    1    0    2                                               
db2000_hybrid.dat                                                      
D-ADENOSINE - with 5' - OH end group and 3' - O[minus]        
                                                              
 DA5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00    180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.52    109.59   -127.70 
  19   C8    CK    B   14  12  11    1.37    131.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.30    113.93    177.00 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    104.00      0.00 
  24   C6    CA    B   18  17  15    1.40    132.42    180.00 
  25   N6    N2    B   19  18  17    1.34    123.50      0.00 
  26   H61   H     E   20  19  18    1.01    120.00    180.00 
  27   H62   H     E   20  19  18    1.01    120.00      0.00 
  28   N1    NC    B   19  18  17    1.34    117.43    180.00 
  29   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  30   C2    CQ    B   23  19  18    1.33    118.80      0.00 
  31   H2    H5    E   24  23  19    1.08    120.00    180.00 
  32   N3    NC    B   24  23  19    1.32    129.17      0.00 
  33   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  34   C4    CB    E   26  24  23    1.35    110.80      0.00 
  35   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  36   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  37   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  38   H2'1  HC    E   30  28   9    1.09    109.50    120.00 
  39   H2'2  HC    E   30  28   9    1.09    109.50    240.00 
  40   O3'   OS    M   28   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + A5E, dft/cc-pvtz polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1213  0.1243
 -0.0191  0.0456  0.1671 -0.0230 -0.3440
  0.0161  0.3636 -0.6837  0.3562  0.3562
  0.0046 -0.3886  0.1181  0.1016  0.0872
 -0.4679  0.1692  0.1568  0.0639 -0.0414
  0.0452  0.0452 -0.4994
                                                              
IMPROPER                        
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-ADENOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 DA   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.52    109.59   -127.70 
  21   C8    CK    B   16  14  13    1.37    131.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.30    113.93    177.00 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    104.00      0.00 
  26   C6    CA    B   20  19  17    1.40    132.42    180.00 
  27   N6    N2    B   21  20  19    1.34    123.50      0.00 
  28   H61   H     E   22  21  20    1.01    120.00    180.00 
  29   H62   H     E   22  21  20    1.01    120.00      0.00 
  30   N1    NC    B   21  20  19    1.34    117.43    180.00 
  31   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  32   C2    CQ    B   25  21  20    1.33    118.80      0.00 
  33   H2    H5    E   26  25  21    1.08    120.00    180.00 
  34   N3    NC    B   26  25  21    1.32    129.17      0.00 
  35   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   28  26  25    1.35    110.80      0.00 
  37   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  38   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  39   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  40   H2'1  HC    E   32  30  11    1.09    109.50    120.00 
  41   H2'2  HC    E   32  30  11    1.09    109.50    240.00 
  42   O3'   OS    M   30  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + A, dft/cc-pvtz polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1213  0.1243 -0.0191  0.0456  0.1671
 -0.0230 -0.3440  0.0161  0.3636 -0.6837
  0.3562  0.3562  0.0046 -0.3886  0.1181
  0.1016  0.0872 -0.4679  0.1692  0.1568
  0.0639 -0.0414  0.0452  0.0452 -0.4994

IMPROPER               
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-ADENOSINE - with 5' - phosphate group and 3' - OH group     
                                                              
 DA3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.52    109.59   -127.70 
  21   C8    CK    B   16  14  13    1.37    131.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.30    113.93    177.00 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    104.00      0.00 
  26   C6    CA    B   20  19  17    1.40    132.42    180.00 
  27   N6    N2    B   21  20  19    1.34    123.50      0.00 
  28   H61   H     E   22  21  20    1.01    120.00    180.00 
  29   H62   H     E   22  21  20    1.01    120.00      0.00 
  30   N1    NC    B   21  20  19    1.34    117.43    180.00 
  31   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  32   C2    CQ    B   25  21  20    1.33    118.80      0.00 
  33   H2    H5    E   26  25  21    1.08    120.00    180.00 
  34   N3    NC    B   26  25  21    1.32    129.17      0.00 
  35   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   28  26  25    1.35    110.80      0.00 
  37   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  38   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  39   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  40   H2'1  HC    E   32  30  11    1.09    109.50    120.00 
  41   H2'2  HC    E   32  30  11    1.09    109.50    240.00 
  42   O3'   OH    M   30  11   8    1.42    116.52   -203.47 
  45   H3T   HO    M   35  30  11    0.96    114.97    180.00 
                                                              
CHARGE + A3E, dft/cc-pvtz polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1213  0.1243 -0.0191  0.0456  0.1671
 -0.0230 -0.3440  0.0161  0.3636 -0.6837
  0.3562  0.3562  0.0046 -0.3886  0.1181
  0.1016  0.0872 -0.4679  0.1692  0.1568
  0.0639 -0.0414  0.0452  0.0452 -0.5941
  0.4026

IMPROPER                       
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-ADENOSINE - with 5' - OH group and 3' - OH group            
                                                              
 DAN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00    180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.52    109.59   -127.70 
  19   C8    CK    B   14  12  11    1.37    131.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.30    113.93    177.00 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    104.00      0.00 
  14   C6    CA    B   18  17  15    1.40    132.42    180.00 
  25   N6    N2    B   19  18  17    1.34    123.50      0.00 
  26   H61   H     E   20  19  18    1.01    120.00    180.00 
  27   H62   H     E   20  19  18    1.01    120.00      0.00 
  28   N1    NC    B   19  18  17    1.34    117.43    180.00 
  29   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  30   C2    CQ    B   23  19  18    1.33    118.80      0.00 
  31   H2    H5    E   24  23  19    1.08    120.00    180.00 
  32   N3    NC    B   24  23  19    1.32    129.17      0.00 
  33   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  34   C4    CB    E   26  24  23    1.35    110.80      0.00 
  35   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  26   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  37   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  38   H2'1  HC    E   30  28   9    1.09    109.50    120.00 
  39   H2'2  HC    E   30  28   9    1.09    109.50    240.00 
  40   O3'   OH    M   28   9   6    1.42    116.52   -203.47 
  43   H3T   HO    M   33  28   9    0.96    114.97    180.00 
                                                              
CHARGE + AN, dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1213  0.1243
 -0.0191  0.0456  0.1671 -0.0230 -0.3440
  0.0161  0.3636 -0.6837  0.3562  0.3562
  0.0046 -0.3886  0.1181  0.1016  0.0872
 -0.4679  0.1692  0.1568  0.0639 -0.0414
  0.0452  0.0452 -0.5941  0.4026

IMPROPER                                 
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-ADENOSINE - with 5' - OH end group and 3' - O[minus]        
                                                              
 RA5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00    180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.52    109.59   -127.70 
  19   C8    CK    B   14  12  11    1.37    131.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.30    113.93    177.00 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    104.00      0.00 
  24   C6    CA    B   18  17  15    1.40    132.42    180.00 
  25   N6    N2    B   19  18  17    1.34    123.50      0.00 
  26   H61   H     E   20  19  18    1.01    120.00    180.00 
  27   H62   H     E   20  19  18    1.01    120.00      0.00 
  28   N1    NC    B   19  18  17    1.34    117.43    180.00 
  29   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  30   C2    CQ    B   23  19  18    1.33    118.80      0.00 
  31   H2    H5    E   24  23  19    1.08    120.00    180.00 
  32   N3    NC    B   24  23  19    1.32    129.17      0.00 
  33   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  34   C4    CB    E   26  24  23    1.35    110.80      0.00 
  35   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  36   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  37   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  38   H2'1  H1    E   30  28   9    1.09    109.50    120.00 
  39   O2'   OH    S   30  28   9    1.43    109.50    240.00 
  42   HO'2  HO    E   32  30  28    0.96    107.00    180.00 
  43   O3'   OS    M   28   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + RA5E, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0214  0.1611
  0.0285  0.0374  0.1542 -0.0013 -0.3616
  0.0327  0.3496 -0.6637  0.3417  0.3417
  0.0204 -0.3931  0.1186  0.0994  0.0538
 -0.4318  0.1141  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.4746

IMPROPER
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-ADENOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 RA   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.52    109.59   -127.70 
  21   C8    CK    B   16  14  13    1.37    131.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.30    113.93    177.00 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    104.00      0.00 
  26   C6    CA    B   20  19  17    1.40    132.42    180.00 
  27   N6    N2    B   21  20  19    1.34    123.50      0.00 
  28   H61   H     E   22  21  20    1.01    120.00    180.00 
  29   H62   H     E   22  21  20    1.01    120.00      0.00 
  30   N1    NC    B   21  20  19    1.34    117.43    180.00 
  31   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  32   C2    CQ    B   25  21  20    1.33    118.80      0.00 
  33   H2    H5    E   26  25  21    1.08    120.00    180.00 
  34   N3    NC    B   26  25  21    1.32    129.17      0.00 
  35   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   28  26  25    1.35    110.80      0.00 
  37   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  38   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  39   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  40   H2'1  H1    E   32  30  11    1.09    109.50    120.00 
  41   O2'   OH    S   32  30  11    1.43    109.50    240.00 
  44   HO'2  HO    E   34  32  30    0.96    107.00    180.00 
  45   O3'   OS    M   30  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + RA, dft/cc-pvtz, polarization correctd
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.0214  0.1611  0.0285  0.0374  0.1542
 -0.0013 -0.3616  0.0327  0.3496 -0.6637
  0.3417  0.3417  0.0204 -0.3931  0.1186
  0.0994  0.0538 -0.4318  0.1141  0.2484
  0.0147  0.0346  0.0875 -0.5105  0.3787
 -0.4746

