# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 09:06:46 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2~{S},4~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-4-azanyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@H](N(C1)C(=O)Nc2cn(C(N)=O)c3ccccc23)C(=O)Nc4cccc(OC(F)(F)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
 8S2  8S2  (2~{S},4~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-4-azanyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide  ligand  56  35  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8S2
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
 8S2  C6   C  CR6   0   0.334  -5.5062  -0.0654   0.2722
 8S2  C7   C  CR16  0  -0.409  -4.3900  -0.6681  -0.2711
 8S2  C10  C  CR16  0  -0.314  -3.3141  -0.5435   1.8809
 8S2  C20  C  CH1   0  -0.182  -0.1126  -2.6535  -0.5442
 8S2  C26  C  CH1   0  -0.113   1.1802  -4.6676  -0.7311
 8S2  C28  C  CH2   0  -0.474  -0.2081  -4.1687  -0.3418
 8S2  F1   F  F     0  -0.299  -5.7663   1.4351  -2.0985
 8S2  C2   C  CT    0   1.072  -6.7456   1.2561  -1.2092
 8S2  F3   F  F     0  -0.298  -6.7442   2.3275  -0.4147
 8S2  F4   F  F     0  -0.277  -7.8969   1.2204  -1.8608
 8S2  O5   O  O2    0  -0.525  -6.6266   0.1072  -0.5332
 8S2  C9   C  CR6   0   0.397  -3.2770  -0.9159   0.5360
 8S2  C12  C  CR16  0  -0.243  -4.4549   0.0579   2.3926
 8S2  C14  C  CR16  0  -0.317  -5.5662   0.3081   1.6032
 8S2  N16  N  NH1   0  -0.752  -2.1894  -1.5322  -0.0826
 8S2  C18  C  C     0   0.553  -1.0012  -1.9133   0.4478
 8S2  O19  O  O     0  -0.455  -0.6751  -1.7564   1.6067
 8S2  N22  N  NT    0  -0.535   1.2883  -2.3738  -0.3083
 8S2  C23  C  CH2   0  -0.300   2.0887  -3.5736  -0.1518
 8S2  N31  N  NH2   0  -0.791   1.4287  -6.0220  -0.3055
 8S2  C34  C  C     0   0.765   1.7163  -1.0912  -0.3319
 8S2  O35  O  O     0  -0.524   0.9595  -0.1618  -0.5872
 8S2  N36  N  NH1   0  -0.800   3.0402  -0.9006  -0.0513
 8S2  C38  C  CR5   0   0.237   3.6840   0.3259  -0.0634
 8S2  C39  C  CR15  0  -0.081   3.2090   1.5690  -0.3279
 8S2  N41  N  NR5   0  -0.636   4.2563   2.4903  -0.2387
 8S2  C42  C  CR56  0   0.376   5.4202   1.8137   0.0846
 8S2  C43  C  CR56  0  -0.028   5.0912   0.4527   0.2103
 8S2  C44  C  CR16  0  -0.335   6.0702  -0.4823   0.5471
 8S2  C46  C  CR16  0  -0.262   7.3616  -0.0417   0.7599
 8S2  C48  C  CR16  0  -0.268   7.6764   1.3170   0.6427
 8S2  C50  C  CR16  0  -0.288   6.7217   2.2609   0.3070
 8S2  C52  C  C     0   0.681   4.1515   3.8687  -0.4421
 8S2  O53  O  O     0  -0.487   5.1397   4.5495  -0.6419
 8S2  N54  N  NH2   0  -0.835   2.8959   4.3531  -0.4316
 8S2  H1   H  HCR6  0   0.292  -4.3858  -0.9668  -1.3125
 8S2  H2   H  HCR6  0   0.289  -2.4735  -0.7210   2.5299
 8S2  H3   H  HCH1  0   0.283  -0.3908  -2.3930  -1.5718
 8S2  H4   H  HCH1  0   0.254   1.2703  -4.6363  -1.8209
 8S2  H5   H  HCH2  0   0.252  -0.3932  -4.4047   0.7103
 8S2  H6   H  HCH2  0   0.272  -1.0051  -4.6134  -0.9350
