# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:23:23 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (2R)-[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl](phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(S[C@@H](C(O)=O)c3ccccc3)nc2C(=O)N1
#
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
 7PM  7PM  '(2R)-[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl](phenyl)acetic acid'  ligand  33  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7PM
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
 7PM  C1   C  CR16  0  -0.258   6.0846  -0.4116  -0.5385
 7PM  C2   C  CR16  0  -0.238   5.3851   0.1080  -1.6189
 7PM  C3   C  CR16  0  -0.237   5.4083  -0.7271   0.6330
 7PM  C4   C  CR16  0  -0.304   4.0152   0.3124  -1.5275
 7PM  C5   C  CR16  0  -0.269   4.0396  -0.5215   0.7272
 7PM  C6   C  CR6   0   0.120   3.3344   0.0015  -0.3553
 7PM  C7   C  CR56  0  -0.074  -2.3952   0.3281  -0.1285
 7PM  C8   C  CR56  0   0.477  -2.8032  -0.9809   0.0463
 7PM  C9   C  CR5   0   0.302  -0.6208  -0.8131  -0.0177
 7PM  C10  C  CR6   0   0.495  -3.3847   1.3441  -0.2403
 7PM  C11  C  CR6   0   0.691  -4.9670  -0.5303   0.0266
 7PM  C12  C  C     0   0.590   1.5604   1.3163   0.7693
 7PM  C13  C  CH1   0  -0.576   1.8461   0.2506  -0.2753
 7PM  N14  N  N     0  -0.442  -1.0234   0.4105  -0.1660
 7PM  N15  N  N     0  -0.504  -4.0497  -1.4617   0.1267
 7PM  N16  N  NR15  0  -0.693  -1.6521  -1.7022   0.1154
 7PM  N17  N  NR16  0  -0.723  -4.6690   0.7904  -0.1445
 7PM  N18  N  NH2   0  -0.833  -6.2636  -0.8556   0.1277
 7PM  O20  O  O     0  -0.474  -3.2374   2.5449  -0.3973
 7PM  O21  O  OH1   0  -0.573   1.3196   0.8299   1.9718
 7PM  S22  S  S2    0   0.118   1.0384  -1.3476   0.0220
 7PM  H1   H  HCR6  0   0.263   7.1525  -0.5712  -0.6094
 7PM  H2   H  HCR6  0   0.264   5.9038   0.3554  -2.5357
 7PM  H3   H  HCR6  0   0.263   5.9466  -1.1335   1.4791
 7PM  H4   H  HCR6  0   0.264   3.4737   0.7160  -2.3739
 7PM  H5   H  HCR6  0   0.263   3.5280  -0.7742   1.6477
 7PM  H6   H  HCH1  0   0.347   1.4935   0.6402  -1.2307
 7PM  H8   H  HNR5  0   0.427  -1.5848  -2.7022   0.2350
 7PM  H9   H  HNR6  0   0.425  -5.4330   1.4512  -0.2071
 7PM  H10  H  HNH2  0   0.413  -6.5010  -1.8330   0.1079
 7PM  H11  H  HNH2  0   0.415  -6.9831  -0.2139  -0.1586
 7PM  H12  H  HOH1  0   0.488   1.1953   1.5545   2.6039
 7PM  O19  O  O     0  -0.429   1.6312   2.4887   0.5092

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
 7PM  O19  C12  double    1.203  0.020  1.203
 7PM  O20  C10  double    1.220  0.020  1.220
 7PM  C12  O21  single    1.319  0.020  1.319
 7PM  C12  C13  single    1.519  0.020  1.519
 7PM  C4   C2   aromatic  1.388  0.020  1.388
 7PM  C4   C6   aromatic  1.391  0.020  1.391
 7PM  C2   C1   aromatic  1.388  0.020  1.388
 7PM  C13  C6   single    1.511  0.020  1.511
 7PM  C13  S22  single    1.815  0.020  1.815
 7PM  C10  C7   single    1.423  0.020  1.423