IMPROPER 
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-ADENOSINE - with 5' - phosphate group and 3' - OH group     
                                                              
 RA3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.52    109.59   -127.70 
  21   C8    CK    B   16  14  13    1.37    131.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.30    113.93    177.00 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    104.00      0.00 
  26   C6    CA    B   20  19  17    1.40    132.42    180.00 
  27   N6    N2    B   21  20  19    1.34    123.50      0.00 
  28   H61   H     E   22  21  20    1.01    120.00    180.00 
  29   H62   H     E   22  21  20    1.01    120.00      0.00 
  30   N1    NC    B   21  20  19    1.34    117.43    180.00 
  31   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  32   C2    CQ    B   25  21  20    1.33    118.80      0.00 
  33   H2    H5    E   26  25  21    1.08    120.00    180.00 
  34   N3    NC    B   26  25  21    1.32    129.17      0.00 
  35   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   28  26  25    1.35    110.80      0.00 
  37   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  38   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  39   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  40   H2'1  H1    E   32  30  11    1.09    109.50    120.00 
  41   O2'   OH    S   32  30  11    1.43    109.50    240.00 
  44   HO'2  HO    E   34  32  30    0.96    107.00    180.00 
  45   O3'   OH    M   30  11   8    1.42    116.52   -203.47 
  48   H3T   HO    M   36  30  11    0.96    114.97    180.00 

CHARGE + RA3E, dft/cc-pvtz, polarization corrected
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.0214  0.1611  0.0285  0.0374  0.1542
 -0.0013 -0.3616  0.0327  0.3496 -0.6637
  0.3417  0.3417  0.0204 -0.3931  0.1186
  0.0994  0.0538 -0.4318  0.1141  0.2484
  0.0147  0.0346  0.0875 -0.5105  0.3787
 -0.5793  0.4126

IMPROPER
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-ADENOSINE - with 5' - OH group and 3' - OH group            
                                                              
 RAN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00    180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.52    109.59   -127.70 
  19   C8    CK    B   14  12  11    1.37    131.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.30    113.93    177.00 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    104.00      0.00 
  24   C6    CA    B   18  17  15    1.40    132.42    180.00 
  25   N6    N2    B   19  18  17    1.34    123.50      0.00 
  26   H61   H     E   20  19  18    1.01    120.00    180.00 
  27   H62   H     E   20  19  18    1.01    120.00      0.00 
  28   N1    NC    B   19  18  17    1.34    117.43    180.00 
  29   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  30   C2    CQ    B   23  19  18    1.33    118.80      0.00 
  31   H2    H5    E   24  23  19    1.08    120.00    180.00 
  32   N3    NC    B   24  23  19    1.32    129.17      0.00 
  33   EP23  EP    E    5   4   3    0.35    120.00    180.00 
  34   C4    CB    E   26  24  23    1.35    110.80      0.00 
  35   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  36   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  37   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  38   H2'1  H1    E   30  28   9    1.09    109.50    120.00 
  39   O2'   OH    S   30  28   9    1.43    109.50    240.00 
  42   HO'2  HO    E   32  30  28    0.96    107.00    180.00 
  43   O3'   OH    M   28   9   6    1.42    116.52   -203.47 
  46   H3T   HO    M   34  28   9    0.96    114.97    180.00 
                                                              
CHARGE + RAN, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0214  0.1611
  0.0285  0.0374  0.1542 -0.0013 -0.3616
  0.0327  0.3496 -0.6637  0.3417  0.3417
  0.0204 -0.3931  0.1186  0.0994  0.0538
 -0.4318  0.1141  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.5793  0.4126

IMPROPER
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-THYMINE - with 5' - OH end group and 3' - O[minus]          
                                                              
 DT5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.53    109.59   -127.70 
  19   C6    CM    B   14  12  11    1.37    123.04     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.34    121.22    177.30 
  22   C7    CT    3   17  15  14    1.50    121.63    180.00 
  23   H71   HC    E   18  17  15    1.09    109.50     60.00 
  24   H72   HC    E   18  17  15    1.09    109.50    180.00 
  25   H73   HC    E   18  17  15    1.09    109.50    300.00 
  26   C4    C     B   17  15  14    1.44    120.78      0.00 
  27   O4    O     B   22  17  15    1.23    125.35    180.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N3    NA    B   22  17  15    1.38    114.07      0.00 
  31   H3    H     E   24  22  17    1.09    116.77    180.00 
  32   C2    C     S   24  22  17    1.38    126.46      0.00 
  33   O2    O     B   26  24  22    1.22    121.70    180.00 
  34   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  35   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  36   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  37   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  38   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  39   H2'1  HC    E   30  28   9    1.09    109.50    120.00 
  40   H2'2  HC    E   30  28   9    1.09    109.50    240.00 
  41   O3'   OS    M   28   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + deoxy-THY-B: T5E, dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.0729  0.1275
  0.0096 -0.1929  0.2403  0.0033 -0.1309
  0.0576  0.0576  0.0576  0.3669 -0.0164
 -0.2106 -0.2106 -0.3515  0.3258  0.3819
 -0.0545 -0.2144 -0.2144  0.1568  0.0639
 -0.0414  0.0452  0.0452 -0.4994

IMPROPER 
 C6   C2   N1   C1'                                           
 C4   C6   C5   C7                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-THYMINE - with 5' - phosphate group and 3' - O[minus] group 
                                                              
 DT   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.53    109.59   -127.70 
  21   C6    CM    B   16  14  13    1.37    123.04     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.34    121.22    177.30 
  24   C7    CT    3   19  17  16    1.50    121.63    180.00 
  25   H71   HC    E   20  19  17    1.09    109.50     60.00 
  26   H72   HC    E   20  19  17    1.09    109.50    180.00 
  27   H73   HC    E   20  19  17    1.09    109.50    300.00 
  28   C4    C     B   19  17  16    1.44    120.78      0.00 
  29   O4    O     B   24  19  17    1.23    125.35    180.00 
  30   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  31   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  32   N3    NA    B   24  19  17    1.38    114.07      0.00 
  33   H3    H     E   26  24  19    1.09    116.77    180.00 
  34   C2    C     S   26  24  19    1.38    126.46      0.00 
  35   O2    O     B   28  26  24    1.22    121.70    180.00 
  36   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  37   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  38   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  39   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  40   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  41   H2'1  HC    E   32  30  11    1.09    109.50    120.00 
  42   H2'2  HC    E   32  30  11    1.09    109.50    240.00 
  43   O3'   OS    M   30  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + deoxy-THY-B: T, dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.0729  0.1275  0.0096 -0.1929  0.2403
  0.0033 -0.1309  0.0576  0.0576  0.0576
  0.3669 -0.0164 -0.2106 -0.2106 -0.3515
  0.3258  0.3819 -0.0545 -0.2144 -0.2144
  0.1568  0.0639 -0.0414  0.0452  0.0452
 -0.4994

IMPROPER 
 C6   C2   N1   C1'                                           
 C4   C6   C5   C7                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-THYMINE - with 5' - phosphate group and 3' - OH group       
                                                              
 DT3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.53    109.59   -127.70 
  21   C6    CM    B   16  14  13    1.37    123.04     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.34    121.22    177.30 
  24   C7    CT    3   19  17  16    1.50    121.63    180.00 
  25   H71   HC    E   20  19  17    1.09    109.50     60.00 
  26   H72   HC    E   20  19  17    1.09    109.50    180.00 
  27   H73   HC    E   20  19  17    1.09    109.50    300.00 
  28   C4    C     B   19  17  16    1.44    120.78      0.00 
  29   O4    O     B   24  19  17    1.23    125.35    180.00 
  30   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  31   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  32   N3    NA    B   24  19  17    1.38    114.07      0.00 
  33   H3    H     E   26  24  19    1.09    116.77    180.00 
  34   C2    C     S   26  24  19    1.38    126.46      0.00 
  35   O2    O     B   28  26  24    1.22    121.70    180.00 
  36   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  37   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  38   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  39   H3'   H1    E   30  11   8    1.09    109.50     30.00 
  40   C2'   CT    B   30  11   8    1.53    102.80    -86.30 
  41   H2'1  HC    E   32  30  11    1.09    109.50    120.00 
  42   H2'2  HC    E   32  30  11    1.09    109.50    240.00 
  43   O3'   OH    M   30  11   8    1.42    116.52   -203.47 
  46   H3T   HO    M   35  30  11    0.96    114.97    180.00 
                                                              
CHARGE + deoxy-THY-B: T3E, dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.0729  0.1275  0.0096 -0.1929  0.2403
  0.0033 -0.1309  0.0576  0.0576  0.0576
  0.3669 -0.0164 -0.2106 -0.2106 -0.3515
  0.3258  0.3819 -0.0545 -0.2144 -0.2144
  0.1568  0.0639 -0.0414  0.0452  0.0452
 -0.5941  0.4026

IMPROPER 
 C6   C2   N1   C1'                                           
 C4   C6   C5   C7                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-THYMINE - with 5' - OH group and 3' - OH group              
                                                              
