# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:05:47 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  62  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  CR16  0  -0.295   -2.5054  -0.9101  -0.8183
 8OM  C13  C  CR16  0  -0.216   -3.8629  -1.1845  -0.8496
 8OM  C8   C  CH2   0  -0.622    3.8252   0.4171   0.5721
 8OM  C7   C  CR16  0  -0.290    0.4460  -1.0852   1.3857
 8OM  C6   C  CR16  0  -0.268    1.7996  -0.7942   1.4279
 8OM  C4   C  CR16  0  -0.263    1.5432   0.6777  -0.4446
 8OM  C2   C  CR6   0   0.080   -0.3798  -0.4988   0.4265
 8OM  C1   C  C     0   0.550   -5.5059   1.6755  -0.1248
 8OM  O2   O  OH1   0  -0.579   -4.8381   1.9859  -1.2229
 8OM  O1   O  O     0  -0.425   -5.1534   1.9656   0.9898
 8OM  C21  C  CH1   0  -0.192   -6.7995   0.9258  -0.4165
 8OM  C22  C  CH1   0  -0.248   -8.0026   1.8919  -0.3756
 8OM  C17  C  CH3   0  -0.666   -7.8100   3.0766  -1.3178
 8OM  C9   C  CH3   0  -0.650   -9.2866   1.1449  -0.7177
 8OM  N18  N  NC1   0  -0.717   -7.0019  -0.1348   0.5552
 8OM  O19  O  OS    0  -0.651   -6.6549  -2.3964   1.4981
 8OM  O20  O  OS    0  -0.650   -6.6710  -2.0552  -0.9996
 8OM  C14  C  CR6   0  -0.235   -4.5491  -1.3443   0.3456
 8OM  C15  C  CR16  0  -0.208   -3.8931  -1.2405   1.5659
 8OM  C16  C  CR16  0  -0.297   -2.5384  -0.9694   1.5817
 8OM  C11  C  CR6   0   0.102   -1.8242  -0.7962   0.3932
 8OM  C5   C  CR6   0   0.082    2.3616   0.0982   0.5209
 8OM  C3   C  CR16  0  -0.289    0.1908   0.3837  -0.4918
 8OM  S10  S  S2    0   0.083    4.6549  -0.7070  -0.5987
 8OM  C28  C  CR6   0   0.345    6.3125  -0.1607  -0.4813
 8OM  N31  N  N     0  -0.454    6.6490   0.8014   0.3167
 8OM  C34  C  CR56  0   0.249    7.9636   1.1335   0.3021
 8OM  C37  C  CH2   0  -0.501    8.5563   2.1971   1.1734
 8OM  C36  C  CH2   0  -0.465    9.9477   2.4129   0.5532
 8OM  C35  C  CH2   0  -0.478   10.2741   1.1178  -0.2215
 8OM  C33  C  CR56  0  -0.148    8.9167   0.5383  -0.4629
 8OM  C32  C  CR6   0   0.521    8.5599  -0.5371  -1.3314
 8OM  N29  N  NR16  0  -0.688    7.1898  -0.8135  -1.2777
 8OM  O38  O  O     0  -0.471    9.2935  -1.1838  -2.0625
 8OM  H1   H  HCR6  0   0.271   -1.9730  -0.8064  -1.7546
 8OM  H2   H  HCR6  0   0.288   -4.3660  -1.2839  -1.8015
 8OM  H3   H  HCH2  0   0.309    4.0265   1.4430   0.2695
 8OM  H4   H  HCH2  0   0.308    4.2369   0.2548   1.5664
 8OM  H5   H  HCR6  0   0.263    0.0346  -1.7898   2.0974
 8OM  H6   H  HCR6  0   0.264    2.4238  -1.2641   2.1780
 8OM  H7   H  HCR6  0   0.263    1.9635   1.3766  -1.1578
 8OM  H8   H  HOH1  0   0.483   -4.0483   2.5040  -1.0027
 8OM  H9   H  HCH1  0   0.293   -6.7550   0.4816  -1.4135
 8OM  H10  H  HCH1  0   0.244   -8.0803   2.2751   0.6481
 8OM  H11  H  HCH3  0   0.228   -7.6443   2.7428  -2.3438
 8OM  H12  H  HCH3  0   0.244   -8.7072   3.6951  -1.3118
 8OM  H13  H  HCH3  0   0.238   -6.9789   3.7213  -1.0319
 8OM  H14  H  HCH3  0   0.241   -9.4757   0.3195  -0.0340
 8OM  H15  H  HCH3  0   0.237  -10.1387   1.8234  -0.6669
 8OM  H16  H  HCH3  0   0.222   -9.2436   0.7417  -1.7319
 8OM  H17  H  HNC1  0   0.415   -6.9756   0.1690   1.5238
 8OM  H18  H  HCR6  0   0.286   -4.4253  -1.3624   2.4997
