# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 02:29:54 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: (3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CN(C[C@H]3OC[C@H](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O
#
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
 WPG  WPG  '(3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid'  ligand  54  32  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WPG
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
 WPG  C4   C  CR56  0   0.507  -41.0564   -9.9620  25.2877
 WPG  C5   C  CR56  0  -0.097  -42.0685   -9.3274  25.9844
 WPG  C6   C  CR6   0   0.505  -41.9628   -9.2240  27.4013
 WPG  C8   C  CR15  0   0.082  -42.6307   -9.2430  23.9503
 WPG  N1   N  NR16  0  -0.728  -40.7791   -9.8228  27.8517
 WPG  N3   N  N     0  -0.513  -39.9373  -10.5183  25.7689
 WPG  PBF  P  P     0   1.351  -44.3166  -15.6079  22.5039
 WPG  OAJ  O  OH1   0  -0.747  -43.9199  -16.3421  23.8807
 WPG  OAE  O  OH1   0  -0.748  -45.4488  -14.5886  22.9940
 WPG  CAZ  C  CH1   0  -0.252  -42.9319  -14.4769  22.1087
 WPG  OAF  O  OH1   0  -0.655  -43.2203  -13.8289  20.8923
 WPG  CAN  C  CH2   0  -0.198  -42.6735  -13.4325  23.1839
 WPG  OAT  O  O2    0  -0.486  -41.4536  -12.7590  22.9856
 WPG  CBA  C  CR15  0   0.056  -41.4601  -11.6163  22.1832
 WPG  CAO  C  CH2   0  -0.294  -40.6860  -11.7634  20.8752
 WPG  NBC  N  NR5   0  -0.491  -40.2621  -10.3986  20.5918
 WPG  CAU  C  C     0   0.585  -39.8340   -9.9307  19.4065
 WPG  OAB  O  O     0  -0.498  -39.5842   -8.7452  19.2419
 WPG  CAL  C  CH2   0  -0.609  -39.7297  -10.9414  18.2814
 WPG  CAM  C  CH2   0  -0.739  -38.7767  -10.5073  17.1730
 WPG  PBE  P  P     0   1.361  -37.0346  -10.8138  17.4893
 WPG  OAG  O  OH1   0  -0.745  -36.8468  -10.2643  18.9902
 WPG  OAH  O  O     0  -0.718  -36.0717  -10.2589  16.5033
 WPG  OAD  O  OH1   0  -0.754  -37.0103  -12.4222  17.6020
 WPG  CAP  C  CH2   0  -0.241  -40.4171   -9.5057  21.7298
 WPG  CBB  C  CR15  0  -0.183  -40.7108  -10.4755  22.8689
 WPG  N9   N  NR5   0  -0.512  -41.4234   -9.8978  23.9802
 WPG  C2   C  CR6   0   0.693  -39.8362  -10.4297  27.0717
 WPG  O6   O  O     0  -0.474  -42.7365   -8.7088  28.1908
 WPG  N7   N  N     0  -0.442  -43.0430   -8.8860  25.1274
 WPG  H1   H  HCR5  0   0.296  -43.1518   -9.0561  23.0233
 WPG  H2   H  HNH2  0   0.413  -38.0186  -11.2977  27.1365
 WPG  H3   H  HNH2  0   0.415  -38.5825  -10.7607  28.6599
 WPG  H5   H  HOH1  0   0.496  -43.4180  -17.1590  23.7612
 WPG  H6   H  HOH1  0   0.498  -46.3398  -14.9640  23.0318
 WPG  H7   H  HCH1  0   0.272  -42.0369  -15.1104  22.0308
 WPG  H8   H  HOH1  0   0.467  -43.0387  -14.4308  20.1637
 WPG  H9   H  HCH2  0   0.232  -43.5108  -12.7274  23.2351
 WPG  H10  H  HCH2  0   0.255  -42.6008  -13.9242  24.1555
 WPG  H11  H  HCR5  0   0.244  -42.4835  -11.2896  21.9584
 WPG  H12  H  HCH2  0   0.271  -41.3119  -12.1678  20.0826
 WPG  H13  H  HCH2  0   0.253  -39.8316  -12.4333  21.0161
 WPG  H14  H  HCH2  0   0.304  -40.7326  -11.0455  17.8544
