# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 15:35:38 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: (3R,4R)-N-(4-chlorophenyl)-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)cc4
#
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
 RR8  RR8  (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(methylsulfonyl)pyrrolidine-3,4-dicarboxamide  ligand  58  36  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RR8
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
 RR8  S1    S   S     0   1.350  -2.9726   4.8577  -0.0155
 RR8  C2    C   CR15  0  -0.452  -0.9578   1.6103  -0.0566
 RR8  C3    C   CR15  0  -0.428  -2.2499   1.0895  -0.6679
 RR8  N4    N   NR5   0  -0.611  -2.4138   3.3973  -0.5058
 RR8  C5    C   C     0   0.589   0.2788   0.9097  -0.5779
 RR8  N6    N   NR6   0  -0.613   6.5581  -1.0018  -0.2358
 RR8  C7    C   C     0   0.594  -2.6379  -0.2754  -0.1385
 RR8  C8    C   CH2   0  -0.255  -3.2460   2.2052  -0.3486
 RR8  C9    C   CH2   0  -0.238  -0.9786   3.0951  -0.4370
 RR8  C10   C   CR6   0   0.553   7.0702  -1.8756   0.7286
 RR8  C11   C   CR6   0   0.295   5.2088  -0.5638  -0.0951
 RR8  N12   N   NH1   0  -0.742   1.2793   0.8200   0.3343
 RR8  C13   C   CR16  0  -0.417   4.8814   0.3504   0.8955
 RR8  N14   N   NH1   0  -0.754  -3.8604  -0.6929  -0.5485
 RR8  C15   C   CR6   0   0.218   2.5692   0.3294   0.1312
 RR8  C16   C   CR6   0   0.487   3.5785   0.7763   0.9852
 RR8  O17   O   OS    0  -0.662  -2.0240   5.8528  -0.4904
 RR8  O18   O   OS    0  -0.664  -4.3668   4.9334  -0.4232
 RR8  C19   C   CR16  0   0.049   7.2722  -0.5721  -1.3142
 RR8  O20   O   O     0  -0.450   0.3626   0.5146  -1.7236
 RR8  O21   O   O     0  -0.450  -1.8927  -0.9189   0.5754
 RR8  C22   C   CR16  0  -0.453   8.4316  -2.2790   0.4987
 RR8  O23   O   O     0  -0.501   6.3707  -2.2372   1.6667
 RR8  C24   C   CR16  0  -0.264   4.2361  -1.0343  -0.9581
 RR8  C25   C   CR16  0  -0.302   2.9245  -0.5929  -0.8494
 RR8  C26   C   CR16  0  -0.399   8.5509  -0.9654  -1.5199
 RR8  C27   C   CR16  0  -0.118   9.1367  -1.8443  -0.5772
 RR8  C28   C   CR6   0   0.387  -4.5306  -1.8869  -0.2658
 RR8  C29   C   CH3   0  -0.800  -2.9202   4.8471   1.7632
 RR8  F30   F   F     0  -0.308   3.2509   1.6673   1.9336
 RR8  C31   C   CR6   0  -0.057  -6.0194  -4.1938   0.1859
 RR8  CL3   CL  CL    0  -0.132  -6.9435  -5.6327   0.4705
 RR8  C34   C   CR16  0  -0.353  -5.7660  -2.0748  -0.8892
 RR8  C33   C   CR16  0  -0.316  -4.0502  -2.8767   0.5917
 RR8  C36   C   CR16  0  -0.200  -4.7975  -4.0249   0.8128
 RR8  C35   C   CR16  0  -0.199  -6.5101  -3.2188  -0.6685
 RR8  H291  H   HCH3  0   0.290  -1.8972   4.6923   2.1007
 RR8  H292  H   HCH3  0   0.310  -3.2794   5.8124   2.1159
 RR8  H293  H   HCH3  0   0.290  -3.5647   4.0567   2.1417
 RR8  H2    H   HCR5  0   0.306  -1.0149   1.5253   1.0325
 RR8  H3    H   HCR5  0   0.323  -2.1381   1.0186  -1.7555
