# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 01:39:36 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCCNC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 2UH  2UH  'N-[3-(propanoylamino)propyl]guanosine 5'-(trihydrogen diphosphate)'  ligand  62  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2UH
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
 2UH  O3B  O  OH1   0  -0.718  -27.4970   5.3970   3.1310
 2UH  PB   P  P     0   1.462  -26.5802   4.4745   2.2287
 2UH  O1B  O  O     0  -0.687  -27.0658   3.1294   1.8835
 2UH  O2B  O  OH1   0  -0.713  -25.2242   4.6342   3.0268
 2UH  O3A  O  O2    0  -0.703  -26.3018   5.3888   0.9049
 2UH  PA   P  P     0   1.513  -26.8357   5.1122  -0.5934
 2UH  O1A  O  OH1   0  -0.741  -28.4060   5.1408  -0.3406
 2UH  O2A  O  O     0  -0.672  -26.2723   3.9510  -1.2940
 2UH  O5'  O  O2    0  -0.578  -26.4420   6.4646  -1.3193
 2UH  C5'  C  CH2   0  -0.204  -26.7631   7.7773  -0.8517
 2UH  C4'  C  CH1   0  -0.022  -26.7193   8.7391  -2.0167
 2UH  O4'  O  O2    0  -0.494  -25.4174   8.7550  -2.5957
 2UH  C3'  C  CH1   0  -0.049  -27.7020   8.4316  -3.1598
 2UH  O3'  O  OH1   0  -0.647  -28.1509   9.6005  -3.7889
 2UH  C2'  C  CH1   0  -0.003  -26.8083   7.6738  -4.1431
 2UH  O2'  O  OH1   0  -0.640  -27.1604   7.7266  -5.4870
 2UH  C1'  C  CH1   0   0.199  -25.4686   8.3841  -3.9473
 2UH  N9   N  NR5   0  -0.544  -24.3289   7.5667  -4.2706
 2UH  C4   C  CR56  0   0.514  -23.3538   7.8734  -5.1719
 2UH  N3   N  N     0  -0.515  -23.2614   9.0023  -5.8828
 2UH  C8   C  CR15  0   0.092  -24.0225   6.3167  -3.7814
 2UH  N7   N  N     0  -0.442  -22.9479   5.8195  -4.3078
 2UH  C5   C  CR56  0  -0.101  -22.5131   6.7771  -5.1888
 2UH  C6   C  CR6   0   0.498  -21.4039   6.7797  -6.0830
 2UH  O6   O  O     0  -0.476  -20.5617   5.9143  -6.2571
 2UH  N1   N  NR16  0  -0.748  -21.3652   7.9701  -6.8174
 2UH  C2   C  CR6   0   0.760  -22.2446   9.0141  -6.7104
 2UH  N4   N  NH1   0  -0.678  -22.0239  10.0746  -7.4935
 2UH  CAO  C  CH2   0  -0.285  -22.8639  11.2541  -7.4842
 2UH  CAM  C  CH2   0  -0.450  -24.2528  11.0356  -8.0721
 2UH  CAN  C  CH2   0  -0.288  -25.0039  12.3576  -8.2074
 2UH  NAS  N  NH1   0  -0.627  -26.4143  12.1694  -8.4557
 2UH  CAY  C  C     0   0.535  -27.3153  12.0385  -7.4629
 2UH  OAB  O  O     0  -0.499  -27.0363  12.2200  -6.2861
 2UH  CAL  C  CH2   0  -0.554  -28.7050  11.6242  -7.8923
 2UH  CAA  C  CH3   0  -0.674  -28.9840  10.1814  -7.4730
 2UH  H1   H  HOH1  0   0.512  -28.4319   5.1507   3.1398
 2UH  H2   H  HOH1  0   0.512  -24.4818   4.1257   2.6714
 2UH  H3   H  HOH1  0   0.509  -28.9328   4.6870  -1.0133
 2UH  H4   H  HCH2  0   0.268  -26.0400   8.0717  -0.0888