 DTN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.53    109.59   -127.70 
  19   C6    CM    B   14  12  11    1.37    123.04     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.34    121.22    177.30 
  22   C7    CT    3   17  15  14    1.50    121.63    180.00 
  23   H71   HC    E   18  17  15    1.09    109.50     60.00 
  24   H72   HC    E   18  17  15    1.09    109.50    180.00 
  25   H73   HC    E   18  17  15    1.09    109.50    300.00 
  26   C4    C     B   17  15  14    1.44    120.78      0.00 
  27   O4    O     B   22  17  15    1.23    125.35    180.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N3    NA    B   22  17  15    1.38    114.07      0.00 
  31   H3    H     E   24  22  17    1.09    116.77    180.00 
  32   C2    C     S   24  22  17    1.38    126.46      0.00 
  33   O2    O     B   26  24  22    1.22    121.70    180.00 
  34   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  35   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  36   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  37   H3'   H1    E   28   9   6    1.09    109.50     30.00 
  38   C2'   CT    B   28   9   6    1.53    102.80    -86.30 
  39   H2'1  HC    E   30  28   9    1.09    109.50    120.00 
  40   H2'2  HC    E   30  28   9    1.09    109.50    240.00 
  41   O3'   OH    M   28   9   6    1.42    116.52   -203.47 
  44   H3T   HO    M   33  28   9    0.96    114.97    180.00 
                                                              
CHARGE + deoxy-THY-B: dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.0729  0.1275
  0.0096 -0.1929  0.2403  0.0033 -0.1309
  0.0576  0.0576  0.0576  0.3669 -0.0164
 -0.2106 -0.2106 -0.3515  0.3258  0.3819
 -0.0545 -0.2144 -0.2144  0.1568  0.0639
 -0.0414  0.0452  0.0452 -0.5941  0.4026

IMPROPER 
 C6   C2   N1   C1'                                           
 C4   C6   C5   C7                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-URACIL - with 5' - OH end group and 3' - O[minus]           
                                                              
 RU5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.53    109.59   -127.70 
  19   C6    CM    B   14  12  11    1.37    123.04     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.34    121.22    177.30 
  22   H5    HA    E   17  15  14    1.09    120.00    180.00 
  23   C4    C     B   17  15  14    1.44    120.78      0.00 
  24   O4    O     B   19  17  15    1.23    125.35    180.00 
  25   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  26   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  27   N3    NA    B   19  17  15    1.38    114.07      0.00 
  28   H3    H     E   21  19  17    1.09    116.77    180.00 
  29   C2    C     S   21  19  17    1.38    126.46      0.00 
  30   O2    O     B   23  21  19    1.22    121.70    180.00 
  31   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  32   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  33   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  34   H3'   H1    E   25   9   6    1.09    109.50     30.00 
  35   C2'   CT    B   25   9   6    1.53    102.80    -86.30 
  36   H2'1  H1    E   27  25   9    1.09    109.50    120.00 
  37   O2'   OH    S   27  25   9    1.43    109.50    240.00 
  40   HO'2  HO    E   29  27  25    0.96    107.00    180.00 
  41   O3'   OS    M   25   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + resp RU5E, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1030  0.1015
  0.0291 -0.1035  0.1860 -0.2499  0.1516
  0.3796 -0.0360 -0.2066 -0.2066 -0.2404
  0.2897  0.2962 -0.0716 -0.1995 -0.1995
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.4746

IMPROPER
 C6   C2   N1   C1'                                           
 C4   C6   C5   H5                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-URACIL - with 5' - phosphate group and 3' - O[minus] group  
                                                              
 RU   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.53    109.59   -127.70 
  21   C6    CM    B   16  14  13    1.37    123.04     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.34    121.22    177.30 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    C     B   19  17  16    1.44    120.78      0.00 
  26   O4    O     B   21  19  17    1.23    125.35    180.00 
  27   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  28   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  29   N3    NA    B   21  19  17    1.38    114.07      0.00 
  30   H3    H     E   23  21  19    1.09    116.77    180.00 
  31   C2    C     S   23  21  19    1.38    126.46      0.00 
  32   O2    O     B   25  23  21    1.22    121.70    180.00 
  33   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   27  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   27  11   8    1.53    102.80    -86.30 
  38   H2'1  H1    E   29  27  11    1.09    109.50    120.00 
  39   O2'   OH    S   29  27  11    1.43    109.50    240.00 
  42   HO'2  HO    E   31  29  27    0.96    107.00    180.00 
  43   O3'   OS    M   27  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + resp RU, dft/cc-pvtz, polarization corrected
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.1030  0.1015  0.0291 -0.1035  0.1860
 -0.2499  0.1516  0.3796 -0.0360 -0.2066
 -0.2066 -0.2404  0.2897  0.2962 -0.0716
 -0.1995 -0.1995  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.4746

IMPROPER
 C6   C2   N1   C1'                                           
 C4   C6   C5   H5                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-URACIL - with 5' - phosphate group and 3' - OH group        
                                                              
 RU3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.53    109.59   -127.70 
  21   C6    CM    B   16  14  13    1.37    123.04     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.34    121.22    177.30 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    C     B   19  17  16    1.44    120.78      0.00 
  26   O4    O     B   21  19  17    1.23    125.35    180.00 
  27   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  28   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  29   N3    NA    B   21  19  17    1.38    114.07      0.00 
  30   H3    H     E   23  21  19    1.09    116.77    180.00 
  31   C2    C     S   23  21  19    1.38    126.46      0.00 
  32   O2    O     B   25  23  21    1.22    121.70    180.00 
  33   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   27  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   27  11   8    1.53    102.80    -86.30 
  38   H2'1  H1    E   29  27  11    1.09    109.50    120.00 
  39   O2'   OH    S   29  27  11    1.43    109.50    240.00 
  42   HO'2  HO    E   31  29  27    0.96    107.00    180.00 
  43   O3'   OH    M   27  11   8    1.42    116.52   -203.47 
  46   H3T   HO    M   33  27  11    0.96    114.97    180.00 
                                                              
CHARGE + resp RU3E, dft/cc-pvtz, polarization corrected
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.1030  0.1015  0.0291 -0.1035  0.1860
 -0.2499  0.1516  0.3796 -0.0360 -0.2066
 -0.2066 -0.2404  0.2897  0.2962 -0.0716
 -0.1995 -0.1995  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.5793  0.4126

IMPROPER
 C6   C2   N1   C1'                                           
 C4   C6   C5   H5                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-URACIL - with 5' - OH group and 3' - OH group               
                                                              
 RUN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   6    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.53    109.59   -127.70 
  19   C6    CM    B   14  12  11    1.37    123.04     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.34    121.22    177.30 
  22   H5    HA    E   17  15  14    1.09    120.00    180.00 
  23   C4    C     B   17  15  14    1.44    120.78      0.00 
  24   O4    O     B   19  17  15    1.23    125.35    180.00 
  25   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  26   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  27   N3    NA    B   19  17  15    1.38    114.07      0.00 
  28   H3    H     E   21  19  17    1.09    116.77    180.00 
  29   C2    C     S   21  19  17    1.38    126.46      0.00 
  30   O2    O     B   23  21  19    1.22    121.70    180.00 
  31   EP+2  EP    E    5   4   3    0.35    120.00      0.00 
  32   EP-2  EP    E    5   4   3    0.35    120.00    180.00 
  33   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  34   H3'   H1    E   25   9   6    1.09    109.50     30.00 
  35   C2'   CT    B   25   9   6    1.53    102.80    -86.30 
  36   H2'1  H1    E   27  25   9    1.09    109.50    120.00 
  37   O2'   OH    S   27  25   9    1.43    109.50    240.00 
  40   HO'2  HO    E   29  27  25    0.96    107.00    180.00 
  41   O3'   OH    M   25   9   6    1.42    116.52   -203.47 
  44   H3T   HO    M   31  25   9    0.96    114.97    180.00 
                                                              
CHARGE + resp RURA, dft/cc-pvtz, polarization corrected 
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1030  0.1015
  0.0291 -0.1035  0.1860 -0.2499  0.1516
  0.3796 -0.0360 -0.2066 -0.2066 -0.2404
  0.2897  0.2962 -0.0716 -0.1995 -0.1995
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.5793  0.4126

IMPROPER 
 C6   C2   N1   C1'                                           
 C4   C6   C5   H5                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-GUANOSINE - with 5' - OH end group and 3' - O[minus] group  
                                                              
 DG5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.49    108.06   -127.70 
  19   C8    CK    B   14  12  11    1.38    129.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.31    114.00   -179.90 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    103.90      0.00 
  24   C6    C     B   18  17  15    1.42    130.40    180.00 
  25   O6    O     B   19  18  17    1.23    128.80      0.00 
  26   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  27   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  28   N1    NA    B   19  18  17    1.40    111.38    180.00 
  29   H1    H     E   21  19  18    1.00    117.36    179.90 
  30   C2    CA    B   21  19  18    1.38    125.24     -0.10 
  31   N2    N2    B   23  21  19    1.34    116.02    180.00 
  32   H21   H     E   24  23  21    1.01    127.00     -0.82 
  33   H22   H     E   24  23  21    1.01    116.53   -179.44 
  34   N3    NC    B   23  21  19    1.33    123.30      0.00 
  35   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   27  23  21    1.36    112.20      0.00 
  37   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  38   H3'   H1    E   29   9   6    1.09    109.50     30.00 
  39   C2'   CT    B   29   9   6    1.53    102.80    -86.30 
  40   H2'1  HC    E   31  29   9    1.09    109.50    120.00 
  41   H2'2  HC    E   31  29   9    1.09    109.50    240.00 
  42   O3'   OS    M   29   9   6    1.42    116.52   -203.47 

CHARGE + deoxy-GUA-B G5E: dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1494  0.1022
  0.0022  0.0092  0.1706 -0.0129 -0.3374
  0.0696  0.3049 -0.0173 -0.2051 -0.2051
 -0.4073  0.3500  0.4834 -0.7230  0.3459
  0.3459  0.0391 -0.4364  0.0769  0.1568
  0.0639 -0.0414  0.0452  0.0452 -0.4994

