# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:31:43 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: N-[(4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-yl)sulfonyl]-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N[S](=O)(=O)c1ccc(cc1)c2ccc(CSC3=NC4=C(CCC4)C(=O)N3)cc2)C(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
 8OM  8OM  N-[(4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-yl)sulfonyl]-L-valine  ligand  61  35  .  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_8OM
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
 8OM  C12  C  C1     0  -0.299  -2.4675  -0.9043  -0.8106
 8OM  C13  C  C1     0  -0.219  -3.8240  -1.1827  -0.8577
 8OM  C8   C  CH2    0  -0.622   3.8479   0.4336   0.5951
 8OM  C7   C  CR16   0  -0.291   0.4317  -0.9553   1.4600
 8OM  C6   C  CR16   0  -0.270   1.7896  -0.6828   1.5034
 8OM  C4   C  CR16   0  -0.262   1.5813   0.6739  -0.4592
 8OM  C2   C  CR6    0   0.078  -0.3716  -0.4197   0.4535
 8OM  C1   C  C      0   0.448  -5.7712   1.9394   0.6398
 8OM  O2   O  OC    -1  -0.590  -5.0406   2.7022  -0.0110
 8OM  O1   O  O      0  -0.601  -5.8507   1.8402   1.8825
 8OM  C21  C  CH1    0  -0.214  -6.7245   1.0189  -0.1655
 8OM  C22  C  CH1    0  -0.224  -8.0449   1.7167  -0.5398
 8OM  C17  C  CH3    0  -0.651  -7.8192   2.9952  -1.3419
 8OM  C9   C  CH3    0  -0.647  -8.9508   0.7729  -1.3241
 8OM  N18  N  NC1    0  -0.709  -7.0314  -0.1664   0.6449
 8OM  O19  O  OS     0  -0.672  -6.6009  -2.4864   1.3920
 8OM  O20  O  OS     0  -0.659  -6.6439  -1.9536  -1.0637
 8OM  C14  C  C      0  -0.208  -4.5415  -1.2672   0.3254
 8OM  C15  C  C1     0  -0.205  -3.9180  -1.0700   1.5512
 8OM  C16  C  C1     0  -0.301  -2.5636  -0.7962   1.5854
 8OM  C11  C  C      0   0.101  -1.8175  -0.7089   0.4073
 8OM  C5   C  CR6    0   0.082   2.3784   0.1412   0.5501
 8OM  C3   C  CR16   0  -0.290   0.2254   0.3980  -0.5076
 8OM  S10  S  S2     0   0.083   4.6550  -0.7417  -0.5411
 8OM  C28  C  C      0   0.345   6.3176  -0.2023  -0.4719
 8OM  N31  N  N      0  -0.454   6.6745   0.7837   0.2872
 8OM  C34  C  C      0   0.249   7.9902   1.1073   0.2363
 8OM  C37  C  CH2    0  -0.501   8.6052   2.1953   1.0607
 8OM  C36  C  CH2    0  -0.465   9.9850   2.3833   0.4065
 8OM  C35  C  CH2    0  -0.478  10.2900   1.0613  -0.3307
 8OM  C33  C  C      0  -0.148   8.9254   0.4815  -0.5264
 8OM  C32  C  C      0   0.521   8.5464  -0.6205  -1.3509
 8OM  N29  N  NH1    0  -0.688   7.1762  -0.8869  -1.2621
 8OM  O38  O  O      0  -0.472   9.2627  -1.2959  -2.0734
 8OM  H1   H  H      0   0.267  -1.9095  -0.8632  -1.7370
 8OM  H2   H  H      0   0.281  -4.3047  -1.3444  -1.8125
 8OM  H3   H  HCH2   0   0.309   4.0700   1.4453   0.2606
 8OM  H4   H  HCH2   0   0.308   4.2552   0.2942   1.5946
 8OM  H5   H  HCR6   0   0.262   0.0002  -1.6086   2.2077
 8OM  H6   H  HCR6   0   0.262   2.3955  -1.1163   2.2897
 8OM  H7   H  HCR6   0   0.262   2.0219   1.3202  -1.2091
