# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 02:54:16 2020
#   Inital geometry file: a 164 line input string
#   Ligand name: (3R,4R)-N-(3-fluoro-4-methoxyphenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(methylsulfonyl)pyrrolidine-3,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)[C@H]2CN(C[C@@H]2C(=O)Nc3ccc(cc3F)N4C=CC=CC4=O)[S](C)(=O)=O)cc1F
#
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
 8NC  8NC  (3R,4R)-N-(3-fluoro-4-methoxyphenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(methylsulfonyl)pyrrolidine-3,4-dicarboxamide  ligand  62  38  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8NC
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
 8NC  S1    S  S     0   1.347    2.1379   5.1936  -0.0129
 8NC  C2    C  CR15  0  -0.436    0.6981   1.6633  -0.7591
 8NC  C3    C  CR15  0  -0.438    2.0672   1.4133  -0.1404
 8NC  N4    N  NR5   0  -0.603    1.8178   3.7016  -0.6157
 8NC  C5    C  C     0   0.581   -0.3926   0.7868  -0.1804
 8NC  N6    N  NR6   0  -0.613   -6.5696  -1.2209   0.6007
 8NC  C7    C  C     0   0.580    2.7085   0.1284  -0.6252
 8NC  C8    C  CH2   0  -0.249    0.4680   3.1504  -0.4732
 8NC  C9    C  CH2   0  -0.251    2.8510   2.6573  -0.5642
 8NC  C10   C  CR6   0   0.553   -7.1016  -2.3053  -0.1026
 8NC  C11   C  CR6   0   0.295   -5.2890  -0.7284   0.2112
 8NC  N12   N  NH1   0  -0.740   -1.5692   0.8734  -0.8537
 8NC  C13   C  CR16  0  -0.421   -5.2078   0.4827  -0.4570
 8NC  N14   N  NH1   0  -0.746    3.2841  -0.6021   0.3539
 8NC  C15   C  CR6   0   0.210   -2.7840   0.2945  -0.4764
 8NC  C16   C  CR6   0   0.498   -3.9615   0.9733  -0.7766
 8NC  C17   C  CR6   0   0.480    5.0760  -3.5737   1.4680
 8NC  C18   C  CR16  0  -0.506    4.3842  -2.3900   1.4704
 8NC  O19   O  OS    0  -0.661    3.4529   5.5784  -0.5003
 8NC  O20   O  OS    0  -0.663    0.9817   6.0227  -0.3159
 8NC  C21   C  CR16  0   0.050   -7.2214  -0.5953   1.6216
 8NC  C22   C  CR6   0   0.375    3.9753  -1.8166   0.2618
 8NC  O23   O  O     0  -0.442   -0.2210   0.0959   0.8028
 8NC  O24   O  O     0  -0.461    2.7023  -0.1763  -1.8048
 8NC  C25   C  CR16  0  -0.453   -8.4012  -2.7250   0.3504
 8NC  C26   C  CR6   0   0.229    5.3978  -4.2528   0.2918
 8NC  O27   O  O     0  -0.501   -6.4727  -2.8136  -1.0226
 8NC  C28   C  CR16  0  -0.264   -4.1400  -1.4367   0.5205
 8NC  C29   C  CR16  0  -0.296   -2.8969  -0.9340   0.1720
 8NC  C30   C  CR16  0  -0.398   -8.4464  -0.9982   2.0326
 8NC  C31   C  CR16  0  -0.118   -9.0426  -2.0982   1.3697
 8NC  C32   C  CR16  0  -0.368    4.9845  -3.6744  -0.8994
 8NC  C33   C  CH3   0  -0.802    2.2386   5.0109   1.7548
 8NC  F34   F  F     0  -0.305   -3.8713   2.1517  -1.4091
 8NC  C36   C  CR16  0  -0.315    4.2835  -2.4714  -0.9242
 8NC  O37   O  O2    0  -0.465    6.0787  -5.4028   0.4229
 8NC  C38   C  CH3   0  -0.438    6.3859  -6.1261  -0.7534
 8NC  H331  H  HCH3  0   0.290    3.0252   4.3022   2.0047
 8NC  H332  H  HCH3  0   0.311    2.4763   5.9845   2.1805
 8NC  H333  H  HCH3  0   0.291    1.2835   4.6646   2.1437
 8NC  H2    H  HCR5  0   0.318    0.7518   1.5145  -1.8425