 8S2  H7   H  HCR6  0   0.273  -4.4735   0.3374   3.4374
 8S2  H8   H  HCR6  0   0.280  -6.4554   0.7634   2.0168
 8S2  H9   H  HNH1  0   0.422  -2.3077  -1.7087  -1.0692
 8S2  H10  H  HCH2  0   0.244   2.3134  -3.7797   0.9015
 8S2  H11  H  HCH2  0   0.255   3.0302  -3.5108  -0.7021
 8S2  H12  H  HNH2  0   0.354   2.3278  -6.3371  -0.6464
 8S2  H13  H  HNH2  0   0.344   1.4718  -6.0700   0.7059
 8S2  H15  H  HNH1  0   0.422   3.6079  -1.6946   0.1949
 8S2  H16  H  HCR5  0   0.306   2.2225   1.8761  -0.6189
 8S2  H17  H  HCR6  0   0.249   5.8345  -1.5351   0.6449
 8S2  H18  H  HCR6  0   0.257   8.1365  -0.7504   1.0204
 8S2  H19  H  HCR6  0   0.258   8.6938   1.6419   0.8177
 8S2  H20  H  HCR6  0   0.275   6.9906   3.3011   0.2200
 8S2  H21  H  HNH2  0   0.417   2.1362   3.8729   0.0196
 8S2  H22  H  HNH2  0   0.414   2.7914   5.3510  -0.5143

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
 8S2  F4   C2   single    1.323  0.020  1.323
 8S2  N54  C52  single    1.346  0.020  1.346
 8S2  F1   C2   single    1.335  0.020  1.335
 8S2  C2   O5   single    1.338  0.020  1.338
 8S2  C2   F3   single    1.334  0.020  1.334
 8S2  O53  C52  double    1.217  0.020  1.217
 8S2  C52  N41  single    1.397  0.020  1.397
 8S2  O5   C6   single    1.391  0.020  1.391
 8S2  N41  C39  aromatic  1.398  0.020  1.398
 8S2  N41  C42  aromatic  1.385  0.020  1.385
 8S2  C39  C38  aromatic  1.357  0.020  1.357
 8S2  C7   C6   aromatic  1.380  0.020  1.380
 8S2  C7   C9   aromatic  1.397  0.020  1.397
 8S2  C6   C14  aromatic  1.384  0.020  1.384
 8S2  O35  C34  double    1.225  0.020  1.225
 8S2  C42  C50  aromatic  1.394  0.020  1.394
 8S2  C42  C43  aromatic  1.406  0.020  1.406
 8S2  C38  N36  single    1.385  0.020  1.385
 8S2  C38  C43  aromatic  1.439  0.020  1.439
 8S2  N16  C9   single    1.395  0.020  1.395
 8S2  N16  C18  single    1.356  0.020  1.356
 8S2  C34  N36  single    1.367  0.020  1.367
 8S2  C34  N22  single    1.352  0.020  1.352
 8S2  C50  C48  aromatic  1.384  0.020  1.384
 8S2  C9   C10  aromatic  1.396  0.020  1.396
 8S2  C20  N22  single    1.448  0.020  1.448
 8S2  C20  C28  single    1.532  0.020  1.532
 8S2  C20  C18  single    1.524  0.020  1.524
 8S2  C14  C12  aromatic  1.386  0.020  1.386
 8S2  C43  C44  aromatic  1.395  0.020  1.395
 8S2  N22  C23  single    1.451  0.020  1.451
 8S2  C28  C26  single    1.526  0.020  1.526
 8S2  C18  O19  double    1.214  0.020  1.214
 8S2  C48  C46  aromatic  1.400  0.020  1.400
 8S2  C23  C26  single    1.536  0.020  1.536
 8S2  C10  C12  aromatic  1.387  0.020  1.387
 8S2  C44  C46  aromatic  1.381  0.020  1.381
 8S2  C26  N31  single    1.441  0.020  1.441
 8S2  C7   H1   single    0.930  0.020  1.080
 8S2  C10  H2   single    0.930  0.020  1.080
 8S2  C20  H3   single    0.970  0.020  1.090
 8S2  C26  H4   single    0.970  0.020  1.090
 8S2  C28  H5   single    0.970  0.020  1.090
 8S2  C28  H6   single    0.970  0.020  1.090
