# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:27:05 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1[nH]c2cc(ccc2n1)c3c(Cl)cccc3OC(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
 XVD  XVD  6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol  ligand  30  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XVD
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
 XVD  N1   N   N     0  -0.516  245.6472  239.2025  142.4030
 XVD  C4   C   CR16  0  -0.282  239.3470  241.3095  146.5017
 XVD  C5   C   CR6   0   0.275  240.4851  240.8216  145.8854
 XVD  C6   C   CR6   0   0.090  240.9390  241.2868  144.6508
 XVD  C7   C   CR6   0   0.026  242.1600  240.7343  144.0220
 XVD  C8   C   CR16  0  -0.319  243.4027  240.9501  144.6086
 XVD  C10  C   CR56  0   0.150  244.4010  239.6338  142.7997
 XVD  C13  C   CR5   0   0.591  246.4545  239.6805  143.3036
 XVD  C1   C   CR6   0  -0.123  240.1793  242.2951  144.0564
 XVD  C11  C   CR16  0  -0.320  243.1526  239.4276  142.2234
 XVD  C12  C   CR16  0  -0.276  242.0466  239.9829  142.8439
 XVD  C14  C   CT    0   1.081  240.9374  238.5881  146.4649
 XVD  C2   C   CR16  0  -0.193  239.0280  242.7980  144.6425
 XVD  C3   C   CR16  0  -0.276  238.6150  242.3000  145.8669
 XVD  C9   C   CR56  0   0.357  244.5003  240.3920  143.9791
 XVD  F1   F   F     0  -0.298  239.7996  238.2942  147.0989
 XVD  F2   F   F     0  -0.276  241.9157  237.9022  147.0344
 XVD  F3   F   F     0  -0.295  240.7948  238.1694  145.2088
 XVD  N2   N   NR15  0  -0.715  245.8446  240.4009  144.2741
 XVD  O1   O   OH1   0  -0.587  247.7631  239.5302  143.3519
 XVD  CL1  CL  CL    0  -0.111  240.6900  242.9754  142.5497
 XVD  H2   H   HCR6  0   0.285  239.0444  240.9352  147.4702
 XVD  H3   H   HCR6  0   0.265  243.5038  241.5341  145.5143
 XVD  H4   H   HCR6  0   0.253  243.0463  238.8459  141.3171
 XVD  H5   H   HCR6  0   0.251  241.0658  239.8266  142.4131
 XVD  H6   H   HCR6  0   0.286  238.4670  243.5818  144.1526
 XVD  H7   H   HCR6  0   0.279  237.7221  242.6931  146.3331
 XVD  H8   H   HNR5  0   0.423  246.2941  240.8501  145.0576
 XVD  H1   H   HOH1  0   0.492  248.0535  238.9897  142.6047
 XVD  O2   O   O2    0  -0.516  241.2592  239.8852  146.5525

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
 XVD  N1   C10  aromatic  1.377  0.020  1.377
 XVD  N1   C13  aromatic  1.301  0.020  1.301
 XVD  C11  C10  aromatic  1.390  0.020  1.390
 XVD  C11  C12  aromatic  1.384  0.020  1.384
 XVD  CL1  C1   single    1.730  0.020  1.730
 XVD  O1   C13  single    1.318  0.020  1.318
 XVD  C10  C9   aromatic  1.406  0.020  1.406
 XVD  C13  N2   aromatic  1.354  0.020  1.354
 XVD  C12  C7   aromatic  1.402  0.020  1.402
 XVD  C9   N2   aromatic  1.376  0.020  1.376
 XVD  C9   C8   aromatic  1.383  0.020  1.383
 XVD  C7   C8   aromatic  1.391  0.020  1.391
 XVD  C7   C6   single    1.480  0.020  1.480
 XVD  C1   C6   aromatic  1.395  0.020  1.395
 XVD  C1   C2   aromatic  1.386  0.020  1.386
 XVD  C6   C5   aromatic  1.395  0.020  1.395
 XVD  C2   C3   aromatic  1.385  0.020  1.385
 XVD  F3   C14  single    1.332  0.020  1.332
 XVD  C5   O2   single    1.386  0.020  1.386
 XVD  C5   C4   aromatic  1.383  0.020  1.383
 XVD  C3   C4   aromatic  1.386  0.020  1.386
 XVD  C14  F2   single    1.324  0.020  1.324
 XVD  C14  O2   single    1.339  0.020  1.339
 XVD  C14  F1   single    1.335  0.020  1.335
 XVD  C4   H2   single    0.930  0.020  1.080
 XVD  C8   H3   single    0.930  0.020  1.080
 XVD  C11  H4   single    0.930  0.020  1.080
 XVD  C12  H5   single    0.930  0.020  1.080
 XVD  C2   H6   single    0.930  0.020  1.080
