# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 04:25:29 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: [3,5-bis(trifluoromethyl)phenyl]methyl (1~{S},5~{R})-6-[(1~{H}-benzotriazol-5-ylcarbonylamino)methyl]-3-azabicyclo[3.1.0]hexane-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc(COC(=O)N2C[C@H]3C(CNC(=O)c4ccc5[nH]nnc5c4)[C@H]3C2)cc(c1)C(F)(F)F
#
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
 9V8  9V8  '[3,5-bis(trifluoromethyl)phenyl]methyl (1~{S},5~{R})-6-[(1~{H}-benzotriazol-5-ylcarbonylamino)methyl]-3-azabicyclo[3.1.0]hexane-3-carboxylate'  ligand  56  37  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9V8
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
 9V8  N3   N  NT    0  -0.518   0.2461   3.2106  -0.8136
 9V8  C4   C  CH2   0  -0.249  -0.4658   4.4617  -1.0401
 9V8  C5   C  CH1   0  -0.296  -1.7739   4.2620  -0.3177
 9V8  C6   C  CH1   0  -0.270  -2.5689   3.0511  -0.6929
 9V8  C7   C  CH2   0  -0.264  -4.0557   3.0528  -0.4749
 9V8  C15  C  CR6   0   0.098   3.6312   0.1684  -0.9466
 9V8  C17  C  CR16  0  -0.348   4.5721  -2.1169   0.3605
 9V8  C20  C  CR16  0  -0.319   4.0977  -0.9154  -1.6733
 9V8  C21  C  C     0   0.542  -5.7167   1.2330  -0.5141
 9V8  C22  C  CR6   0  -0.055  -5.9895  -0.1896  -0.1353
 9V8  C24  C  CR16  0  -0.297  -4.9461  -1.1367   0.0170
 9V8  C26  C  CR16  0  -0.312  -7.3078  -0.5623   0.0333
 9V8  C28  C  CR56  0   0.372  -6.5205  -2.8035   0.5395
 9V8  C1   C  CH1   0  -0.292  -1.6642   3.0137   0.5040
 9V8  C11  C  C     0   0.782   1.3842   2.9433  -1.4694
 9V8  C14  C  CH2   0  -0.209   3.1621   1.4060  -1.6546
 9V8  C16  C  CR6   0  -0.149   4.5723  -2.0484  -1.0227
 9V8  C18  C  CR6   0  -0.148   4.0996  -1.0324   1.0874
 9V8  C19  C  CR16  0  -0.302   3.6352   0.1036   0.4421
 9V8  C2   C  CH2   0  -0.249  -0.2913   2.4268   0.2948
 9V8  C25  C  CR16  0  -0.270  -5.1836  -2.4489   0.3505
 9V8  C27  C  CR56  0   0.159  -7.5633  -1.8869   0.3864
 9V8  C32  C  CT    0   1.062   5.0560  -3.1966  -1.8548
 9V8  C36  C  CT    0   1.061   4.0585  -1.0680   2.5850
 9V8  F33  F  F     0  -0.299   5.6015  -4.1699  -1.1230
 9V8  F34  F  F     0  -0.312   4.0556  -3.7451  -2.5577
 9V8  F35  F  F     0  -0.310   5.9778  -2.8045  -2.7431
 9V8  F37  F  F     0  -0.312   2.7975  -1.0784   3.0382
 9V8  F38  F  F     0  -0.299   4.6669  -2.1423   3.0915
 9V8  F39  F  F     0  -0.310   4.6482   0.0086   3.1198
 9V8  N10  N  NH1   0  -0.653  -4.5104   1.7114  -0.1716
 9V8  N29  N  NR15  0  -0.531  -7.1619  -3.9446   0.8666
 9V8  N30  N  N     0  -0.044  -8.4737  -3.7527   0.9138
 9V8  N31  N  N     0  -0.325  -8.7405  -2.5373   0.6324
 9V8  O12  O  O     0  -0.526   1.8816   3.6566  -2.3192
 9V8  O13  O  O2    0  -0.483   1.9141   1.7749  -1.0816
 9V8  O23  O  O     0  -0.491  -6.5596   1.9014  -1.0982
 9V8  H1   H  HCH2  0   0.246   0.0765   5.3137  -0.6195
 9V8  H2   H  HCH2  0   0.252  -0.5954   4.6405  -2.1086
