# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 12:13:20 2021
#   Inital geometry file: a 155 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-(2-{[(2-aminophenyl)carbonyl]oxy}ethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OCCOC(=O)c3ccccc3N)[C@@H](O)[C@H]2O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 1AA  1AA  5'-O-[(S)-{[(R)-(2-{[(2-aminophenyl)carbonyl]oxy}ethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  61  37  .  2021-08-03  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1AA
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 1AA  O1    O  O     0  -0.434   3.7605   2.4778  12.2475
 1AA  C1    C  CR6   0   0.614   2.9435   3.2146  12.7879
 1AA  N4    N  N     0  -0.553   2.1188   2.8023  13.7693
 1AA  C9'   C  CR6   0   0.480   1.2312   3.6239  14.2966
 1AA  N3    N  NH2   0  -0.807   0.4382   3.1613  15.2625
 1AA  C8'   C  CR16  0  -0.442   1.1024   4.9778  13.8643
 1AA  C7'   C  CR16  0   0.056   1.9570   5.3921  12.9060
 1AA  N2    N  NR6   0  -0.598   2.8697   4.5522  12.3688
 1AA  C2    C  CH1   0   0.234   3.8332   4.9821  11.3444
 1AA  O2'   O  O2    0  -0.502   3.9293   6.3791  11.3551
 1AA  C3    C  CH1   0  -0.086   3.3909   4.5722   9.9340
 1AA  O4'   O  OH1   0  -0.644   4.5354   4.2958   9.1734
 1AA  C4    C  CH1   0   0.003   2.7033   5.8538   9.4496
 1AA  O3'   O  OH1   0  -0.618   2.6780   6.0087   8.0638
 1AA  C5    C  CH1   0  -0.133   3.5845   6.9196  10.0865
 1AA  C6    C  CH2   0  -0.197   2.9693   8.2870  10.2312
 1AA  O2    O  O2    0  -0.561   1.7026   8.1856  10.8998
 1AA  P1    P  P     0   1.404   0.4283   8.9916  10.3993
 1AA  O1'   O  O     0  -0.699   0.6384  10.4183  10.1072
 1AA  O9    O  OH1   0  -0.674  -0.6773   8.5618  11.4424
 1AA  O3    O  O2    0  -0.706  -0.0951   8.1274   9.1298
 1AA  P2    P  P     0   1.422  -0.0154   8.5782   7.5727
 1AA  O8    O  O     0  -0.652   1.3169   8.9711   7.0958
 1AA  O7    O  OH1   0  -0.625  -1.1676   9.6714   7.5158
 1AA  O4    O  O2    0  -0.643  -0.5795   7.2863   6.8563
 1AA  C7    C  CH2   0  -0.189  -1.9379   6.8336   6.9347
 1AA  C8    C  CH2   0  -0.263  -1.9837   5.3925   7.3710
 1AA  O5    O  O2    0  -0.419  -1.3396   4.5554   6.4099
 1AA  C9    C  C     0   0.562  -0.1054   4.1280   6.6349
 1AA  O6    O  O     0  -0.393   0.4684   4.3247   7.6936
 1AA  C1'   C  CR6   0  -0.133   0.4668   3.3775   5.5140
 1AA  C2'   C  CR16  0  -0.254  -0.2136   3.3239   4.2856
 1AA  C3'   C  CR16  0  -0.315   0.2981   2.6533   3.1997
 1AA  C4'   C  CR16  0  -0.260   1.5273   2.0023   3.3311
 1AA  C5'   C  CR16  0  -0.309   2.2153   2.0321   4.5203
 1AA  C6'   C  CR6   0   0.207   1.7153   2.7174   5.6461
 1AA  N1    N  NH2   0  -0.758   2.4719   2.7298   6.7763
 1AA  HN31  H  HNH2  0   0.414  -0.2409   3.7497  15.7118