 8NC  H3    H  HCR5  0   0.299    1.9702   1.4134   0.9482
 8NC  H81C  H  HCH2  0   0.284   -0.2199   3.6121  -1.1791
 8NC  H82C  H  HCH2  0   0.257    0.0686   3.2887   0.5381
 8NC  H91C  H  HCH2  0   0.276    3.6458   2.8853   0.1468
 8NC  H92C  H  HCH2  0   0.273    3.3053   2.5348  -1.5482
 8NC  H12   H  HNH1  0   0.421   -1.5942   1.4884  -1.6536
 8NC  H21   H  HCR6  0   0.314   -6.6947   0.2302   2.0786
 8NC  H14   H  HNH1  0   0.423    3.1875  -0.2405   1.2904
 8NC  H25   H  HCR6  0   0.276   -8.8517  -3.5622  -0.1653
 8NC  H13   H  HCR6  0   0.299   -6.0959   1.0456  -0.7148
 8NC  H28   H  HCR6  0   0.278   -4.2059  -2.3836   1.0389
 8NC  H29   H  HCR6  0   0.291   -2.0144  -1.5074   0.4061
 8NC  H18   H  HCR6  0   0.296    4.1634  -1.9116   2.4171
 8NC  H30   H  HCR6  0   0.281   -8.9403  -0.4872   2.8444
 8NC  H36   H  HCR6  0   0.287    3.9932  -2.0668  -1.8788
 8NC  H31   H  HCR6  0   0.282  -10.0214  -2.4412   1.6793
 8NC  H32   H  HCR6  0   0.294    5.2023  -4.1500  -1.8457
 8NC  H381  H  HCH3  0   0.232    5.4839  -6.4258  -1.2931
 8NC  H382  H  HCH3  0   0.231    7.0285  -5.5549  -1.4283
 8NC  H383  H  HCH3  0   0.263    6.9182  -7.0187  -0.4355
 8NC  F35   F  F     0  -0.310    5.4618  -4.1084   2.6349

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
 8NC  S1   N4    single    1.641  0.020  1.641
 8NC  S1   O19   double    1.454  0.020  1.454
 8NC  S1   O20   double    1.455  0.020  1.455
 8NC  S1   C33   single    1.780  0.020  1.780
 8NC  C2   C3    single    1.523  0.020  1.523
 8NC  C2   C5    single    1.514  0.020  1.514
 8NC  C2   C8    single    1.532  0.020  1.532
 8NC  C3   C7    single    1.516  0.020  1.516
 8NC  C3   C9    single    1.530  0.020  1.530
 8NC  N4   C8    single    1.465  0.020  1.465
 8NC  N4   C9    single    1.470  0.020  1.470
 8NC  C5   N12   single    1.358  0.020  1.358
 8NC  C5   O23   double    1.214  0.020  1.214
 8NC  N6   C10   single    1.398  0.020  1.398
 8NC  N6   C11   single    1.426  0.020  1.426
 8NC  N6   C21   single    1.363  0.020  1.363
 8NC  C7   N14   single    1.350  0.020  1.350
 8NC  C7   O24   double    1.218  0.020  1.218
 8NC  C10  C25   single    1.439  0.020  1.439
 8NC  C10  O27   double    1.225  0.020  1.225
 8NC  C11  C13   aromatic  1.386  0.020  1.386
 8NC  C11  C28   aromatic  1.385  0.020  1.385
 8NC  N12  C15   single    1.398  0.020  1.398
 8NC  C13  C16   aromatic  1.377  0.020  1.377
 8NC  N14  C22   single    1.400  0.020  1.400
 8NC  C15  C16   aromatic  1.392  0.020  1.392
 8NC  C15  C29   aromatic  1.394  0.020  1.394
 8NC  C16  F34   single    1.340  0.020  1.340
 8NC  C17  C18   aromatic  1.371  0.020  1.371
 8NC  C17  C26   aromatic  1.396  0.020  1.396
 8NC  C17  F35   single    1.340  0.020  1.340
 8NC  C18  C22   aromatic  1.399  0.020  1.399
 8NC  C21  C30   double    1.353  0.020  1.353
 8NC  C22  C36   aromatic  1.389  0.020  1.389
 8NC  C25  C31   double    1.358  0.020  1.358
 8NC  C26  C32   aromatic  1.387  0.020  1.387
 8NC  C26  O37   single    1.343  0.020  1.343
 8NC  C28  C29   aromatic  1.385  0.020  1.385
 8NC  C30  C31   single    1.416  0.020  1.416
