# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:54:42 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-fluoranyl-3-[[(1~{S},2~{S})-2-phenylcyclopropyl]carbonylamino]-1~{H}-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2ccc(F)cc2c1NC(=O)[C@H]3C[C@@H]3c4ccccc4
#
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
 QJS  QJS  '5-fluoranyl-3-[[(1~{S},2~{S})-2-phenylcyclopropyl]carbonylamino]-1~{H}-indole-2-carboxylic acid'  ligand  39  25  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QJS
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
 QJS  C2   C  CR6    0   0.528  -3.1033   2.9291  -0.9490
 QJS  C3   C  CR16   0  -0.508  -2.0922   2.0247  -0.7589
 QJS  C13  C  C      0   0.571   0.5202  -0.3370  -0.8178
 QJS  C15  C  CH1    0  -0.423   1.8797  -0.9232  -0.6610
 QJS  C17  C  CH1    0  -0.357   3.0659  -0.0418  -1.0077
 QJS  C19  C  CH2    0  -0.453   2.6928  -1.1822  -1.8917
 QJS  C22  C  CR6    0   0.231   4.2830  -0.0557  -0.1605
 QJS  C23  C  CR16   0  -0.325   4.8969   1.1525   0.1662
 QJS  C25  C  CR16   0  -0.239   6.0407   1.1848   0.9528
 QJS  C27  C  CR16   0  -0.275   6.5902   0.0045   1.4333
 QJS  C29  C  CR16   0  -0.235   5.9848  -1.2059   1.1175
 QJS  F1   F  F      0  -0.331  -2.8144   4.1094  -1.5397
 QJS  C5   C  CR56   0   0.068  -2.4169   0.8044  -0.1416
 QJS  C6   C  CR56   0   0.320  -3.7574   0.5814   0.2631
 QJS  N7   N  NR15   0  -0.719  -3.8204  -0.6306   0.8698
 QJS  C9   C  CR5    0   0.061  -2.5835  -1.2066   0.8851
 QJS  C10  C  CR5    0   0.180  -1.6919  -0.3624   0.2584
 QJS  N11  N  NH1    0  -0.744  -0.3311  -0.6653   0.1759
 QJS  O14  O  O      0  -0.490   0.2312   0.3913  -1.7573
 QJS  C31  C  CR16   0  -0.353   4.8444  -1.2359   0.3286
 QJS  C33  C  C      0   0.418  -2.3443  -2.5235   1.5587
 QJS  O34  O  OC    -1  -0.584  -3.3446  -3.0971   2.0200
 QJS  O35  O  O      0  -0.589  -1.1542  -2.9108   1.6012
 QJS  C37  C  CR16   0  -0.288  -4.7668   1.5192   0.0459
 QJS  C39  C  CR16   0  -0.439  -4.4306   2.7052  -0.5695
 QJS  H1   H  HCR6   0   0.269  -1.0868   2.2508  -1.0799
 QJS  H2   H  HCH1   0   0.284   2.0228  -1.6042   0.1710
 QJS  H3   H  HCH1   0   0.270   2.7964   0.9404  -1.3800
 QJS  H4   H  HCH2   0   0.269   3.3207  -2.0641  -1.8926
 QJS  H5   H  HCH2   0   0.270   2.2447  -0.9453  -2.8477
 QJS  H6   H  HCR6   0   0.251   4.4753   2.0808  -0.2012
 QJS  H7   H  HCR6   0   0.255   6.5017   2.1356   1.1880
 QJS  H8   H  HCR6   0   0.254   7.4819   0.0254   2.0461
 QJS  H9   H  HCR6   0   0.256   6.4047  -2.1341   1.4834
 QJS  H10  H  HNR5   0   0.401  -4.6264  -1.0348   1.3174
 QJS  H11  H  HNH1   0   0.405  -0.0880  -1.4476   0.7788
 QJS  H12  H  HCR6   0   0.250   4.3978  -2.1951   0.0942
 QJS  H14  H  HCR6   0   0.271  -5.7857   1.3257   0.3549