 1AA  HN32  H  HNH2  0   0.393   0.5355   2.2149  15.5885
 1AA  H8'   H  HCR6  0   0.259   0.3783   5.6531  14.2942
 1AA  H7'   H  HCR6  0   0.300   1.9427   6.4082  12.5464
 1AA  H2    H  HCH1  0   0.272   4.7956   4.5358  11.6010
 1AA  H3    H  HCH1  0   0.282   2.7049   3.7176   9.9600
 1AA  H4'   H  HOH1  0   0.445   4.3325   4.5059   8.2529
 1AA  H4    H  HCH1  0   0.272   1.6952   5.8902   9.8789
 1AA  H6    H  HOH1  0   0.454   1.9270   5.4972   7.7270
 1AA  H5    H  HCH1  0   0.294   4.4904   7.0520   9.4801
 1AA  H61   H  HCH2  0   0.251   2.8706   8.7176   9.2322
 1AA  H62   H  HCH2  0   0.340   3.6133   8.9449  10.8161
 1AA  HO9   H  HOH1  0   0.514  -0.7276   9.1252  12.2270
 1AA  HO7   H  HOH1  0   0.535  -0.9879  10.4094   6.9165
 1AA  H71   H  HCH2  0   0.301  -2.3778   6.9561   5.9448
 1AA  H72   H  HCH2  0   0.237  -2.5356   7.4173   7.6377
 1AA  H81   H  HCH2  0   0.287  -3.0276   5.0810   7.4010
 1AA  H82   H  HCH2  0   0.261  -1.5555   5.2602   8.3637
 1AA  H2'   H  HCR6  0   0.257  -1.1627   3.8309   4.1846
 1AA  H3'   H  HCR6  0   0.246  -0.2419   2.6328   2.2635
 1AA  H1    H  HCR6  0   0.273   1.9478   1.4632   2.4917
 1AA  H5'   H  HCR6  0   0.269   3.1653   1.5185   4.6067
 1AA  HN11  H  HNH2  0   0.366   2.0260   2.9459   7.6504
 1AA  HN12  H  HNH2  0   0.363   3.2062   2.0437   6.8338

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 1AA  O1   C1    double    1.226  0.020  1.226
 1AA  C1   N4    single    1.347  0.020  1.347
 1AA  C1   N2    single    1.404  0.020  1.404
 1AA  N4   C9'   double    1.319  0.020  1.319
 1AA  C9'  N3    single    1.333  0.020  1.333
 1AA  C9'  C8'   single    1.427  0.020  1.427
 1AA  N3   HN31  single    0.860  0.020  1.020
 1AA  N3   HN32  single    0.860  0.020  1.020
 1AA  C8'  C7'   double    1.349  0.020  1.349
 1AA  C8'  H8'   single    0.930  0.020  1.080
 1AA  C7'  N2    single    1.352  0.020  1.352
 1AA  C7'  H7'   single    0.930  0.020  1.080
 1AA  N2   C2    single    1.471  0.020  1.471
 1AA  C2   O2'   single    1.400  0.020  1.400
 1AA  C2   C3    single    1.534  0.020  1.534
 1AA  C2   H2    single    0.970  0.020  1.090
 1AA  O2'  C5    single    1.421  0.020  1.421
 1AA  C3   O4'   single    1.402  0.020  1.402
 1AA  C3   C4    single    1.533  0.020  1.533
 1AA  C3   H3    single    0.970  0.020  1.090
 1AA  O4'  H4'   single    0.850  0.020  0.980
 1AA  C4   O3'   single    1.395  0.020  1.395
 1AA  C4   C5    single    1.523  0.020  1.523
 1AA  C4   H4    single    0.970  0.020  1.090
 1AA  O3'  H6    single    0.850  0.020  0.980
 1AA  C5   C6    single    1.506  0.020  1.506
 1AA  C5   H5    single    0.970  0.020  1.090
 1AA  C6   O2    single    1.436  0.020  1.436
 1AA  C6   H61   single    0.970  0.020  1.090
 1AA  C6   H62   single    0.970  0.020  1.090
 1AA  O2   P1    single    1.589  0.020  1.589