 RR8  H91C  H   HCH2  0   0.274  -0.4548   3.7012   0.3028
 RR8  H92C  H   HCH2  0   0.273  -0.5130   3.2741  -1.4077
 RR8  H81C  H   HCH2  0   0.282  -4.0892   2.2283  -1.0370
 RR8  H82C  H   HCH2  0   0.258  -3.6329   2.0952   0.6709
 RR8  H12   H   HNH1  0   0.423   1.0888   1.2039   1.2473
 RR8  H19   H   HCR6  0   0.314   6.7542   0.1026  -1.9807
 RR8  H14   H   HNH1  0   0.423  -4.3512  -0.0796  -1.1823
 RR8  H22   H   HCR6  0   0.276   8.8715  -2.9528   1.2210
 RR8  H13   H   HCR6  0   0.296   5.6266   0.7423   1.5749
 RR8  H24   H   HCR6  0   0.280   4.4896  -1.7564  -1.7229
 RR8  H25   H   HCR6  0   0.294   2.1847  -0.9842  -1.5279
 RR8  H26   H   HCR6  0   0.280   9.0964  -0.6049  -2.3782
 RR8  H27   H   HCR6  0   0.282  10.1586  -2.1724  -0.7174
 RR8  H33   H   HCR6  0   0.291  -3.1027  -2.7711   1.0927
 RR8  H34   H   HCR6  0   0.283  -6.1569  -1.3167  -1.5574
 RR8  H35   H   HCR6  0   0.284  -7.4642  -3.3426  -1.1619
 RR8  H36   H   HCR6  0   0.283  -4.4130  -4.7845   1.4798

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
 RR8  S1   N4    single    1.639  0.020  1.639
 RR8  S1   O17   double    1.455  0.020  1.455
 RR8  S1   O18   double    1.455  0.020  1.455
 RR8  S1   C29   single    1.779  0.020  1.779
 RR8  C2   C3    single    1.521  0.020  1.521
 RR8  C2   C5    single    1.514  0.020  1.514
 RR8  C2   C9    single    1.533  0.020  1.533
 RR8  C3   C7    single    1.515  0.020  1.515
 RR8  C3   C8    single    1.529  0.020  1.529
 RR8  N4   C8    single    1.462  0.020  1.462
 RR8  N4   C9    single    1.468  0.020  1.468
 RR8  C5   N12   single    1.357  0.020  1.357
 RR8  C5   O20   double    1.215  0.020  1.215
 RR8  N6   C10   single    1.398  0.020  1.398
 RR8  N6   C11   single    1.426  0.020  1.426
 RR8  N6   C19   single    1.363  0.020  1.363
 RR8  C7   N14   single    1.355  0.020  1.355
 RR8  C7   O21   double    1.216  0.020  1.216
 RR8  C10  C22   single    1.438  0.020  1.438
 RR8  C10  O23   double    1.225  0.020  1.225
 RR8  C11  C13   aromatic  1.387  0.020  1.387
 RR8  C11  C24   aromatic  1.383  0.020  1.383
 RR8  N12  C15   single    1.395  0.020  1.395
 RR8  C13  C16   aromatic  1.374  0.020  1.374
 RR8  N14  C28   single    1.398  0.020  1.398
 RR8  C15  C16   aromatic  1.396  0.020  1.396
 RR8  C15  C25   aromatic  1.392  0.020  1.392
 RR8  C16  F30   single    1.342  0.020  1.342
 RR8  C19  C26   double    1.354  0.020  1.354
 RR8  C22  C27   double    1.358  0.020  1.358
 RR8  C24  C25   aromatic  1.388  0.020  1.388
 RR8  C26  C27   single    1.416  0.020  1.416
 RR8  C28  C33   aromatic  1.395  0.020  1.395
 RR8  C28  C34   aromatic  1.396  0.020  1.396
 RR8  C31  CL3   single    1.734  0.020  1.734
 RR8  C31  C35   aromatic  1.386  0.020  1.386
 RR8  C31  C36   aromatic  1.384  0.020  1.384
 RR8  C33  C36   aromatic  1.388  0.020  1.388
 RR8  C34  C35   aromatic  1.383  0.020  1.383
 RR8  C29  H291  single    0.970  0.020  1.090
