# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 20:20:25 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  40  25  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.529  -2.6514   3.0386  -0.4799
 QJS  C3   C  CR16  0  -0.493  -1.7620   2.0119  -0.3239
 QJS  C13  C  C     0   0.585   0.4831  -0.5849  -0.7622
 QJS  C15  C  CH1   0  -0.428   1.8713  -1.0641  -0.5462
 QJS  C17  C  CH1   0  -0.356   2.9976  -0.1913  -1.0695
 QJS  C19  C  CH2   0  -0.451   2.6758  -1.4815  -1.7400
 QJS  C22  C  CR6   0   0.232   4.2274   0.0034  -0.2633
 QJS  C23  C  CR16  0  -0.325   4.8010   1.2721  -0.1980
 QJS  C25  C  CR16  0  -0.240   5.9523   1.4984   0.5447
 QJS  C27  C  CR16  0  -0.274   6.5502   0.4561   1.2390
 QJS  C29  C  CR16  0  -0.236   5.9862  -0.8126   1.1822
 QJS  F1   F  F     0  -0.324  -2.1862   4.2661  -0.7827
 QJS  C5   C  CR56  0   0.086  -2.2927   0.7511  -0.0056
 QJS  C6   C  CR56  0   0.333  -3.6872   0.5971   0.1481
 QJS  N7   N  NR15  0  -0.739  -3.9388  -0.6904   0.4913
 QJS  C9   C  CR5   0   0.154  -2.7568  -1.3777   0.5659
 QJS  C10  C  CR5   0   0.208  -1.7171  -0.5229   0.2614
 QJS  N11  N  NH1   0  -0.749  -0.3641  -0.8494   0.2673
 QJS  O14  O  O     0  -0.474   0.1363   0.0068  -1.7699
 QJS  C31  C  CR16  0  -0.353   4.8379  -1.0371   0.4374
 QJS  C33  C  C     0   0.521  -2.6727  -2.7901   0.9208
 QJS  O34  O  OH1   0  -0.601  -3.8692  -3.3499   1.0324
 QJS  O35  O  O     0  -0.439  -1.6291  -3.3772   1.0908
 QJS  C37  C  CR16  0  -0.280  -4.5724   1.6646  -0.0261
 QJS  C39  C  CR16  0  -0.427  -4.0397   2.8914  -0.3444
 QJS  H1   H  HCR6  0   0.272  -0.7001   2.1771  -0.4374
 QJS  H2   H  HCH1  0   0.291   2.0683  -1.5853   0.3838
 QJS  H3   H  HCH1  0   0.273   2.6662   0.6986  -1.5935
 QJS  H4   H  HCH2  0   0.272   3.3530  -2.3155  -1.6088
 QJS  H5   H  HCH2  0   0.274   2.1947  -1.4355  -2.7084
 QJS  H6   H  HCR6  0   0.252   4.3423   2.0925  -0.7374
 QJS  H7   H  HCR6  0   0.255   6.3804   2.4919   0.5803
 QJS  H8   H  HCR6  0   0.255   7.4479   0.6284   1.8183
 QJS  H9   H  HCR6  0   0.256   6.4426  -1.6331   1.7207
 QJS  H10  H  HNR5  0   0.421  -4.8483  -1.0702   0.6982
 QJS  H11  H  HNH1  0   0.411  -0.0476  -1.4789   0.9889
 QJS  H12  H  HCR6  0   0.250   4.4228  -2.0379   0.4059
 QJS  H13  H  HOH1  0   0.495  -3.7836  -4.2834   1.2780
 QJS  H14  H  HCR6  0   0.281  -5.6402   1.5347   0.0876
 QJS  H15  H  HCR6  0   0.283  -4.6846   3.7479  -0.4895

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  1.375  0.020  1.375
 QJS  C37  C6   aromatic  1.398  0.020  1.398
 QJS  C39  C2   aromatic  1.403  0.020  1.403
 QJS  C6   N7   aromatic  1.356  0.020  1.356
 QJS  C6   C5   aromatic  1.411  0.020  1.411
 QJS  N7   C9   aromatic  1.369  0.020  1.369
 QJS  C2   F1   single    1.347  0.020  1.347
 QJS  C2   C3   aromatic  1.367  0.020  1.367
 QJS  O35  C33  double    1.209  0.020  1.209
 QJS  C5   C3   aromatic  1.404  0.020  1.404
 QJS  C5   C10  aromatic  1.423  0.020  1.423
 QJS  C9   C33  single    1.459  0.020  1.459
 QJS  C9   C10  aromatic  1.380  0.020  1.380
 QJS  C33  O34  single    1.326  0.020  1.326
 QJS  C10  N11  single    1.392  0.020  1.392
 QJS  N11  C13  single    1.359  0.020  1.359
 QJS  O14  C13  double    1.219  0.020  1.219
 QJS  C13  C15  single    1.484  0.020  1.484