 QJS  H15  H  HCR6   0   0.272  -5.1813   3.4607  -0.7596

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
 QJS  C37  C39  aromatic  1.378  0.020  1.378
 QJS  C37  C6   aromatic  1.395  0.020  1.395
 QJS  C39  C2   aromatic  1.399  0.020  1.399
 QJS  C6   N7   aromatic  1.357  0.020  1.357
 QJS  C6   C5   aromatic  1.418  0.020  1.418
 QJS  N7   C9   aromatic  1.365  0.020  1.365
 QJS  C2   F1   single    1.351  0.020  1.351
 QJS  C2   C3   aromatic  1.370  0.020  1.370
 QJS  O35  C33  deloc     1.252  0.020  1.252
 QJS  C5   C3   aromatic  1.406  0.020  1.406
 QJS  C5   C10  aromatic  1.431  0.020  1.431
 QJS  C9   C33  single    1.498  0.020  1.498
 QJS  C9   C10  aromatic  1.379  0.020  1.379
 QJS  C33  O34  deloc     1.242  0.020  1.242
 QJS  C10  N11  single    1.397  0.020  1.397
 QJS  N11  C13  single    1.349  0.020  1.349
 QJS  O14  C13  double    1.223  0.020  1.223
 QJS  C13  C15  single    1.489  0.020  1.489
 QJS  C15  C19  single    1.498  0.020  1.498
 QJS  C15  C17  single    1.518  0.020  1.518
 QJS  C19  C17  single    1.490  0.020  1.490
 QJS  C17  C22  single    1.483  0.020  1.483
 QJS  C22  C23  aromatic  1.394  0.020  1.394
 QJS  C22  C31  aromatic  1.395  0.020  1.395
 QJS  C23  C25  aromatic  1.389  0.020  1.389
 QJS  C31  C29  aromatic  1.387  0.020  1.387
 QJS  C25  C27  aromatic  1.388  0.020  1.388
 QJS  C29  C27  aromatic  1.390  0.020  1.390
 QJS  C3   H1   single    0.930  0.020  1.080
 QJS  C15  H2   single    0.970  0.020  1.090
 QJS  C17  H3   single    0.970  0.020  1.090
 QJS  C19  H4   single    0.970  0.020  1.090
 QJS  C19  H5   single    0.970  0.020  1.090
 QJS  C23  H6   single    0.930  0.020  1.080
 QJS  C25  H7   single    0.930  0.020  1.080
 QJS  C27  H8   single    0.930  0.020  1.080
 QJS  C29  H9   single    0.930  0.020  1.080
 QJS  N7   H10  single    0.860  0.020  1.020
 QJS  N11  H11  single    0.890  0.020  1.040
 QJS  C31  H12  single    0.930  0.020  1.080
 QJS  C37  H14  single    0.930  0.020  1.080
 QJS  C39  H15  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
 QJS  C39  C2   F1   117.48  3.000
 QJS  F1   C2   C3   118.66  3.000
 QJS  C39  C2   C3   123.86  3.000
 QJS  H1   C3   C5   121.85  3.000
 QJS  H1   C3   C2   120.53  3.000
 QJS  C5   C3   C2   117.62  3.000
 QJS  O14  C13  N11  124.16  3.000
 QJS  O14  C13  C15  122.07  3.000
 QJS  N11  C13  C15  113.76  3.000
 QJS  H2   C15  C19  116.75  3.000
 QJS  H2   C15  C17  115.89  3.000
 QJS  C19  C15  C17   59.23  3.000
 QJS  H2   C15  C13  116.65  3.000
 QJS  C17  C15  C13  117.45  3.000
 QJS  C19  C15  C13  118.51  3.000
 QJS  H3   C17  C22  114.11  3.000
 QJS  H3   C17  C19  115.29  3.000
 QJS  C22  C17  C19  122.49  3.000
 QJS  H3   C17  C15  114.21  3.000
 QJS  C22  C17  C15  120.36  3.000