 8NC  C32  C36   aromatic  1.393  0.020  1.393
 8NC  O37  C38   single    1.415  0.020  1.415
 8NC  C33  H331  single    0.970  0.020  1.090
 8NC  C33  H332  single    0.970  0.020  1.090
 8NC  C33  H333  single    0.970  0.020  1.090
 8NC  C2   H2    single    0.970  0.020  1.090
 8NC  C3   H3    single    0.970  0.020  1.090
 8NC  C8   H81C  single    0.970  0.020  1.090
 8NC  C8   H82C  single    0.970  0.020  1.090
 8NC  C9   H91C  single    0.970  0.020  1.090
 8NC  C9   H92C  single    0.970  0.020  1.090
 8NC  N12  H12   single    0.860  0.020  1.020
 8NC  C21  H21   single    0.930  0.020  1.080
 8NC  N14  H14   single    0.860  0.020  1.020
 8NC  C25  H25   single    0.930  0.020  1.080
 8NC  C13  H13   single    0.930  0.020  1.080
 8NC  C28  H28   single    0.930  0.020  1.080
 8NC  C29  H29   single    0.930  0.020  1.080
 8NC  C18  H18   single    0.930  0.020  1.080
 8NC  C30  H30   single    0.930  0.020  1.080
 8NC  C36  H36   single    0.930  0.020  1.080
 8NC  C31  H31   single    0.930  0.020  1.080
 8NC  C32  H32   single    0.930  0.020  1.080
 8NC  C38  H381  single    0.970  0.020  1.090
 8NC  C38  H382  single    0.970  0.020  1.090
 8NC  C38  H383  single    0.970  0.020  1.090

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
 8NC  C33   S1   O20   108.08  3.000
 8NC  C33   S1   O19   107.99  3.000
 8NC  O20   S1   O19   119.88  3.000
 8NC  C33   S1   N4    106.41  3.000
 8NC  O20   S1   N4    106.66  3.000
 8NC  O19   S1   N4    107.09  3.000
 8NC  H2    C2   C8    108.90  3.000
 8NC  H2    C2   C5    109.56  3.000
 8NC  C8    C2   C5    112.49  3.000
 8NC  H2    C2   C3    109.60  3.000
 8NC  C8    C2   C3    102.63  3.000
 8NC  C5    C2   C3    113.41  3.000
 8NC  H3    C3   C9    108.74  3.000
 8NC  H3    C3   C7    110.87  3.000
 8NC  C9    C3   C7    112.58  3.000
 8NC  H3    C3   C2    108.95  3.000
 8NC  C9    C3   C2    102.39  3.000
 8NC  C7    C3   C2    112.93  3.000
 8NC  C9    N4   C8    112.14  3.000
 8NC  C9    N4   S1    119.74  3.000
 8NC  C8    N4   S1    119.09  3.000
 8NC  O23   C5   N12   124.07  3.000
 8NC  O23   C5   C2    122.50  3.000
 8NC  N12   C5   C2    113.43  3.000
 8NC  C21   N6   C11   118.39  3.000
 8NC  C21   N6   C10   123.43  3.000
 8NC  C11   N6   C10   118.18  3.000
 8NC  O24   C7   N14   124.67  3.000
 8NC  O24   C7   C3    121.30  3.000
 8NC  N14   C7   C3    114.02  3.000
 8NC  H82C  C8   H81C  108.33  3.000
 8NC  H82C  C8   N4    112.21  3.000
 8NC  H81C  C8   N4    111.08  3.000
 8NC  H82C  C8   C2    110.46  3.000
 8NC  H81C  C8   C2    112.69  3.000
 8NC  N4    C8   C2    102.05  3.000
 8NC  H92C  C9   H91C  107.95  3.000
 8NC  H92C  C9   N4    109.93  3.000
 8NC  H91C  C9   N4    112.74  3.000
 8NC  H92C  C9   C3    111.83  3.000
 8NC  H91C  C9   C3    111.27  3.000
 8NC  N4    C9   C3    103.13  3.000
 8NC  O27   C10  C25   125.39  3.000
 8NC  O27   C10  N6    120.30  3.000
 8NC  C25   C10  N6    114.31  3.000
 8NC  C28   C11  C13   120.41  3.000
 8NC  C28   C11  N6    120.49  3.000
 8NC  C13   C11  N6    119.09  3.000
 8NC  H12   N12  C15   116.41  3.000
 8NC  H12   N12  C5    116.94  3.000