 8OM  H9   H  HCH1   0   0.239  -6.2329   0.7155  -1.0953
 8OM  H10  H  HCH1   0   0.216  -8.5499   1.9831   0.3966
 8OM  H11  H  HCH3   0   0.211  -7.2614   2.7867  -2.2577
 8OM  H12  H  HCH3   0   0.219  -8.7787   3.4253  -1.6339
 8OM  H13  H  HCH3   0   0.231  -7.2724   3.7522  -0.7846
 8OM  H14  H  HCH3   0   0.231  -9.1660  -0.1425  -0.7757
 8OM  H15  H  HCH3   0   0.222  -9.9007   1.2588  -1.5528
 8OM  H16  H  HCH3   0   0.211  -8.4863   0.4931  -2.2726
 8OM  H17  H  HNC1   0   0.396  -6.9187   0.0820   1.6296
 8OM  H18  H  H      0   0.279  -4.4736  -1.1283   2.4776
 8OM  H19  H  H      0   0.267  -2.0867  -0.6271   2.5421
 8OM  H20  H  HCR6   0   0.262  -0.3765   0.8442  -1.2890
 8OM  H21  H  HCH2   0   0.260   8.0013   3.1038   1.0694
 8OM  H22  H  HCH2   0   0.245   9.9304   3.1955  -0.3197
 8OM  H23  H  HCH2   0   0.250  10.8243   1.2242  -1.2681
 8OM  H24  H  HCH2   0   0.262   8.6850   1.8585   2.0993
 8OM  H25  H  HCH2   0   0.243  10.7569   2.6428   1.1293
 8OM  H26  H  HCH2   0   0.248  10.9108   0.3943   0.2753
 8OM  H27  H  HNH1   0   0.429   6.8303  -1.6530  -1.8284
 8OM  S17  S  S      0   1.362  -6.2879  -1.5792   0.2965

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
 8OM  C9   C22  single    1.525  0.020  1.525
 8OM  C17  C22  single    1.526  0.020  1.526
 8OM  C22  C21  single    1.540  0.020  1.540
 8OM  C21  N18  single    1.468  0.020  1.468
 8OM  C21  C1   single    1.551  0.020  1.551
 8OM  N18  S17  single    1.634  0.020  1.634
 8OM  C1   O1   deloc     1.249  0.020  1.249
 8OM  C1   O2   deloc     1.241  0.020  1.241
 8OM  O19  S17  double    1.456  0.020  1.456
 8OM  S17  O20  double    1.455  0.020  1.455
 8OM  S17  C14  single    1.774  0.020  1.774
 8OM  C14  C15  aromatic  1.389  0.020  1.389
 8OM  C14  C13  aromatic  1.386  0.020  1.386
 8OM  C15  C16  aromatic  1.382  0.020  1.382
 8OM  C13  C12  aromatic  1.386  0.020  1.386
 8OM  C16  C11  aromatic  1.397  0.020  1.397
 8OM  C12  C11  aromatic  1.394  0.020  1.394
 8OM  C11  C2   single    1.475  0.020  1.475
 8OM  C2   C7   aromatic  1.395  0.020  1.395
 8OM  C2   C3   aromatic  1.396  0.020  1.396
 8OM  C7   C6   aromatic  1.386  0.020  1.386
 8OM  C3   C4   aromatic  1.385  0.020  1.385
 8OM  C6   C5   aromatic  1.391  0.020  1.391
 8OM  C4   C5   aromatic  1.392  0.020  1.392
 8OM  C5   C8   single    1.499  0.020  1.499
 8OM  C8   S10  single    1.823  0.020  1.823
 8OM  S10  C28  single    1.749  0.020  1.749
 8OM  N31  C28  double    1.295  0.020  1.295
 8OM  N31  C34  single    1.356  0.020  1.356
 8OM  C28  N29  single    1.353  0.020  1.353
 8OM  C34  C37  single    1.497  0.020  1.497
 8OM  C34  C33  double    1.359  0.020  1.359
 8OM  C37  C36  single    1.539  0.020  1.539
 8OM  N29  C32  single    1.399  0.020  1.399
 8OM  C33  C32  single    1.428  0.020  1.428
 8OM  C33  C35  single    1.496  0.020  1.496
 8OM  C32  O38  double    1.221  0.020  1.221
