# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 15 20:20:25 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: (3R,4R)-N-(4-chloro-3-fluorophenyl)-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: C[S](=O)(=O)N1C[C@@H]([C@H](C1)C(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)C(=O)Nc4ccc(Cl)c(F)c4
#
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
 OYJ  OYJ  (3R,4R)-N-(4-chloro-3-fluorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(methylsulfonyl)pyrrolidine-3,4-dicarboxamide  ligand  58  37  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYJ
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
 OYJ  S1    S   S     0   1.347    1.8918   5.1414   0.0241
 OYJ  C2    C   CR15  0  -0.439    0.5407   1.5770  -0.7397
 OYJ  C3    C   CR15  0  -0.449    1.8851   1.3639  -0.0662
 OYJ  N4    N   NR5   0  -0.602    1.6176   3.6382  -0.5750
 OYJ  C5    C   C     0   0.582   -0.5512   0.6835  -0.1909
 OYJ  N6    N   NR6   0  -0.613   -6.7161  -1.3729   0.5005
 OYJ  C7    C   C     0   0.590    2.5794   0.0825  -0.4775
 OYJ  C8    C   CH2   0  -0.247    0.2730   3.0631  -0.4783
 OYJ  C9    C   CH2   0  -0.253    2.6665   2.6146  -0.4814
 OYJ  C10   C   CR6   0   0.553   -7.2568  -2.4240  -0.2452
 OYJ  C11   C   CR6   0   0.295   -5.4350  -0.8701   0.1258
 OYJ  N12   N   NH1   0  -0.741   -1.7147   0.7620  -0.8869
 OYJ  C13   C   CR16  0  -0.421   -5.3541   0.3620  -0.5029
 OYJ  N14   N   NH1   0  -0.753    3.4971  -0.3396   0.4286
 OYJ  C15   C   CR6   0   0.208   -2.9312   0.1728  -0.5300
 OYJ  C16   C   CR6   0   0.500   -4.1078   0.8622  -0.8074
 OYJ  C17   C   CR6   0   0.631    6.0391  -2.7063   1.5160
 OYJ  C18   C   CR16  0  -0.514    5.1547  -1.6530   1.4972
 OYJ  O19   O   OS    0  -0.661    3.2164   5.5423  -0.4221
 OYJ  O20   O   OS    0  -0.662    0.7335   5.9481  -0.3265
 OYJ  C21   C   CR16  0   0.050   -7.3604  -0.7864   1.5490
 OYJ  C22   C   CR6   0   0.411    4.3612  -1.4322   0.3697
 OYJ  O23   O   O     0  -0.443   -0.3927  -0.0121   0.7913
 OYJ  O24   O   O     0  -0.447    2.3451  -0.4739  -1.5321
 OYJ  C25   C   CR16  0  -0.453   -8.5576  -2.8539   0.1944
 OYJ  C26   C   CR6   0  -0.249    6.1670  -3.5646   0.4368
 OYJ  O27   O   O     0  -0.501   -6.6335  -2.8977  -1.1872
 OYJ  C28   C   CR16  0  -0.264   -4.2866  -1.5895   0.4111
 OYJ  C29   C   CR16  0  -0.294   -3.0436  -1.0760   0.0779
 OYJ  C30   C   CR16  0  -0.398   -8.5864  -1.1984   1.9473
 OYJ  C31   C   CR16  0  -0.118   -9.1918  -2.2659   1.2410
 OYJ  C32   C   CR16  0  -0.197    5.3797  -3.3438  -0.6795
 OYJ  C33   C   CH3   0  -0.802    1.9333   4.9778   1.7961
 OYJ  F34   F   F     0  -0.305   -4.0177   2.0608  -1.4002
 OYJ  C36   C   CR16  0  -0.329    4.4796  -2.2900  -0.7252
 OYJ  CL    CL  CL    0  -0.094    7.2884  -4.8698   0.5052
 OYJ  H331  H   HCH3  0   0.290    2.7244   4.2882   2.0826
 OYJ  H332  H   HCH3  0   0.312    2.1370   5.9602   2.2190
 OYJ  H333  H   HCH3  0   0.291    0.9718   4.6169   2.1544
