# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 19:19:32 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-[(4-{[3-(trifluoromethyl)pyridin-2-yl]oxy}phenyl)amino]-1H-benzimidazole-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccnc1Oc2ccc(Nc3[nH]c4cc(ccc4n3)C#N)cc2
#
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
 0VM  0VM  2-[(4-{[3-(trifluoromethyl)pyridin-2-yl]oxy}phenyl)amino]-1H-benzimidazole-6-carbonitrile  ligand  41  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0VM
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
 0VM  C8   C  CR6   0  -0.029   -7.4422  -0.3183   0.4281
 0VM  C9   C  CR16  0  -0.297   -6.7661   0.6805  -0.2795
 0VM  C10  C  CR56  0   0.347   -5.3907   0.6371  -0.2286
 0VM  C11  C  CR56  0   0.222   -4.6806  -0.3462   0.4901
 0VM  C13  C  CR16  0  -0.333   -5.3751  -1.3320   1.1867
 0VM  C14  C  CR16  0  -0.256   -6.7565  -1.3097   1.1497
 0VM  N3   N  NR15  0  -0.747   -4.4187   1.4303  -0.7824
 0VM  C12  C  CR5   0   0.723   -3.2179   0.9184  -0.3930
 0VM  N4   N  N     0  -0.531   -3.3344  -0.1448   0.3683
 0VM  C15  C  CR6   0   0.346    1.9305   0.6511  -0.0050
 0VM  C16  C  CR16  0  -0.297    1.5781   1.7208  -0.8095
 0VM  C17  C  CR16  0  -0.358    0.2414   1.9791  -1.0520
 0VM  C18  C  CR6   0   0.366   -0.7569   1.1715  -0.5004
 0VM  C19  C  CR16  0  -0.317   -0.3863   0.0947   0.3063
 0VM  C20  C  CR16  0  -0.294    0.9563  -0.1578   0.5483
 0VM  N1   N  NH1   0  -0.807   -2.0744   1.5110  -0.7980
 0VM  C7   C  CSP   0   0.044   -8.8660  -0.3307   0.4180
 0VM  N2   N  NS    0  -0.265  -10.0195  -0.3464   0.4141
 0VM  C1   C  CR16  0  -0.339    5.4188  -2.2525  -1.8322
 0VM  C2   C  CR16  0  -0.158    6.0291  -1.5736  -0.7848
 0VM  C3   C  CR6   0  -0.379    5.3027  -0.6518  -0.0541
 0VM  C4   C  CR6   0   0.539    3.9627  -0.4530  -0.4202
 0VM  N5   N  N     0  -0.440    3.3821  -1.0857  -1.4083
 0VM  C6   C  CR16  0  -0.040    4.0954  -1.9700  -2.1022
 0VM  F1   F  F     0  -0.302    7.1905  -0.2123   1.2660
 0VM  F3   F  F     0  -0.310    5.8550   1.4295   0.8958
 0VM  F2   F  F     0  -0.310    5.2775  -0.1447   2.2426
 0VM  H1   H  HCR6  0   0.289   -7.3015   1.4414  -0.8308
 0VM  H2   H  HCR6  0   0.267   -4.8478  -2.0968   1.7408
 0VM  H3   H  HCR6  0   0.275   -7.3214  -2.0647   1.6791
 0VM  H4   H  HNR5  0   0.428   -4.5662   2.2409  -1.3636
 0VM  H6   H  HCR6  0   0.276    2.3378   2.3581  -1.2429
 0VM  H7   H  HCR6  0   0.278   -0.0285   2.8227  -1.6763
 0VM  H8   H  HCR6  0   0.297   -1.1359  -0.5442   0.7450
 0VM  H9   H  HCR6  0   0.274    1.2334  -0.9942   1.1773
 0VM  H10  H  HNH1  0   0.424   -2.1853   2.3219  -1.3873
 0VM  H11  H  HCR6  0   0.282    5.9628  -2.9786  -2.4178
 0VM  H12  H  HCR6  0   0.292    7.0652  -1.7734  -0.5500
 0VM  H13  H  HCR6  0   0.281    3.5768  -2.4715  -2.9102
 0VM  O1   O  O2    0  -0.519    3.2616   0.4385   0.2961