 2UH  H5   H  HCH2  0   0.253  -27.7608   7.8097  -0.4076
 2UH  H6   H  HCH1  0   0.269  -26.9410   9.7282  -1.5992
 2UH  H7   H  HCH1  0   0.249  -28.5409   7.8167  -2.8078
 2UH  H8   H  HOH1  0   0.454  -28.7267  10.0706  -3.1778
 2UH  H9   H  HCH1  0   0.240  -26.7263   6.6384  -3.7920
 2UH  H10  H  HOH1  0   0.459  -27.9767   7.2336  -5.6133
 2UH  H11  H  HCH1  0   0.269  -25.4182   9.2580  -4.6063
 2UH  H12  H  HCR5  0   0.285  -24.6289   5.8305  -3.0334
 2UH  H13  H  HNR6  0   0.422  -20.6076   8.0463  -7.4840
 2UH  H14  H  HNH1  0   0.412  -21.2549  10.0497  -8.1416
 2UH  H15  H  HCH2  0   0.258  -22.3271  12.0129  -8.0539
 2UH  H16  H  HCH2  0   0.243  -22.9551  11.6278  -6.4613
 2UH  H17  H  HCH2  0   0.253  -24.8166  10.3643  -7.4236
 2UH  H18  H  HCH2  0   0.229  -24.1695  10.5556  -9.0507
 2UH  H19  H  HCH2  0   0.249  -24.5847  12.9491  -9.0229
 2UH  H20  H  HCH2  0   0.238  -24.8956  12.9517  -7.2993
 2UH  H21  H  HNH1  0   0.396  -26.6956  11.9312  -9.3922
 2UH  H22  H  HCH2  0   0.240  -28.8392  11.7358  -8.9702
 2UH  H23  H  HCH2  0   0.252  -29.4199  12.2942  -7.4105
 2UH  H24  H  HCH3  0   0.229  -30.0190   9.9171  -7.6893
 2UH  H25  H  HCH3  0   0.222  -28.3422   9.4849  -8.0132
 2UH  H26  H  HCH3  0   0.256  -28.8032  10.0347  -6.4094

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
 2UH  CAA  CAL  single    1.528  0.020  1.528
 2UH  CAL  CAY  single    1.512  0.020  1.512
 2UH  NAS  CAY  single    1.347  0.020  1.347
 2UH  NAS  CAN  single    1.444  0.020  1.444
 2UH  CAM  CAN  single    1.526  0.020  1.526
 2UH  CAM  CAO  single    1.524  0.020  1.524
 2UH  CAY  OAB  double    1.223  0.020  1.223
 2UH  N4   CAO  single    1.448  0.020  1.448
 2UH  N4   C2   single    1.337  0.020  1.337
 2UH  N1   C2   single    1.369  0.020  1.369
 2UH  N1   C6   single    1.399  0.020  1.399
 2UH  O6   C6   double    1.220  0.020  1.220
 2UH  C2   N3   double    1.311  0.020  1.311
 2UH  C6   C5   single    1.425  0.020  1.425
 2UH  N3   C4   single    1.337  0.020  1.337
 2UH  C5   C4   aromatic  1.382  0.020  1.382
 2UH  C5   N7   aromatic  1.372  0.020  1.372
 2UH  C4   N9   aromatic  1.363  0.020  1.363
 2UH  O2'  C2'  single    1.390  0.020  1.390
 2UH  N7   C8   aromatic  1.296  0.020  1.296
 2UH  N9   C8   aromatic  1.377  0.020  1.377
 2UH  N9   C1'  single    1.439  0.020  1.439
 2UH  C2'  C1'  single    1.529  0.020  1.529
 2UH  C2'  C3'  single    1.530  0.020  1.530
 2UH  C1'  O4'  single    1.403  0.020  1.403
 2UH  O3'  C3'  single    1.401  0.020  1.401
 2UH  C3'  C4'  single    1.538  0.020  1.538
 2UH  O4'  C4'  single    1.425  0.020  1.425
 2UH  C4'  C5'  single    1.511  0.020  1.511
 2UH  O2A  PA   double    1.468  0.020  1.468