 OYJ  H2    H   HCR5  0   0.319    0.6353   1.4170  -1.8182
 OYJ  H3    H   HCR5  0   0.307    1.7473   1.3805   1.0189
 OYJ  H81C  H   HCH2  0   0.284   -0.3949   3.5065  -1.2143
 OYJ  H82C  H   HCH2  0   0.257   -0.1658   3.2040   0.5159
 OYJ  H91C  H   HCH2  0   0.276    3.4385   2.8664   0.2464
 OYJ  H92C  H   HCH2  0   0.276    3.1513   2.4867  -1.4508
 OYJ  H12   H   HNH1  0   0.421   -1.7329   1.3847  -1.6807
 OYJ  H21   H   HCR6  0   0.315   -6.8271   0.0159   2.0384
 OYJ  H14   H   HNH1  0   0.428    3.5551   0.1999   1.2796
 OYJ  H25   H   HCR6  0   0.276   -9.0154  -3.6658  -0.3542
 OYJ  H13   H   HCR6  0   0.298   -6.2424   0.9334  -0.7402
 OYJ  H28   H   HCR6  0   0.278   -4.3533  -2.5528   0.8979
 OYJ  H29   H   HCR6  0   0.290   -2.1602  -1.6564   0.2913
 OYJ  H18   H   HCR6  0   0.305    5.0867  -1.0070   2.3643
 OYJ  H30   H   HCR6  0   0.281   -9.0743  -0.7188   2.7816
 OYJ  H36   H   HCR6  0   0.294    3.8858  -2.1531  -1.6125
 OYJ  H31   H   HCR6  0   0.282  -10.1720  -2.6153   1.5391
 OYJ  H32   H   HCR6  0   0.293    5.4675  -4.0023  -1.5329
 OYJ  F35   F   F     0  -0.293    6.7884  -2.9060   2.6005

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
 OYJ  S1   N4    single    1.641  0.020  1.641
 OYJ  S1   O19   double    1.454  0.020  1.454
 OYJ  S1   O20   double    1.454  0.020  1.454
 OYJ  S1   C33   single    1.780  0.020  1.780
 OYJ  C2   C3    single    1.519  0.020  1.519
 OYJ  C2   C5    single    1.514  0.020  1.514
 OYJ  C2   C8    single    1.533  0.020  1.533
 OYJ  C3   C7    single    1.514  0.020  1.514
 OYJ  C3   C9    single    1.532  0.020  1.532
 OYJ  N4   C8    single    1.466  0.020  1.466
 OYJ  N4   C9    single    1.469  0.020  1.469
 OYJ  C5   N12   single    1.358  0.020  1.358
 OYJ  C5   O23   double    1.214  0.020  1.214
 OYJ  N6   C10   single    1.398  0.020  1.398
 OYJ  N6   C11   single    1.426  0.020  1.426
 OYJ  N6   C21   single    1.363  0.020  1.363
 OYJ  C7   N14   single    1.357  0.020  1.357
 OYJ  C7   O24   double    1.215  0.020  1.215
 OYJ  C10  C25   single    1.439  0.020  1.439
 OYJ  C10  O27   double    1.225  0.020  1.225
 OYJ  C11  C13   aromatic  1.386  0.020  1.386
 OYJ  C11  C28   aromatic  1.385  0.020  1.385
 OYJ  N12  C15   single    1.398  0.020  1.398
 OYJ  C13  C16   aromatic  1.377  0.020  1.377
 OYJ  N14  C22   single    1.394  0.020  1.394
 OYJ  C15  C16   aromatic  1.392  0.020  1.392
 OYJ  C15  C29   aromatic  1.393  0.020  1.393
 OYJ  C16  F34   single    1.340  0.020  1.340
 OYJ  C17  C18   aromatic  1.376  0.020  1.376
 OYJ  C17  C26   aromatic  1.385  0.020  1.385
 OYJ  C17  F35   single    1.333  0.020  1.333
 OYJ  C18  C22   aromatic  1.396  0.020  1.396
 OYJ  C21  C30   double    1.353  0.020  1.353
 OYJ  C22  C36   aromatic  1.396  0.020  1.396
 OYJ  C25  C31   double    1.358  0.020  1.358
 OYJ  C26  C32   aromatic  1.384  0.020  1.384
 OYJ  C26  CL    single    1.722  0.020  1.722
 OYJ  C28  C29   aromatic  1.386  0.020  1.386