 8OM  H19  H  HCR6  0   0.271   -2.0356  -0.8695   2.5347
 8OM  H20  H  HCR6  0   0.260   -0.4288   0.8689  -1.2351
 8OM  H21  H  HCH2  0   0.260    7.9476   3.1021   1.1993
 8OM  H22  H  HCH2  0   0.245    9.9037   3.2489  -0.1462
 8OM  H23  H  HCH2  0   0.250   10.8255   1.3146  -1.1422
 8OM  H24  H  HCH2  0   0.262    8.6175   1.8274   2.2020
 8OM  H25  H  HCH2  0   0.243   10.7040   2.6513   1.2995
 8OM  H26  H  HCH2  0   0.248   10.8864   0.4339   0.3742
 8OM  H27  H  HNR6  0   0.430    6.8589  -1.5618  -1.8760
 8OM  S17  S  S     0   1.387   -6.2987  -1.6083   0.3317

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    1.524  0.020  1.524
 8OM  C17  C22  single    1.526  0.020  1.526
 8OM  C22  C21  single    1.544  0.020  1.544
 8OM  C21  N18  single    1.453  0.020  1.453
 8OM  C21  C1   single    1.523  0.020  1.523
 8OM  N18  S17  single    1.648  0.020  1.648
 8OM  C1   O1   double    1.204  0.020  1.204
 8OM  C1   O2   single    1.322  0.020  1.322
 8OM  O19  S17  double    1.452  0.020  1.452
 8OM  S17  O20  double    1.453  0.020  1.453
 8OM  S17  C14  single    1.769  0.020  1.769
 8OM  C14  C15  aromatic  1.389  0.020  1.389
 8OM  C14  C13  aromatic  1.387  0.020  1.387
 8OM  C15  C16  aromatic  1.382  0.020  1.382
 8OM  C13  C12  aromatic  1.385  0.020  1.385
 8OM  C16  C11  aromatic  1.397  0.020  1.397
 8OM  C12  C11  aromatic  1.395  0.020  1.395
 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  1.385  0.020  1.385
 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    1.294  0.020  1.294
 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  O2   H8   single    0.850  0.020  0.980
 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  120.23  3.000
 8OM  H1   C12  C13  118.79  3.000
 8OM  C11  C12  C13  120.97  3.000
 8OM  H2   C13  C14  121.18  3.000
 8OM  H2   C13  C12  119.61  3.000
 8OM  C14  C13  C12  119.21  3.000
 8OM  H4   C8   H3   108.94  3.000
 8OM  H4   C8   S10  108.83  3.000
 8OM  H3   C8   S10  108.57  3.000
 8OM  H4   C8   C5   111.65  3.000
 8OM  H3   C8   C5   111.82  3.000
 8OM  S10  C8   C5   106.94  3.000
 8OM  H5   C7   C2   120.04  3.000
 8OM  H5   C7   C6   119.21  3.000
 8OM  C2   C7   C6   120.74  3.000
 8OM  H6   C6   C5   119.80  3.000
 8OM  H6   C6   C7   119.55  3.000
 8OM  C5   C6   C7   120.65  3.000
 8OM  H7   C4   C3   119.56  3.000
 8OM  H7   C4   C5   119.80  3.000
 8OM  C3   C4   C5   120.63  3.000
 8OM  C3   C2   C11  120.86  3.000
 8OM  C3   C2   C7   118.44  3.000
 8OM  C11  C2   C7   120.70  3.000
 8OM  C21  C1   O1   122.97  3.000
 8OM  O1   C1   O2   124.34  3.000
 8OM  C21  C1   O2   112.67  3.000
 8OM  H8   O2   C1   110.38  3.000
 8OM  H9   C21  N18  108.62  3.000
 8OM  H9   C21  C22  108.08  3.000
 8OM  N18  C21  C22  109.31  3.000
 8OM  H9   C21  C1   109.90  3.000
 8OM  N18  C21  C1   110.47  3.000
 8OM  C22  C21  C1   110.41  3.000
 8OM  H10  C22  C9   108.74  3.000
 8OM  H10  C22  C17  108.31  3.000
 8OM  C9   C22  C17  110.38  3.000
 8OM  H10  C22  C21  107.39  3.000
 8OM  C17  C22  C21  111.79  3.000
 8OM  C9   C22  C21  110.11  3.000
 8OM  H13  C17  H12  106.89  3.000
 8OM  H13  C17  H11  108.16  3.000