 8NC  C15   N12  C5    126.35  3.000
 8NC  H13   C13  C16   120.13  3.000
 8NC  H13   C13  C11   121.42  3.000
 8NC  C16   C13  C11   118.45  3.000
 8NC  H14   N14  C22   114.78  3.000
 8NC  H14   N14  C7    116.01  3.000
 8NC  C22   N14  C7    129.19  3.000
 8NC  C29   C15  C16   117.50  3.000
 8NC  C29   C15  N12   124.13  3.000
 8NC  C16   C15  N12   118.37  3.000
 8NC  F34   C16  C15   118.26  3.000
 8NC  F34   C16  C13   118.92  3.000
 8NC  C15   C16  C13   122.81  3.000
 8NC  F35   C17  C26   118.24  3.000
 8NC  F35   C17  C18   119.22  3.000
 8NC  C26   C17  C18   122.54  3.000
 8NC  H18   C18  C22   120.95  3.000
 8NC  H18   C18  C17   119.05  3.000
 8NC  C22   C18  C17   119.99  3.000
 8NC  H21   C21  C30   122.69  3.000
 8NC  H21   C21  N6    115.73  3.000
 8NC  C30   C21  N6    121.57  3.000
 8NC  C36   C22  C18   118.65  3.000
 8NC  C36   C22  N14   125.05  3.000
 8NC  C18   C22  N14   116.30  3.000
 8NC  H25   C25  C31   121.24  3.000
 8NC  H25   C25  C10   116.87  3.000
 8NC  C31   C25  C10   121.90  3.000
 8NC  O37   C26  C32   126.30  3.000
 8NC  O37   C26  C17   116.83  3.000
 8NC  C32   C26  C17   116.87  3.000
 8NC  H28   C28  C29   119.53  3.000
 8NC  H28   C28  C11   120.29  3.000
 8NC  C29   C28  C11   120.18  3.000
 8NC  H29   C29  C28   119.13  3.000
 8NC  H29   C29  C15   120.23  3.000
 8NC  C28   C29  C15   120.63  3.000
 8NC  H30   C30  C31   121.83  3.000
 8NC  H30   C30  C21   120.12  3.000
 8NC  C31   C30  C21   118.05  3.000
 8NC  H31   C31  C30   119.54  3.000
 8NC  H31   C31  C25   119.71  3.000
 8NC  C30   C31  C25   120.75  3.000
 8NC  H32   C32  C36   117.76  3.000
 8NC  H32   C32  C26   120.53  3.000
 8NC  C36   C32  C26   121.71  3.000
 8NC  H333  C33  H332  109.67  3.000
 8NC  H333  C33  H331  110.20  3.000
 8NC  H332  C33  H331  109.56  3.000
 8NC  H333  C33  S1    109.76  3.000
 8NC  H332  C33  S1    107.99  3.000
 8NC  H331  C33  S1    109.63  3.000
 8NC  H36   C36  C32   118.44  3.000
 8NC  H36   C36  C22   121.33  3.000
 8NC  C32   C36  C22   120.23  3.000
 8NC  C38   O37  C26   117.83  3.000
 8NC  H383  C38  H382  108.78  3.000
 8NC  H383  C38  H381  108.87  3.000
 8NC  H382  C38  H381  108.88  3.000
 8NC  H383  C38  O37   106.44  3.000
 8NC  H382  C38  O37   111.95  3.000
 8NC  H381  C38  O37   111.81  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
 8NC  CONST_01  C15   C16  C13  C11     0.00   0.0  0
 8NC  CONST_02  C15   C29  C28  C11     0.00   0.0  0
 8NC  CONST_03  C29   C28  C11  C13     0.00   0.0  0
 8NC  CONST_04  C29   C15  C16  C13     0.00   0.0  0
 8NC  CONST_05  C28   C11  C13  C16     0.00   0.0  0
 8NC  CONST_06  C28   C29  C15  C16     0.00   0.0  0
 8NC  CONST_07  C36   C22  C18  C17     0.00   0.0  0
 8NC  CONST_08  C36   C32  C26  C17     0.00   0.0  0
 8NC  CONST_09  C32   C26  C17  C18     0.00   0.0  0
 8NC  CONST_10  C32   C36  C22  C18     0.00   0.0  0
 8NC  CONST_11  C26   C17  C18  C22     0.00   0.0  0
 8NC  CONST_12  C26   C32  C36  C22     0.00   0.0  0
 8NC  CONST_13  C16   C13  C11  N6    180.00   0.0  0
 8NC  CONST_14  C29   C28  C11  N6    180.00   0.0  0
 8NC  CONST_15  C25   C10  N6   C11   180.00   0.0  0