 1AA  P1   O1'   double    1.471  0.020  1.471
 1AA  P1   O9    single    1.580  0.020  1.580
 1AA  P1   O3    single    1.623  0.020  1.623
 1AA  O9   HO9   single    0.850  0.020  0.980
 1AA  O3   P2    single    1.623  0.020  1.623
 1AA  P2   O8    double    1.469  0.020  1.469
 1AA  P2   O7    single    1.589  0.020  1.589
 1AA  P2   O4    single    1.581  0.020  1.581
 1AA  O7   HO7   single    0.850  0.020  0.980
 1AA  O4   C7    single    1.434  0.020  1.434
 1AA  C7   C8    single    1.506  0.020  1.506
 1AA  C7   H71   single    0.970  0.020  1.090
 1AA  C7   H72   single    0.970  0.020  1.090
 1AA  C8   O5    single    1.428  0.020  1.428
 1AA  C8   H81   single    0.970  0.020  1.090
 1AA  C8   H82   single    0.970  0.020  1.090
 1AA  O5   C9    single    1.325  0.020  1.325
 1AA  C9   O6    double    1.220  0.020  1.220
 1AA  C9   C1'   single    1.465  0.020  1.465
 1AA  C1'  C2'   aromatic  1.405  0.020  1.405
 1AA  C1'  C6'   aromatic  1.418  0.020  1.418
 1AA  C2'  C3'   aromatic  1.375  0.020  1.375
 1AA  C2'  H2'   single    0.930  0.020  1.080
 1AA  C3'  C4'   aromatic  1.397  0.020  1.397
 1AA  C3'  H3'   single    0.930  0.020  1.080
 1AA  C4'  C5'   aromatic  1.374  0.020  1.374
 1AA  C4'  H1    single    0.930  0.020  1.080
 1AA  C5'  C6'   aromatic  1.410  0.020  1.410
 1AA  C5'  H5'   single    0.930  0.020  1.080
 1AA  C6'  N1    single    1.360  0.020  1.360
 1AA  N1   HN11  single    0.890  0.020  1.040
 1AA  N1   HN12  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 1AA  N2    C1   N4    118.50  3.000
 1AA  N2    C1   O1    118.44  3.000
 1AA  N4    C1   O1    123.06  3.000
 1AA  C9'   N4   C1    120.84  3.000
 1AA  C8'   C9'  N3    119.68  3.000
 1AA  C8'   C9'  N4    122.03  3.000
 1AA  N3    C9'  N4    118.29  3.000
 1AA  HN32  N3   HN31  118.14  3.000
 1AA  HN32  N3   C9'   120.27  3.000
 1AA  HN31  N3   C9'   121.54  3.000
 1AA  H8'   C8'  C7'   121.04  3.000
 1AA  H8'   C8'  C9'   122.24  3.000
 1AA  C7'   C8'  C9'   116.70  3.000
 1AA  H7'   C7'  N2    117.52  3.000
 1AA  H7'   C7'  C8'   121.20  3.000
 1AA  N2    C7'  C8'   121.28  3.000
 1AA  C2    N2   C7'   122.52  3.000
 1AA  C2    N2   C1    116.88  3.000
 1AA  C7'   N2   C1    120.59  3.000
 1AA  H2    C2   C3    111.17  3.000
 1AA  H2    C2   O2'   110.22  3.000
 1AA  C3    C2   O2'   107.06  3.000
 1AA  H2    C2   N2    107.13  3.000
 1AA  C3    C2   N2    111.93  3.000
 1AA  O2'   C2   N2    109.34  3.000
 1AA  C5    O2'  C2    110.85  3.000
 1AA  H3    C3   C4    112.25  3.000
 1AA  H3    C3   O4'   111.72  3.000
 1AA  C4    C3   O4'   111.08  3.000
 1AA  H3    C3   C2    111.52  3.000
 1AA  C4    C3   C2    101.33  3.000
 1AA  O4'   C3   C2    108.43  3.000
 1AA  H4'   O4'  C3    107.62  3.000
 1AA  H4    C4   C5    110.19  3.000