 OYJ  C30  C31   single    1.416  0.020  1.416
 OYJ  C32  C36   aromatic  1.387  0.020  1.387
 OYJ  C33  H331  single    0.970  0.020  1.090
 OYJ  C33  H332  single    0.970  0.020  1.090
 OYJ  C33  H333  single    0.970  0.020  1.090
 OYJ  C2   H2    single    0.970  0.020  1.090
 OYJ  C3   H3    single    0.970  0.020  1.090
 OYJ  C8   H81C  single    0.970  0.020  1.090
 OYJ  C8   H82C  single    0.970  0.020  1.090
 OYJ  C9   H91C  single    0.970  0.020  1.090
 OYJ  C9   H92C  single    0.970  0.020  1.090
 OYJ  N12  H12   single    0.860  0.020  1.020
 OYJ  C21  H21   single    0.930  0.020  1.080
 OYJ  N14  H14   single    0.860  0.020  1.020
 OYJ  C25  H25   single    0.930  0.020  1.080
 OYJ  C13  H13   single    0.930  0.020  1.080
 OYJ  C28  H28   single    0.930  0.020  1.080
 OYJ  C29  H29   single    0.930  0.020  1.080
 OYJ  C18  H18   single    0.930  0.020  1.080
 OYJ  C30  H30   single    0.930  0.020  1.080
 OYJ  C36  H36   single    0.930  0.020  1.080
 OYJ  C31  H31   single    0.930  0.020  1.080
 OYJ  C32  H32   single    0.930  0.020  1.080

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
 OYJ  C33   S1   O20   108.03  3.000
 OYJ  C33   S1   O19   108.03  3.000
 OYJ  O20   S1   O19   119.90  3.000
 OYJ  C33   S1   N4    106.45  3.000
 OYJ  O20   S1   N4    106.68  3.000
 OYJ  O19   S1   N4    107.02  3.000
 OYJ  H2    C2   C8    108.96  3.000
 OYJ  H2    C2   C5    109.47  3.000
 OYJ  C8    C2   C5    112.62  3.000
 OYJ  H2    C2   C3    109.87  3.000
 OYJ  C8    C2   C3    102.42  3.000
 OYJ  C5    C2   C3    113.26  3.000
 OYJ  H3    C3   C9    108.70  3.000
 OYJ  H3    C3   C7    109.88  3.000
 OYJ  C9    C3   C7    112.54  3.000
 OYJ  H3    C3   C2    109.04  3.000
 OYJ  C9    C3   C2    102.52  3.000
 OYJ  C7    C3   C2    113.84  3.000
 OYJ  C9    N4   C8    112.18  3.000
 OYJ  C9    N4   S1    119.73  3.000
 OYJ  C8    N4   S1    119.25  3.000
 OYJ  O23   C5   N12   124.03  3.000
 OYJ  O23   C5   C2    122.50  3.000
 OYJ  N12   C5   C2    113.45  3.000
 OYJ  C21   N6   C11   118.36  3.000
 OYJ  C21   N6   C10   123.44  3.000
 OYJ  C11   N6   C10   118.19  3.000
 OYJ  O24   C7   N14   124.57  3.000
 OYJ  O24   C7   C3    122.33  3.000
 OYJ  N14   C7   C3    113.07  3.000
 OYJ  H82C  C8   H81C  108.39  3.000
 OYJ  H82C  C8   N4    112.13  3.000
 OYJ  H81C  C8   N4    111.01  3.000
 OYJ  H82C  C8   C2    110.45  3.000
 OYJ  H81C  C8   C2    112.76  3.000
 OYJ  N4    C8   C2    102.06  3.000
 OYJ  H92C  C9   H91C  107.77  3.000
 OYJ  H92C  C9   N4    110.02  3.000
 OYJ  H91C  C9   N4    112.78  3.000
 OYJ  H92C  C9   C3    111.82  3.000
 OYJ  H91C  C9   C3    111.64  3.000
 OYJ  N4    C9   C3    102.83  3.000
 OYJ  O27   C10  C25   125.42  3.000
 OYJ  O27   C10  N6    120.29  3.000
 OYJ  C25   C10  N6    114.30  3.000
 OYJ  C28   C11  C13   120.46  3.000
 OYJ  C28   C11  N6    120.51  3.000
 OYJ  C13   C11  N6    119.02  3.000
 OYJ  H12   N12  C15   116.44  3.000