 RR8  C29  H292  single    0.970  0.020  1.090
 RR8  C29  H293  single    0.970  0.020  1.090
 RR8  C2   H2    single    0.970  0.020  1.090
 RR8  C3   H3    single    0.970  0.020  1.090
 RR8  C9   H91C  single    0.970  0.020  1.090
 RR8  C9   H92C  single    0.970  0.020  1.090
 RR8  C8   H81C  single    0.970  0.020  1.090
 RR8  C8   H82C  single    0.970  0.020  1.090
 RR8  N12  H12   single    0.860  0.020  1.020
 RR8  C19  H19   single    0.930  0.020  1.080
 RR8  N14  H14   single    0.860  0.020  1.020
 RR8  C22  H22   single    0.930  0.020  1.080
 RR8  C13  H13   single    0.930  0.020  1.080
 RR8  C24  H24   single    0.930  0.020  1.080
 RR8  C25  H25   single    0.930  0.020  1.080
 RR8  C26  H26   single    0.930  0.020  1.080
 RR8  C27  H27   single    0.930  0.020  1.080
 RR8  C33  H33   single    0.930  0.020  1.080
 RR8  C34  H34   single    0.930  0.020  1.080
 RR8  C35  H35   single    0.930  0.020  1.080
 RR8  C36  H36   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
 RR8  C29   S1   O18   107.98  3.000
 RR8  C29   S1   O17   108.13  3.000
 RR8  O18   S1   O17   119.87  3.000
 RR8  C29   S1   N4    106.48  3.000
 RR8  O18   S1   N4    106.82  3.000
 RR8  O17   S1   N4    106.84  3.000
 RR8  H2    C2   C9    108.76  3.000
 RR8  H2    C2   C5    110.46  3.000
 RR8  C9    C2   C5    111.95  3.000
 RR8  H2    C2   C3    109.22  3.000
 RR8  C9    C2   C3    102.73  3.000
 RR8  C5    C2   C3    113.39  3.000
 RR8  H3    C3   C8    108.72  3.000
 RR8  H3    C3   C7    108.35  3.000
 RR8  C8    C3   C7    114.68  3.000
 RR8  H3    C3   C2    109.54  3.000
 RR8  C8    C3   C2    102.68  3.000
 RR8  C7    C3   C2    112.68  3.000
 RR8  C9    N4   C8    112.55  3.000
 RR8  C9    N4   S1    120.18  3.000
 RR8  C8    N4   S1    120.02  3.000
 RR8  O20   C5   N12   124.18  3.000
 RR8  O20   C5   C2    122.11  3.000
 RR8  N12   C5   C2    113.67  3.000
 RR8  C19   N6   C11   118.50  3.000
 RR8  C19   N6   C10   123.42  3.000
 RR8  C11   N6   C10   118.06  3.000
 RR8  O21   C7   N14   124.57  3.000
 RR8  O21   C7   C3    121.67  3.000
 RR8  N14   C7   C3    113.76  3.000
 RR8  H82C  C8   H81C  108.48  3.000
 RR8  H82C  C8   N4    112.51  3.000
 RR8  H81C  C8   N4    110.82  3.000
 RR8  H82C  C8   C3    110.54  3.000
 RR8  H81C  C8   C3    112.82  3.000
 RR8  N4    C8   C3    101.63  3.000
 RR8  H92C  C9   H91C  107.90  3.000
 RR8  H92C  C9   N4    109.97  3.000
 RR8  H91C  C9   N4    112.76  3.000
 RR8  H92C  C9   C2    111.95  3.000
 RR8  H91C  C9   C2    111.32  3.000
 RR8  N4    C9   C2    102.96  3.000
 RR8  O23   C10  C22   125.46  3.000
 RR8  O23   C10  N6    120.24  3.000
 RR8  C22   C10  N6    114.30  3.000
 RR8  C24   C11  C13   120.26  3.000
 RR8  C24   C11  N6    119.98  3.000
 RR8  C13   C11  N6    119.76  3.000
 RR8  H12   N12  C15   116.12  3.000
 RR8  H12   N12  C5    116.37  3.000
 RR8  C15   N12  C5    127.39  3.000
