# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:19:04 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@@H](CC(C)(C)C1)n2c(Nc3ccc(cc3)C(C)C)nc4cc(ccc24)C(O)=O
#
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
 6VN  6VN  '2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid'  ligand  63  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6VN
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
 6VN  C1   C  CR56   0   0.336  -2.2595   0.5140  -0.0242
 6VN  C2   C  CR16   0  -0.394  -2.3774   2.9297   0.0415
 6VN  C3   C  CR16   0  -0.308  -3.6404   0.3990  -0.0940
 6VN  C4   C  CR6    0  -0.123  -3.7639   2.8388  -0.0281
 6VN  C8   C  CR6    0   0.154   5.0259   1.2699  -0.1156
 6VN  C9   C  CR16   0  -0.302   4.7629   0.0405   0.4868
 6VN  C10  C  CR16   0  -0.324   3.9390   1.9768  -0.6174
 6VN  C11  C  CR16   0  -0.342   3.4749  -0.4556   0.5803
 6VN  C12  C  CR16   0  -0.286   2.6385   1.4966  -0.5357
 6VN  C13  C  CR6    0   0.351   2.3931   0.2652   0.0685
 6VN  C15  C  CH2    0  -0.411  -1.1058  -2.6176   1.1509
 6VN  C16  C  CT     0  -0.100  -1.4181  -4.1194   1.0504
 6VN  C17  C  CH1    0  -0.127  -1.4466  -1.8593  -0.1310
 6VN  C18  C  CH2    0  -0.380  -0.7531  -4.6841  -0.2129
 6VN  C19  C  CH2    0  -0.410  -0.7616  -2.4549  -1.3584
 6VN  C20  C  CH1    0  -0.250  -1.1077  -3.9367  -1.4967
 6VN  C21  C  CH3    0  -0.652  -0.4064  -4.5484  -2.7023
 6VN  C24  C  CH3    0  -0.641   6.9071   2.2945   1.1804
 6VN  C25  C  CH3    0  -0.649   7.4121   0.8350  -0.8089
 6VN  N1   N  NR5    0  -0.601  -1.2426  -0.4195  -0.0047
 6VN  C5   C  CR16   0  -0.313  -4.3727   1.5773  -0.0961
 6VN  C7   C  C      0   0.396  -4.6137   4.1009  -0.0273
 6VN  O1   O  OC    -1  -0.599  -5.8505   3.9473  -0.0824
 6VN  O    O  O      0  -0.598  -4.0053   5.1883   0.0297
 6VN  C    C  CR56   0   0.185  -1.6249   1.7624   0.0435
 6VN  N    N  N      0  -0.525  -0.2621   1.5943   0.1179
 6VN  C6   C  CR5    0   0.702  -0.0779   0.3022   0.0892
 6VN  N2   N  NH1    0  -0.819   1.1302  -0.3227   0.1466
 6VN  H1   H  HCR6   0   0.236  -1.8941   3.8963   0.0965
 6VN  H2   H  HCR6   0   0.257  -4.1439  -0.5581  -0.1459
 6VN  H3   H  HCR6   0   0.246   5.5746  -0.5485   0.8986
 6VN  H4   H  HCR6   0   0.246   4.1056   2.9353  -1.0960
 6VN  H5   H  HCR6   0   0.259   3.3056  -1.4139   1.0582
 6VN  H6   H  HCR6   0   0.268   1.8256   2.0816  -0.9369
 6VN  H7   H  HCH1   0   0.237   6.3918   2.7059  -0.8489
 6VN  H8   H  HCH2   0   0.252  -1.6476  -2.1758   1.9925
 6VN  H9   H  HCH2   0   0.218  -0.0414  -2.5143   1.3912
 6VN  H10  H  HCH1   0   0.266  -2.5202  -1.9605  -0.2981
 6VN  H11  H  HCH2   0   0.213   0.3363  -4.6480  -0.0822
 6VN  H12  H  HCH2   0   0.228  -1.0133  -5.7425  -0.3184
 6VN  H13  H  HCH2   0   0.249  -1.0768  -1.9072  -2.2503
 6VN  H14  H  HCH2   0   0.215   0.3259  -2.3510  -1.2926
 6VN  H15  H  HCH1   0   0.224  -2.1883  -4.0179  -1.6628
 6VN  H16  H  HCH3   0   0.228  -0.6560  -5.6055  -2.8078
 6VN  H17  H  HCH3   0   0.228  -0.6947  -4.0453  -3.6268