IMPROPER                                                      
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-GUANOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 DG   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.49    108.06   -127.70 
  21   C8    CK    B   16  14  13    1.38    129.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.31    114.00   -179.90 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    103.90      0.00 
  26   C6    C     B   20  19  17    1.42    130.40    180.00 
  27   O6    O     B   21  20  19    1.23    128.80      0.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N1    NA    B   21  20  19    1.40    111.38    180.00 
  31   H1    H     E   23  21  20    1.00    117.36    179.90 
  32   C2    CA    B   23  21  20    1.38    125.24     -0.10 
  33   N2    N2    B   25  23  21    1.34    116.02    180.00 
  34   H21   H     E   26  25  23    1.01    127.00     -0.82 
  35   H22   H     E   26  25  23    1.01    116.53   -179.44 
  36   N3    NC    B   25  23  21    1.33    123.30      0.00 
  37   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  38   C4    CB    E   29  25  23    1.36    112.20      0.00 
  39   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  40   H3'   H1    E   31  11   8    1.09    109.50     30.00 
  41   C2'   CT    B   31  11   8    1.53    102.80    -86.30 
  42   H2'1  HC    E   33  31  11    1.09    109.50    120.00 
  43   H2'2  HC    E   33  31  11    1.09    109.50    240.00 
  44   O3'   OS    M   31  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + deoxy-GUA-B G: dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1493  0.1022  0.0022  0.0092  0.1706
 -0.0129 -0.3374  0.0696  0.3049 -0.0173
 -0.2051 -0.2051 -0.4073  0.3500  0.4834
 -0.7230  0.3459  0.3459  0.0391 -0.4364
  0.0769  0.1568  0.0639 -0.0414  0.0452
  0.0452 -0.4994

IMPROPER                                                      
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-GUANOSINE - with 5' - phosphate group and 3' - OH group     
                                                              
 DG3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.49    108.06   -127.70 
  21   C8    CK    B   16  14  13    1.38    129.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.31    114.00   -179.90 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    103.90      0.00 
  26   C6    C     B   20  19  17    1.42    130.40    180.00 
  27   O6    O     B   21  20  19    1.23    128.80      0.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N1    NA    B   21  20  19    1.40    111.38    180.00 
  31   H1    H     E   23  21  20    1.00    117.36    179.90 
  32   C2    CA    B   23  21  20    1.38    125.24     -0.10 
  33   N2    N2    B   25  23  21    1.34    116.02    180.00 
  34   H21   H     E   26  25  23    1.01    127.00     -0.82 
  35   H22   H     E   26  25  23    1.01    116.53   -179.44 
  36   N3    NC    B   25  23  21    1.33    123.30      0.00 
  37   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  38   C4    CB    E   29  25  23    1.36    112.20      0.00 
  39   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  40   H3'   H1    E   31  11   8    1.09    109.50     30.00 
  41   C2'   CT    B   31  11   8    1.53    102.80    -86.30 
  42   H2'1  HC    E   33  31  11    1.09    109.50    120.00 
  43   H2'2  HC    E   33  31  11    1.09    109.50    240.00 
  44   O3'   OH    M   31  11   8    1.42    116.52   -203.47 
  47   H3T   HO    M   36  31  11    0.96    114.97    180.00 
                                                              
CHARGE + deoxy-GUA-B G3E: dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1494  0.1022  0.0022  0.0092  0.1706
 -0.0129 -0.3374  0.0696  0.3049 -0.0173
 -0.2051 -0.2051 -0.4073  0.3500  0.4834
 -0.7230  0.3459  0.3459  0.0391 -0.4364
  0.0769  0.1568  0.0639 -0.0414  0.0452
  0.0452 -0.5941  0.4026

IMPROPER                                                      
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-GUANOSINE - with 5' - OH group and 3' - OH group            
                                                              
 DGN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.49    108.06   -127.70 
  19   C8    CK    B   14  12  11    1.38    129.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.31    114.00   -179.90 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    103.90      0.00 
  24   C6    C     B   18  17  15    1.42    130.40    180.00 
  25   O6    O     B   19  18  17    1.23    128.80      0.00 
  26   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  27   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  28   N1    NA    B   19  18  17    1.40    111.38    180.00 
  29   H1    H     E   21  19  18    1.00    117.36    179.90 
  30   C2    CA    B   21  19  18    1.38    125.24     -0.10 
  31   N2    N2    B   23  21  19    1.34    116.02    180.00 
  32   H21   H     E   24  23  21    1.01    127.00     -0.82 
  33   H22   H     E   24  23  21    1.01    116.53   -179.44 
  34   N3    NC    B   23  21  19    1.33    123.30      0.00 
  35   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   27  23  21    1.36    112.20      0.00 
  37   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  38   H3'   H1    E   29   9   6    1.09    109.50     30.00 
  39   C2'   CT    B   29   9   6    1.53    102.80    -86.30 
  40   H2'1  HC    E   31  29   9    1.09    109.50    120.00 
  41   H2'2  HC    E   31  29   9    1.09    109.50    240.00 
  42   O3'   OH    M   29   9   6    1.42    116.52   -203.47 
  45   H3T   HO    M   34  29   9    0.96    114.97    180.00 
                                                              
CHARGE + deoxy-GUA-B: dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1494  0.1022
  0.0022  0.0092  0.1706 -0.0129 -0.3374
  0.0696  0.3049 -0.0173 -0.2051 -0.2051
 -0.4073  0.3500  0.4834 -0.7230  0.3459
  0.3459  0.0391 -0.4364  0.0769  0.1568
  0.0639 -0.0414  0.0452  0.0452 -0.5941
  0.4026

IMPROPER 
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-GUANOSINE - with 5' - OH end group and 3' - O[minus] group  
                                                              
 RG5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.49    108.06   -127.70 
  19   C8    CK    B   14  12  11    1.38    129.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.31    114.00   -179.90 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    103.90      0.00 
  24   C6    C     B   18  17  15    1.42    130.40    180.00 
  25   O6    O     B   19  18  17    1.23    128.80      0.00 
  26   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  27   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  28   N1    NA    B   19  18  17    1.40    111.38    180.00 
  29   H1    H     E   21  19  18    1.00    117.36    179.90 
  30   C2    CA    B   21  19  18    1.38    125.24     -0.10 
  31   N2    N2    B   23  21  19    1.34    116.02    180.00 
  32   H21   H     E   24  23  21    1.01    127.00     -0.82 
  33   H22   H     E   24  23  21    1.01    116.53   -179.44 
  34   N3    NC    B   23  21  19    1.33    123.30      0.00 
  35   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   27  23  21    1.36    112.20      0.00 
  37   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  38   H3'   H1    E   29   9   6    1.09    109.50     30.00 
  39   C2'   CT    B   29   9   6    1.53    102.80    -86.30 
  40   H2'1  H1    E   31  29   9    1.09    109.50    120.00 
  41   O2'   OH    S   31  29   9    1.43    109.50    240.00 
  44   HO'2  HO    E   33  31  29    0.96    107.00    180.00 
  45   O3'   OS    M   29   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + resp RG5E, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1426  0.0860
 -0.0180  0.0162  0.1555  0.0197 -0.3612
  0.0795  0.2803 -0.0133 -0.2038 -0.2038
 -0.3586  0.3364  0.4549 -0.7249  0.3457
  0.3457  0.0063 -0.4016  0.0395  0.2484
  0.0147  0.0346  0.0875 -0.5105  0.3787
 -0.4746

IMPROPER
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-GUANOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 RG   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.49    108.06   -127.70 
  21   C8    CK    B   16  14  13    1.38    129.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.31    114.00   -179.90 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    103.90      0.00 
  26   C6    C     B   20  19  17    1.42    130.40    180.00 
  27   O6    O     B   21  20  19    1.23    128.80      0.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N1    NA    B   21  20  19    1.40    111.38    180.00 
  31   H1    H     E   23  21  20    1.00    117.36    179.90 
  32   C2    CA    B   23  21  20    1.38    125.24     -0.10 
  33   N2    N2    B   25  23  21    1.34    116.02    180.00 
  34   H21   H     E   26  25  23    1.01    127.00     -0.82 
  35   H22   H     E   26  25  23    1.01    116.53   -179.44 
  36   N3    NC    B   25  23  21    1.33    123.30      0.00 
  37   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  38   C4    CB    E   29  25  23    1.36    112.20      0.00 
  39   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  40   H3'   H1    E   31  11   8    1.09    109.50     30.00 
  41   C2'   CT    B   31  11   8    1.53    102.80    -86.30 
  42   H2'1  H1    E   33  31  11    1.09    109.50    120.00 
  43   O2'   OH    S   33  31  11    1.43    109.50    240.00 
  46   HO'2  HO    E   35  33  31    0.96    107.00    180.00 
  47   O3'   OS    M   31  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + resp RG, dft/cc-pvtz, polarization corrected
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.1426  0.0860 -0.0180  0.0162  0.1555
  0.0197 -0.3612  0.0795  0.2803 -0.0133
 -0.2038 -0.2038 -0.3586  0.3364  0.4549
 -0.7249  0.3457  0.3457  0.0063 -0.4016
  0.0395  0.2484  0.0147  0.0346  0.0875
 -0.5105  0.3787 -0.4746

IMPROPER
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-GUANOSINE - with 5' - phosphate group and 3' - OH group     
                                                              