 8OM  C36  C35  single    1.544  0.020  1.544
 8OM  C12  H1   single    0.930  0.020  1.080
 8OM  C13  H2   single    0.930  0.020  1.080
 8OM  C8   H3   single    0.970  0.020  1.090
 8OM  C8   H4   single    0.970  0.020  1.090
 8OM  C7   H5   single    0.930  0.020  1.080
 8OM  C6   H6   single    0.930  0.020  1.080
 8OM  C4   H7   single    0.930  0.020  1.080
 8OM  C21  H9   single    0.970  0.020  1.090
 8OM  C22  H10  single    0.970  0.020  1.090
 8OM  C17  H11  single    0.970  0.020  1.090
 8OM  C17  H12  single    0.970  0.020  1.090
 8OM  C17  H13  single    0.970  0.020  1.090
 8OM  C9   H14  single    0.970  0.020  1.090
 8OM  C9   H15  single    0.970  0.020  1.090
 8OM  C9   H16  single    0.970  0.020  1.090
 8OM  N18  H17  single    0.890  0.020  1.040
 8OM  C15  H18  single    0.930  0.020  1.080
 8OM  C16  H19  single    0.930  0.020  1.080
 8OM  C3   H20  single    0.930  0.020  1.080
 8OM  C37  H21  single    0.970  0.020  1.090
 8OM  C36  H22  single    0.970  0.020  1.090
 8OM  C35  H23  single    0.970  0.020  1.090
 8OM  C37  H24  single    0.970  0.020  1.090
 8OM  C36  H25  single    0.970  0.020  1.090
 8OM  C35  H26  single    0.970  0.020  1.090
 8OM  N29  H27  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
 8OM  H1   C12  C11  120.14  3.000
 8OM  H1   C12  C13  118.90  3.000
 8OM  C11  C12  C13  120.95  3.000
 8OM  H2   C13  C14  120.96  3.000
 8OM  H2   C13  C12  119.70  3.000
 8OM  C14  C13  C12  119.33  3.000
 8OM  H4   C8   H3   108.96  3.000
 8OM  H4   C8   S10  108.91  3.000
 8OM  H3   C8   S10  108.50  3.000
 8OM  H4   C8   C5   111.69  3.000
 8OM  H3   C8   C5   111.85  3.000
 8OM  S10  C8   C5   106.83  3.000
 8OM  H5   C7   C2   120.03  3.000
 8OM  H5   C7   C6   119.19  3.000
 8OM  C2   C7   C6   120.77  3.000
 8OM  H6   C6   C5   119.86  3.000
 8OM  H6   C6   C7   119.49  3.000
 8OM  C5   C6   C7   120.66  3.000
 8OM  H7   C4   C3   119.53  3.000
 8OM  H7   C4   C5   119.81  3.000
 8OM  C3   C4   C5   120.65  3.000
 8OM  C3   C2   C11  120.83  3.000
 8OM  C3   C2   C7   118.39  3.000
 8OM  C11  C2   C7   120.78  3.000
 8OM  C21  C1   O1   115.49  3.000
 8OM  O1   C1   O2   127.46  3.000
 8OM  C21  C1   O2   117.04  3.000
 8OM  H9   C21  N18  109.81  3.000
 8OM  H9   C21  C22  107.71  3.000
 8OM  N18  C21  C22  108.71  3.000
 8OM  H9   C21  C1   109.24  3.000
 8OM  N18  C21  C1   108.72  3.000
 8OM  C22  C21  C1   112.61  3.000
 8OM  H10  C22  C9   108.41  3.000
 8OM  H10  C22  C17  108.26  3.000
 8OM  C9   C22  C17  109.63  3.000
 8OM  H10  C22  C21  107.30  3.000
 8OM  C17  C22  C21  112.37  3.000
 8OM  C9   C22  C21  110.73  3.000
 8OM  H13  C17  H12  107.75  3.000
 8OM  H13  C17  H11  107.80  3.000
 8OM  H12  C17  H11  107.45  3.000
 8OM  H13  C17  C22  112.85  3.000
 8OM  H12  C17  C22  109.93  3.000
 8OM  H11  C17  C22  110.87  3.000
 8OM  H16  C9   H15  107.59  3.000
 8OM  H16  C9   H14  107.82  3.000