 6VN  H18  H  HCH3   0   0.215   0.6792  -4.4723  -2.6064
 6VN  H19  H  HCH3   0   0.230   6.2425   3.0528   1.5962
 6VN  H20  H  HCH3   0   0.218   6.9471   1.4628   1.8870
 6VN  H21  H  HCH3   0   0.226   7.9087   2.7240   1.1169
 6VN  H22  H  HCH3   0   0.218   7.5316  -0.0515  -0.1833
 6VN  H23  H  HCH3   0   0.231   7.0829   0.5054  -1.7952
 6VN  H24  H  HCH3   0   0.230   8.3968   1.2920  -0.9182
 6VN  H25  H  HCH3   0   0.226  -1.2667  -4.4168   3.1996
 6VN  H26  H  HCH3   0   0.227  -1.0381  -5.8893   2.2547
 6VN  H27  H  HCH3   0   0.224   0.2474  -4.6849   2.3313
 6VN  H28  H  HCH3   0   0.228  -3.4367  -3.8852   0.1901
 6VN  H29  H  HCH3   0   0.230  -3.1482  -5.4268   0.9766
 6VN  H30  H  HCH3   0   0.229  -3.3916  -3.9765   1.9464
 6VN  H31  H  HCR6   0   0.238  -5.4515   1.5221  -0.1486
 6VN  H33  H  HNH1   0   0.406   1.1264  -1.2843   0.4406
 6VN  C23  C  CH3    0  -0.641  -0.8357  -4.8165   2.2790
 6VN  C22  C  CH3    0  -0.653  -2.9308  -4.3583   1.0326
 6VN  C14  C  CH1    0  -0.323   6.4269   1.8287  -0.1951

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
 6VN  C22  C16  single    1.531  0.020  1.531
 6VN  C21  C20  single    1.523  0.020  1.523
 6VN  C14  C25  single    1.528  0.020  1.528
 6VN  C14  C24  single    1.530  0.020  1.530
 6VN  C14  C8   single    1.510  0.020  1.510
 6VN  C18  C20  single    1.527  0.020  1.527
 6VN  C18  C16  single    1.535  0.020  1.535
 6VN  C9   C11  aromatic  1.383  0.020  1.383
 6VN  C9   C8   aromatic  1.394  0.020  1.394
 6VN  C20  C19  single    1.528  0.020  1.528
 6VN  C23  C16  single    1.528  0.020  1.528
 6VN  C16  C15  single    1.537  0.020  1.537
 6VN  C11  C13  aromatic  1.397  0.020  1.397
 6VN  C8   C10  aromatic  1.390  0.020  1.390
 6VN  C19  C17  single    1.527  0.020  1.527
 6VN  C15  C17  single    1.528  0.020  1.528
 6VN  C13  N2   single    1.395  0.020  1.395
 6VN  C13  C12  aromatic  1.393  0.020  1.393
 6VN  C10  C12  aromatic  1.389  0.020  1.389
 6VN  C17  N1   single    1.460  0.020  1.460
 6VN  N2   C6   single    1.361  0.020  1.361
 6VN  N1   C6   aromatic  1.373  0.020  1.373
 6VN  N1   C1   aromatic  1.381  0.020  1.381
 6VN  C6   N    aromatic  1.305  0.020  1.305
 6VN  C1   C3   aromatic  1.387  0.020  1.387
 6VN  C1   C    aromatic  1.402  0.020  1.402
 6VN  N    C    aromatic  1.375  0.020  1.375
 6VN  C3   C5   aromatic  1.387  0.020  1.387
 6VN  C    C2   aromatic  1.389  0.020  1.389
 6VN  C5   C4   aromatic  1.402  0.020  1.402
 6VN  C2   C4   aromatic  1.391  0.020  1.391
 6VN  C4   C7   single    1.522  0.020  1.522
 6VN  C7   O    deloc     1.247  0.020  1.247
 6VN  C7   O1   deloc     1.247  0.020  1.247
 6VN  C2   H1   single    0.930  0.020  1.080
 6VN  C3   H2   single    0.930  0.020  1.080
 6VN  C9   H3   single    0.930  0.020  1.080
 6VN  C10  H4   single    0.930  0.020  1.080
 6VN  C11  H5   single    0.930  0.020  1.080
 6VN  C12  H6   single    0.930  0.020  1.080
 6VN  C14  H7   single    0.970  0.020  1.090
 6VN  C15  H8   single    0.970  0.020  1.090