 RR8  H13   C13  C16   120.00  3.000
 RR8  H13   C13  C11   121.65  3.000
 RR8  C16   C13  C11   118.35  3.000
 RR8  H14   N14  C28   114.38  3.000
 RR8  H14   N14  C7    116.20  3.000
 RR8  C28   N14  C7    129.36  3.000
 RR8  C25   C15  C16   117.29  3.000
 RR8  C25   C15  N12   124.86  3.000
 RR8  C16   C15  N12   117.84  3.000
 RR8  F30   C16  C15   117.94  3.000
 RR8  F30   C16  C13   118.92  3.000
 RR8  C15   C16  C13   123.14  3.000
 RR8  H19   C19  C26   122.72  3.000
 RR8  H19   C19  N6    115.70  3.000
 RR8  C26   C19  N6    121.58  3.000
 RR8  H22   C22  C27   121.16  3.000
 RR8  H22   C22  C10   116.94  3.000
 RR8  C27   C22  C10   121.89  3.000
 RR8  H24   C24  C25   119.28  3.000
 RR8  H24   C24  C11   120.22  3.000
 RR8  C25   C24  C11   120.50  3.000
 RR8  H25   C25  C24   118.94  3.000
 RR8  H25   C25  C15   120.59  3.000
 RR8  C24   C25  C15   120.46  3.000
 RR8  H26   C26  C27   121.87  3.000
 RR8  H26   C26  C19   120.09  3.000
 RR8  C27   C26  C19   118.04  3.000
 RR8  H27   C27  C26   119.51  3.000
 RR8  H27   C27  C22   119.73  3.000
 RR8  C26   C27  C22   120.76  3.000
 RR8  C33   C28  C34   118.92  3.000
 RR8  C34   C28  N14   116.66  3.000
 RR8  C33   C28  N14   124.42  3.000
 RR8  H293  C29  H292  109.63  3.000
 RR8  H293  C29  H291  110.22  3.000
 RR8  H292  C29  H291  109.62  3.000
 RR8  H293  C29  S1    109.55  3.000
 RR8  H292  C29  S1    107.99  3.000
 RR8  H291  C29  S1    109.79  3.000
 RR8  C35   C31  C36   120.40  3.000
 RR8  C36   C31  CL3   119.85  3.000
 RR8  C35   C31  CL3   119.75  3.000
 RR8  H34   C34  C35   118.89  3.000
 RR8  H34   C34  C28   120.03  3.000
 RR8  C35   C34  C28   121.08  3.000
 RR8  H33   C33  C36   118.74  3.000
 RR8  H33   C33  C28   121.28  3.000
 RR8  C36   C33  C28   119.97  3.000
 RR8  H36   C36  C33   119.20  3.000
 RR8  H36   C36  C31   120.51  3.000
 RR8  C33   C36  C31   120.29  3.000
 RR8  H35   C35  C34   119.79  3.000
 RR8  H35   C35  C31   120.87  3.000
 RR8  C34   C35  C31   119.33  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
 RR8  CONST_01  C15   C16  C13  C11     0.00   0.0  0
 RR8  CONST_02  C15   C25  C24  C11     0.00   0.0  0
 RR8  CONST_03  C25   C24  C11  C13     0.00   0.0  0
 RR8  CONST_04  C25   C15  C16  C13     0.00   0.0  0
 RR8  CONST_05  C24   C11  C13  C16     0.00   0.0  0
 RR8  CONST_06  C24   C25  C15  C16     0.00   0.0  0
 RR8  CONST_07  C31   C36  C33  C28     0.00   0.0  0
 RR8  CONST_08  C31   C35  C34  C28     0.00   0.0  0
 RR8  CONST_09  C36   C33  C28  C34     0.00   0.0  0
 RR8  CONST_10  C36   C31  C35  C34     0.00   0.0  0
 RR8  CONST_11  C35   C34  C28  C33     0.00   0.0  0
 RR8  CONST_12  C35   C31  C36  C33     0.00   0.0  0
 RR8  CONST_13  C16   C13  C11  N6    180.00   0.0  0
 RR8  CONST_14  C25   C24  C11  N6    180.00   0.0  0
 RR8  CONST_15  C22   C10  N6   C11   180.00   0.0  0
 RR8  CONST_16  C22   C10  N6   C19     0.00   0.0  0