 0VM  C5   C  CT    0   1.078    5.9045   0.1051   1.0860

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
 0VM  N2   C7   triple    1.154  0.020  1.154
 0VM  C1   C6   aromatic  1.380  0.020  1.380
 0VM  C1   C2   aromatic  1.389  0.020  1.389
 0VM  C6   N5   aromatic  1.331  0.020  1.331
 0VM  C7   C8   single    1.424  0.020  1.424
 0VM  C2   C3   aromatic  1.382  0.020  1.382
 0VM  C9   C8   aromatic  1.398  0.020  1.398
 0VM  C9   C10  aromatic  1.377  0.020  1.377
 0VM  N5   C4   aromatic  1.309  0.020  1.309
 0VM  C8   C14  aromatic  1.405  0.020  1.405
 0VM  C3   C4   aromatic  1.403  0.020  1.403
 0VM  C3   C5   single    1.495  0.020  1.495
 0VM  F3   C5   single    1.339  0.020  1.339
 0VM  C4   O1   single    1.341  0.020  1.341
 0VM  C10  N3   aromatic  1.371  0.020  1.371
 0VM  C10  C11  aromatic  1.410  0.020  1.410
 0VM  N3   C12  aromatic  1.362  0.020  1.362
 0VM  C5   F1   single    1.337  0.020  1.337
 0VM  C5   F2   single    1.339  0.020  1.339
 0VM  C16  C17  aromatic  1.383  0.020  1.383
 0VM  C16  C15  aromatic  1.384  0.020  1.384
 0VM  C14  C13  aromatic  1.382  0.020  1.382
 0VM  O1   C15  single    1.381  0.020  1.381
 0VM  C17  C18  aromatic  1.397  0.020  1.397
 0VM  C15  C20  aromatic  1.382  0.020  1.382
 0VM  C11  C13  aromatic  1.393  0.020  1.393
 0VM  C11  N4   aromatic  1.367  0.020  1.367
 0VM  C12  N1   single    1.350  0.020  1.350
 0VM  C12  N4   aromatic  1.313  0.020  1.313
 0VM  C18  N1   single    1.393  0.020  1.393
 0VM  C18  C19  aromatic  1.396  0.020  1.396
 0VM  C20  C19  aromatic  1.387  0.020  1.387
 0VM  C9   H1   single    0.930  0.020  1.080
 0VM  C13  H2   single    0.930  0.020  1.080
 0VM  C14  H3   single    0.930  0.020  1.080
 0VM  N3   H4   single    0.860  0.020  1.020
 0VM  C16  H6   single    0.930  0.020  1.080
 0VM  C17  H7   single    0.930  0.020  1.080
 0VM  C19  H8   single    0.930  0.020  1.080
 0VM  C20  H9   single    0.930  0.020  1.080
 0VM  N1   H10  single    0.860  0.020  1.020
 0VM  C1   H11  single    0.930  0.020  1.080
 0VM  C2   H12  single    0.930  0.020  1.080
 0VM  C6   H13  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
 0VM  C7   C8   C14  119.05  3.000
 0VM  C14  C8   C9   121.86  3.000
 0VM  C7   C8   C9   119.09  3.000
 0VM  H1   C9   C10  122.38  3.000
 0VM  H1   C9   C8   121.40  3.000
 0VM  C10  C9   C8   116.21  3.000
 0VM  N3   C10  C11  104.61  3.000
 0VM  C11  C10  C9   122.95  3.000
 0VM  N3   C10  C9   132.44  3.000
 0VM  N4   C11  C13  129.80  3.000
 0VM  N4   C11  C10  110.36  3.000
 0VM  C13  C11  C10  119.84  3.000
 0VM  H2   C13  C14  120.83  3.000
 0VM  H2   C13  C11  120.90  3.000
 0VM  C14  C13  C11  118.27  3.000
 0VM  H3   C14  C13  119.85  3.000
 0VM  H3   C14  C8   119.29  3.000
 0VM  C13  C14  C8   120.86  3.000
 0VM  H4   N3   C12  126.57  3.000
 0VM  H4   N3   C10  126.45  3.000
 0VM  C12  N3   C10  106.98  3.000