 9V8  H3   H  HCH1  0   0.273  -2.2849   5.1392   0.0586
 9V8  H4   H  HCH1  0   0.267  -2.2422   2.5003  -1.5727
 9V8  H5   H  HCH2  0   0.242  -4.3198   3.7394   0.3370
 9V8  H6   H  HCH2  0   0.261  -4.5717   3.4036  -1.3677
 9V8  H7   H  HCR6  0   0.287   4.9363  -2.9992   0.8665
 9V8  H8   H  HCR6  0   0.286   4.0869  -0.8681  -2.7556
 9V8  H9   H  HCR6  0   0.264  -3.9208  -0.8382  -0.1578
 9V8  H10  H  HCR6  0   0.277  -8.1145   0.1467  -0.0935
 9V8  H11  H  HCH1  0   0.275  -2.0969   2.9523   1.4954
 9V8  H12  H  HCH2  0   0.262   3.8940   2.2080  -1.5296
 9V8  H13  H  HCH2  0   0.256   3.0576   1.2137  -2.7246
 9V8  H14  H  HCR6  0   0.281   3.2737   0.9490   1.0145
 9V8  H15  H  HCH2  0   0.255  -0.3269   1.3661   0.0432
 9V8  H16  H  HCH2  0   0.247   0.3167   2.5402   1.1973
 9V8  H17  H  HCR6  0   0.289  -4.3768  -3.1614   0.4470
 9V8  H18  H  HNH1  0   0.406  -3.9263   1.1738   0.4486
 9V8  H19  H  HNR5  0   0.437  -6.7826  -4.8578   1.0684

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
 9V8  F35  C32  single    1.339  0.020  1.339
 9V8  F34  C32  single    1.340  0.020  1.340
 9V8  C32  F33  single    1.334  0.020  1.334
 9V8  C32  C16  single    1.498  0.020  1.498
 9V8  F37  C36  single    1.340  0.020  1.340
 9V8  C17  C16  aromatic  1.385  0.020  1.385
 9V8  C17  C18  aromatic  1.388  0.020  1.388
 9V8  C16  C20  aromatic  1.390  0.020  1.390
 9V8  C36  F38  single    1.334  0.020  1.334
 9V8  C36  C18  single    1.499  0.020  1.499
 9V8  C36  F39  single    1.339  0.020  1.339
 9V8  C18  C19  aromatic  1.387  0.020  1.387
 9V8  C20  C15  aromatic  1.386  0.020  1.386
 9V8  C19  C15  aromatic  1.390  0.020  1.390
 9V8  C15  C14  single    1.501  0.020  1.501
 9V8  C14  O13  single    1.422  0.020  1.422
 9V8  O13  C11  single    1.340  0.020  1.340
 9V8  N30  N29  aromatic  1.327  0.020  1.327
 9V8  N30  N31  aromatic  1.276  0.020  1.276
 9V8  N29  C28  aromatic  1.349  0.020  1.349
 9V8  C2   N3   single    1.460  0.020  1.460
 9V8  C2   C1   single    1.508  0.020  1.508
 9V8  C11  N3   single    1.340  0.020  1.340
 9V8  C11  O12  double    1.216  0.020  1.216
 9V8  N31  C27  aromatic  1.367  0.020  1.367
 9V8  C28  C25  aromatic  1.396  0.020  1.396
 9V8  C28  C27  aromatic  1.397  0.020  1.397
 9V8  C25  C24  aromatic  1.375  0.020  1.375
 9V8  N3   C4   single    1.457  0.020  1.457
 9V8  C27  C26  aromatic  1.394  0.020  1.394
 9V8  C1   C6   single    1.501  0.020  1.501
 9V8  C1   C5   single    1.499  0.020  1.499
 9V8  C24  C22  aromatic  1.417  0.020  1.417
 9V8  C26  C22  aromatic  1.380  0.020  1.380
 9V8  C22  C21  single    1.497  0.020  1.497
 9V8  C6   C5   single    1.496  0.020  1.496
 9V8  C6   C7   single    1.503  0.020  1.503
 9V8  C4   C5   single    1.508  0.020  1.508
 9V8  C21  N10  single    1.342  0.020  1.342
 9V8  C21  O23  double    1.224  0.020  1.224