 8OM  H12  C17  H11  107.68  3.000
 8OM  H13  C17  C22  113.18  3.000
 8OM  H12  C17  C22  109.47  3.000
 8OM  H11  C17  C22  111.23  3.000
 8OM  H16  C9   H15  107.68  3.000
 8OM  H16  C9   H14  108.08  3.000
 8OM  H15  C9   H14  107.87  3.000
 8OM  H16  C9   C22  110.86  3.000
 8OM  H15  C9   C22  110.05  3.000
 8OM  H14  C9   C22  112.15  3.000
 8OM  H17  N18  S17  112.70  3.000
 8OM  H17  N18  C21  114.58  3.000
 8OM  S17  N18  C21  120.17  3.000
 8OM  C15  C14  S17  119.01  3.000
 8OM  C15  C14  C13  120.97  3.000
 8OM  S17  C14  C13  119.96  3.000
 8OM  H18  C15  C16  119.65  3.000
 8OM  H18  C15  C14  121.17  3.000
 8OM  C16  C15  C14  119.19  3.000
 8OM  H19  C16  C11  120.01  3.000
 8OM  H19  C16  C15  118.93  3.000
 8OM  C11  C16  C15  121.05  3.000
 8OM  C16  C11  C2   120.41  3.000
 8OM  C2   C11  C12  120.96  3.000
 8OM  C16  C11  C12  118.62  3.000
 8OM  C4   C5   C6   118.80  3.000
 8OM  C4   C5   C8   120.62  3.000
 8OM  C6   C5   C8   120.58  3.000
 8OM  H20  C3   C2   120.08  3.000
 8OM  H20  C3   C4   119.16  3.000
 8OM  C2   C3   C4   120.74  3.000
 8OM  C28  S10  C8   101.28  3.000
 8OM  N29  C28  N31  123.57  3.000
 8OM  N29  C28  S10  115.11  3.000
 8OM  N31  C28  S10  121.32  3.000
 8OM  C34  N31  C28  115.30  3.000
 8OM  C33  C34  C37  111.16  3.000
 8OM  C33  C34  N31  125.35  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  113.44  3.000
 8OM  H24  C37  C34  109.21  3.000
 8OM  H21  C37  C34  112.47  3.000
 8OM  C36  C37  C34  102.89  3.000
 8OM  H25  C36  H22  107.44  3.000
 8OM  H25  C36  C35  112.37  3.000
 8OM  H22  C36  C35  109.25  3.000
 8OM  H25  C36  C37  112.49  3.000
 8OM  H22  C36  C37  109.23  3.000
 8OM  C35  C36  C37  106.01  3.000
 8OM  H26  C35  H23  106.81  3.000
 8OM  H26  C35  C33  110.71  3.000
 8OM  H23  C35  C33  113.10  3.000
 8OM  H26  C35  C36  111.68  3.000
 8OM  H23  C35  C36  112.27  3.000
 8OM  C33  C35  C36  102.36  3.000
 8OM  C32  C33  C35  128.09  3.000
 8OM  C35  C33  C34  112.08  3.000
 8OM  C32  C33  C34  119.80  3.000
 8OM  O38  C32  N29  120.45  3.000
 8OM  O38  C32  C33  127.81  3.000
 8OM  N29  C32  C33  111.74  3.000
 8OM  H27  N29  C32  116.30  3.000
 8OM  H27  N29  C28  119.47  3.000
 8OM  C32  N29  C28  124.23  3.000
 8OM  C14  S17  O20  107.85  3.000
 8OM  C14  S17  O19  108.49  3.000
 8OM  O20  S17  O19  120.41  3.000
 8OM  C14  S17  N18  106.71  3.000
 8OM  O20  S17  N18  106.86  3.000
 8OM  O19  S17  N18  105.76  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  CONST_40  H8   O2   C1   O1      0.00   0.0  0
 8OM  Var_01    C36  C37  C34  N31  -167.03  30.0  1
 8OM  Var_02    C35  C36  C37  C34   -22.50  30.0  1
 8OM  Var_03    C36  C35  C33  C34   -13.99  30.0  1
 8OM  Var_04    C33  C35  C36  C37    22.23  30.0  1
 8OM  Var_05    N18  S17  C14  C13   -95.62  30.0  2
 8OM  Var_06    N31  C28  S10  C8      0.97  30.0  3
 8OM  Var_07    S10  C8   C5   C6     94.10  30.0  2
 8OM  Var_08    C14  S17  N18  C21    62.21  30.0  3
 8OM  Var_09    H14  C9   C22  C21    58.67  30.0  3
 8OM  Var_10    H11  C17  C22  C21    57.19  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
 8OM  plan-4  H8   0.020