 WPG  H15  H  HCH2  0   0.279  -39.4704  -11.9324  18.6561
 WPG  H16  H  HCH2  0   0.302  -39.0165  -11.0380  16.2493
 WPG  H17  H  HCH2  0   0.295  -38.8918   -9.4445  16.9563
 WPG  H18  H  HOH1  0   0.492  -35.9240  -10.1717  19.2630
 WPG  H19  H  HOH1  0   0.490  -36.1217  -12.8025  17.6114
 WPG  H20  H  HCH2  0   0.271  -39.5146   -8.9226  21.9113
 WPG  H21  H  HCH2  0   0.253  -41.2407   -8.8027  21.5722
 WPG  H22  H  HCR5  0   0.302  -39.7713  -10.8651  23.2676
 WPG  H23  H  HNR6  0   0.425  -40.6274   -9.7945  28.8523
 WPG  N2   N  NH2   0  -0.832  -38.7880  -10.9791  27.7003
 WPG  OAI  O  O     0  -0.707  -44.6743  -16.5143  21.3856

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
 WPG  OAH  PBE  double    1.486  0.020  1.486
 WPG  CAM  CAL  single    1.525  0.020  1.525
 WPG  CAM  PBE  single    1.797  0.020  1.797
 WPG  CAL  CAU  single    1.516  0.020  1.516
 WPG  PBE  OAD  single    1.612  0.020  1.612
 WPG  PBE  OAG  single    1.609  0.020  1.609
 WPG  CAU  OAB  double    1.223  0.020  1.223
 WPG  CAU  NBC  single    1.344  0.020  1.344
 WPG  OAI  PBF  double    1.483  0.020  1.483
 WPG  OAF  CAZ  single    1.408  0.020  1.408
 WPG  NBC  CAO  single    1.457  0.020  1.457
 WPG  NBC  CAP  single    1.455  0.020  1.455
 WPG  CAO  CBA  single    1.527  0.020  1.527
 WPG  CAZ  PBF  single    1.831  0.020  1.831
 WPG  CAZ  CAN  single    1.521  0.020  1.521
 WPG  PBF  OAE  single    1.600  0.020  1.600
 WPG  PBF  OAJ  single    1.610  0.020  1.610
 WPG  CAP  CBB  single    1.525  0.020  1.525
 WPG  CBA  OAT  single    1.396  0.020  1.396
 WPG  CBA  CBB  single    1.527  0.020  1.527
 WPG  OAT  CAN  single    1.407  0.020  1.407
 WPG  CBB  N9   single    1.441  0.020  1.441
 WPG  N9   C8   aromatic  1.374  0.020  1.374
 WPG  N9   C4   aromatic  1.360  0.020  1.360
 WPG  N3   C4   single    1.339  0.020  1.339
 WPG  N3   C2   double    1.310  0.020  1.310
 WPG  C8   N7   aromatic  1.297  0.020  1.297
 WPG  C4   C5   aromatic  1.383  0.020  1.383
 WPG  N2   C2   single    1.340  0.020  1.340
 WPG  C2   N1   single    1.366  0.020  1.366
 WPG  N7   C5   aromatic  1.371  0.020  1.371
 WPG  C5   C6   single    1.425  0.020  1.425
 WPG  N1   C6   single    1.401  0.020  1.401
 WPG  C6   O6   double    1.220  0.020  1.220
 WPG  C8   H1   single    0.930  0.020  1.080
 WPG  N2   H2   single    0.890  0.020  1.040
 WPG  N2   H3   single    0.890  0.020  1.040
 WPG  OAJ  H5   single    0.850  0.020  0.980
 WPG  OAE  H6   single    0.850  0.020  0.980
 WPG  CAZ  H7   single    0.970  0.020  1.090
 WPG  OAF  H8   single    0.850  0.020  0.980
 WPG  CAN  H9   single    0.970  0.020  1.090
 WPG  CAN  H10  single    0.970  0.020  1.090
 WPG  CBA  H11  single    0.970  0.020  1.090
 WPG  CAO  H12  single    0.970  0.020  1.090
 WPG  CAO  H13  single    0.970  0.020  1.090
 WPG  CAL  H14  single    0.970  0.020  1.090
 WPG  CAL  H15  single    0.970  0.020  1.090
 WPG  CAM  H16  single    0.970  0.020  1.090
 WPG  CAM  H17  single    0.970  0.020  1.090
 WPG  OAG  H18  single    0.850  0.020  0.980