 RG3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N9    N*    S   14  13  11    1.49    108.06   -127.70 
  21   C8    CK    B   16  14  13    1.38    129.20     81.59 
  22   H8    H5    E   17  16  14    1.08    120.00      0.00 
  23   N7    NB    B   17  16  14    1.31    114.00   -179.90 
  24   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  25   C5    CB    S   19  17  16    1.39    103.90      0.00 
  26   C6    C     B   20  19  17    1.42    130.40    180.00 
  27   O6    O     B   21  20  19    1.23    128.80      0.00 
  28   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  29   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  30   N1    NA    B   21  20  19    1.40    111.38    180.00 
  31   H1    H     E   23  21  20    1.00    117.36    179.90 
  32   C2    CA    B   23  21  20    1.38    125.24     -0.10 
  33   N2    N2    B   25  23  21    1.34    116.02    180.00 
  34   H21   H     E   26  25  23    1.01    127.00     -0.82 
  35   H22   H     E   26  25  23    1.01    116.53   -179.44 
  36   N3    NC    B   25  23  21    1.33    123.30      0.00 
  37   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  38   C4    CB    E   29  25  23    1.36    112.20      0.00 
  39   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  40   H3'   H1    E   31  11   8    1.09    109.50     30.00 
  41   C2'   CT    B   31  11   8    1.53    102.80    -86.30 
  42   H2'1  H1    E   33  31  11    1.09    109.50    120.00 
  43   O2'   OH    S   33  31  11    1.43    109.50    240.00 
  46   HO'2  HO    E   35  33  31    0.96    107.00    180.00 
  47   O3'   OH    M   31  11   8    1.42    116.52   -203.47 
  50   H3T   HO    M   37  31  11    0.96    114.97    180.00 
                                                              
CHARGE + resp RG3E, dft/cc-pvtz, polarization corrected
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.1426  0.0860 -0.0180  0.0162  0.1555
  0.0197 -0.3612  0.0795  0.2803 -0.0133
 -0.2038 -0.2038 -0.3586  0.3364  0.4549
 -0.7249  0.3457  0.3457  0.0063 -0.4016
  0.0395  0.2484  0.0147  0.0346  0.0875
 -0.5105  0.3787 -0.5793  0.4126

IMPROPER
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
R-GUANOSINE - with 5' - OH group and 3' - OH group            
                                                              
 RGN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N9    N*    S   12  11   9    1.49    108.06   -127.70 
  19   C8    CK    B   14  12  11    1.38    129.20     81.59 
  20   H8    H5    E   15  14  12    1.08    120.00      0.00 
  21   N7    NB    B   15  14  12    1.31    114.00   -179.90 
  22   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  23   C5    CB    S   17  15  14    1.39    103.90      0.00 
  24   C6    C     B   18  17  15    1.42    130.40    180.00 
  25   O6    O     B   19  18  17    1.23    128.80      0.00 
  26   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  27   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  28   N1    NA    B   19  18  17    1.40    111.38    180.00 
  29   H1    H     E   21  19  18    1.00    117.36    179.90 
  30   C2    CA    B   21  19  18    1.38    125.24     -0.10 
  31   N2    N2    B   23  21  19    1.34    116.02    180.00 
  32   H21   H     E   24  23  21    1.01    127.00     -0.82 
  33   H22   H     E   24  23  21    1.01    116.53   -179.44 
  34   N3    NC    B   23  21  19    1.33    123.30      0.00 
  35   EP22  EP    E    5   4   3    0.35    120.00    180.00 
  36   C4    CB    E   27  23  21    1.36    112.20      0.00 
  37   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  38   H3'   H1    E   29   9   6    1.09    109.50     30.00 
  39   C2'   CT    B   29   9   6    1.53    102.80    -86.30 
  40   H2'1  H1    E   31  29   9    1.09    109.50    120.00 
  41   O2'   OH    S   31  29   9    1.43    109.50    240.00 
  44   HO'2  HO    E   33  31  29    0.96    107.00    180.00 
  45   O3'   OH    M   29   9   6    1.42    116.52   -203.47 
  48   H3T   HO    M   35  29   9    0.96    114.97    180.00 
                                                              
CHARGE + resp RGUA, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1426  0.0860
 -0.0180  0.0162  0.1555  0.0197 -0.3612
  0.0795  0.2803 -0.0133 -0.2038 -0.2038
 -0.3586  0.3364  0.4549 -0.7249  0.3457
  0.3457  0.0063 -0.4016  0.0395  0.2484
  0.0147  0.0346  0.0875 -0.5105  0.3787
 -0.5793  0.4126

IMPROPER 
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
D-CYTOSINE - with 5' - OH end group and 3' - O[minus] group   
                                                              
 DC5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.49    108.10   -127.70 
  19   C6    CM    B   14  12  11    1.36    121.10     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.36    121.00    180.00 
  22   H5    HA    E   17  15  14    1.09    120.00    180.00 
  23   C4    CA    B   17  15  14    1.43    116.90      0.00 
  24   N4    N2    B   19  17  15    1.32    120.10    180.00 
  25   H41   H     E   20  19  17    1.01    117.70    180.00 
  26   H42   H     E   20  19  17    1.01    120.27      0.00 
  27   N3    NC    B   19  17  15    1.33    121.70      0.00 
  28   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  29   C2    C     S   23  19  17    1.36    120.50      0.00 
  30   O2    O     B   24  23  19    1.24    122.40    180.00 
  31   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  32   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  33   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  34   H3'   H1    E   26   9   6    1.09    109.50     30.00 
  35   C2'   CT    B   26   9   6    1.53    102.80    -86.30 
  36   H2'1  HC    E   28  26   9    1.09    109.50    120.00 
  37   H2'2  HC    E   28  26   9    1.09    109.50    240.00 
  38   O3'   OS    M   26   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + deoxy cyt C5E, dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1314  0.0949
 -0.0350 -0.0594  0.1971 -0.3813  0.1745
  0.4751 -0.7150  0.3550  0.3550  0.0329
 -0.4554  0.4292 -0.0726 -0.2108 -0.2108
  0.1568  0.0639 -0.0414  0.0452  0.0452
 -0.4994

IMPROPER
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-CYTOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 DC   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.49    108.10   -127.70 
  21   C6    CM    B   16  14  13    1.36    121.10     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.36    121.00    180.00 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    CA    B   19  17  16    1.43    116.90      0.00 
  26   N4    N2    B   21  19  17    1.32    120.10    180.00 
  27   H41   H     E   22  21  19    1.01    117.70    180.00 
  28   H42   H     E   22  21  19    1.01    120.27      0.00 
  29   N3    NC    B   21  19  17    1.33    121.70      0.00 
  30   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  31   C2    C     S   25  21  19    1.36    120.50      0.00 
  32   O2    O     B   26  25  21    1.24    122.40    180.00 
  33   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   28  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   28  11   8    1.53    102.80    -86.30 
  38   H2'1  HC    E   30  28  11    1.09    109.50    120.00 
  39   H2'2  HC    E   30  28  11    1.09    109.50    240.00 
  40   O3'   OS    M   28  11   8    1.42    116.52   -203.47 

CHARGE + deoxy cyt C, dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1314  0.0949 -0.0350 -0.0594  0.1971
 -0.3813  0.1745  0.4751 -0.7150  0.3550
  0.3550  0.0329 -0.4554  0.4292 -0.0726
 -0.2108 -0.2108  0.1568  0.0639 -0.0414
  0.0452  0.0452 -0.4994


IMPROPER
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-CYTOSINE - with 5' - phosphate group and 3' - OH group      
                                                              
 DC3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.49    108.10   -127.70 
  21   C6    CM    B   16  14  13    1.36    121.10     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.36    121.00    180.00 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    CA    B   19  17  16    1.43    116.90      0.00 
  26   N4    N2    B   21  19  17    1.32    120.10    180.00 
  27   H41   H     E   22  21  19    1.01    117.70    180.00 
  28   H42   H     E   22  21  19    1.01    120.27      0.00 
  29   N3    NC    B   21  19  17    1.33    121.70      0.00 
  30   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  31   C2    C     S   25  21  19    1.36    120.50      0.00 
  32   O2    O     B   26  25  21    1.24    122.40    180.00 
  33   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   28  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   28  11   8    1.53    102.80    -86.30 
  38   H2'1  HC    E   30  28  11    1.09    109.50    120.00 
  39   H2'2  HC    E   30  28  11    1.09    109.50    240.00 
  40   O3'   OH    M   28  11   8    1.42    116.52   -203.47 
  43   H3T   HO    M   30  25   8    0.96    114.97    180.00 
                                                              
CHARGE + deoxy cyt C3E, dft/cc-pvtz, polarization corrected
  1.0733 -0.7545 -0.7545 -0.4112 -0.0091
  0.0663  0.0663  0.0623  0.0913 -0.3053
  0.1314  0.0949 -0.0350 -0.0594  0.1971
 -0.3813  0.1745  0.4751 -0.7150  0.3550
  0.3550  0.0329 -0.4554  0.4292 -0.0726
 -0.2108 -0.2108  0.1568  0.0639 -0.0414
  0.0452  0.0452 -0.5941  0.4026

IMPROPER
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
D-CYTOSINE - with 5' - OH group and 3' - OH group             
                                                              