 1AA  H4    C4   O3'   111.63  3.000
 1AA  C5    C4   O3'   110.39  3.000
 1AA  H4    C4   C3    108.45  3.000
 1AA  C5    C4   C3    101.16  3.000
 1AA  O3'   C4   C3    114.52  3.000
 1AA  H6    O3'  C4    107.50  3.000
 1AA  H5    C5   C6    106.29  3.000
 1AA  H5    C5   C4    109.32  3.000
 1AA  C6    C5   C4    116.06  3.000
 1AA  H5    C5   O2'   109.79  3.000
 1AA  C6    C5   O2'   111.01  3.000
 1AA  C4    C5   O2'   104.33  3.000
 1AA  H62   C6   H61   107.82  3.000
 1AA  H62   C6   O2    108.28  3.000
 1AA  H61   C6   O2    111.96  3.000
 1AA  H62   C6   C5    110.97  3.000
 1AA  H61   C6   C5    107.88  3.000
 1AA  O2    C6   C5    109.93  3.000
 1AA  P1    O2   C6    121.67  3.000
 1AA  O3    P1   O9     98.39  3.000
 1AA  O3    P1   O1'   114.03  3.000
 1AA  O9    P1   O1'   119.66  3.000
 1AA  O3    P1   O2    103.60  3.000
 1AA  O9    P1   O2    102.44  3.000
 1AA  O1'   P1   O2    116.10  3.000
 1AA  HO9   O9   P1    114.43  3.000
 1AA  P2    O3   P1    125.94  3.000
 1AA  O4    P2   O7    106.69  3.000
 1AA  O4    P2   O8    113.27  3.000
 1AA  O7    P2   O8    117.52  3.000
 1AA  O4    P2   O3    100.97  3.000
 1AA  O7    P2   O3    100.94  3.000
 1AA  O8    P2   O3    115.49  3.000
 1AA  HO7   O7   P2    114.35  3.000
 1AA  C7    O4   P2    124.83  3.000
 1AA  H72   C7   H71   107.67  3.000
 1AA  H72   C7   C8    107.96  3.000
 1AA  H71   C7   C8    110.99  3.000
 1AA  H72   C7   O4    112.65  3.000
 1AA  H71   C7   O4    107.29  3.000
 1AA  C8    C7   O4    110.29  3.000
 1AA  H82   C8   H81   108.47  3.000
 1AA  H82   C8   O5    111.40  3.000
 1AA  H81   C8   O5    106.44  3.000
 1AA  H82   C8   C7    111.60  3.000
 1AA  H81   C8   C7    108.09  3.000
 1AA  O5    C8   C7    110.61  3.000
 1AA  C9    O5   C8    119.65  3.000
 1AA  C1'   C9   O6    124.24  3.000
 1AA  C1'   C9   O5    113.51  3.000
 1AA  O6    C9   O5    122.23  3.000
 1AA  C6'   C1'  C2'   119.32  3.000
 1AA  C6'   C1'  C9    120.72  3.000
 1AA  C2'   C1'  C9    119.95  3.000
 1AA  H2'   C2'  C3'   118.81  3.000
 1AA  H2'   C2'  C1'   119.27  3.000
 1AA  C3'   C2'  C1'   121.92  3.000
 1AA  H3'   C3'  C4'   120.80  3.000
 1AA  H3'   C3'  C2'   120.49  3.000
 1AA  C4'   C3'  C2'   118.71  3.000
 1AA  H1    C4'  C5'   119.17  3.000
 1AA  H1    C4'  C3'   120.05  3.000
 1AA  C5'   C4'  C3'   120.78  3.000
 1AA  H5'   C5'  C6'   118.55  3.000
 1AA  H5'   C5'  C4'   119.85  3.000
 1AA  C6'   C5'  C4'   121.60  3.000
 1AA  N1    C6'  C5'   118.08  3.000
 1AA  N1    C6'  C1'   124.24  3.000
 1AA  C5'   C6'  C1'   117.66  3.000
 1AA  HN12  N1   HN11  114.87  3.000
 1AA  HN12  N1   C6'   116.55  3.000