 WPG  OAD  H19  single    0.850  0.020  0.980
 WPG  CAP  H20  single    0.970  0.020  1.090
 WPG  CAP  H21  single    0.970  0.020  1.090
 WPG  CBB  H22  single    0.970  0.020  1.090
 WPG  N1   H23  single    0.860  0.020  1.020

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
 WPG  N9   C4   N3   126.21  3.000
 WPG  N3   C4   C5   128.41  3.000
 WPG  N9   C4   C5   105.38  3.000
 WPG  N7   C5   C6   130.63  3.000
 WPG  C6   C5   C4   118.69  3.000
 WPG  N7   C5   C4   110.68  3.000
 WPG  O6   C6   N1   120.57  3.000
 WPG  O6   C6   C5   128.86  3.000
 WPG  N1   C6   C5   110.57  3.000
 WPG  H1   C8   N7   125.31  3.000
 WPG  H1   C8   N9   121.69  3.000
 WPG  N7   C8   N9   113.00  3.000
 WPG  H23  N1   C2   118.25  3.000
 WPG  H23  N1   C6   115.62  3.000
 WPG  C2   N1   C6   126.13  3.000
 WPG  C2   N3   C4   113.19  3.000
 WPG  CAZ  PBF  OAE  101.98  3.000
 WPG  OAE  PBF  OAJ  101.71  3.000
 WPG  CAZ  PBF  OAJ  106.25  3.000
 WPG  OAJ  PBF  OAI  115.19  3.000
 WPG  OAE  PBF  OAI  116.71  3.000
 WPG  CAZ  PBF  OAI  113.40  3.000
 WPG  H5   OAJ  PBF  114.06  3.000
 WPG  H6   OAE  PBF  114.60  3.000
 WPG  H7   CAZ  CAN  107.91  3.000
 WPG  H7   CAZ  OAF  111.76  3.000
 WPG  CAN  CAZ  OAF  109.23  3.000
 WPG  H7   CAZ  PBF  105.96  3.000
 WPG  CAN  CAZ  PBF  113.58  3.000
 WPG  OAF  CAZ  PBF  108.41  3.000
 WPG  H8   OAF  CAZ  109.12  3.000
 WPG  H10  CAN  H9   107.40  3.000
 WPG  H10  CAN  OAT  106.46  3.000
 WPG  H9   CAN  OAT  111.16  3.000
 WPG  H10  CAN  CAZ  109.34  3.000
 WPG  H9   CAN  CAZ  110.18  3.000
 WPG  OAT  CAN  CAZ  112.10  3.000
 WPG  CBA  OAT  CAN  117.94  3.000
 WPG  H11  CBA  CBB  109.09  3.000
 WPG  H11  CBA  CAO  109.02  3.000
 WPG  CBB  CBA  CAO  101.99  3.000
 WPG  H11  CBA  OAT  111.45  3.000
 WPG  CBB  CBA  OAT  110.55  3.000
 WPG  CAO  CBA  OAT  114.27  3.000
 WPG  H13  CAO  H12  108.38  3.000
 WPG  H13  CAO  NBC  111.79  3.000
 WPG  H12  CAO  NBC  111.96  3.000
 WPG  H13  CAO  CBA  110.14  3.000
 WPG  H12  CAO  CBA  111.61  3.000
 WPG  NBC  CAO  CBA  102.94  3.000
 WPG  CAP  NBC  CAU  120.67  3.000
 WPG  CAP  NBC  CAO  113.07  3.000
 WPG  CAU  NBC  CAO  126.17  3.000
 WPG  CAL  CAU  OAB  122.17  3.000
 WPG  OAB  CAU  NBC  121.42  3.000
 WPG  CAL  CAU  NBC  116.37  3.000
 WPG  H15  CAL  H14  105.39  3.000
 WPG  H15  CAL  CAM  111.09  3.000
 WPG  H14  CAL  CAM  108.42  3.000
 WPG  H15  CAL  CAU  111.54  3.000
 WPG  H14  CAL  CAU  106.85  3.000
 WPG  CAM  CAL  CAU  113.12  3.000
 WPG  H17  CAM  H16  106.39  3.000
 WPG  H17  CAM  PBE  107.67  3.000
 WPG  H16  CAM  PBE  106.19  3.000
 WPG  H17  CAM  CAL  110.85  3.000
 WPG  H16  CAM  CAL  109.83  3.000
 WPG  PBE  CAM  CAL  115.43  3.000
 WPG  OAD  PBE  OAH  114.15  3.000
 WPG  OAD  PBE  OAG  105.88  3.000
 WPG  OAH  PBE  OAG  114.57  3.000
 WPG  OAG  PBE  CAM  102.65  3.000
 WPG  OAD  PBE  CAM  101.36  3.000
 WPG  OAH  PBE  CAM  116.60  3.000
 WPG  H18  OAG  PBE  114.03  3.000
 WPG  H19  OAD  PBE  114.01  3.000
 WPG  H21  CAP  H20  107.68  3.000
 WPG  H21  CAP  CBB  111.79  3.000
 WPG  H20  CAP  CBB  112.05  3.000