 8S2  C12  H7   single    0.930  0.020  1.080
 8S2  C14  H8   single    0.930  0.020  1.080
 8S2  N16  H9   single    0.860  0.020  1.020
 8S2  C23  H10  single    0.970  0.020  1.090
 8S2  C23  H11  single    0.970  0.020  1.090
 8S2  N31  H12  single    0.890  0.020  1.040
 8S2  N31  H13  single    0.890  0.020  1.040
 8S2  N36  H15  single    0.860  0.020  1.020
 8S2  C39  H16  single    0.930  0.020  1.080
 8S2  C44  H17  single    0.930  0.020  1.080
 8S2  C46  H18  single    0.930  0.020  1.080
 8S2  C48  H19  single    0.930  0.020  1.080
 8S2  C50  H20  single    0.930  0.020  1.080
 8S2  N54  H21  single    0.890  0.020  1.040
 8S2  N54  H22  single    0.890  0.020  1.040

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
 8S2  C14  C6   O5   119.25  3.000
 8S2  C14  C6   C7   122.12  3.000
 8S2  O5   C6   C7   118.55  3.000
 8S2  H1   C7   C9   120.23  3.000
 8S2  H1   C7   C6   120.13  3.000
 8S2  C9   C7   C6   119.63  3.000
 8S2  H2   C10  C12  119.41  3.000
 8S2  H2   C10  C9   121.06  3.000
 8S2  C12  C10  C9   119.53  3.000
 8S2  H3   C20  N22  110.64  3.000
 8S2  H3   C20  C18  110.30  3.000
 8S2  N22  C20  C18  111.36  3.000
 8S2  H3   C20  C28  110.07  3.000
 8S2  C18  C20  C28  110.99  3.000
 8S2  N22  C20  C28  103.29  3.000
 8S2  H4   C26  N31  107.87  3.000
 8S2  H4   C26  C23  107.86  3.000
 8S2  N31  C26  C23  117.13  3.000
 8S2  H4   C26  C28  108.65  3.000
 8S2  N31  C26  C28  112.88  3.000
 8S2  C23  C26  C28  102.08  3.000
 8S2  H6   C28  H5   108.18  3.000
 8S2  H6   C28  C26  113.18  3.000
 8S2  H5   C28  C26  109.20  3.000
 8S2  H6   C28  C20  112.19  3.000
 8S2  H5   C28  C20  110.55  3.000
 8S2  C26  C28  C20  103.48  3.000
 8S2  O5   C2   F4   107.63  3.000
 8S2  O5   C2   F3   112.87  3.000
 8S2  F4   C2   F3   108.41  3.000
 8S2  F3   C2   F1   106.76  3.000
 8S2  O5   C2   F1   112.73  3.000
 8S2  F4   C2   F1   108.29  3.000
 8S2  C2   O5   C6   118.08  3.000
 8S2  N16  C9   C10  124.47  3.000
 8S2  C10  C9   C7   119.22  3.000
 8S2  N16  C9   C7   116.32  3.000
 8S2  H7   C12  C14  119.33  3.000
 8S2  H7   C12  C10  118.84  3.000
 8S2  C14  C12  C10  121.83  3.000
 8S2  H8   C14  C12  121.17  3.000
 8S2  H8   C14  C6   121.15  3.000
 8S2  C12  C14  C6   117.67  3.000
 8S2  H9   N16  C18  115.85  3.000
 8S2  H9   N16  C9   114.80  3.000
 8S2  C18  N16  C9   129.35  3.000
 8S2  O19  C18  N16  124.92  3.000
 8S2  O19  C18  C20  121.84  3.000
 8S2  N16  C18  C20  113.14  3.000
 8S2  C34  N22  C23  127.70  3.000
 8S2  C23  N22  C20  113.06  3.000
 8S2  C34  N22  C20  119.12  3.000
 8S2  H11  C23  H10  108.55  3.000
 8S2  H11  C23  N22  111.94  3.000
 8S2  H10  C23  N22  111.84  3.000
 8S2  H11  C23  C26  111.16  3.000
 8S2  H10  C23  C26  110.47  3.000
 8S2  N22  C23  C26  102.83  3.000
 8S2  H13  N31  H12  106.48  3.000
 8S2  H13  N31  C26  110.28  3.000
 8S2  H12  N31  C26  110.27  3.000
 8S2  N36  C34  O35  122.36  3.000