 6VN  C15  H9   single    0.970  0.020  1.090
 6VN  C17  H10  single    0.970  0.020  1.090
 6VN  C18  H11  single    0.970  0.020  1.090
 6VN  C18  H12  single    0.970  0.020  1.090
 6VN  C19  H13  single    0.970  0.020  1.090
 6VN  C19  H14  single    0.970  0.020  1.090
 6VN  C20  H15  single    0.970  0.020  1.090
 6VN  C21  H16  single    0.970  0.020  1.090
 6VN  C21  H17  single    0.970  0.020  1.090
 6VN  C21  H18  single    0.970  0.020  1.090
 6VN  C24  H19  single    0.970  0.020  1.090
 6VN  C24  H20  single    0.970  0.020  1.090
 6VN  C24  H21  single    0.970  0.020  1.090
 6VN  C25  H22  single    0.970  0.020  1.090
 6VN  C25  H23  single    0.970  0.020  1.090
 6VN  C25  H24  single    0.970  0.020  1.090
 6VN  C23  H25  single    0.970  0.020  1.090
 6VN  C23  H26  single    0.970  0.020  1.090
 6VN  C23  H27  single    0.970  0.020  1.090
 6VN  C22  H28  single    0.970  0.020  1.090
 6VN  C22  H29  single    0.970  0.020  1.090
 6VN  C22  H30  single    0.970  0.020  1.090
 6VN  C5   H31  single    0.930  0.020  1.080
 6VN  N2   H33  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
 6VN  C    C1   N1   105.54  3.000
 6VN  C    C1   C3   121.79  3.000
 6VN  N1   C1   C3   132.67  3.000
 6VN  H1   C2   C    120.58  3.000
 6VN  H1   C2   C4   120.40  3.000
 6VN  C    C2   C4   119.02  3.000
 6VN  H2   C3   C5   120.35  3.000
 6VN  H2   C3   C1   122.58  3.000
 6VN  C5   C3   C1   117.07  3.000
 6VN  C7   C4   C5   120.24  3.000
 6VN  C7   C4   C2   120.16  3.000
 6VN  C5   C4   C2   119.59  3.000
 6VN  C14  C8   C10  121.20  3.000
 6VN  C10  C8   C9   117.19  3.000
 6VN  C14  C8   C9   121.60  3.000
 6VN  H3   C9   C11  118.46  3.000
 6VN  H3   C9   C8   120.13  3.000
 6VN  C11  C9   C8   121.40  3.000
 6VN  H4   C10  C12  118.40  3.000
 6VN  H4   C10  C8   119.25  3.000
 6VN  C12  C10  C8   122.35  3.000
 6VN  H5   C11  C13  119.78  3.000
 6VN  H5   C11  C9   119.48  3.000
 6VN  C13  C11  C9   120.74  3.000
 6VN  H6   C12  C13  120.51  3.000
 6VN  H6   C12  C10  119.76  3.000
 6VN  C13  C12  C10  119.73  3.000
 6VN  N2   C13  C12  123.78  3.000
 6VN  C12  C13  C11  118.58  3.000
 6VN  N2   C13  C11  117.58  3.000
 6VN  H9   C15  H8   105.92  3.000
 6VN  H9   C15  C17  110.72  3.000
 6VN  H8   C15  C17  109.54  3.000
 6VN  H9   C15  C16  107.68  3.000
 6VN  H8   C15  C16  110.13  3.000
 6VN  C17  C15  C16  112.62  3.000
 6VN  C22  C16  C23  108.34  3.000
 6VN  C23  C16  C18  109.19  3.000
 6VN  C22  C16  C18  111.16  3.000
 6VN  C23  C16  C15  108.40  3.000
 6VN  C18  C16  C15  108.98  3.000
 6VN  C22  C16  C15  110.72  3.000
 6VN  H10  C17  N1   104.02  3.000
 6VN  H10  C17  C19  106.39  3.000
 6VN  N1   C17  C19  113.06  3.000
 6VN  H10  C17  C15  107.57  3.000
 6VN  N1   C17  C15  112.69  3.000
 6VN  C19  C17  C15  112.39  3.000
 6VN  H12  C18  H11  106.20  3.000
 6VN  H12  C18  C20  109.69  3.000
 6VN  H11  C18  C20  108.32  3.000
 6VN  H12  C18  C16  109.38  3.000
 6VN  H11  C18  C16  108.64  3.000
 6VN  C20  C18  C16  114.27  3.000