 QJS  C15  C19  single    1.499  0.020  1.499
 QJS  C15  C17  single    1.518  0.020  1.518
 QJS  C19  C17  single    1.489  0.020  1.489
 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    0.860  0.020  1.020
 QJS  C31  H12  single    0.930  0.020  1.080
 QJS  O34  H13  single    0.850  0.020  0.980
 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   117.33  3.000
 QJS  F1   C2   C3   119.03  3.000
 QJS  C39  C2   C3   123.64  3.000
 QJS  H1   C3   C5   122.17  3.000
 QJS  H1   C3   C2   120.82  3.000
 QJS  C5   C3   C2   117.01  3.000
 QJS  O14  C13  N11  122.90  3.000
 QJS  O14  C13  C15  122.89  3.000
 QJS  N11  C13  C15  114.20  3.000
 QJS  H2   C15  C19  116.86  3.000
 QJS  H2   C15  C17  115.93  3.000
 QJS  C19  C15  C17   59.16  3.000
 QJS  H2   C15  C13  116.74  3.000
 QJS  C17  C15  C13  117.27  3.000
 QJS  C19  C15  C13  118.42  3.000
 QJS  H3   C17  C22  114.09  3.000
 QJS  H3   C17  C19  115.29  3.000
 QJS  C22  C17  C19  122.52  3.000
 QJS  H3   C17  C15  114.31  3.000
 QJS  C22  C17  C15  120.22  3.000
 QJS  C19  C17  C15   59.78  3.000
 QJS  H5   C19  H4   114.79  3.000
 QJS  H5   C19  C17  117.52  3.000
 QJS  H4   C19  C17  118.54  3.000
 QJS  H5   C19  C15  117.53  3.000
 QJS  H4   C19  C15  116.99  3.000
 QJS  C17  C19  C15   61.06  3.000
 QJS  C31  C22  C23  118.38  3.000
 QJS  C31  C22  C17  122.54  3.000
 QJS  C23  C22  C17  119.09  3.000
 QJS  H6   C23  C25  119.59  3.000
 QJS  H6   C23  C22  119.44  3.000
 QJS  C25  C23  C22  120.97  3.000
 QJS  H7   C25  C27  120.17  3.000
 QJS  H7   C25  C23  119.67  3.000
 QJS  C27  C25  C23  120.16  3.000
 QJS  H8   C27  C29  120.26  3.000
 QJS  H8   C27  C25  120.38  3.000
 QJS  C29  C27  C25  119.37  3.000
 QJS  H9   C29  C31  119.58  3.000
 QJS  H9   C29  C27  120.04  3.000
 QJS  C31  C29  C27  120.38  3.000
 QJS  C10  C5   C6   106.35  3.000
 QJS  C10  C5   C3   133.88  3.000
 QJS  C6   C5   C3   119.74  3.000
 QJS  C37  C6   N7   129.73  3.000
 QJS  N7   C6   C5   108.33  3.000
 QJS  C37  C6   C5   121.93  3.000
 QJS  H10  N7   C9   125.38  3.000
 QJS  H10  N7   C6   125.29  3.000
 QJS  C9   N7   C6   109.28  3.000
 QJS  C33  C9   C10  127.59  3.000
 QJS  C10  C9   N7   109.11  3.000
 QJS  C33  C9   N7   123.30  3.000
 QJS  N11  C10  C9   125.88  3.000
 QJS  N11  C10  C5   127.15  3.000
 QJS  C9   C10  C5   106.93  3.000
 QJS  H11  N11  C10  117.04  3.000
 QJS  H11  N11  C13  117.89  3.000
 QJS  C10  N11  C13  123.85  3.000
 QJS  H12  C31  C29  118.82  3.000
 QJS  H12  C31  C22  120.43  3.000
 QJS  C29  C31  C22  120.75  3.000
 QJS  O35  C33  O34  124.20  3.000
 QJS  O34  C33  C9   112.17  3.000
 QJS  O35  C33  C9   123.63  3.000
 QJS  H13  O34  C33  110.39  3.000
 QJS  H14  C37  C39  120.92  3.000
 QJS  H14  C37  C6   121.36  3.000
 QJS  C39  C37  C6   117.71  3.000
 QJS  H15  C39  C37  120.44  3.000
 QJS  H15  C39  C2   119.59  3.000
 QJS  C37  C39  C2   119.97  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  CONST_47  H13  O34  C33  C9    180.00   0.0  0
 QJS  Var_01    C22  C17  C19  C15   108.63  30.0  1
 QJS  Var_02    C23  C22  C17  C15  -138.76  30.0  2
 QJS  Var_03    C17  C19  C15  C13   106.47  30.0  1
 QJS  Var_04    N11  C13  C15  C17  -143.02  30.0  2
 QJS  Var_05    O35  C33  C9   N7   -173.99  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
 QJS  plan-4  H13  0.020