 OYJ  H12   N12  C5    117.02  3.000
 OYJ  C15   N12  C5    126.18  3.000
 OYJ  H13   C13  C16   120.16  3.000
 OYJ  H13   C13  C11   121.39  3.000
 OYJ  C16   C13  C11   118.44  3.000
 OYJ  H14   N14  C22   114.77  3.000
 OYJ  H14   N14  C7    115.82  3.000
 OYJ  C22   N14  C7    129.40  3.000
 OYJ  C29   C15  C16   117.56  3.000
 OYJ  C29   C15  N12   124.01  3.000
 OYJ  C16   C15  N12   118.43  3.000
 OYJ  F34   C16  C15   118.32  3.000
 OYJ  F34   C16  C13   118.92  3.000
 OYJ  C15   C16  C13   122.76  3.000
 OYJ  F35   C17  C26   119.29  3.000
 OYJ  F35   C17  C18   119.16  3.000
 OYJ  C26   C17  C18   121.56  3.000
 OYJ  H18   C18  C22   121.09  3.000
 OYJ  H18   C18  C17   119.08  3.000
 OYJ  C22   C18  C17   119.83  3.000
 OYJ  H21   C21  C30   122.67  3.000
 OYJ  H21   C21  N6    115.76  3.000
 OYJ  C30   C21  N6    121.57  3.000
 OYJ  C36   C22  C18   119.21  3.000
 OYJ  C36   C22  N14   124.56  3.000
 OYJ  C18   C22  N14   116.23  3.000
 OYJ  H25   C25  C31   121.23  3.000
 OYJ  H25   C25  C10   116.87  3.000
 OYJ  C31   C25  C10   121.90  3.000
 OYJ  CL    C26  C32   121.57  3.000
 OYJ  CL    C26  C17   119.93  3.000
 OYJ  C32   C26  C17   118.51  3.000
 OYJ  H28   C28  C29   119.59  3.000
 OYJ  H28   C28  C11   120.28  3.000
 OYJ  C29   C28  C11   120.13  3.000
 OYJ  H29   C29  C28   119.20  3.000
 OYJ  H29   C29  C15   120.17  3.000
 OYJ  C28   C29  C15   120.63  3.000
 OYJ  H30   C30  C31   121.84  3.000
 OYJ  H30   C30  C21   120.12  3.000
 OYJ  C31   C30  C21   118.04  3.000
 OYJ  H31   C31  C30   119.55  3.000
 OYJ  H31   C31  C25   119.70  3.000
 OYJ  C30   C31  C25   120.75  3.000
 OYJ  H32   C32  C36   119.31  3.000
 OYJ  H32   C32  C26   119.55  3.000
 OYJ  C36   C32  C26   121.14  3.000
 OYJ  H333  C33  H332  109.68  3.000
 OYJ  H333  C33  H331  110.23  3.000
 OYJ  H332  C33  H331  109.49  3.000
 OYJ  H333  C33  S1    109.74  3.000
 OYJ  H332  C33  S1    107.95  3.000
 OYJ  H331  C33  S1    109.72  3.000
 OYJ  H36   C36  C32   118.81  3.000
 OYJ  H36   C36  C22   121.44  3.000
 OYJ  C32   C36  C22   119.75  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
 OYJ  CONST_01  C15   C16  C13  C11     0.00   0.0  0
 OYJ  CONST_02  C15   C29  C28  C11     0.00   0.0  0
 OYJ  CONST_03  C29   C28  C11  C13     0.00   0.0  0
 OYJ  CONST_04  C29   C15  C16  C13     0.00   0.0  0
 OYJ  CONST_05  C28   C11  C13  C16     0.00   0.0  0
 OYJ  CONST_06  C28   C29  C15  C16     0.00   0.0  0
 OYJ  CONST_07  C36   C22  C18  C17     0.00   0.0  0
 OYJ  CONST_08  C36   C32  C26  C17     0.00   0.0  0
 OYJ  CONST_09  C32   C26  C17  C18     0.00   0.0  0
 OYJ  CONST_10  C32   C36  C22  C18     0.00   0.0  0
 OYJ  CONST_11  C26   C17  C18  C22     0.00   0.0  0
 OYJ  CONST_12  C26   C32  C36  C22     0.00   0.0  0
 OYJ  CONST_13  C16   C13  C11  N6    180.00   0.0  0
 OYJ  CONST_14  C29   C28  C11  N6    180.00   0.0  0
 OYJ  CONST_15  C25   C10  N6   C11   180.00   0.0  0
 OYJ  CONST_16  C25   C10  N6   C21     0.00   0.0  0