 7PM  C10  N17  single    1.402  0.020  1.402
 7PM  C6   C5   aromatic  1.394  0.020  1.394
 7PM  C1   C3   aromatic  1.389  0.020  1.389
 7PM  N14  C7   aromatic  1.375  0.020  1.375
 7PM  N14  C9   aromatic  1.297  0.020  1.297
 7PM  C5   C3   aromatic  1.387  0.020  1.387
 7PM  C7   C8   aromatic  1.382  0.020  1.382
 7PM  N17  C11  single    1.365  0.020  1.365
 7PM  C9   S22  single    1.744  0.020  1.744
 7PM  C9   N16  aromatic  1.368  0.020  1.368
 7PM  C8   N16  aromatic  1.360  0.020  1.360
 7PM  C8   N15  single    1.338  0.020  1.338
 7PM  C11  N18  single    1.341  0.020  1.341
 7PM  C11  N15  double    1.311  0.020  1.311
 7PM  C1   H1   single    0.930  0.020  1.080
 7PM  C2   H2   single    0.930  0.020  1.080
 7PM  C3   H3   single    0.930  0.020  1.080
 7PM  C4   H4   single    0.930  0.020  1.080
 7PM  C5   H5   single    0.930  0.020  1.080
 7PM  C13  H6   single    0.970  0.020  1.090
 7PM  N16  H8   single    0.860  0.020  1.020
 7PM  N17  H9   single    0.860  0.020  1.020
 7PM  N18  H10  single    0.890  0.020  1.040
 7PM  N18  H11  single    0.890  0.020  1.040
 7PM  O21  H12  single    0.850  0.020  0.980

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
 7PM  H1   C1   C3   120.14  3.000
 7PM  H1   C1   C2   120.11  3.000
 7PM  C3   C1   C2   119.75  3.000
 7PM  H2   C2   C4   119.68  3.000
 7PM  H2   C2   C1   120.23  3.000
 7PM  C4   C2   C1   120.08  3.000
 7PM  H3   C3   C5   119.56  3.000
 7PM  H3   C3   C1   120.18  3.000
 7PM  C5   C3   C1   120.26  3.000
 7PM  H4   C4   C6   119.83  3.000
 7PM  H4   C4   C2   119.80  3.000
 7PM  C6   C4   C2   120.37  3.000
 7PM  H5   C5   C6   120.58  3.000
 7PM  H5   C5   C3   119.28  3.000
 7PM  C6   C5   C3   120.14  3.000
 7PM  C13  C6   C5   121.27  3.000
 7PM  C5   C6   C4   119.40  3.000
 7PM  C13  C6   C4   119.33  3.000
 7PM  N14  C7   C10  130.47  3.000
 7PM  N14  C7   C8   110.78  3.000
 7PM  C10  C7   C8   118.75  3.000
 7PM  N16  C8   N15  126.48  3.000
 7PM  N15  C8   C7   128.51  3.000
 7PM  N16  C8   C7   105.00  3.000
 7PM  S22  C9   N16  121.05  3.000
 7PM  N16  C9   N14  112.98  3.000
 7PM  S22  C9   N14  125.97  3.000
 7PM  O20  C10  N17  120.55  3.000
 7PM  N17  C10  C7   110.47  3.000
 7PM  O20  C10  C7   128.98  3.000
 7PM  N18  C11  N17  117.10  3.000
 7PM  N18  C11  N15  119.90  3.000
 7PM  N17  C11  N15  122.98  3.000
 7PM  O21  C12  O19  124.55  3.000
 7PM  O21  C12  C13  113.73  3.000
 7PM  O19  C12  C13  121.59  3.000
 7PM  H6   C13  S22  108.32  3.000
 7PM  H6   C13  C12  106.91  3.000
 7PM  S22  C13  C12  114.91  3.000
 7PM  H6   C13  C6   109.33  3.000
 7PM  S22  C13  C6   107.56  3.000
 7PM  C12  C13  C6   109.70  3.000
 7PM  C9   N14  C7   104.48  3.000
 7PM  C11  N15  C8   113.06  3.000
 7PM  H8   N16  C9   127.24  3.000
 7PM  H8   N16  C8   126.01  3.000
 7PM  C9   N16  C8   106.76  3.000
 7PM  H9   N17  C11  118.34  3.000