 QJS  C19  C17  C15   59.70  3.000
 QJS  H5   C19  H4   114.69  3.000
 QJS  H5   C19  C17  117.41  3.000
 QJS  H4   C19  C17  118.59  3.000
 QJS  H5   C19  C15  117.61  3.000
 QJS  H4   C19  C15  117.16  3.000
 QJS  C17  C19  C15   61.07  3.000
 QJS  C31  C22  C23  118.27  3.000
 QJS  C31  C22  C17  122.57  3.000
 QJS  C23  C22  C17  119.16  3.000
 QJS  H6   C23  C25  119.51  3.000
 QJS  H6   C23  C22  119.45  3.000
 QJS  C25  C23  C22  121.04  3.000
 QJS  H7   C25  C27  120.21  3.000
 QJS  H7   C25  C23  119.62  3.000
 QJS  C27  C25  C23  120.17  3.000
 QJS  H8   C27  C29  120.30  3.000
 QJS  H8   C27  C25  120.39  3.000
 QJS  C29  C27  C25  119.32  3.000
 QJS  H9   C29  C31  119.52  3.000
 QJS  H9   C29  C27  120.07  3.000
 QJS  C31  C29  C27  120.41  3.000
 QJS  C10  C5   C6   105.72  3.000
 QJS  C10  C5   C3   135.54  3.000
 QJS  C6   C5   C3   118.71  3.000
 QJS  C37  C6   N7   129.54  3.000
 QJS  N7   C6   C5   108.18  3.000
 QJS  C37  C6   C5   122.28  3.000
 QJS  H10  N7   C9   123.45  3.000
 QJS  H10  N7   C6   126.49  3.000
 QJS  C9   N7   C6   109.88  3.000
 QJS  C33  C9   C10  129.75  3.000
 QJS  C10  C9   N7   108.82  3.000
 QJS  C33  C9   N7   121.38  3.000
 QJS  N11  C10  C9   121.61  3.000
 QJS  N11  C10  C5   130.85  3.000
 QJS  C9   C10  C5   107.39  3.000
 QJS  H11  N11  C10  111.39  3.000
 QJS  H11  N11  C13  118.22  3.000
 QJS  C10  N11  C13  127.27  3.000
 QJS  H12  C31  C29  118.74  3.000
 QJS  H12  C31  C22  120.47  3.000
 QJS  C29  C31  C22  120.79  3.000
 QJS  O35  C33  O34  127.59  3.000
 QJS  O34  C33  C9   116.38  3.000
 QJS  O35  C33  C9   116.03  3.000
 QJS  H14  C37  C39  120.74  3.000
 QJS  H14  C37  C6   121.12  3.000
 QJS  C39  C37  C6   118.14  3.000
 QJS  H15  C39  C37  120.69  3.000
 QJS  H15  C39  C2   119.93  3.000
 QJS  C37  C39  C2   119.38  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
 QJS  CONST_01  C6   C37  C39  C2      0.00   0.0  0
 QJS  CONST_02  C6   C5   C3   C2      0.00   0.0  0
 QJS  CONST_03  C10  C5   C3   C2    180.00   0.0  0
 QJS  CONST_04  C37  C39  C2   C3      0.00   0.0  0
 QJS  CONST_05  C37  C6   C5   C3      0.00   0.0  0
 QJS  CONST_06  N7   C6   C5   C3    180.00   0.0  0
 QJS  CONST_07  C9   C10  C5   C3    180.00   0.0  0
 QJS  CONST_08  C27  C25  C23  C22     0.00   0.0  0
 QJS  CONST_09  C27  C29  C31  C22     0.00   0.0  0
 QJS  CONST_10  C29  C31  C22  C23     0.00   0.0  0
 QJS  CONST_11  C29  C27  C25  C23     0.00   0.0  0
 QJS  CONST_12  C31  C22  C23  C25     0.00   0.0  0
 QJS  CONST_13  C31  C29  C27  C25     0.00   0.0  0
 QJS  CONST_14  C39  C37  C6   C5      0.00   0.0  0
 QJS  CONST_15  C9   N7   C6   C5      0.00   0.0  0
 QJS  CONST_16  C39  C2   C3   C5      0.00   0.0  0
 QJS  CONST_17  N7   C9   C10  C5      0.00   0.0  0