 OYJ  CONST_17  F34   C16  C13  C11   180.00   0.0  0
 OYJ  CONST_18  C13   C16  C15  N12   180.00   0.0  0
 OYJ  CONST_19  C28   C29  C15  N12   180.00   0.0  0
 OYJ  CONST_20  C17   C18  C22  N14   180.00   0.0  0
 OYJ  CONST_21  C32   C36  C22  N14   180.00   0.0  0
 OYJ  CONST_22  CL    C26  C17  C18   180.00   0.0  0
 OYJ  CONST_23  F35   C17  C18  C22   180.00   0.0  0
 OYJ  CONST_24  F34   C16  C15  C29   180.00   0.0  0
 OYJ  CONST_25  F35   C17  C26  C32   180.00   0.0  0
 OYJ  CONST_26  CL    C26  C32  C36   180.00   0.0  0
 OYJ  CONST_27  O27   C10  N6   C11     0.00   0.0  0
 OYJ  CONST_28  O27   C10  N6   C21   180.00   0.0  0
 OYJ  CONST_29  H13   C13  C11  N6      0.00   0.0  0
 OYJ  CONST_30  H28   C28  C11  N6      0.00   0.0  0
 OYJ  CONST_31  H29   C29  C28  C11   180.00   0.0  0
 OYJ  CONST_32  H32   C32  C26  C17   180.00   0.0  0
 OYJ  CONST_33  H36   C36  C22  C18   180.00   0.0  0
 OYJ  CONST_34  H18   C18  C17  C26   180.00   0.0  0
 OYJ  CONST_35  C15   N12  C5   C2    180.00   0.0  0
 OYJ  CONST_36  C22   N14  C7   C3    180.00   0.0  0
 OYJ  CONST_39  C18   C22  N14  C7    180.00   0.0  0
 OYJ  CONST_40  C36   C22  N14  C7      0.00   0.0  0
 OYJ  CONST_42  H14   N14  C22  C18     0.00   0.0  0
 OYJ  CONST_43  O23   C5   N12  C15     0.00   0.0  0
 OYJ  CONST_44  O24   C7   N14  C22     0.00   0.0  0
 OYJ  Var_01    C9    N4   C8   C2    -16.40  30.0  1
 OYJ  Var_02    C8    N4   C9   C3     -9.71  30.0  1
 OYJ  Var_03    C13   C11  N6   C10   106.60  30.0  2
 OYJ  Var_04    O19   S1   N4   C8   -169.81  30.0  3
 OYJ  Var_05    H331  C33  S1   N4     59.48  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
 OYJ  chir_01  C2  C3  C5  C8  negativ
 OYJ  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
 OYJ  plan-1  N6   0.020
 OYJ  plan-1  C10  0.020
 OYJ  plan-1  C11  0.020
 OYJ  plan-1  C21  0.020
 OYJ  plan-1  C25  0.020
 OYJ  plan-1  O27  0.020
 OYJ  plan-1  C30  0.020
 OYJ  plan-1  C31  0.020
 OYJ  plan-1  H21  0.020
 OYJ  plan-1  H25  0.020
 OYJ  plan-1  H30  0.020
 OYJ  plan-1  H31  0.020
 OYJ  plan-2  N6   0.020
 OYJ  plan-2  C11  0.020
 OYJ  plan-2  N12  0.020
 OYJ  plan-2  C13  0.020
 OYJ  plan-2  C15  0.020
 OYJ  plan-2  C16  0.020
 OYJ  plan-2  C28  0.020
 OYJ  plan-2  C29  0.020
 OYJ  plan-2  F34  0.020
 OYJ  plan-2  H13  0.020
 OYJ  plan-2  H28  0.020
 OYJ  plan-2  H29  0.020
 OYJ  plan-3  N14  0.020
 OYJ  plan-3  C17  0.020
 OYJ  plan-3  C18  0.020
 OYJ  plan-3  C22  0.020
 OYJ  plan-3  C26  0.020
 OYJ  plan-3  C32  0.020
 OYJ  plan-3  C36  0.020
 OYJ  plan-3  CL   0.020
 OYJ  plan-3  H18  0.020
 OYJ  plan-3  H36  0.020
 OYJ  plan-3  H32  0.020
 OYJ  plan-3  F35  0.020
 OYJ  plan-4  C3   0.020
 OYJ  plan-4  C7   0.020
 OYJ  plan-4  N14  0.020
 OYJ  plan-4  C22  0.020
 OYJ  plan-4  O24  0.020
 OYJ  plan-4  H14  0.020
 OYJ  plan-5  C2   0.020
 OYJ  plan-5  C5   0.020
 OYJ  plan-5  N12  0.020
 OYJ  plan-5  C15  0.020
 OYJ  plan-5  O23  0.020
 OYJ  plan-5  H12  0.020