 RR8  CONST_17  F30   C16  C13  C11   180.00   0.0  0
 RR8  CONST_18  C13   C16  C15  N12   180.00   0.0  0
 RR8  CONST_19  C24   C25  C15  N12   180.00   0.0  0
 RR8  CONST_20  C36   C33  C28  N14   180.00   0.0  0
 RR8  CONST_21  C35   C34  C28  N14   180.00   0.0  0
 RR8  CONST_22  F30   C16  C15  C25   180.00   0.0  0
 RR8  CONST_23  C34   C35  C31  CL3   180.00   0.0  0
 RR8  CONST_24  C33   C36  C31  CL3   180.00   0.0  0
 RR8  CONST_25  O23   C10  N6   C11     0.00   0.0  0
 RR8  CONST_26  O23   C10  N6   C19   180.00   0.0  0
 RR8  CONST_27  H13   C13  C11  N6      0.00   0.0  0
 RR8  CONST_28  H24   C24  C11  N6      0.00   0.0  0
 RR8  CONST_29  H25   C25  C24  C11   180.00   0.0  0
 RR8  CONST_30  H36   C36  C33  C28   180.00   0.0  0
 RR8  CONST_31  H35   C35  C34  C28   180.00   0.0  0
 RR8  CONST_32  H34   C34  C35  C31   180.00   0.0  0
 RR8  CONST_33  H33   C33  C36  C31   180.00   0.0  0
 RR8  CONST_34  C15   N12  C5   C2    180.00   0.0  0
 RR8  CONST_35  C28   N14  C7   C3    180.00   0.0  0
 RR8  CONST_38  C33   C28  N14  C7      0.00   0.0  0
 RR8  CONST_39  C34   C28  N14  C7    180.00   0.0  0
 RR8  CONST_41  H14   N14  C28  C34     0.00   0.0  0
 RR8  CONST_42  O20   C5   N12  C15     0.00   0.0  0
 RR8  CONST_43  C28   N14  C7   O21     0.00   0.0  0
 RR8  Var_01    C8    N4   C9   C2     -6.31  30.0  1
 RR8  Var_02    C9    N4   C8   C3    -19.20  30.0  1
 RR8  Var_03    C13   C11  N6   C10    72.71  30.0  2
 RR8  Var_04    O17   S1   N4   C8   -171.24  30.0  2
 RR8  Var_05    H291  C29  S1   N4     60.05  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
 RR8  chir_01  C2  C3  C5  C9  negativ
 RR8  chir_02  C3  C2  C7  C8  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
 RR8  plan-1  N6   0.020
 RR8  plan-1  C10  0.020
 RR8  plan-1  C11  0.020
 RR8  plan-1  C19  0.020
 RR8  plan-1  C22  0.020
 RR8  plan-1  O23  0.020
 RR8  plan-1  C26  0.020
 RR8  plan-1  C27  0.020
 RR8  plan-1  H19  0.020
 RR8  plan-1  H22  0.020
 RR8  plan-1  H26  0.020
 RR8  plan-1  H27  0.020
 RR8  plan-2  N6   0.020
 RR8  plan-2  C11  0.020
 RR8  plan-2  N12  0.020
 RR8  plan-2  C13  0.020
 RR8  plan-2  C15  0.020
 RR8  plan-2  C16  0.020
 RR8  plan-2  C24  0.020
 RR8  plan-2  C25  0.020
 RR8  plan-2  F30  0.020
 RR8  plan-2  H13  0.020
 RR8  plan-2  H24  0.020
 RR8  plan-2  H25  0.020
 RR8  plan-3  N14  0.020
 RR8  plan-3  C28  0.020
 RR8  plan-3  C31  0.020
 RR8  plan-3  CL3  0.020
 RR8  plan-3  C34  0.020
 RR8  plan-3  C33  0.020
 RR8  plan-3  C36  0.020
 RR8  plan-3  C35  0.020
 RR8  plan-3  H33  0.020
 RR8  plan-3  H34  0.020
 RR8  plan-3  H35  0.020
 RR8  plan-3  H36  0.020
 RR8  plan-4  C3   0.020
 RR8  plan-4  C7   0.020
 RR8  plan-4  N14  0.020
 RR8  plan-4  O21  0.020
 RR8  plan-4  C28  0.020
 RR8  plan-4  H14  0.020
 RR8  plan-5  C2   0.020
 RR8  plan-5  C5   0.020
 RR8  plan-5  N12  0.020
 RR8  plan-5  C15  0.020
 RR8  plan-5  O20  0.020
 RR8  plan-5  H12  0.020