 8NC  CONST_16  C25   C10  N6   C21     0.00   0.0  0
 8NC  CONST_17  F34   C16  C13  C11   180.00   0.0  0
 8NC  CONST_18  C13   C16  C15  N12   180.00   0.0  0
 8NC  CONST_19  C28   C29  C15  N12   180.00   0.0  0
 8NC  CONST_20  C17   C18  C22  N14   180.00   0.0  0
 8NC  CONST_21  C32   C36  C22  N14   180.00   0.0  0
 8NC  CONST_22  O37   C26  C17  C18   180.00   0.0  0
 8NC  CONST_23  F35   C17  C18  C22   180.00   0.0  0
 8NC  CONST_24  F34   C16  C15  C29   180.00   0.0  0
 8NC  CONST_25  F35   C17  C26  C32   180.00   0.0  0
 8NC  CONST_26  O37   C26  C32  C36   180.00   0.0  0
 8NC  CONST_27  O27   C10  N6   C11     0.00   0.0  0
 8NC  CONST_28  O27   C10  N6   C21   180.00   0.0  0
 8NC  CONST_29  H13   C13  C11  N6      0.00   0.0  0
 8NC  CONST_30  H28   C28  C11  N6      0.00   0.0  0
 8NC  CONST_31  H29   C29  C28  C11   180.00   0.0  0
 8NC  CONST_32  H32   C32  C26  C17   180.00   0.0  0
 8NC  CONST_33  H36   C36  C22  C18   180.00   0.0  0
 8NC  CONST_34  H18   C18  C17  C26   180.00   0.0  0
 8NC  CONST_35  C15   N12  C5   C2    180.00   0.0  0
 8NC  CONST_36  C22   N14  C7   C3    180.00   0.0  0
 8NC  CONST_39  C18   C22  N14  C7    180.00   0.0  0
 8NC  CONST_40  C36   C22  N14  C7      0.00   0.0  0
 8NC  CONST_42  H14   N14  C22  C18     0.00   0.0  0
 8NC  CONST_43  O23   C5   N12  C15     0.00   0.0  0
 8NC  CONST_44  O24   C7   N14  C22     0.00   0.0  0
 8NC  Var_01    C9    N4   C8   C2    -16.74  30.0  1
 8NC  Var_02    C8    N4   C9   C3     -9.19  30.0  1
 8NC  Var_03    C13   C11  N6   C10   107.24  30.0  2
 8NC  Var_04    O19   S1   N4   C8   -169.95  30.0  2
 8NC  Var_05    H331  C33  S1   N4     59.26  30.0  3
 8NC  Var_06    H381  C38  O37  C26   -60.42  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
 8NC  chir_01  C2  C3  C5  C8  negativ
 8NC  chir_02  C3  C2  C7  C9  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
 8NC  plan-1  N6   0.020
 8NC  plan-1  C10  0.020
 8NC  plan-1  C11  0.020
 8NC  plan-1  C21  0.020
 8NC  plan-1  C25  0.020
 8NC  plan-1  O27  0.020
 8NC  plan-1  C30  0.020
 8NC  plan-1  C31  0.020
 8NC  plan-1  H21  0.020
 8NC  plan-1  H25  0.020
 8NC  plan-1  H30  0.020
 8NC  plan-1  H31  0.020
 8NC  plan-2  N6   0.020
 8NC  plan-2  C11  0.020
 8NC  plan-2  N12  0.020
 8NC  plan-2  C13  0.020
 8NC  plan-2  C15  0.020
 8NC  plan-2  C16  0.020
 8NC  plan-2  C28  0.020
 8NC  plan-2  C29  0.020
 8NC  plan-2  F34  0.020
 8NC  plan-2  H13  0.020
 8NC  plan-2  H28  0.020
 8NC  plan-2  H29  0.020
 8NC  plan-3  N14  0.020
 8NC  plan-3  C17  0.020
 8NC  plan-3  C18  0.020
 8NC  plan-3  C22  0.020
 8NC  plan-3  C26  0.020
 8NC  plan-3  C32  0.020
 8NC  plan-3  C36  0.020
 8NC  plan-3  O37  0.020
 8NC  plan-3  H18  0.020
 8NC  plan-3  H36  0.020
 8NC  plan-3  H32  0.020
 8NC  plan-3  F35  0.020
 8NC  plan-4  C3   0.020
 8NC  plan-4  C7   0.020
 8NC  plan-4  N14  0.020
 8NC  plan-4  C22  0.020
 8NC  plan-4  O24  0.020
 8NC  plan-4  H14  0.020
 8NC  plan-5  C2   0.020
 8NC  plan-5  C5   0.020
 8NC  plan-5  N12  0.020
 8NC  plan-5  C15  0.020
 8NC  plan-5  O23  0.020
 8NC  plan-5  H12  0.020