 WPG  H21  CAP  NBC  111.22  3.000
 WPG  H20  CAP  NBC  111.75  3.000
 WPG  CBB  CAP  NBC  102.39  3.000
 WPG  H22  CBB  N9   106.67  3.000
 WPG  H22  CBB  CAP  109.50  3.000
 WPG  N9   CBB  CAP  114.61  3.000
 WPG  H22  CBB  CBA  108.62  3.000
 WPG  N9   CBB  CBA  113.77  3.000
 WPG  CAP  CBB  CBA  103.54  3.000
 WPG  CBB  N9   C8   127.51  3.000
 WPG  C8   N9   C4   106.30  3.000
 WPG  CBB  N9   C4   126.10  3.000
 WPG  N3   C2   N2   119.95  3.000
 WPG  N2   C2   N1   117.02  3.000
 WPG  N3   C2   N1   123.01  3.000
 WPG  C8   N7   C5   104.64  3.000
 WPG  H3   N2   H2   116.58  3.000
 WPG  H3   N2   C2   121.24  3.000
 WPG  H2   N2   C2   117.74  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
 WPG  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 WPG  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 WPG  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 WPG  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 WPG  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 WPG  CONST_06  CBB  N9   C4   C5    180.00   0.0  0
 WPG  CONST_07  CBB  N9   C4   N3      0.00   0.0  0
 WPG  CONST_08  N7   C8   N9   CBB   180.00   0.0  0
 WPG  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 WPG  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 WPG  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 WPG  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 WPG  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 WPG  CONST_14  O6   C6   N1   C2    180.00   0.0  0
 WPG  CONST_15  H1   C8   N9   C4    180.00   0.0  0
 WPG  CONST_16  H23  N1   C6   C5    180.00   0.0  0
 WPG  CONST_17  CAL  CAU  NBC  CAO     0.00   0.0  0
 WPG  CONST_18  OAB  CAU  NBC  CAO   180.00   0.0  0
 WPG  CONST_19  CAP  NBC  CAU  OAB     0.00   0.0  0
 WPG  CONST_20  CAP  NBC  CAU  CAL   180.00   0.0  0
 WPG  CONST_21  H2   N2   C2   N1    180.00   0.0  0
 WPG  CONST_22  H3   N2   C2   N1      0.00   0.0  0
 WPG  Var_01    CAP  NBC  CAO  CBA    13.77  30.0  1
 WPG  Var_02    CBB  CAP  NBC  CAO    11.26  30.0  1
 WPG  Var_03    CAM  CAL  CAU  NBC  -158.12  30.0  1
 WPG  Var_04    H9   CAN  OAT  CBA   -35.31  30.0  3
 WPG  Var_05    PBE  CAM  CAL  CAU    81.77  30.0  1
 WPG  Var_06    OAH  PBE  CAM  CAL  -173.01  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
 WPG  chir_01  CAZ  OAF  PBF  CAN  positiv
 WPG  chir_02  CBA  OAT  CBB  CAO  negativ
 WPG  chir_03  CBB  N9   CAP  CBA  positiv

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
 WPG  plan-1  C4   0.020
 WPG  plan-1  C5   0.020
 WPG  plan-1  C6   0.020
 WPG  plan-1  C8   0.020
 WPG  plan-1  N1   0.020
 WPG  plan-1  N3   0.020
 WPG  plan-1  CBB  0.020
 WPG  plan-1  N9   0.020
 WPG  plan-1  C2   0.020
 WPG  plan-1  O6   0.020
 WPG  plan-1  N7   0.020
 WPG  plan-1  H1   0.020
 WPG  plan-1  H2   0.020
 WPG  plan-1  H3   0.020
 WPG  plan-1  H23  0.020
 WPG  plan-1  N2   0.020
 WPG  plan-2  CAO  0.020
 WPG  plan-2  NBC  0.020
 WPG  plan-2  CAU  0.020
 WPG  plan-2  OAB  0.020
 WPG  plan-2  CAL  0.020
 WPG  plan-2  CAP  0.020