 DCN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  11   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  12   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  15   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  16   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  17   N1    N*    S   12  11   9    1.49    108.10   -127.70 
  18   C6    CM    B   14  12  11    1.36    121.10     81.59 
  19   H6    H4    E   15  14  12    1.08    120.00      0.00 
  20   C5    CM    B   15  14  12    1.36    121.00    180.00 
  21   H5    HA    E   17  15  14    1.09    120.00    180.00 
  22   C4    CA    B   17  15  14    1.43    116.90      0.00 
  23   N4    N2    B   19  17  15    1.32    120.10    180.00 
  24   H41   H     E   20  19  17    1.01    117.70    180.00 
  25   H42   H     E   20  19  17    1.01    120.27      0.00 
  26   N3    NC    B   19  17  15    1.33    121.70      0.00 
  27   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  28   C2    C     S   23  19  17    1.36    120.50      0.00 
  29   O2    O     B   24  23  19    1.24    122.40    180.00 
  30   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  31   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  32   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  33   H3'   H1    E   26   9   6    1.09    109.50     30.00 
  34   C2'   CT    B   26   9   6    1.53    102.80    -86.30 
  35   H2'1  HC    E   28  26   9    1.09    109.50    120.00 
  36   H2'2  HC    E   28  26   9    1.09    109.50    240.00 
  37   O3'   OH    M   26   9   6    1.42    116.52   -203.47 
  40   H3T   HO    M   31  26   9    0.96    114.97    180.00 
                                                              
CHARGE + deoxy cyt, dft/cc-pvtz, polarization corrected
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1314  0.0949
 -0.0350 -0.0594  0.1971 -0.3813  0.1745
  0.4751 -0.7150  0.3550  0.3550  0.0329
 -0.4554  0.4292 -0.0726 -0.2108 -0.2108
  0.1568  0.0639 -0.0414  0.0452  0.0452
 -0.5941  0.4026


IMPROPER
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-CYTOSINE - with 5' - OH end group and 3' - O[minus] group   
                                                              
 RC5  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.49    108.10   -127.70 
  19   C6    CM    B   14  12  11    1.36    121.10     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.36    121.00    180.00 
  22   H5    HA    E   17  15  14    1.09    120.00    180.00 
  23   C4    CA    B   17  15  14    1.43    116.90      0.00 
  24   N4    N2    B   19  17  15    1.32    120.10    180.00 
  25   H41   H     E   20  19  17    1.01    117.70    180.00 
  26   H42   H     E   20  19  17    1.01    120.27      0.00 
  27   N3    NC    B   19  17  15    1.33    121.70      0.00 
  28   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  29   C2    C     S   23  19  17    1.36    120.50      0.00 
  30   O2    O     B   24  23  19    1.24    122.40    180.00 
  31   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  32   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  33   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  34   H3'   H1    E   26   9   6    1.09    109.50     30.00 
  35   C2'   CT    B   26   9   6    1.53    102.80    -86.30 
  36   H2'1  H1    E   28  26   9    1.09    109.50    120.00 
  37   O2'   OH    S   28  26   9    1.43    109.50    240.00 
  40   HO'2  HO    E   30  28  26    0.96    107.00    180.00 
  41   O3'   OS    M   26   9   6    1.42    116.52   -203.47 
                                                              
CHARGE + resp RC5E, dft/cc-pvtz, polarization corrected 
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0247  0.1403
  0.0249 -0.0880  0.1856 -0.3548  0.1679
  0.4521 -0.7135  0.3501  0.3501  0.0324
 -0.4310  0.3722 -0.0511 -0.2194 -0.2194
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.4746

IMPROPER
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-CYTOSINE - with 5' - phosphate group and 3' - O[minus] group
                                                              
 RC   INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.49    108.10   -127.70 
  21   C6    CM    B   16  14  13    1.36    121.10     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.36    121.00    180.00 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    CA    B   19  17  16    1.43    116.90      0.00 
  26   N4    N2    B   21  19  17    1.32    120.10    180.00 
  27   H41   H     E   22  21  19    1.01    117.70    180.00 
  28   H42   H     E   22  21  19    1.01    120.27      0.00 
  29   N3    NC    B   21  19  17    1.33    121.70      0.00 
  30   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  31   C2    C     S   25  21  19    1.36    120.50      0.00 
  32   O2    O     B   26  25  21    1.24    122.40    180.00 
  33   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   28  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   28  11   8    1.53    102.80    -86.30 
  38   H2'1  H1    E   30  28  11    1.09    109.50    120.00 
  39   O2'   OH    S   30  28  11    1.43    109.50    240.00 
  42   HO'2  HO    E   32  30  28    0.96    107.00    180.00 
  43   O3'   OS    M   28  11   8    1.42    116.52   -203.47 
                                                              
CHARGE + resp RC, dft/cc-pvtz, polarization corrected 
  1.0720 -0.7552 -0.7552 -0.4087  0.0955
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.0247  0.1403  0.0249 -0.0880  0.1856
 -0.3548  0.1679  0.4521 -0.7135  0.3501
  0.3501  0.0324 -0.4310  0.3722 -0.0511
 -0.2194 -0.2194  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.4746

IMPROPER 
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-CYTOSINE - with 5' - phosphate group and 3' - OH group      
                                                              
 RC3  INT     1                                               
 CORRECT OMIT DU   BEG                                        
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   P     P     M    3   2   1    1.60    119.04    200.00 
   5   O1P   O2    E    4   3   2    1.48    109.61    150.00 
   6   O2P   O2    E    4   3   2    1.48    109.58     20.00 
   7   O5'   OS    M    4   3   2    1.60    101.43    -98.89 
  10   C5'   CT    M    7   4   3    1.44    119.00    -39.22 
  11   H5'1  H1    E    8   7   4    1.09    109.50     60.00 
  12   H5'2  H1    E    8   7   4    1.09    109.50    -60.00 
  13   C4'   CT    M    8   7   4    1.52    110.00    180.00 
  14   H4'   H1    E   11   8   7    1.09    109.50   -200.00 
  15   O4'   OS    S   11   8   7    1.46    108.86    -86.31 
  18   C1'   CT    B   13  11   8    1.42    110.04    105.60 
  19   H1'   H2    E   14  13  11    1.09    109.50   -240.00 
  20   N1    N*    S   14  13  11    1.49    108.10   -127.70 
  21   C6    CM    B   16  14  13    1.36    121.10     81.59 
  22   H6    H4    E   17  16  14    1.08    120.00      0.00 
  23   C5    CM    B   17  16  14    1.36    121.00    180.00 
  24   H5    HA    E   19  17  16    1.09    120.00    180.00 
  25   C4    CA    B   19  17  16    1.43    116.90      0.00 
  26   N4    N2    B   21  19  17    1.32    120.10    180.00 
  27   H41   H     E   22  21  19    1.01    117.70    180.00 
  28   H42   H     E   22  21  19    1.01    120.27      0.00 
  29   N3    NC    B   21  19  17    1.33    121.70      0.00 
  30   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  31   C2    C     S   25  21  19    1.36    120.50      0.00 
  32   O2    O     B   26  25  21    1.24    122.40    180.00 
  33   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  34   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  35   C3'   CT    M   11   8   7    1.53    115.78   -329.11 
  36   H3'   H1    E   28  11   8    1.09    109.50     30.00 
  37   C2'   CT    B   28  11   8    1.53    102.80    -86.30 
  38   H2'1  H1    E   30  28  11    1.09    109.50    120.00 
  39   O2'   OH    S   30  28  11    1.43    109.50    240.00 
  42   HO'2  HO    E   32  30  28    0.96    107.00    180.00 
  43   O3'   OH    M   28  11   8    1.42    116.52   -203.47 
  46   H3T   HO    M   34  28  11    0.96    114.97    180.00 
                                                              
CHARGE + resp RC3E, dft/cc-pvtz, polarization corrected 
  1.0720 -0.7552 -0.7552 -0.4087  0.0955 
  0.0462  0.0462  0.0195  0.0998 -0.2620
  0.0247  0.1403  0.0249 -0.0880  0.1856
 -0.3548  0.1679  0.4521 -0.7135  0.3501
  0.3501  0.0324 -0.4310  0.3722 -0.0511
 -0.2194 -0.2194  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.5793  0.4126

IMPROPER           
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
R-CYTOSINE - with 5' - OH group and 3' - OH group             
                                                              
 RCN  INT     1                                               
 CORRECT NOMIT DU   BEG                                       
   0.0                                                        
   1   DUMM  DU    M    0  -1  -2    0.00      0.00      0.00 
   2   DUMM  DU    M    1   0  -1    1.00      0.00      0.00 
   3   DUMM  DU    M    2   1   0    1.00     90.00      0.00 
   4   H5T   HO    M    3   2   1    1.00    120.00    180.00 
   5   O5'   OH    M    4   3   2    0.96    101.43    -98.89 
   8   C5'   CT    M    5   4   3    1.44    119.00    -39.22 
   9   H5'1  H1    E    6   5   4    1.09    109.50     60.00 
  10   H5'2  H1    E    6   5   4    1.09    109.50    -60.00 
  11   C4'   CT    M    6   5   4    1.52    110.00   -180.00 
  12   H4'   H1    E    9   6   5    1.09    109.50   -200.00 
  13   O4'   OS    S    9   6   5    1.46    108.86    -86.31 
  16   C1'   CT    B   11   9   5    1.42    110.04    105.60 
  17   H1'   H2    E   12  11   9    1.09    109.50   -240.00 
  18   N1    N*    S   12  11   9    1.49    108.10   -127.70 
  19   C6    CM    B   14  12  11    1.36    121.10     81.59 
  20   H6    H4    E   15  14  12    1.08    120.00      0.00 
  21   C5    CM    B   15  14  12    1.36    121.00    180.00 
  22   H5    HA    E   17  15  14    1.09    120.00    180.00 
  23   C4    CA    B   17  15  14    1.43    116.90      0.00 
  24   N4    N2    B   19  17  15    1.32    120.10    180.00 
  25   H41   H     E   20  19  17    1.01    117.70    180.00 
  26   H42   H     E   20  19  17    1.01    120.27      0.00 
  27   N3    NC    B   19  17  15    1.33    121.70      0.00 
  28   EP21  EP    E    5   4   3    0.35    120.00    180.00 
  29   C2    C     S   23  19  17    1.36    120.50      0.00 
  30   O2    O     B   24  23  19    1.24    122.40    180.00 
  31   EP+1  EP    E    5   4   3    0.35    120.00      0.00 
  32   EP-1  EP    E    5   4   3    0.35    120.00    180.00 
  33   C3'   CT    M    9   6   5    1.53    115.78   -329.11 
  34   H3'   H1    E   26   9   6    1.09    109.50     30.00 
  35   C2'   CT    B   26   9   6    1.53    102.80    -86.30 
  36   H2'1  H1    E   28  26   9    1.09    109.50    120.00 
  37   O2'   OH    S   28  26   9    1.43    109.50    240.00 
  40   HO'2  HO    E   30  28  26    0.96    107.00    180.00 
  41   O3'   OH    M   26   9   6    1.42    116.52   -203.47 
  44   H3T   HO    M   32  26   9    0.96    114.97    180.00 
                                                              