 0VM  N1   C12  N4   127.20  3.000
 0VM  N4   C12  N3   113.07  3.000
 0VM  N1   C12  N3   119.73  3.000
 0VM  C12  N4   C11  104.98  3.000
 0VM  O1   C15  C20  120.14  3.000
 0VM  C20  C15  C16  120.37  3.000
 0VM  O1   C15  C16  119.41  3.000
 0VM  H6   C16  C17  119.89  3.000
 0VM  H6   C16  C15  120.61  3.000
 0VM  C17  C16  C15  119.50  3.000
 0VM  H7   C17  C18  119.95  3.000
 0VM  H7   C17  C16  119.15  3.000
 0VM  C18  C17  C16  120.89  3.000
 0VM  N1   C18  C19  124.25  3.000
 0VM  C19  C18  C17  118.96  3.000
 0VM  N1   C18  C17  116.78  3.000
 0VM  H8   C19  C20  119.60  3.000
 0VM  H8   C19  C18  120.51  3.000
 0VM  C20  C19  C18  119.89  3.000
 0VM  H9   C20  C19  119.32  3.000
 0VM  H9   C20  C15  120.29  3.000
 0VM  C19  C20  C15  120.39  3.000
 0VM  H10  N1   C18  115.15  3.000
 0VM  H10  N1   C12  115.79  3.000
 0VM  C18  N1   C12  129.06  3.000
 0VM  N2   C7   C8   180.00  3.000
 0VM  H11  C1   C6   120.97  3.000
 0VM  H11  C1   C2   121.07  3.000
 0VM  C6   C1   C2   117.95  3.000
 0VM  H12  C2   C3   120.80  3.000
 0VM  H12  C2   C1   119.63  3.000
 0VM  C3   C2   C1   119.57  3.000
 0VM  C5   C3   C4   120.77  3.000
 0VM  C5   C3   C2   121.95  3.000
 0VM  C4   C3   C2   117.27  3.000
 0VM  O1   C4   N5   119.50  3.000
 0VM  O1   C4   C3   117.00  3.000
 0VM  N5   C4   C3   123.50  3.000
 0VM  C6   N5   C4   118.47  3.000
 0VM  H13  C6   N5   116.09  3.000
 0VM  H13  C6   C1   120.69  3.000
 0VM  N5   C6   C1   123.22  3.000
 0VM  C4   O1   C15  119.31  3.000
 0VM  F2   C5   F3   106.85  3.000
 0VM  F2   C5   F1   106.84  3.000
 0VM  F3   C5   F1   106.83  3.000
 0VM  F2   C5   C3   112.07  3.000
 0VM  F1   C5   C3   111.70  3.000
 0VM  F3   C5   C3   112.19  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
 0VM  CONST_01  N3   C10  C9   C8    180.00   0.0  0
 0VM  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 0VM  CONST_03  C11  C13  C14  C8      0.00   0.0  0
 0VM  CONST_04  C13  C14  C8   C9      0.00   0.0  0
 0VM  CONST_05  C12  N3   C10  C9    180.00   0.0  0
 0VM  CONST_06  C13  C11  C10  C9      0.00   0.0  0
 0VM  CONST_07  N4   C11  C10  C9    180.00   0.0  0
 0VM  CONST_08  C14  C8   C9   C10     0.00   0.0  0
 0VM  CONST_09  N4   C12  N3   C10     0.00   0.0  0
 0VM  CONST_10  C14  C13  C11  C10     0.00   0.0  0
 0VM  CONST_11  C12  N4   C11  C10     0.00   0.0  0
 0VM  CONST_12  C12  N3   C10  C11     0.00   0.0  0
 0VM  CONST_13  N3   C12  N4   C11     0.00   0.0  0
 0VM  CONST_14  N3   C10  C11  C13   180.00   0.0  0
 0VM  CONST_15  C12  N4   C11  C13   180.00   0.0  0
 0VM  CONST_16  N4   C11  C13  C14   180.00   0.0  0
 0VM  CONST_17  N4   C11  C10  N3      0.00   0.0  0
 0VM  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 0VM  CONST_19  C18  C19  C20  C15     0.00   0.0  0
 0VM  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 0VM  CONST_21  C19  C20  C15  C16     0.00   0.0  0