 9V8  N10  C7   single    1.448  0.020  1.448
 9V8  C4   H1   single    0.970  0.020  1.090
 9V8  C4   H2   single    0.970  0.020  1.090
 9V8  C5   H3   single    0.970  0.020  1.090
 9V8  C6   H4   single    0.970  0.020  1.090
 9V8  C7   H5   single    0.970  0.020  1.090
 9V8  C7   H6   single    0.970  0.020  1.090
 9V8  C17  H7   single    0.930  0.020  1.080
 9V8  C20  H8   single    0.930  0.020  1.080
 9V8  C24  H9   single    0.930  0.020  1.080
 9V8  C26  H10  single    0.930  0.020  1.080
 9V8  C1   H11  single    0.970  0.020  1.090
 9V8  C14  H12  single    0.970  0.020  1.090
 9V8  C14  H13  single    0.970  0.020  1.090
 9V8  C19  H14  single    0.930  0.020  1.080
 9V8  C2   H15  single    0.970  0.020  1.090
 9V8  C2   H16  single    0.970  0.020  1.090
 9V8  C25  H17  single    0.930  0.020  1.080
 9V8  N10  H18  single    0.860  0.020  1.020
 9V8  N29  H19  single    0.860  0.020  1.020

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
 9V8  C2   N3   C11  125.23  3.000
 9V8  C11  N3   C4   120.66  3.000
 9V8  C2   N3   C4   113.52  3.000
 9V8  H2   C4   H1   107.93  3.000
 9V8  H2   C4   C5   112.83  3.000
 9V8  H1   C4   C5   110.43  3.000
 9V8  H2   C4   N3   110.55  3.000
 9V8  H1   C4   N3   111.51  3.000
 9V8  C5   C4   N3   103.63  3.000
 9V8  H3   C5   C1   121.26  3.000
 9V8  H3   C5   C6   119.47  3.000
 9V8  C1   C5   C6    60.15  3.000
 9V8  H3   C5   C4   117.95  3.000
 9V8  C6   C5   C4   116.62  3.000
 9V8  C1   C5   C4   108.03  3.000
 9V8  H4   C6   C1   116.82  3.000
 9V8  H4   C6   C7   114.51  3.000
 9V8  C1   C6   C7   118.73  3.000
 9V8  H4   C6   C5   116.93  3.000
 9V8  C7   C6   C5   119.24  3.000
 9V8  C1   C6   C5    60.00  3.000
 9V8  H6   C7   H5   106.94  3.000
 9V8  H6   C7   N10  108.73  3.000
 9V8  H5   C7   N10  110.46  3.000
 9V8  H6   C7   C6   110.50  3.000
 9V8  H5   C7   C6   110.29  3.000
 9V8  N10  C7   C6   109.87  3.000
 9V8  C19  C15  C14  120.70  3.000
 9V8  C14  C15  C20  120.18  3.000
 9V8  C19  C15  C20  119.10  3.000
 9V8  H7   C17  C18  120.50  3.000
 9V8  H7   C17  C16  120.54  3.000
 9V8  C18  C17  C16  118.96  3.000
 9V8  H8   C20  C16  120.43  3.000
 9V8  H8   C20  C15  119.10  3.000
 9V8  C16  C20  C15  120.46  3.000
 9V8  O23  C21  N10  123.09  3.000
 9V8  O23  C21  C22  120.94  3.000
 9V8  N10  C21  C22  115.97  3.000
 9V8  C26  C22  C24  120.63  3.000
 9V8  C26  C22  C21  117.48  3.000
 9V8  C24  C22  C21  121.87  3.000
 9V8  H9   C24  C25  117.79  3.000
 9V8  H9   C24  C22  119.73  3.000
 9V8  C25  C24  C22  122.47  3.000
 9V8  H10  C26  C27  121.05  3.000
 9V8  H10  C26  C22  121.41  3.000
 9V8  C27  C26  C22  117.54  3.000
 9V8  N29  C28  C27  103.10  3.000
 9V8  C27  C28  C25  122.23  3.000
 9V8  N29  C28  C25  134.66  3.000
 9V8  H11  C1   C2   117.95  3.000
 9V8  H11  C1   C6   119.37  3.000
 9V8  C2   C1   C6   116.61  3.000
 9V8  H11  C1   C5   121.31  3.000