CHARGE + resp RCYT, dft/cc-pvtz, polarization corrected
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0247  0.1403
  0.0249 -0.0880  0.1856 -0.3548  0.1679
  0.4521 -0.7135  0.3501  0.3501  0.0324
 -0.4310  0.3722 -0.0511 -0.2194 -0.2194
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.5793  0.4126

IMPROPER 
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C1'  C2'                                                     
 C2   N1                                                      
                                                              
DONE                                                          
N-methyl-ADENINE                                                     
      
AME INT     1
 CORRECT NOMIT DU   BEG
   0.0
   1 DUMM  DU   M   0  -1  -2      .00000      .0000     .0000
   2 DUMM  DU   M   1   0  -1     1.00000      .0000     .0000
   3 DUMM  DU   M   2   1   0     1.00000    90.0000     .0000
   4 H11'  H1   M   3   2   1     3.88600    92.5070   92.0960
   5 C1'   CT   M   4   3   2     1.09000   102.0370   71.2940
   6 H12'  H1   E   5   4   3     1.09000   109.4780  183.2340
   7 H13'  H1   E   5   4   3     1.09000   107.8200   59.2900
   8 N9    N*   M   5   4   3     1.52100   109.6030  295.5360
   9 C8    CK   M   8   5   4     1.37000   131.1870   81.6070
  10 H8    H5   E   9   8   5     1.08000   120.0060     .0050
  11 N7    NB   M   9   8   5     1.30000   113.8870  177.0200
  12 EP21  EP   E   8   5   4     0.35000   128.0000  180.0000
  13 C5    CB   M  11   9   8     1.38900   104.0390     .0040
  14 C6    CA   M  12  11   9     1.40000   132.4290  180.0430
  15 N6    N2   B  13  12  11     1.34000   123.4980  359.9610
  16 H61   H    E  14  13  12     1.01000   119.9420  180.0440
  17 H62   H    E  14  13  12     1.01000   120.0050     .0060
  18 N1    NC   M  13  12  11     1.34000   117.4080  179.9600
  19 EP22  EP   E  17  13  12     0.35000   120.6000  180.0000
  20 C2    CQ   M  17  13  12     1.33000   118.8320     .0080
  21 H2    H5   E  18  17  13     1.08000   120.0130  179.9930
  22 N3    NC   M  18  17  13     1.31900   129.1490  359.9310
  23 EP23  EP   E  20  18  17     0.35000   124.6000  180.0000
  24 C4    CB   M  20  18  17     1.35000   110.8300     .0830
 
CHARGE + ADE new-resp, polarization corrected, dft/cc-pvtz (corrected Aug8,2001)
  0.102021 -0.177538  0.102021  0.102021  0.037703
 -0.027818  0.163874 -0.023835 -0.325864  0.017577
  0.365596 -0.730374  0.382107  0.382107  0.002795
 -0.401713  0.136005  0.104593  0.051620 -0.447903
  0.185005

IMPROPER                                                      
 C8   C4   N9   C1'                                           
 C6   H61  N6   H62                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   H2                                            
 C5   N1   C6   N6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
N-methyl-CYTOSINE                                                    
       
CME INT     1
 CORRECT NOMIT DU   BEG
   0.0
   1 DUMM  DU   M   0  -1  -2      .00000      .0000     .0000    .0000
   2 DUMM  DU   M   1   0  -1     1.00000      .0000     .0000    .0000
   3 DUMM  DU   M   2   1   0     1.00000    90.0000     .0000    .0000
   4 H11'  H1   M   3   2   1     3.88600    92.5070   92.0960    .0000
   5 C1'   CT   M   4   3   2     1.09000   102.0370   71.2940    .0000
   6 H12'  H1   E   5   4   3     1.09000   109.4780  183.2340    .0000
   7 H13'  H1   E   5   4   3     1.09000   107.8200   59.2900    .0000
   8 N1    N*   M   5   4   3     1.49000   108.1190  295.5500    .0000
   9 C6    CM   M   8   5   4     1.36000   121.1340   81.5730    .0000
  10 H6    H4   E   9   8   5     1.08000   119.9490     .0420    .0000
  11 C5    CM   M   9   8   5     1.36000   121.0290  180.0410    .0000
  12 H5    HA   E  11   9   8     1.09000   119.9940  180.0670    .0000
  13 C4    CA   M  11   9   8     1.43000   116.8750  359.9720    .0000
  14 N4    N2   B  13  11   9     1.31900   120.0770  179.9930    .0000
  15 H41   H    E  14  13  11     1.01000   117.7460  180.0300    .0000
  16 H42   H    E  14  13  11     1.01000   120.2950     .0610    .0000
  17 N3    NC   M  13  11   9     1.33000   121.7030     .0750    .0000
  18 EP21  EP   E  17  13  11     0.35000   120.0000  180.0000    .0000
  19 C2    C    M  17  13  11     1.36000   120.5330  359.9230    .0000
  20 O2    O    B  18  17  13     1.23900   122.4570  180.0510    .0000
  21 EP+1  EP   E  18  17  13     0.35000   120.0000    0.0000    .0000
  22 EP-1  EP   E  18  17  13     0.35000   120.0000  180.0000    .0000
 
CHARGE + deoxy-CYT-B polarization corrected charges: CYT, df/cc-pvtz (Aug82001)
  0.066681 -0.069856  0.066681  0.066681  0.022218
 -0.110255  0.173830 -0.412853  0.185270  0.569685
 -0.848028  0.401758  0.401758  0.005018 -0.447333
  0.393416 -0.048423 -0.208124 -0.208124

 
IMPROPER                                                      
 C6   C2   N1   C1'                                           
 N1   N3   C2   O2                                            
 C4   H41  N4   H42                                           
 N1   C5   C6   H6                                            
 C6   C4   C5   H5                                            
 N3   C5   C4   N4                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C2   N1                                                      
                                                              
DONE                                                          
N-methyl-GUANINE                                                     
     
GME INT     1
 CORRECT NOMIT DU   BEG
   0.0
   1 DUMM  DU   M   0  -1  -2      .00000      .0000     .0000
   2 DUMM  DU   M   1   0  -1     1.00000      .0000     .0000
   3 DUMM  DU   M   2   1   0     1.00000    90.0000     .0000
   4 H11'  H1   M   3   2   1     3.88600    92.5070   92.0960
   5 C1'   CT   M   4   3   2     1.09000   102.0370   71.2940
   6 H12'  H1   E   5   4   3     1.09000   109.4780  183.2340
   7 H13'  H1   E   5   4   3     1.09000   107.8200   59.2900
   8 N9    N*   M   5   4   3     1.49000   108.0830  295.5380
   9 C8    CK   M   8   5   4     1.38000   129.2070   81.5690
  10 H8    H5   E   9   8   5     1.08000   119.9900     .0590
  11 N7    NB   M   9   8   5     1.31000   114.0170  180.1070
  12 EP21  EP   E  11   9   8     0.35000   128.1000  180.0000
  13 C5    CB   M  11   9   8     1.39000   103.8950     .0350
  14 C6    C    M  12  11   9     1.42000   130.4290  179.9530
  15 O6    O    B  13  12  11     1.23100   128.7830     .0290
  16 EP+1  EP   E  13  12  11     0.35000   120.0000    0.0000
  17 EP-1  EP   E  13  12  11     0.35000   120.0000  180.0000
  18 N1    NA   M  13  12  11     1.40000   111.4060  180.0170
  19 H1    H    E  15  13  12     1.00100   117.3610  179.9310
  20 C2    CA   M  15  13  12     1.38000   125.2260  359.8940
  21 N2    N2   B  17  15  13     1.34100   116.0360  180.0230
  22 H21   H    E  18  17  15     1.01000   126.9570  359.1960
  23 H22   H    E  18  17  15     1.01000   116.5580  180.5620
  24 N3    NC   M  17  15  13     1.33000   123.3460     .0130
  25 EP22  EP   E  21  17  15     0.35000   124.0000  180.0000
  26 C4    CB   M  21  17  15     1.36000   112.1600  359.9980
 