 0VM  CONST_22  C20  C15  C16  C17     0.00   0.0  0
 0VM  CONST_23  C20  C19  C18  C17     0.00   0.0  0
 0VM  CONST_24  C4   N5   C6   C1      0.00   0.0  0
 0VM  CONST_25  C4   C3   C2   C1      0.00   0.0  0
 0VM  CONST_26  N5   C6   C1   C2      0.00   0.0  0
 0VM  CONST_27  N5   C4   C3   C2      0.00   0.0  0
 0VM  CONST_28  C6   C1   C2   C3      0.00   0.0  0
 0VM  CONST_29  C6   N5   C4   C3      0.00   0.0  0
 0VM  CONST_30  C7   C8   C9   C10   180.00   0.0  0
 0VM  CONST_31  N1   C12  N3   C10   180.00   0.0  0
 0VM  CONST_32  N1   C12  N4   C11   180.00   0.0  0
 0VM  CONST_33  C7   C8   C14  C13   180.00   0.0  0
 0VM  CONST_34  N1   C18  C17  C16   180.00   0.0  0
 0VM  CONST_35  O1   C15  C16  C17   180.00   0.0  0
 0VM  CONST_36  O1   C15  C20  C19   180.00   0.0  0
 0VM  CONST_37  N1   C18  C19  C20   180.00   0.0  0
 0VM  CONST_38  C5   C3   C2   C1    180.00   0.0  0
 0VM  CONST_39  O1   C4   C3   C2    180.00   0.0  0
 0VM  CONST_40  C5   C3   C4   N5    180.00   0.0  0
 0VM  CONST_41  O1   C4   N5   C6    180.00   0.0  0
 0VM  CONST_42  H2   C13  C14  C8    180.00   0.0  0
 0VM  CONST_43  H3   C14  C8   C9    180.00   0.0  0
 0VM  CONST_44  H4   N3   C10  C9      0.00   0.0  0
 0VM  CONST_45  H1   C9   C10  C11   180.00   0.0  0
 0VM  CONST_46  H7   C17  C16  C15   180.00   0.0  0
 0VM  CONST_47  H8   C19  C20  C15   180.00   0.0  0
 0VM  CONST_48  H9   C20  C15  C16   180.00   0.0  0
 0VM  CONST_49  H6   C16  C17  C18   180.00   0.0  0
 0VM  CONST_50  H13  C6   C1   C2    180.00   0.0  0
 0VM  CONST_51  H11  C1   C2   C3    180.00   0.0  0
 0VM  CONST_52  H12  C2   C3   C4    180.00   0.0  0
 0VM  Var_01    C18  N1   C12  N3    178.71  30.0  2
 0VM  Var_02    C17  C18  N1   C12  -179.30  30.0  3
 0VM  Var_03    N5   C4   O1   C15     1.37  30.0  3
 0VM  Var_04    F3   C5   C3   C2    120.95  30.0  2

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
 0VM  plan-1  C15  0.020
 0VM  plan-1  C16  0.020
 0VM  plan-1  C17  0.020
 0VM  plan-1  C18  0.020
 0VM  plan-1  C19  0.020
 0VM  plan-1  C20  0.020
 0VM  plan-1  N1   0.020
 0VM  plan-1  H6   0.020
 0VM  plan-1  H7   0.020
 0VM  plan-1  H8   0.020
 0VM  plan-1  H9   0.020
 0VM  plan-1  O1   0.020
 0VM  plan-2  C1   0.020
 0VM  plan-2  C2   0.020
 0VM  plan-2  C3   0.020
 0VM  plan-2  C4   0.020
 0VM  plan-2  N5   0.020
 0VM  plan-2  C6   0.020
 0VM  plan-2  H11  0.020
 0VM  plan-2  H12  0.020
 0VM  plan-2  H13  0.020
 0VM  plan-2  O1   0.020
 0VM  plan-2  C5   0.020
 0VM  plan-3  C8   0.020
 0VM  plan-3  C9   0.020
 0VM  plan-3  C10  0.020
 0VM  plan-3  C11  0.020
 0VM  plan-3  C13  0.020
 0VM  plan-3  C14  0.020
 0VM  plan-3  N3   0.020
 0VM  plan-3  C12  0.020
 0VM  plan-3  N4   0.020
 0VM  plan-3  N1   0.020
 0VM  plan-3  C7   0.020
 0VM  plan-3  N2   0.020
 0VM  plan-3  H1   0.020
 0VM  plan-3  H2   0.020
 0VM  plan-3  H3   0.020
 0VM  plan-3  H4   0.020