 9V8  C6   C1   C5    59.85  3.000
 9V8  C2   C1   C5   108.35  3.000
 9V8  O13  C11  O12  123.50  3.000
 9V8  O12  C11  N3   124.91  3.000
 9V8  O13  C11  N3   111.59  3.000
 9V8  H13  C14  H12  107.78  3.000
 9V8  H13  C14  O13  110.89  3.000
 9V8  H12  C14  O13  110.56  3.000
 9V8  H13  C14  C15  110.30  3.000
 9V8  H12  C14  C15  109.99  3.000
 9V8  O13  C14  C15  107.34  3.000
 9V8  C32  C16  C20  118.36  3.000
 9V8  C20  C16  C17  120.51  3.000
 9V8  C32  C16  C17  121.12  3.000
 9V8  C36  C18  C19  118.38  3.000
 9V8  C19  C18  C17  120.68  3.000
 9V8  C36  C18  C17  120.93  3.000
 9V8  H14  C19  C18  120.35  3.000
 9V8  H14  C19  C15  119.38  3.000
 9V8  C18  C19  C15  120.27  3.000
 9V8  H16  C2   H15  108.01  3.000
 9V8  H16  C2   C1   110.56  3.000
 9V8  H15  C2   C1   112.39  3.000
 9V8  H16  C2   N3   111.47  3.000
 9V8  H15  C2   N3   111.04  3.000
 9V8  C1   C2   N3   103.39  3.000
 9V8  H17  C25  C28  122.37  3.000
 9V8  H17  C25  C24  121.47  3.000
 9V8  C28  C25  C24  116.16  3.000
 9V8  N31  C27  C28  108.11  3.000
 9V8  C28  C27  C26  120.95  3.000
 9V8  N31  C27  C26  130.94  3.000
 9V8  F35  C32  F34  106.61  3.000
 9V8  F34  C32  F33  107.12  3.000
 9V8  F35  C32  F33  107.22  3.000
 9V8  F33  C32  C16  112.73  3.000
 9V8  F34  C32  C16  111.34  3.000
 9V8  F35  C32  C16  111.49  3.000
 9V8  F39  C36  F38  107.16  3.000
 9V8  F39  C36  F37  106.60  3.000
 9V8  F38  C36  F37  107.12  3.000
 9V8  F39  C36  C18  111.59  3.000
 9V8  F38  C36  C18  112.70  3.000
 9V8  F37  C36  C18  111.34  3.000
 9V8  H18  N10  C21  119.21  3.000
 9V8  H18  N10  C7   116.18  3.000
 9V8  C21  N10  C7   123.97  3.000
 9V8  H19  N29  N30  119.70  3.000
 9V8  H19  N29  C28  129.42  3.000
 9V8  N30  N29  C28  110.88  3.000
 9V8  N31  N30  N29  109.67  3.000
 9V8  N30  N31  C27  108.23  3.000
 9V8  C14  O13  C11  117.16  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
 9V8  CONST_01  C17  C16  C20  C15     0.00   0.0  0
 9V8  CONST_02  C17  C18  C19  C15     0.00   0.0  0
 9V8  CONST_03  C18  C17  C16  C20     0.00   0.0  0
 9V8  CONST_04  C18  C19  C15  C20     0.00   0.0  0
 9V8  CONST_05  C28  C25  C24  C22     0.00   0.0  0
 9V8  CONST_06  N31  C27  C26  C22   180.00   0.0  0
 9V8  CONST_07  C28  C27  C26  C22     0.00   0.0  0
 9V8  CONST_08  N29  C28  C25  C24   180.00   0.0  0
 9V8  CONST_09  C27  C28  C25  C24     0.00   0.0  0
 9V8  CONST_10  C27  C26  C22  C24     0.00   0.0  0
 9V8  CONST_11  N30  N31  C27  C26   180.00   0.0  0
 9V8  CONST_12  N29  C28  C27  C26   180.00   0.0  0
 9V8  CONST_13  C25  C28  C27  C26     0.00   0.0  0
 9V8  CONST_14  C25  C24  C22  C26     0.00   0.0  0
 9V8  CONST_15  N31  N30  N29  C28     0.00   0.0  0
 9V8  CONST_16  N30  N31  C27  C28     0.00   0.0  0
 9V8  CONST_17  C19  C18  C17  C16     0.00   0.0  0
 9V8  CONST_18  C19  C15  C20  C16     0.00   0.0  0
 9V8  CONST_19  N30  N29  C28  C25   180.00   0.0  0