 8S2  N36  C34  N22  115.80  3.000
 8S2  O35  C34  N22  121.83  3.000
 8S2  H15  N36  C38  116.00  3.000
 8S2  H15  N36  C34  119.11  3.000
 8S2  C38  N36  C34  124.88  3.000
 8S2  C43  C38  C39  107.38  3.000
 8S2  C43  C38  N36  122.06  3.000
 8S2  C39  C38  N36  130.55  3.000
 8S2  H16  C39  N41  121.16  3.000
 8S2  H16  C39  C38  129.55  3.000
 8S2  N41  C39  C38  109.21  3.000
 8S2  C52  N41  C42  125.39  3.000
 8S2  C42  N41  C39  108.83  3.000
 8S2  C52  N41  C39  125.78  3.000
 8S2  C50  C42  C43  120.98  3.000
 8S2  C43  C42  N41  107.29  3.000
 8S2  C50  C42  N41  131.71  3.000
 8S2  C44  C43  C42  120.41  3.000
 8S2  C44  C43  C38  132.30  3.000
 8S2  C42  C43  C38  107.28  3.000
 8S2  H17  C44  C46  119.97  3.000
 8S2  H17  C44  C43  121.37  3.000
 8S2  C46  C44  C43  118.66  3.000
 8S2  H18  C46  C48  119.66  3.000
 8S2  H18  C46  C44  119.86  3.000
 8S2  C48  C46  C44  120.47  3.000
 8S2  H19  C48  C50  118.88  3.000
 8S2  H19  C48  C46  119.30  3.000
 8S2  C50  C48  C46  121.82  3.000
 8S2  H20  C50  C48  120.38  3.000
 8S2  H20  C50  C42  121.97  3.000
 8S2  C48  C50  C42  117.65  3.000
 8S2  N54  C52  O53  123.89  3.000
 8S2  O53  C52  N41  121.00  3.000
 8S2  N54  C52  N41  115.08  3.000
 8S2  H22  N54  H21  115.58  3.000
 8S2  H22  N54  C52  116.94  3.000
 8S2  H21  N54  C52  122.44  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
 8S2  CONST_01  C10  C9   C7   C6      0.00   0.0  0
 8S2  CONST_02  C10  C12  C14  C6      0.00   0.0  0
 8S2  CONST_03  C12  C14  C6   C7      0.00   0.0  0
 8S2  CONST_04  C12  C10  C9   C7      0.00   0.0  0
 8S2  CONST_05  C14  C6   C7   C9      0.00   0.0  0
 8S2  CONST_06  C14  C12  C10  C9      0.00   0.0  0
 8S2  CONST_07  C42  N41  C39  C38     0.00   0.0  0
 8S2  CONST_08  N41  C42  C43  C38     0.00   0.0  0
 8S2  CONST_09  C50  C42  C43  C38   180.00   0.0  0
 8S2  CONST_10  C46  C44  C43  C38   180.00   0.0  0
 8S2  CONST_11  C50  C42  N41  C39   180.00   0.0  0
 8S2  CONST_12  C43  C42  N41  C39     0.00   0.0  0
 8S2  CONST_13  C42  C43  C38  C39     0.00   0.0  0
 8S2  CONST_14  C44  C43  C38  C39   180.00   0.0  0
 8S2  CONST_15  C43  C38  C39  N41     0.00   0.0  0
 8S2  CONST_16  C48  C50  C42  N41   180.00   0.0  0
 8S2  CONST_17  C44  C43  C42  N41   180.00   0.0  0
 8S2  CONST_18  C46  C48  C50  C42     0.00   0.0  0
 8S2  CONST_19  C46  C44  C43  C42     0.00   0.0  0
 8S2  CONST_20  C48  C50  C42  C43     0.00   0.0  0
 8S2  CONST_21  C48  C46  C44  C43     0.00   0.0  0
 8S2  CONST_22  C50  C42  C43  C44     0.00   0.0  0
 8S2  CONST_23  C50  C48  C46  C44     0.00   0.0  0
 8S2  CONST_24  N16  C9   C7   C6    180.00   0.0  0
 8S2  CONST_25  C9   C7   C6   O5    180.00   0.0  0
 8S2  CONST_26  C12  C14  C6   O5    180.00   0.0  0
 8S2  CONST_27  N16  C9   C10  C12   180.00   0.0  0
 8S2  CONST_28  N41  C39  C38  N36   180.00   0.0  0
 8S2  CONST_29  C42  C43  C38  N36   180.00   0.0  0
 8S2  CONST_30  C44  C43  C38  N36     0.00   0.0  0