 8OM  H15  C9   H14  107.93  3.000
 8OM  H16  C9   C22  110.63  3.000
 8OM  H15  C9   C22  110.44  3.000
 8OM  H14  C9   C22  112.25  3.000
 8OM  H17  N18  S17  111.43  3.000
 8OM  H17  N18  C21  108.22  3.000
 8OM  S17  N18  C21  119.03  3.000
 8OM  C15  C14  S17  118.75  3.000
 8OM  C15  C14  C13  120.81  3.000
 8OM  S17  C14  C13  120.42  3.000
 8OM  H18  C15  C16  119.52  3.000
 8OM  H18  C15  C14  121.16  3.000
 8OM  C16  C15  C14  119.32  3.000
 8OM  H19  C16  C11  120.01  3.000
 8OM  H19  C16  C15  118.99  3.000
 8OM  C11  C16  C15  120.98  3.000
 8OM  C16  C11  C2   120.62  3.000
 8OM  C2   C11  C12  120.78  3.000
 8OM  C16  C11  C12  118.61  3.000
 8OM  C4   C5   C6   118.77  3.000
 8OM  C4   C5   C8   120.56  3.000
 8OM  C6   C5   C8   120.67  3.000
 8OM  H20  C3   C2   120.03  3.000
 8OM  H20  C3   C4   119.18  3.000
 8OM  C2   C3   C4   120.77  3.000
 8OM  C28  S10  C8   101.38  3.000
 8OM  N29  C28  N31  123.57  3.000
 8OM  N29  C28  S10  115.09  3.000
 8OM  N31  C28  S10  121.34  3.000
 8OM  C34  N31  C28  115.30  3.000
 8OM  C33  C34  C37  111.16  3.000
 8OM  C33  C34  N31  125.36  3.000
 8OM  C37  C34  N31  123.46  3.000
 8OM  H24  C37  H21  106.80  3.000
 8OM  H24  C37  C36  112.06  3.000
 8OM  H21  C37  C36  113.45  3.000
 8OM  H24  C37  C34  109.19  3.000
 8OM  H21  C37  C34  112.47  3.000
 8OM  C36  C37  C34  102.89  3.000
 8OM  H25  C36  H22  107.46  3.000
 8OM  H25  C36  C35  112.39  3.000
 8OM  H22  C36  C35  109.24  3.000
 8OM  H25  C36  C37  112.49  3.000
 8OM  H22  C36  C37  109.21  3.000
 8OM  C35  C36  C37  105.99  3.000
 8OM  H26  C35  H23  106.79  3.000
 8OM  H26  C35  C33  110.72  3.000
 8OM  H23  C35  C33  113.10  3.000
 8OM  H26  C35  C36  111.69  3.000
 8OM  H23  C35  C36  112.27  3.000
 8OM  C33  C35  C36  102.37  3.000
 8OM  C32  C33  C35  128.10  3.000
 8OM  C35  C33  C34  112.08  3.000
 8OM  C32  C33  C34  119.79  3.000
 8OM  O38  C32  N29  120.46  3.000
 8OM  O38  C32  C33  127.80  3.000
 8OM  N29  C32  C33  111.74  3.000
 8OM  H27  N29  C32  116.29  3.000
 8OM  H27  N29  C28  119.48  3.000
 8OM  C32  N29  C28  124.23  3.000
 8OM  C14  S17  O20  107.54  3.000
 8OM  C14  S17  O19  107.99  3.000
 8OM  O20  S17  O19  119.36  3.000
 8OM  C14  S17  N18  107.00  3.000
 8OM  O20  S17  N18  108.09  3.000
 8OM  O19  S17  N18  106.29  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
 8OM  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 8OM  CONST_02  C15  C16  C11  C12     0.00   0.0  0
 8OM  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 8OM  CONST_06  C16  C11  C12  C13     0.00   0.0  0
 8OM  CONST_07  C2   C11  C12  C13   180.00   0.0  0
 8OM  CONST_09  C4   C3   C2   C7      0.00   0.0  0
 8OM  CONST_10  C4   C5   C6   C7      0.00   0.0  0
 8OM  CONST_11  C11  C2   C7   C6    180.00   0.0  0
 8OM  CONST_12  C3   C2   C7   C6      0.00   0.0  0
 8OM  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 8OM  CONST_14  C11  C2   C3   C4    180.00   0.0  0