 6VN  H14  C19  H13  106.74  3.000
 6VN  H14  C19  C20  108.82  3.000
 6VN  H13  C19  C20  110.29  3.000
 6VN  H14  C19  C17  111.13  3.000
 6VN  H13  C19  C17  109.34  3.000
 6VN  C20  C19  C17  110.46  3.000
 6VN  H15  C20  C21  107.71  3.000
 6VN  H15  C20  C19  107.99  3.000
 6VN  C21  C20  C19  110.91  3.000
 6VN  H15  C20  C18  108.66  3.000
 6VN  C19  C20  C18  110.24  3.000
 6VN  C21  C20  C18  111.22  3.000
 6VN  H18  C21  H17  107.74  3.000
 6VN  H18  C21  H16  107.65  3.000
 6VN  H17  C21  H16  107.71  3.000
 6VN  H18  C21  C20  111.11  3.000
 6VN  H17  C21  C20  111.34  3.000
 6VN  H16  C21  C20  111.12  3.000
 6VN  H21  C24  H20  107.67  3.000
 6VN  H21  C24  H19  107.92  3.000
 6VN  H20  C24  H19  107.77  3.000
 6VN  H21  C24  C14  110.83  3.000
 6VN  H20  C24  C14  111.19  3.000
 6VN  H19  C24  C14  111.30  3.000
 6VN  H24  C25  H23  107.96  3.000
 6VN  H24  C25  H22  107.38  3.000
 6VN  H23  C25  H22  107.81  3.000
 6VN  H24  C25  C14  110.47  3.000
 6VN  H23  C25  C14  111.42  3.000
 6VN  H22  C25  C14  111.62  3.000
 6VN  C6   N1   C17  130.00  3.000
 6VN  C6   N1   C1   105.68  3.000
 6VN  C17  N1   C1   124.25  3.000
 6VN  H31  C5   C4   118.77  3.000
 6VN  H31  C5   C3   118.90  3.000
 6VN  C4   C5   C3   122.33  3.000
 6VN  O    C7   O1   126.37  3.000
 6VN  O1   C7   C4   116.85  3.000
 6VN  O    C7   C4   116.79  3.000
 6VN  N    C    C2   129.78  3.000
 6VN  C2   C    C1   120.20  3.000
 6VN  N    C    C1   110.02  3.000
 6VN  C6   N    C    105.05  3.000
 6VN  N2   C6   N    125.35  3.000
 6VN  N    C6   N1   113.70  3.000
 6VN  N2   C6   N1   120.95  3.000
 6VN  H33  N2   C6   116.61  3.000
 6VN  H33  N2   C13  115.00  3.000
 6VN  C6   N2   C13  127.41  3.000
 6VN  H27  C23  H26  107.65  3.000
 6VN  H27  C23  H25  107.87  3.000
 6VN  H26  C23  H25  107.77  3.000
 6VN  H27  C23  C16  111.19  3.000
 6VN  H26  C23  C16  111.08  3.000
 6VN  H25  C23  C16  111.12  3.000
 6VN  H30  C22  H29  107.51  3.000
 6VN  H30  C22  H28  107.40  3.000
 6VN  H29  C22  H28  107.01  3.000
 6VN  H30  C22  C16  110.64  3.000
 6VN  H29  C22  C16  110.48  3.000
 6VN  H28  C22  C16  113.54  3.000
 6VN  H7   C14  C25  107.57  3.000
 6VN  H7   C14  C24  107.65  3.000
 6VN  C25  C14  C24  110.91  3.000
 6VN  H7   C14  C8   107.35  3.000
 6VN  C24  C14  C8   110.89  3.000
 6VN  C25  C14  C8   112.25  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
 6VN  CONST_01  N    C6   N1   C1     0.00   0.0  0
 6VN  CONST_02  C4   C5   C3   C1     0.00   0.0  0
 6VN  CONST_03  C6   N    C    C1     0.00   0.0  0
 6VN  CONST_04  C4   C2   C    C1     0.00   0.0  0
 6VN  CONST_05  N1   C1   C    C2   180.00   0.0  0
 6VN  CONST_06  C3   C1   C    C2     0.00   0.0  0
 6VN  CONST_07  C6   N    C    C2   180.00   0.0  0
 6VN  CONST_08  C3   C5   C4   C2     0.00   0.0  0
 6VN  CONST_09  C6   N1   C1   C3   180.00   0.0  0
 6VN  CONST_10  N    C    C1   C3   180.00   0.0  0
 6VN  CONST_11  N    C    C2   C4   180.00   0.0  0
 6VN  CONST_12  C13  C11  C9   C8     0.00   0.0  0