 7PM  H9   N17  C10  115.43  3.000
 7PM  C11  N17  C10  126.22  3.000
 7PM  H11  N18  H10  116.46  3.000
 7PM  H11  N18  C11  121.04  3.000
 7PM  H10  N18  C11  117.55  3.000
 7PM  H12  O21  C12  110.00  3.000
 7PM  C13  S22  C9    98.61  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
 7PM  CONST_01  C6   C4   C2   C1     0.00   0.0  0
 7PM  CONST_02  C6   C5   C3   C1     0.00   0.0  0
 7PM  CONST_03  C5   C6   C4   C2     0.00   0.0  0
 7PM  CONST_04  C5   C3   C1   C2     0.00   0.0  0
 7PM  CONST_05  C4   C2   C1   C3     0.00   0.0  0
 7PM  CONST_06  C4   C6   C5   C3     0.00   0.0  0
 7PM  CONST_07  N16  C9   N14  C7     0.00   0.0  0
 7PM  CONST_08  C9   N16  C8   C7     0.00   0.0  0
 7PM  CONST_09  C9   N14  C7   C8     0.00   0.0  0
 7PM  CONST_10  N14  C9   N16  C8     0.00   0.0  0
 7PM  CONST_11  N16  C8   C7   N14    0.00   0.0  0
 7PM  CONST_12  C11  N17  C10  C7     0.00   0.0  0
 7PM  CONST_13  N17  C11  N15  C8     0.00   0.0  0
 7PM  CONST_14  N15  C11  N17  C10    0.00   0.0  0
 7PM  CONST_15  C13  C6   C4   C2   180.00   0.0  0
 7PM  CONST_16  C13  C6   C5   C3   180.00   0.0  0
 7PM  CONST_17  S22  C9   N14  C7   180.00   0.0  0
 7PM  CONST_18  S22  C9   N16  C8   180.00   0.0  0
 7PM  CONST_19  N18  C11  N15  C8   180.00   0.0  0
 7PM  CONST_20  N18  C11  N17  C10  180.00   0.0  0
 7PM  CONST_21  O20  C10  N17  C11  180.00   0.0  0
 7PM  CONST_22  H4   C4   C2   C1   180.00   0.0  0
 7PM  CONST_23  H5   C5   C3   C1   180.00   0.0  0
 7PM  CONST_24  H3   C3   C1   C2   180.00   0.0  0
 7PM  CONST_25  H2   C2   C1   C3   180.00   0.0  0
 7PM  CONST_26  H1   C1   C2   C4   180.00   0.0  0
 7PM  CONST_27  H8   N16  C8   C7   180.00   0.0  0
 7PM  CONST_28  H9   N17  C10  C7   180.00   0.0  0
 7PM  CONST_29  H10  N18  C11  N15    0.00   0.0  0
 7PM  CONST_30  H11  N18  C11  N15  180.00   0.0  0
 7PM  CONST_31  H12  O21  C12  C13  180.00   0.0  0
 7PM  Var_01    N14  C9   S22  C13   -2.57  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
 7PM  chir_01  C13  C12  C6  S22  negativ

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
 7PM  plan-1  C1   0.020
 7PM  plan-1  C2   0.020
 7PM  plan-1  C3   0.020
 7PM  plan-1  C4   0.020
 7PM  plan-1  C5   0.020
 7PM  plan-1  C6   0.020
 7PM  plan-1  C13  0.020
 7PM  plan-1  H1   0.020
 7PM  plan-1  H2   0.020
 7PM  plan-1  H3   0.020
 7PM  plan-1  H4   0.020
 7PM  plan-1  H5   0.020
 7PM  plan-2  C7   0.020
 7PM  plan-2  C8   0.020
 7PM  plan-2  C9   0.020
 7PM  plan-2  C10  0.020
 7PM  plan-2  C11  0.020
 7PM  plan-2  N14  0.020
 7PM  plan-2  N15  0.020
 7PM  plan-2  N16  0.020
 7PM  plan-2  N17  0.020
 7PM  plan-2  N18  0.020
 7PM  plan-2  O20  0.020
 7PM  plan-2  S22  0.020
 7PM  plan-2  H8   0.020
 7PM  plan-2  H9   0.020
 7PM  plan-2  H10  0.020
 7PM  plan-2  H11  0.020
 7PM  plan-3  C12  0.020
 7PM  plan-3  C13  0.020
 7PM  plan-3  O21  0.020
 7PM  plan-3  H12  0.020
 7PM  plan-3  O19  0.020