CHARGE + deoxy-GUA-B, polarization corrected, dft/cc-pvtz
   .089706  -.121440   .089706   .089706   .074281
  -.085651   .184829  -.038870  -.296403  -.007060
   .277587  -.004970  -.208286  -.208286  -.312501
   .352318   .355163  -.667710   .350143   .350143
   .050411  -.444315   .131499

IMPROPER                                                      
 C8   C4   N9   C1'                                           
 C5   N1   C6   O6                                            
 C6   C2   N1   H1                                            
 C2   H21  N2   H22                                           
 N7   N9   C8   H8                                            
 N1   N3   C2   N2                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C4   C5                                                      
 C4   N9                                                      
                                                              
DONE                                                          
N-methyl- THYMINE
     
TME INT     1
 CORRECT NOMIT DU   BEG
   0.0
   1 DUMM  DU   M   0  -1  -2      .00000      .0000     .0000
   2 DUMM  DU   M   1   0  -1     1.00000      .0000     .0000
   3 DUMM  DU   M   2   1   0     1.00000    90.0000     .0000
   4 H11'  H1   M   3   2   1     1.10000    92.5070   92.0960
   5 C1'   CT   M   4   3   2     1.09000   102.0370   71.2940
   6 H12'  H1   E   5   4   3     1.09000   109.4780  183.2340
   7 H13'  H1   E   5   4   3     1.09000   107.8200   59.2900
   8 N1    N*   M   5   4   3     1.53000   109.5990  295.5450
   9 C6    CM   M   8   5   4     1.36900   123.0650   81.6170
  10 H6    H4   E   9   8   5     1.08100   120.0030  359.9610
  11 C5    CM   M   9   8   5     1.34000   121.2490  177.3250
  12 C7    CT   3  11   9   8     1.50000   121.6610  179.9620
  13 H71   HC   E  12  11   9     1.09000   109.5000   59.9870
  14 H72   HC   E  12  11   9     1.08900   109.5040  179.9530
  15 H73   HC   E  12  11   9     1.09000   109.5220  300.0240
  16 C4    C    M  11   9   8     1.44000   120.7500  359.9570
  17 O4    O    B  16  11   9     1.23000   125.3460  180.0040
  18 EP+1  EP   E  16  11   9     0.35000   120.0000     .0000
  19 EP-1  EP   E  16  11   9     0.35000   120.0000  180.0000
  20 N3    NA   M  16  11   9     1.38000   114.1000     .0440
  21 H3    H    E  18  16  11     1.08900   116.7820  180.0400
  22 C2    C    M  18  16  11     1.38000   126.4030  359.9360
  23 O2    O    B  20  18  16     1.22100   121.6390  179.9800
  24 EP+2  EP   E  16  11   9     0.35000   120.0000     .0000
  25 EP-2  EP   E  16  11   9     0.35000   120.0000  180.0000
 
CHARGE + THY polarization corrected, dft/cc-pvtz
   .078229  -.084621   .078229   .078229   .003711
  -.153266   .181908   .030564  -.246962   .089321
   .089321   .089321   .303685  -.008777  -.208710
  -.208710  -.304312   .310876   .310292  -.040962
  -.193683  -.193683

IMPROPER                                                      
 C6   C2   N1   C1'                                           
 C4   C6   C5   C7                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C2   N1                                                      
                                                              
DONE                                                          
N-methyl-URACIL                                                      
         
UME INT     1
 CORRECT NOMIT DU   BEG
   0.0
   1 DUMM  DU   M   0  -1  -2      .00000      .0000     .0000
   2 DUMM  DU   M   1   0  -1     1.00000      .0000     .0000
   3 DUMM  DU   M   2   1   0     1.00000    90.0000     .0000
   4 H11'  H1   M   3   2   1     3.88600    92.5070   92.0960
   5 C1'   CT   M   4   3   2     1.09000   102.0370   71.2940
   6 H12'  H1   E   5   4   3     1.09000   109.4780  183.2340
   7 H13'  H1   E   5   4   3     1.09000   107.8200   59.2900
   8 N1    N*   M   5   4   3     1.53000   109.5990  295.5450
   9 C6    CM   M   8   5   4     1.36900   123.0650   81.6170
  10 H6    H4   E   9   8   5     1.08100   120.0030  359.9610
  11 C5    CM   M   9   8   5     1.34000   121.2490  177.3250
  12 H5    HA   E  11   9   8     1.09100   120.0290  179.9930
  13 C4    C    M  11   9   8     1.44000   120.7500  359.9570
  14 O4    O    B  13  11   9     1.23000   125.3460  180.0040
  15 EP+1  EP   E  13  11   9     0.35000   120.0000     .0000
  16 EP-1  EP   E  13  11   9     0.35000   120.0000  180.0000
  17 N3    NA   M  13  11   9     1.38000   114.1000     .0440
  18 H3    H    E  15  13  11     1.08900   116.7820  180.0400
  19 C2    C    M  15  13  11     1.38000   126.4030  359.9360
  20 O2    O    B  17  15  13     1.22100   121.6390  179.9800
  21 EP+2  EP   E  13  11   9     0.35000   120.0000     .0000
  22 EP-2  EP   E  13  11   9     0.35000   120.0000  180.0000
 
CHARGE + URA polarization corrected, dft/cc-pvtz
   .081554  -.098784   .081554   .081554   .044668
  -.118713   .180204  -.280178   .160353   .429305
  -.049990  -.206374  -.206374  -.309324   .300993
   .367041  -.074697  -.191396  -.191396

IMPROPER                                                      
 C6   C2   N1   C1'                                           
 C4   C6   C5   H5                                            
 N1   N3   C2   O2                                            
 C5   N3   C4   O4                                            
 C2   C4   N3   H3                                            
 N1   C5   C6   H6                                            
                                                              
LOOP CLOSING EXPLICIT                                         
 C2   N1                                                      
                                                              
DONE                                                          
STOP
--------------------------------------------------------------
hybrid model: lp at 0.35 on bases and no on sugar and phosphate 
DEOXY
- - - - - - - - - - - - - - - - - - - - -  - 
dade
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1213  0.1250
 -0.0191  0.0456  0.1671 -0.0230 -0.3440
  0.0161  0.3636 -0.6837  0.3562  0.3562
  0.0046 -0.3886  0.1181  0.1016  0.0872
 -0.4679  0.1692  0.1568  0.0639 -0.0414
  0.0452  0.0452 -0.5941  0.4026
dcyt
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1314  0.0927
 -0.0350 -0.0594  0.1971 -0.3813  0.1745
  0.4751 -0.7150  0.3550  0.3550  0.0329
 -0.4554  0.4292 -0.0726 -0.2108 -0.2108
  0.1568  0.0639 -0.0414  0.0452  0.0452
 -0.5941  0.4026
dgua
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.1494  0.1039
  0.0022  0.0092  0.1706 -0.0129 -0.3374
  0.0696  0.3049 -0.0173 -0.2051 -0.2051
 -0.4073  0.3500  0.4834 -0.7230  0.3459
  0.3459  0.0391 -0.4364  0.0769  0.1568
  0.0639 -0.0414  0.0452  0.0452 -0.5941
  0.4026
dthy
  0.4096 -0.5644 -0.0091  0.0663  0.0663
  0.0623  0.0913 -0.3053  0.0729  0.1273
  0.0096 -0.1929  0.2403  0.0033 -0.1309
  0.0576  0.0576  0.0576  0.3669 -0.0164
 -0.2106 -0.2106 -0.3515  0.3258  0.3819
 -0.0545 -0.2144 -0.2144  0.1568  0.0639
 -0.0414  0.0452  0.0452 -0.5941  0.4026
pom
  0.0580  0.1234  0.0066  0.0034 -0.4747
  1.0733 -0.7545 -0.7545 -0.4357 -0.0281
  0.0404  0.0484  0.0940

--------------------------------------------------------------
RIBO
- - - - - - - - - - - - - - - - - - - - -  - 
rade
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0214  0.1607
  0.0285  0.0374  0.1542 -0.0013 -0.3616
  0.0327  0.3496 -0.6637  0.3417  0.3417
  0.0204 -0.3931  0.1186  0.0994  0.0538
 -0.4318  0.1141  0.2484  0.0147  0.0346
  0.0875 -0.5105  0.3787 -0.5793  0.4126
rcyt
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.0247  0.1402
  0.0249 -0.0880  0.1856 -0.3548  0.1679
  0.4521 -0.7135  0.3501  0.3501  0.0324
 -0.4310  0.3722 -0.0511 -0.2194 -0.2194
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.5793  0.4126
rgua
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1426  0.0858
 -0.0180  0.0162  0.1555  0.0197 -0.3612
  0.0795  0.2803 -0.0133 -0.2038 -0.2038
 -0.3586  0.3364  0.4549 -0.7249  0.3457
  0.3457  0.0063 -0.4016  0.0395  0.2484
  0.0147  0.0346  0.0875 -0.5105  0.3787
 -0.5793  0.4126
rura
  0.4052 -0.5602  0.0955  0.0462  0.0462
  0.0195  0.0998 -0.2620  0.1030  0.1011
  0.0291 -0.1035  0.1860 -0.2499  0.1516
  0.3796 -0.0360 -0.2066 -0.2066 -0.2404
  0.2897  0.2962 -0.0716 -0.1995 -0.1995
  0.2484  0.0147  0.0346  0.0875 -0.5105
  0.3787 -0.5793  0.4126
pom
  0.0825  0.0228  0.0333  0.0280 -0.4483
  1.0720 -0.7552 -0.7552 -0.4349 -0.0212
  0.0383  0.0454  0.0926