 2UH  O5'  C5'  single    1.430  0.020  1.430
 2UH  O5'  PA   single    1.585  0.020  1.585
 2UH  PA   O1A  single    1.591  0.020  1.591
 2UH  PA   O3A  single    1.614  0.020  1.614
 2UH  O3A  PB   single    1.633  0.020  1.633
 2UH  O1B  PB   double    1.471  0.020  1.471
 2UH  PB   O2B  single    1.582  0.020  1.582
 2UH  PB   O3B  single    1.583  0.020  1.583
 2UH  O3B  H1   single    0.850  0.020  0.980
 2UH  O2B  H2   single    0.850  0.020  0.980
 2UH  O1A  H3   single    0.850  0.020  0.980
 2UH  C5'  H4   single    0.970  0.020  1.090
 2UH  C5'  H5   single    0.970  0.020  1.090
 2UH  C4'  H6   single    0.970  0.020  1.090
 2UH  C3'  H7   single    0.970  0.020  1.090
 2UH  O3'  H8   single    0.850  0.020  0.980
 2UH  C2'  H9   single    0.970  0.020  1.090
 2UH  O2'  H10  single    0.850  0.020  0.980
 2UH  C1'  H11  single    0.970  0.020  1.090
 2UH  C8   H12  single    0.930  0.020  1.080
 2UH  N1   H13  single    0.860  0.020  1.020
 2UH  N4   H14  single    0.860  0.020  1.020
 2UH  CAO  H15  single    0.970  0.020  1.090
 2UH  CAO  H16  single    0.970  0.020  1.090
 2UH  CAM  H17  single    0.970  0.020  1.090
 2UH  CAM  H18  single    0.970  0.020  1.090
 2UH  CAN  H19  single    0.970  0.020  1.090
 2UH  CAN  H20  single    0.970  0.020  1.090
 2UH  NAS  H21  single    0.860  0.020  1.020
 2UH  CAL  H22  single    0.970  0.020  1.090
 2UH  CAL  H23  single    0.970  0.020  1.090
 2UH  CAA  H24  single    0.970  0.020  1.090
 2UH  CAA  H25  single    0.970  0.020  1.090
 2UH  CAA  H26  single    0.970  0.020  1.090

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
 2UH  H1   O3B  PB   114.63  3.000
 2UH  O3A  PB   O2B  101.92  3.000
 2UH  O2B  PB   O1B  119.59  3.000
 2UH  O3A  PB   O1B  112.21  3.000
 2UH  O2B  PB   O3B   98.63  3.000
 2UH  O1B  PB   O3B  118.38  3.000
 2UH  O3A  PB   O3B  103.57  3.000
 2UH  H2   O2B  PB   114.80  3.000
 2UH  PA   O3A  PB   126.88  3.000
 2UH  O5'  PA   O2A  111.16  3.000
 2UH  O5'  PA   O1A  107.62  3.000
 2UH  O2A  PA   O1A  117.95  3.000
 2UH  O1A  PA   O3A  100.13  3.000
 2UH  O5'  PA   O3A  101.35  3.000
 2UH  O2A  PA   O3A  116.83  3.000
 2UH  H3   O1A  PA   114.74  3.000
 2UH  C5'  O5'  PA   125.31  3.000
 2UH  H5   C5'  H4   108.23  3.000
 2UH  H5   C5'  C4'  108.72  3.000
 2UH  H4   C5'  C4'  110.36  3.000
 2UH  H5   C5'  O5'  111.42  3.000
 2UH  H4   C5'  O5'  109.11  3.000
 2UH  C4'  C5'  O5'  109.01  3.000
 2UH  H6   C4'  C3'  109.52  3.000
 2UH  H6   C4'  O4'  109.24  3.000
 2UH  C3'  C4'  O4'  106.50  3.000
 2UH  H6   C4'  C5'  105.94  3.000
 2UH  O4'  C4'  C5'  110.29  3.000
 2UH  C3'  C4'  C5'  115.28  3.000
 2UH  C1'  O4'  C4'  110.81  3.000
 2UH  H7   C3'  C2'  112.02  3.000
