# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:03:35 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  32  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.267   6.0835  -0.4115  -0.2512
 7PM  C2   C  CR16   0  -0.241   5.5681   0.3909  -1.2594
 7PM  C3   C  CR16   0  -0.241   5.2244  -0.9705   0.6882
 7PM  C4   C  CR16   0  -0.316   4.2013   0.6313  -1.3280
 7PM  C5   C  CR16   0  -0.270   3.8607  -0.7285   0.6189
 7PM  C6   C  CR6    0   0.124   3.3348   0.0788  -0.3901
 7PM  C7   C  CR56   0  -0.093  -2.4895   0.2212  -0.8126
 7PM  C8   C  CR56   0   0.479  -2.7060  -0.8986  -0.0275
 7PM  C9   C  CR5    0   0.257  -0.6211  -0.7626  -0.6966
 7PM  C10  C  CR6    0   0.493  -3.5824   1.0944  -1.0742
 7PM  C11  C  CR6    0   0.693  -4.8553  -0.5015   0.3122
 7PM  C12  C  C      0   0.449   1.3538   0.9861   0.8695
 7PM  C13  C  CH1    0  -0.547   1.8569   0.3533  -0.4597
 7PM  N14  N  N      0  -0.423  -1.1847   0.2786  -1.2317
 7PM  N15  N  N      0  -0.507  -3.8453  -1.3018   0.5522
 7PM  N16  N  NR15   0  -0.659  -1.5010  -1.5145   0.0362
 7PM  N17  N  NR16   0  -0.724  -4.7468   0.6260  -0.4511
 7PM  N18  N  NH2    0  -0.835  -6.0659  -0.7876   0.8053
 7PM  O20  O  O      0  -0.477  -3.6032   2.1217  -1.7327
 7PM  S22  S  S2     0   0.042   1.0489  -1.2369  -0.8564
 7PM  H1   H  HCR6   0   0.255   7.1475  -0.6028  -0.1971
 7PM  H2   H  HCR6   0   0.255   6.2283   0.8305  -1.9960
 7PM  H3   H  HCR6   0   0.255   5.6197  -1.5954   1.4788
 7PM  H4   H  HCR6   0   0.253   3.8032   1.2529  -2.1213
 7PM  H5   H  HCR6   0   0.252   3.1974  -1.1651   1.3555
 7PM  H6   H  HCH1   0   0.289   1.6612   1.0408  -1.2833
 7PM  H8   H  HNR5   0   0.420  -1.2792  -2.3404   0.5709
 7PM  H9   H  HNR6   0   0.424  -5.5761   1.1873  -0.5979
 7PM  H10  H  HNH2   0   0.413  -6.1537  -1.5591   1.4436
 7PM  H11  H  HNH2   0   0.416  -6.8283  -0.1347   0.7605
 7PM  O19  O  O      0  -0.594   1.5803   2.2059   0.9501
 7PM  O21  O  OC    -1  -0.573   0.8320   0.2414   1.7095

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  deloc     1.243  0.020  1.243
 7PM  O20  C10  double    1.220  0.020  1.220
 7PM  C12  O21  deloc     1.238  0.020  1.238
 7PM  C12  C13  single    1.556  0.020  1.556
 7PM  C4   C2   aromatic  1.389  0.020  1.389
 7PM  C4   C6   aromatic  1.391  0.020  1.391
 7PM  C2   C1   aromatic  1.388  0.020  1.388
 7PM  C13  C6   single    1.505  0.020  1.505
 7PM  C13  S22  single    1.827  0.020  1.827
 7PM  C10  C7   single    1.423  0.020  1.423
 7PM  C10  N17  single    1.401  0.020  1.401
 7PM  C6   C5   aromatic  1.395  0.020  1.395
 7PM  C1   C3   aromatic  1.390  0.020  1.390
 7PM  N14  C7   aromatic  1.372  0.020  1.372
 7PM  N14  C9   aromatic  1.299  0.020  1.299
 7PM  C5   C3   aromatic  1.387  0.020  1.387
 7PM  C7   C8   aromatic  1.385  0.020  1.385
 7PM  N17  C11  single    1.366  0.020  1.366
 7PM  C9   S22  single    1.743  0.020  1.743
 7PM  C9   N16  aromatic  1.370  0.020  1.370
 7PM  C8   N16  aromatic  1.355  0.020  1.355
 7PM  C8   N15  single    1.340  0.020  1.340
 7PM  C11  N18  single    1.338  0.020  1.338
 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    0.860  0.020  1.020
 7PM  N18  H11  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
 7PM  H1   C1   C3   120.17  3.000
 7PM  H1   C1   C2   120.24  3.000
 7PM  C3   C1   C2   119.59  3.000
 7PM  H2   C2   C4   119.74  3.000
 7PM  H2   C2   C1   120.18  3.000
 7PM  C4   C2   C1   120.08  3.000
 7PM  H3   C3   C5   119.75  3.000
 7PM  H3   C3   C1   120.00  3.000
 7PM  C5   C3   C1   120.25  3.000
 7PM  H4   C4   C6   119.50  3.000
 7PM  H4   C4   C2   119.79  3.000
 7PM  C6   C4   C2   120.71  3.000
 7PM  H5   C5   C6   119.62  3.000
 7PM  H5   C5   C3   119.86  3.000
 7PM  C6   C5   C3   120.52  3.000
 7PM  C13  C6   C5   120.61  3.000
 7PM  C5   C6   C4   118.85  3.000
 7PM  C13  C6   C4   120.53  3.000
 7PM  N14  C7   C10  130.44  3.000
 7PM  N14  C7   C8   110.84  3.000
 7PM  C10  C7   C8   118.71  3.000
 7PM  N16  C8   N15  126.79  3.000
 7PM  N15  C8   C7   128.42  3.000
 7PM  N16  C8   C7   104.79  3.000
 7PM  S22  C9   N16  121.00  3.000
 7PM  N16  C9   N14  112.43  3.000
 7PM  S22  C9   N14  126.57  3.000
 7PM  O20  C10  N17  120.47  3.000
 7PM  N17  C10  C7   110.57  3.000
 7PM  O20  C10  C7   128.96  3.000
 7PM  N18  C11  N17  117.02  3.000
 7PM  N18  C11  N15  119.94  3.000
 7PM  N17  C11  N15  123.03  3.000
 7PM  O21  C12  O19  128.53  3.000
 7PM  O21  C12  C13  118.13  3.000
 7PM  O19  C12  C13  113.30  3.000
 7PM  H6   C13  S22  107.78  3.000
 7PM  H6   C13  C12  109.32  3.000
 7PM  S22  C13  C12  113.36  3.000
 7PM  H6   C13  C6   109.04  3.000
 7PM  S22  C13  C6   106.59  3.000
 7PM  C12  C13  C6   110.63  3.000
 7PM  C9   N14  C7   104.67  3.000
 7PM  C11  N15  C8   113.08  3.000
 7PM  H8   N16  C9   126.29  3.000
 7PM  H8   N16  C8   126.36  3.000
 7PM  C9   N16  C8   107.25  3.000
 7PM  H9   N17  C11  118.28  3.000
 7PM  H9   N17  C10  115.53  3.000
 7PM  C11  N17  C10  126.19  3.000
 7PM  H11  N18  H10  117.44  3.000
 7PM  H11  N18  C11  122.08  3.000
 7PM  H10  N18  C11  118.50  3.000
 7PM  C13  S22  C9    99.61  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  Var_01    N14  C9   S22  C13   49.37  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  O19  0.020
 7PM  plan-3  O21  0.020