 9V8  CONST_20  N31  C27  C28  C25   180.00   0.0  0
 9V8  CONST_21  N29  N30  N31  C27     0.00   0.0  0
 9V8  CONST_22  N30  N29  C28  C27     0.00   0.0  0
 9V8  CONST_23  N31  C27  C28  N29     0.00   0.0  0
 9V8  CONST_24  C32  C16  C20  C15   180.00   0.0  0
 9V8  CONST_25  C36  C18  C19  C15   180.00   0.0  0
 9V8  CONST_26  C25  C24  C22  C21   180.00   0.0  0
 9V8  CONST_27  C27  C26  C22  C21   180.00   0.0  0
 9V8  CONST_28  C16  C20  C15  C14   180.00   0.0  0
 9V8  CONST_29  C18  C19  C15  C14   180.00   0.0  0
 9V8  CONST_30  C36  C18  C17  C16   180.00   0.0  0
 9V8  CONST_31  C32  C16  C17  C18   180.00   0.0  0
 9V8  CONST_32  H8   C20  C16  C17   180.00   0.0  0
 9V8  CONST_33  H14  C19  C18  C17   180.00   0.0  0
 9V8  CONST_34  H7   C17  C16  C20   180.00   0.0  0
 9V8  CONST_35  H17  C25  C24  C22   180.00   0.0  0
 9V8  CONST_36  H10  C26  C22  C24   180.00   0.0  0
 9V8  CONST_37  H9   C24  C22  C26   180.00   0.0  0
 9V8  CONST_38  H19  N29  C28  C25     0.00   0.0  0
 9V8  CONST_39  C22  C21  N10  C7    180.00   0.0  0
 9V8  CONST_40  H18  N10  C21  C22     0.00   0.0  0
 9V8  CONST_41  O23  C21  N10  C7      0.00   0.0  0
 9V8  Var_01    C6   C1   C2   N3     54.86  30.0  1
 9V8  Var_02    C1   C5   C4   N3     10.30  30.0  1
 9V8  Var_03    C1   C2   N3   C4     17.66  30.0  1
 9V8  Var_04    C2   C1   C5   C4     -0.20  30.0  1
 9V8  Var_05    C2   N3   C4   C5    -17.82  30.0  1
 9V8  Var_06    O13  C11  N3   C4    177.30  30.0  1
 9V8  Var_07    N10  C7   C6   C5   -148.22  30.0  3
 9V8  Var_08    F35  C32  C16  C17  -127.77  30.0  2
 9V8  Var_09    F37  C36  C18  C17  -112.38  30.0  3
 9V8  Var_10    O13  C14  C15  C20   132.73  30.0  2
 9V8  Var_11    N10  C21  C22  C24   -26.71  30.0  2
 9V8  Var_12    C21  N10  C7   C6   -148.07  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
 9V8  chir_01  C5  C1  C6  C4  both
 9V8  chir_02  C6  C7  C5  C1  both
 9V8  chir_03  C1  C5  C6  C2  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
 9V8  plan-1  C15  0.020
 9V8  plan-1  C17  0.020
 9V8  plan-1  C20  0.020
 9V8  plan-1  C14  0.020
 9V8  plan-1  C16  0.020
 9V8  plan-1  C18  0.020
 9V8  plan-1  C19  0.020
 9V8  plan-1  C32  0.020
 9V8  plan-1  C36  0.020
 9V8  plan-1  H7   0.020
 9V8  plan-1  H8   0.020
 9V8  plan-1  H14  0.020
 9V8  plan-2  C21  0.020
 9V8  plan-2  C22  0.020
 9V8  plan-2  C24  0.020
 9V8  plan-2  C26  0.020
 9V8  plan-2  C28  0.020
 9V8  plan-2  C25  0.020
 9V8  plan-2  C27  0.020
 9V8  plan-2  N29  0.020
 9V8  plan-2  N30  0.020
 9V8  plan-2  N31  0.020
 9V8  plan-2  H9   0.020
 9V8  plan-2  H10  0.020
 9V8  plan-2  H17  0.020
 9V8  plan-2  H19  0.020
 9V8  plan-3  C7   0.020
 9V8  plan-3  C21  0.020
 9V8  plan-3  C22  0.020
 9V8  plan-3  N10  0.020
 9V8  plan-3  O23  0.020
 9V8  plan-3  H18  0.020
 9V8  plan-4  N3   0.020
 9V8  plan-4  C11  0.020
 9V8  plan-4  O12  0.020
 9V8  plan-4  O13  0.020