 2UH  H7   C3'  O3'  111.48  3.000
 2UH  C2'  C3'  O3'  108.17  3.000
 2UH  H7   C3'  C4'  111.21  3.000
 2UH  O3'  C3'  C4'  111.81  3.000
 2UH  C2'  C3'  C4'  101.74  3.000
 2UH  H8   O3'  C3'  108.31  3.000
 2UH  H9   C2'  C1'  109.40  3.000
 2UH  H9   C2'  O2'  111.37  3.000
 2UH  C1'  C2'  O2'  109.15  3.000
 2UH  H9   C2'  C3'  107.79  3.000
 2UH  C1'  C2'  C3'  101.50  3.000
 2UH  O2'  C2'  C3'  117.04  3.000
 2UH  H10  O2'  C2'  108.81  3.000
 2UH  H11  C1'  N9   106.35  3.000
 2UH  H11  C1'  C2'  109.50  3.000
 2UH  N9   C1'  C2'  113.65  3.000
 2UH  H11  C1'  O4'  111.53  3.000
 2UH  C2'  C1'  O4'  106.16  3.000
 2UH  N9   C1'  O4'  109.74  3.000
 2UH  C8   N9   C4   106.26  3.000
 2UH  C8   N9   C1'  127.74  3.000
 2UH  C4   N9   C1'  125.97  3.000
 2UH  C5   C4   N3   128.41  3.000
 2UH  C5   C4   N9   105.36  3.000
 2UH  N3   C4   N9   126.23  3.000
 2UH  C2   N3   C4   113.38  3.000
 2UH  H12  C8   N7   125.10  3.000
 2UH  H12  C8   N9   122.03  3.000
 2UH  N7   C8   N9   112.87  3.000
 2UH  C5   N7   C8   104.82  3.000
 2UH  C6   C5   N7   130.62  3.000
 2UH  N7   C5   C4   110.68  3.000
 2UH  C6   C5   C4   118.68  3.000
 2UH  N1   C6   O6   120.63  3.000
 2UH  O6   C6   C5   128.73  3.000
 2UH  N1   C6   C5   110.64  3.000
 2UH  H13  N1   C2   118.35  3.000
 2UH  H13  N1   C6   115.50  3.000
 2UH  C2   N1   C6   126.15  3.000
 2UH  N4   C2   N1   116.94  3.000
 2UH  N1   C2   N3   122.72  3.000
 2UH  N4   C2   N3   120.33  3.000
 2UH  H14  N4   CAO  117.89  3.000
 2UH  H14  N4   C2   118.95  3.000
 2UH  CAO  N4   C2   123.14  3.000
 2UH  H16  CAO  H15  106.99  3.000
 2UH  H16  CAO  CAM  109.51  3.000
 2UH  H15  CAO  CAM  110.30  3.000
 2UH  H16  CAO  N4   109.45  3.000
 2UH  H15  CAO  N4   106.14  3.000
 2UH  CAM  CAO  N4   114.17  3.000
 2UH  H18  CAM  H17  107.54  3.000
 2UH  H18  CAM  CAN  109.78  3.000
 2UH  H17  CAM  CAN  109.36  3.000
 2UH  H18  CAM  CAO  109.81  3.000
 2UH  H17  CAM  CAO  109.27  3.000
 2UH  CAN  CAM  CAO  111.01  3.000
 2UH  H20  CAN  H19  106.79  3.000
 2UH  H20  CAN  NAS  108.12  3.000
 2UH  H19  CAN  NAS  108.50  3.000
 2UH  H20  CAN  CAM  110.43  3.000
 2UH  H19  CAN  CAM  110.29  3.000
 2UH  NAS  CAN  CAM  112.51  3.000
 2UH  H21  NAS  CAY  118.41  3.000
 2UH  H21  NAS  CAN  117.62  3.000
 2UH  CAY  NAS  CAN  122.63  3.000
 2UH  CAL  CAY  OAB  121.56  3.000
 2UH  OAB  CAY  NAS  122.83  3.000
 2UH  CAL  CAY  NAS  115.60  3.000
 2UH  H23  CAL  H22  107.00  3.000
 2UH  H23  CAL  CAA  109.80  3.000
 2UH  H22  CAL  CAA  110.18  3.000
 2UH  H23  CAL  CAY  107.95  3.000
 2UH  H22  CAL  CAY  111.42  3.000
 2UH  CAA  CAL  CAY  110.40  3.000
 2UH  H26  CAA  H25  107.47  3.000
 2UH  H26  CAA  H24  108.59  3.000