 8OM  CONST_15  C15  C16  C11  C2    180.00   0.0  0
 8OM  CONST_16  C5   C6   C7   C2      0.00   0.0  0
 8OM  CONST_17  C5   C4   C3   C2      0.00   0.0  0
 8OM  CONST_18  C11  C16  C15  C14     0.00   0.0  0
 8OM  CONST_19  C11  C12  C13  C14     0.00   0.0  0
 8OM  CONST_21  C33  C32  N29  C28     0.00   0.0  0
 8OM  CONST_22  C32  N29  C28  N31     0.00   0.0  0
 8OM  CONST_23  N29  C28  N31  C34     0.00   0.0  0
 8OM  CONST_24  S17  C14  C13  C12   180.00   0.0  0
 8OM  CONST_25  C7   C6   C5   C8    180.00   0.0  0
 8OM  CONST_26  C3   C4   C5   C8    180.00   0.0  0
 8OM  CONST_27  C16  C15  C14  S17   180.00   0.0  0
 8OM  CONST_28  C34  N31  C28  S10   180.00   0.0  0
 8OM  CONST_29  C32  N29  C28  S10   180.00   0.0  0
 8OM  CONST_30  O38  C32  N29  C28   180.00   0.0  0
 8OM  CONST_31  H19  C16  C11  C12   180.00   0.0  0
 8OM  CONST_32  H18  C15  C14  C13   180.00   0.0  0
 8OM  CONST_33  H20  C3   C2   C7    180.00   0.0  0
 8OM  CONST_34  H7   C4   C5   C6    180.00   0.0  0
 8OM  CONST_35  H6   C6   C5   C4    180.00   0.0  0
 8OM  CONST_36  H1   C12  C11  C2      0.00   0.0  0
 8OM  CONST_37  H2   C13  C14  C15   180.00   0.0  0
 8OM  CONST_38  H5   C7   C2   C11     0.00   0.0  0
 8OM  CONST_39  H27  N29  C28  N31   180.00   0.0  0
 8OM  Var_01    C36  C37  C34  N31  -167.00  30.0  1
 8OM  Var_02    C35  C36  C37  C34   -22.56  30.0  1
 8OM  Var_03    C36  C35  C33  C34   -13.97  30.0  1
 8OM  Var_04    C33  C35  C36  C37    22.25  30.0  1
 8OM  Var_05    N18  S17  C14  C13  -105.24  30.0  2
 8OM  Var_06    N31  C28  S10  C8      1.43  30.0  3
 8OM  Var_07    S10  C8   C5   C6     95.92  30.0  2
 8OM  Var_08    C14  S17  N18  C21    54.92  30.0  3
 8OM  Var_09    H14  C9   C22  C21    57.26  30.0  3
 8OM  Var_10    H11  C17  C22  C21    58.13  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
 8OM  chir_01  C21  C22  N18  C1  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
 8OM  plan-1  C8   0.020
 8OM  plan-1  C7   0.020
 8OM  plan-1  C6   0.020
 8OM  plan-1  C4   0.020
 8OM  plan-1  C2   0.020
 8OM  plan-1  C11  0.020
 8OM  plan-1  C5   0.020
 8OM  plan-1  C3   0.020
 8OM  plan-1  H5   0.020
 8OM  plan-1  H6   0.020
 8OM  plan-1  H7   0.020
 8OM  plan-1  H20  0.020
 8OM  plan-2  C12  0.020
 8OM  plan-2  C13  0.020
 8OM  plan-2  C2   0.020
 8OM  plan-2  C14  0.020
 8OM  plan-2  C15  0.020
 8OM  plan-2  C16  0.020
 8OM  plan-2  C11  0.020
 8OM  plan-2  H1   0.020
 8OM  plan-2  H2   0.020
 8OM  plan-2  H18  0.020
 8OM  plan-2  H19  0.020
 8OM  plan-2  S17  0.020
 8OM  plan-3  S10  0.020
 8OM  plan-3  C28  0.020
 8OM  plan-3  N31  0.020
 8OM  plan-3  C34  0.020
 8OM  plan-3  C37  0.020
 8OM  plan-3  C35  0.020
 8OM  plan-3  C33  0.020
 8OM  plan-3  C32  0.020
 8OM  plan-3  N29  0.020
 8OM  plan-3  O38  0.020
 8OM  plan-3  H27  0.020
 8OM  plan-4  C1   0.020
 8OM  plan-4  O2   0.020
 8OM  plan-4  O1   0.020
 8OM  plan-4  C21  0.020