 8S2  CONST_31  C52  N41  C39  C38   180.00   0.0  0
 8S2  CONST_32  C52  N41  C42  C43   180.00   0.0  0
 8S2  CONST_33  C52  N41  C42  C50     0.00   0.0  0
 8S2  CONST_34  H7   C12  C14  C6    180.00   0.0  0
 8S2  CONST_35  H8   C14  C6   C7    180.00   0.0  0
 8S2  CONST_36  H2   C10  C9   C7    180.00   0.0  0
 8S2  CONST_37  H1   C7   C9   C10   180.00   0.0  0
 8S2  CONST_38  H17  C44  C43  C38     0.00   0.0  0
 8S2  CONST_39  H20  C50  C42  N41     0.00   0.0  0
 8S2  CONST_40  H16  C39  N41  C42   180.00   0.0  0
 8S2  CONST_41  H19  C48  C50  C42   180.00   0.0  0
 8S2  CONST_42  H18  C46  C44  C43   180.00   0.0  0
 8S2  CONST_43  O35  C34  N22  C20     0.00   0.0  0
 8S2  CONST_44  C9   N16  C18  C20   180.00   0.0  0
 8S2  CONST_45  O35  C34  N22  C23   180.00   0.0  0
 8S2  CONST_48  C18  N16  C9   C7    180.00   0.0  0
 8S2  CONST_49  C18  N16  C9   C10     0.00   0.0  0
 8S2  CONST_50  C38  N36  C34  N22   180.00   0.0  0
 8S2  CONST_51  C39  C38  N36  C34     0.00   0.0  0
 8S2  CONST_52  C43  C38  N36  C34   180.00   0.0  0
 8S2  CONST_53  N36  C34  N22  C20   180.00   0.0  0
 8S2  CONST_54  N36  C34  N22  C23     0.00   0.0  0
 8S2  CONST_57  H9   N16  C9   C7      0.00   0.0  0
 8S2  CONST_58  H15  N36  C38  C39   180.00   0.0  0
 8S2  CONST_59  O19  C18  N16  C9      0.00   0.0  0
 8S2  CONST_60  C38  N36  C34  O35     0.00   0.0  0
 8S2  CONST_62  H22  N54  C52  N41   180.00   0.0  0
 8S2  Var_01    C26  C23  N22  C20    16.86  30.0  1
 8S2  Var_02    C14  C6   O5   C2     91.51  30.0  2
 8S2  Var_03    F4   C2   O5   C6   -177.73  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
 8S2  chir_01  C20  N22  C28  C18  negativ
 8S2  chir_02  C26  N31  C23  C28  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
 8S2  plan-1  C20  0.020
 8S2  plan-1  C9   0.020
 8S2  plan-1  N16  0.020
 8S2  plan-1  C18  0.020
 8S2  plan-1  O19  0.020
 8S2  plan-1  H9   0.020
 8S2  plan-2  C6   0.020
 8S2  plan-2  C7   0.020
 8S2  plan-2  C10  0.020
 8S2  plan-2  O5   0.020
 8S2  plan-2  C9   0.020
 8S2  plan-2  C12  0.020
 8S2  plan-2  C14  0.020
 8S2  plan-2  N16  0.020
 8S2  plan-2  H1   0.020
 8S2  plan-2  H2   0.020
 8S2  plan-2  H7   0.020
 8S2  plan-2  H8   0.020
 8S2  plan-3  C20  0.020
 8S2  plan-3  N22  0.020
 8S2  plan-3  C23  0.020
 8S2  plan-3  C34  0.020
 8S2  plan-3  O35  0.020
 8S2  plan-3  N36  0.020
 8S2  plan-3  C38  0.020
 8S2  plan-3  H15  0.020
 8S2  plan-4  N36  0.020
 8S2  plan-4  C38  0.020
 8S2  plan-4  C39  0.020
 8S2  plan-4  N41  0.020
 8S2  plan-4  C42  0.020
 8S2  plan-4  C43  0.020
 8S2  plan-4  C44  0.020
 8S2  plan-4  C46  0.020
 8S2  plan-4  C48  0.020
 8S2  plan-4  C50  0.020
 8S2  plan-4  C52  0.020
 8S2  plan-4  O53  0.020
 8S2  plan-4  N54  0.020
 8S2  plan-4  H16  0.020
 8S2  plan-4  H17  0.020
 8S2  plan-4  H18  0.020
 8S2  plan-4  H19  0.020
 8S2  plan-4  H20  0.020
 8S2  plan-4  H21  0.020
 8S2  plan-4  H22  0.020