 QJS  CONST_18  C10  C9   N7   C6      0.00   0.0  0
 QJS  CONST_19  C9   C10  C5   C6      0.00   0.0  0
 QJS  CONST_20  C39  C37  C6   N7    180.00   0.0  0
 QJS  CONST_21  C10  C5   C6   N7      0.00   0.0  0
 QJS  CONST_22  C37  C6   N7   C9    180.00   0.0  0
 QJS  CONST_23  C37  C6   C5   C10   180.00   0.0  0
 QJS  CONST_24  C25  C23  C22  C17   180.00   0.0  0
 QJS  CONST_25  C29  C31  C22  C17   180.00   0.0  0
 QJS  CONST_26  N11  C10  C5   C3      0.00   0.0  0
 QJS  CONST_27  C37  C39  C2   F1    180.00   0.0  0
 QJS  CONST_28  C5   C3   C2   F1    180.00   0.0  0
 QJS  CONST_29  C33  C9   C10  C5    180.00   0.0  0
 QJS  CONST_30  C33  C9   N7   C6    180.00   0.0  0
 QJS  CONST_31  N11  C10  C5   C6    180.00   0.0  0
 QJS  CONST_32  N11  C10  C9   N7    180.00   0.0  0
 QJS  CONST_33  H14  C37  C39  C2    180.00   0.0  0
 QJS  CONST_34  H15  C39  C2   C3    180.00   0.0  0
 QJS  CONST_35  H6   C23  C22  C17     0.00   0.0  0
 QJS  CONST_36  H12  C31  C22  C17     0.00   0.0  0
 QJS  CONST_37  H7   C25  C23  C22   180.00   0.0  0
 QJS  CONST_38  H9   C29  C31  C22   180.00   0.0  0
 QJS  CONST_39  H8   C27  C25  C23   180.00   0.0  0
 QJS  CONST_40  H10  N7   C6   C5    180.00   0.0  0
 QJS  CONST_41  H1   C3   C5   C6    180.00   0.0  0
 QJS  CONST_42  C10  N11  C13  C15   180.00   0.0  0
 QJS  CONST_46  O14  C13  N11  C10     0.00   0.0  0
 QJS  Var_01    C22  C17  C19  C15   108.78  30.0  1
 QJS  Var_02    C23  C22  C17  C15  -136.62  30.0  2
 QJS  Var_03    C17  C19  C15  C13   106.68  30.0  1
 QJS  Var_04    N11  C13  C15  C17  -139.43  30.0  1
 QJS  Var_05    O35  C33  C9   N7   -174.74  30.0  2

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
 QJS  chir_01  C15  C13  C19  C17  both
 QJS  chir_02  C17  C15  C19  C22  both

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
 QJS  plan-1  C17  0.020
 QJS  plan-1  C22  0.020
 QJS  plan-1  C23  0.020
 QJS  plan-1  C25  0.020
 QJS  plan-1  C27  0.020
 QJS  plan-1  C29  0.020
 QJS  plan-1  C31  0.020
 QJS  plan-1  H6   0.020
 QJS  plan-1  H7   0.020
 QJS  plan-1  H8   0.020
 QJS  plan-1  H9   0.020
 QJS  plan-1  H12  0.020
 QJS  plan-2  C2   0.020
 QJS  plan-2  C3   0.020
 QJS  plan-2  F1   0.020
 QJS  plan-2  C5   0.020
 QJS  plan-2  C6   0.020
 QJS  plan-2  N7   0.020
 QJS  plan-2  C9   0.020
 QJS  plan-2  C10  0.020
 QJS  plan-2  N11  0.020
 QJS  plan-2  C33  0.020
 QJS  plan-2  C37  0.020
 QJS  plan-2  C39  0.020
 QJS  plan-2  H1   0.020
 QJS  plan-2  H10  0.020
 QJS  plan-2  H14  0.020
 QJS  plan-2  H15  0.020
 QJS  plan-3  C13  0.020
 QJS  plan-3  C15  0.020
 QJS  plan-3  C10  0.020
 QJS  plan-3  N11  0.020
 QJS  plan-3  O14  0.020
 QJS  plan-3  H11  0.020
 QJS  plan-4  C9   0.020
 QJS  plan-4  C33  0.020
 QJS  plan-4  O34  0.020
 QJS  plan-4  O35  0.020