 6VN  CONST_13  C13  C12  C10  C8     0.00   0.0  0
 6VN  CONST_14  C12  C13  C11  C9     0.00   0.0  0
 6VN  CONST_15  C12  C10  C8   C9     0.00   0.0  0
 6VN  CONST_16  C11  C9   C8   C10    0.00   0.0  0
 6VN  CONST_17  C11  C13  C12  C10    0.00   0.0  0
 6VN  CONST_18  C    N    C6   N1     0.00   0.0  0
 6VN  CONST_19  C5   C3   C1   N1   180.00   0.0  0
 6VN  CONST_20  N    C    C1   N1     0.00   0.0  0
 6VN  CONST_21  C    C1   C3   C5     0.00   0.0  0
 6VN  CONST_22  C    C2   C4   C5     0.00   0.0  0
 6VN  CONST_23  C6   N1   C1   C      0.00   0.0  0
 6VN  CONST_24  C17  N1   C1   C3     0.00   0.0  0
 6VN  CONST_25  N    C6   N1   C17  180.00   0.0  0
 6VN  CONST_26  C    C1   N1   C17  180.00   0.0  0
 6VN  CONST_27  N2   C6   N1   C1   180.00   0.0  0
 6VN  CONST_28  C7   C4   C5   C3   180.00   0.0  0
 6VN  CONST_29  N2   C13  C11  C9   180.00   0.0  0
 6VN  CONST_30  N2   C13  C12  C10  180.00   0.0  0
 6VN  CONST_31  C14  C8   C9   C11  180.00   0.0  0
 6VN  CONST_32  C14  C8   C10  C12  180.00   0.0  0
 6VN  CONST_33  N2   C6   N1   C17    0.00   0.0  0
 6VN  CONST_34  C    C2   C4   C7   180.00   0.0  0
 6VN  CONST_35  N2   C6   N    C    180.00   0.0  0
 6VN  CONST_36  H31  C5   C3   C1   180.00   0.0  0
 6VN  CONST_37  H1   C2   C    C1   180.00   0.0  0
 6VN  CONST_38  H2   C3   C5   C4   180.00   0.0  0
 6VN  CONST_39  H5   C11  C9   C8   180.00   0.0  0
 6VN  CONST_40  H6   C12  C10  C8   180.00   0.0  0
 6VN  CONST_41  H4   C10  C8   C9   180.00   0.0  0
 6VN  CONST_42  H3   C9   C8   C10  180.00   0.0  0
 6VN  Var_01    C20  C18  C16  C15  -53.76  30.0  1
 6VN  Var_02    C18  C16  C15  C17   52.09  30.0  1
 6VN  Var_03    C6   N2   C13  C11  159.20  30.0  2
 6VN  Var_04    N1   C6   N2   C13  170.97  30.0  2
 6VN  Var_05    O    C7   C4   C2     0.41  30.0  2
 6VN  Var_06    C25  C14  C8   C9    52.79  30.0  2
 6VN  Var_07    H28  C22  C16  C15   60.65  30.0  3
 6VN  Var_08    H25  C23  C16  C15   59.72  30.0  3
 6VN  Var_09    H22  C25  C14  C8   -64.64  30.0  3
 6VN  Var_10    H19  C24  C14  C8   -58.29  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
 6VN  chir_01  C17  C19  C15  N1   negativ
 6VN  chir_02  C20  C19  C18  C21  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
 6VN  plan-1  C8   0.020
 6VN  plan-1  C9   0.020
 6VN  plan-1  C10  0.020
 6VN  plan-1  C11  0.020
 6VN  plan-1  C12  0.020
 6VN  plan-1  C13  0.020
 6VN  plan-1  N2   0.020
 6VN  plan-1  H3   0.020
 6VN  plan-1  H4   0.020
 6VN  plan-1  H5   0.020
 6VN  plan-1  H6   0.020
 6VN  plan-1  C14  0.020
 6VN  plan-2  C1   0.020
 6VN  plan-2  C2   0.020
 6VN  plan-2  C3   0.020
 6VN  plan-2  C4   0.020
 6VN  plan-2  C17  0.020
 6VN  plan-2  N1   0.020
 6VN  plan-2  C5   0.020
 6VN  plan-2  C7   0.020
 6VN  plan-2  C    0.020
 6VN  plan-2  N    0.020
 6VN  plan-2  C6   0.020
 6VN  plan-2  N2   0.020
 6VN  plan-2  H1   0.020
 6VN  plan-2  H2   0.020
 6VN  plan-2  H31  0.020
 6VN  plan-3  C4   0.020
 6VN  plan-3  C7   0.020
 6VN  plan-3  O1   0.020
 6VN  plan-3  O    0.020