 1AA  HN11  N1   C6'   118.55  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 1AA  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 1AA  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 1AA  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 1AA  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 1AA  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 1AA  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 1AA  CONST_07  C8'   C9'  N4   C1      0.00   0.0  0
 1AA  CONST_08  C7'   N2   C1   N4      0.00   0.0  0
 1AA  CONST_09  C2    N2   C1   N4    180.00   0.0  0
 1AA  CONST_10  N2    C1   N4   C9'     0.00   0.0  0
 1AA  CONST_11  C3'   C2'  C1'  C9    180.00   0.0  0
 1AA  CONST_12  C5'   C6'  C1'  C9    180.00   0.0  0
 1AA  CONST_13  N1    C6'  C1'  C2'   180.00   0.0  0
 1AA  CONST_14  N1    C6'  C5'  C4'   180.00   0.0  0
 1AA  CONST_15  C9'   N4   C1   O1    180.00   0.0  0
 1AA  CONST_16  C7'   N2   C1   O1    180.00   0.0  0
 1AA  CONST_17  C2    N2   C1   O1      0.00   0.0  0
 1AA  CONST_18  N3    C9'  N4   C1    180.00   0.0  0
 1AA  CONST_19  H3'   C3'  C2'  C1'   180.00   0.0  0
 1AA  CONST_20  H5'   C5'  C6'  C1'   180.00   0.0  0
 1AA  CONST_21  H1    C4'  C3'  C2'   180.00   0.0  0
 1AA  CONST_22  H2'   C2'  C3'  C4'   180.00   0.0  0
 1AA  CONST_25  HN31  N3   C9'  N4    180.00   0.0  0
 1AA  CONST_26  HN32  N3   C9'  N4      0.00   0.0  0
 1AA  Var_01    C2'   C1'  C9   O5      8.37  30.0  2
 1AA  Var_02    C1'   C9   O5   C8   -174.99  30.0  3
 1AA  Var_03    O1'   P1   O2   C6    -47.35  30.0  3
 1AA  Var_04    O8    P2   O3   P1     53.60  30.0  3
 1AA  Var_05    C8    C7   O4   P2   -126.98  30.0  3
 1AA  Var_06    O5    C8   C7   O4    -62.81  30.0  3
 1AA  Var_07    H61   C6   O2   P1    -16.45  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1AA  chir_01  C2  N2   O2'  C3  positiv
 1AA  chir_02  C3  O4'  C2   C4  negativ
 1AA  chir_03  C4  O3'  C5   C3  positiv
 1AA  chir_04  C5  O2'  C4   C6  negativ
 1AA  chir_05  P1  O1'  O9   O3  both
 1AA  chir_06  P2  O8   O7   O4  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 1AA  plan-1  O5    0.020
 1AA  plan-1  C9    0.020
 1AA  plan-1  O6    0.020
 1AA  plan-1  C1'   0.020
 1AA  plan-2  O1    0.020
 1AA  plan-2  C1    0.020
 1AA  plan-2  N4    0.020
 1AA  plan-2  C9'   0.020
 1AA  plan-2  N3    0.020
 1AA  plan-2  C8'   0.020
 1AA  plan-2  C7'   0.020
 1AA  plan-2  N2    0.020
 1AA  plan-2  C2    0.020
 1AA  plan-2  HN31  0.020
 1AA  plan-2  HN32  0.020
 1AA  plan-2  H8'   0.020
 1AA  plan-2  H7'   0.020
 1AA  plan-3  C9    0.020
 1AA  plan-3  C1'   0.020
 1AA  plan-3  C2'   0.020
 1AA  plan-3  C3'   0.020
 1AA  plan-3  C4'   0.020
 1AA  plan-3  C5'   0.020
 1AA  plan-3  C6'   0.020
 1AA  plan-3  N1    0.020
 1AA  plan-3  H2'   0.020
 1AA  plan-3  H3'   0.020
 1AA  plan-3  H1    0.020
 1AA  plan-3  H5'   0.020
 1AA  plan-4  C6'   0.020
 1AA  plan-4  N1    0.020
 1AA  plan-4  HN11  0.020
 1AA  plan-4  HN12  0.020