 2UH  H25  CAA  H24  107.81  3.000
 2UH  H26  CAA  CAL  111.40  3.000
 2UH  H25  CAA  CAL  111.08  3.000
 2UH  H24  CAA  CAL  110.36  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
 2UH  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 2UH  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 2UH  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 2UH  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 2UH  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 2UH  CONST_06  N3   C4   N9   C1'     0.00   0.0  0
 2UH  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 2UH  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 2UH  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 2UH  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 2UH  CONST_11  C2   N1   C6   C5      0.00   0.0  0
 2UH  CONST_12  N4   C2   N3   C4    180.00   0.0  0
 2UH  CONST_13  N4   C2   N1   C6    180.00   0.0  0
 2UH  CONST_14  C2   N1   C6   O6    180.00   0.0  0
 2UH  CONST_15  H12  C8   N9   C1'     0.00   0.0  0
 2UH  CONST_16  H13  N1   C2   N3    180.00   0.0  0
 2UH  CONST_17  CAO  N4   C2   N3      0.00   0.0  0
 2UH  CONST_18  CAO  N4   C2   N1    180.00   0.0  0
 2UH  CONST_19  H14  N4   C2   N3    180.00   0.0  0
 2UH  CONST_20  CAL  CAY  NAS  CAN   180.00   0.0  0
 2UH  CONST_21  OAB  CAY  NAS  CAN     0.00   0.0  0
 2UH  CONST_22  H21  NAS  CAY  OAB   180.00   0.0  0
 2UH  Var_01    C4'  C5'  O5'  PA   -157.97  30.0  3
 2UH  Var_02    CAM  CAO  N4   C2    -69.94  30.0  3
 2UH  Var_03    O2A  PA   O3A  PB    -68.51  30.0  1
 2UH  Var_04    CAN  CAM  CAO  N4   -172.04  30.0  1
 2UH  Var_05    NAS  CAN  CAM  CAO  -166.24  30.0  3
 2UH  Var_06    CAY  NAS  CAN  CAM    88.03  30.0  2
 2UH  Var_07    CAA  CAL  CAY  NAS   108.30  30.0  2
 2UH  Var_08    H24  CAA  CAL  CAY   174.12  30.0  3

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
 2UH  chir_02  C4'  C3'  O4'  C5'  positiv
 2UH  chir_03  C3'  O3'  C2'  C4'  negativ
 2UH  chir_04  C2'  O2'  C1'  C3'  negativ
 2UH  chir_05  C1'  O4'  N9   C2'  negativ
 2UH  chir_06  PA   O5'  O1A  O3A  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
 2UH  plan-1  C1'  0.020
 2UH  plan-1  N9   0.020
 2UH  plan-1  C4   0.020
 2UH  plan-1  N3   0.020
 2UH  plan-1  C8   0.020
 2UH  plan-1  N7   0.020
 2UH  plan-1  C5   0.020
 2UH  plan-1  C6   0.020
 2UH  plan-1  O6   0.020
 2UH  plan-1  N1   0.020
 2UH  plan-1  C2   0.020
 2UH  plan-1  N4   0.020
 2UH  plan-1  CAO  0.020
 2UH  plan-1  H12  0.020
 2UH  plan-1  H13  0.020
 2UH  plan-1  H14  0.020
 2UH  plan-2  CAN  0.020
 2UH  plan-2  NAS  0.020
 2UH  plan-2  CAY  0.020
 2UH  plan-2  OAB  0.020
 2UH  plan-2  CAL  0.020
 2UH  plan-2  H21  0.020