 XVD  C3   H7   single    0.930  0.020  1.080
 XVD  N2   H8   single    0.860  0.020  1.020
 XVD  O1   H1   single    0.850  0.020  0.980

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
 XVD  C13  N1   C10  104.31  3.000
 XVD  H2   C4   C3   120.66  3.000
 XVD  H2   C4   C5   120.48  3.000
 XVD  C3   C4   C5   118.86  3.000
 XVD  O2   C5   C6   118.00  3.000
 XVD  O2   C5   C4   118.90  3.000
 XVD  C6   C5   C4   122.98  3.000
 XVD  C1   C6   C7   122.53  3.000
 XVD  C1   C6   C5   116.16  3.000
 XVD  C7   C6   C5   121.31  3.000
 XVD  C12  C7   C8   120.65  3.000
 XVD  C8   C7   C6   119.99  3.000
 XVD  C12  C7   C6   119.36  3.000
 XVD  H3   C8   C9   121.63  3.000
 XVD  H3   C8   C7   121.33  3.000
 XVD  C9   C8   C7   117.03  3.000
 XVD  C9   C10  C11  119.42  3.000
 XVD  C9   C10  N1   110.29  3.000
 XVD  C11  C10  N1   130.29  3.000
 XVD  O1   C13  N2   118.79  3.000
 XVD  N2   C13  N1   114.35  3.000
 XVD  O1   C13  N1   126.86  3.000
 XVD  CL1  C1   C2   118.08  3.000
 XVD  C2   C1   C6   122.28  3.000
 XVD  CL1  C1   C6   119.63  3.000
 XVD  H4   C11  C12  120.83  3.000
 XVD  H4   C11  C10  121.00  3.000
 XVD  C12  C11  C10  118.17  3.000
 XVD  H5   C12  C11  119.18  3.000
 XVD  H5   C12  C7   119.02  3.000
 XVD  C11  C12  C7   121.80  3.000
 XVD  O2   C14  F3   113.07  3.000
 XVD  O2   C14  F2   107.22  3.000
 XVD  F3   C14  F2   108.79  3.000
 XVD  O2   C14  F1   112.77  3.000
 XVD  F2   C14  F1   108.15  3.000
 XVD  F3   C14  F1   106.71  3.000
 XVD  H6   C2   C3   120.43  3.000
 XVD  H6   C2   C1   120.15  3.000
 XVD  C3   C2   C1   119.41  3.000
 XVD  H7   C3   C2   119.79  3.000
 XVD  H7   C3   C4   119.91  3.000
 XVD  C2   C3   C4   120.30  3.000
 XVD  N2   C9   C10  104.62  3.000
 XVD  N2   C9   C8   132.45  3.000
 XVD  C10  C9   C8   122.93  3.000
 XVD  H8   N2   C9   127.20  3.000
 XVD  H8   N2   C13  126.37  3.000
 XVD  C9   N2   C13  106.43  3.000
 XVD  H1   O1   C13  109.49  3.000
 XVD  C14  O2   C5   119.25  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
 XVD  CONST_01  C12  C11  C10  N1   180.00   0.0  0
 XVD  CONST_02  N2   C9   C10  N1     0.00   0.0  0
 XVD  CONST_03  C8   C9   C10  N1   180.00   0.0  0
 XVD  CONST_04  C9   N2   C13  N1     0.00   0.0  0
 XVD  CONST_05  C7   C6   C5   C4   180.00   0.0  0
 XVD  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 XVD  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 XVD  CONST_10  C2   C1   C6   C5     0.00   0.0  0
 XVD  CONST_11  C2   C3   C4   C5     0.00   0.0  0
 XVD  CONST_12  C11  C12  C7   C6   180.00   0.0  0
 XVD  CONST_13  C9   C8   C7   C6   180.00   0.0  0
 XVD  CONST_14  C3   C2   C1   C6     0.00   0.0  0
 XVD  CONST_15  C3   C4   C5   C6     0.00   0.0  0
 XVD  CONST_16  C10  C11  C12  C7     0.00   0.0  0
 XVD  CONST_17  C10  C9   C8   C7     0.00   0.0  0
 XVD  CONST_18  N2   C9   C8   C7   180.00   0.0  0
 XVD  CONST_19  C2   C1   C6   C7   180.00   0.0  0
 XVD  CONST_20  C11  C10  C9   C8     0.00   0.0  0
 XVD  CONST_21  C13  N2   C9   C8   180.00   0.0  0
 XVD  CONST_22  C11  C12  C7   C8     0.00   0.0  0
 XVD  CONST_24  N2   C13  N1   C10    0.00   0.0  0
 XVD  CONST_25  C13  N2   C9   C10    0.00   0.0  0
 XVD  CONST_26  C11  C10  N1   C13  180.00   0.0  0
 XVD  CONST_27  C9   C10  N1   C13    0.00   0.0  0
 XVD  CONST_29  N2   C9   C10  C11  180.00   0.0  0
 XVD  CONST_30  C9   C10  C11  C12    0.00   0.0  0
 XVD  CONST_31  C9   C8   C7   C12    0.00   0.0  0
 XVD  CONST_32  CL1  C1   C6   C5   180.00   0.0  0
 XVD  CONST_33  CL1  C1   C6   C7     0.00   0.0  0
 XVD  CONST_34  O2   C5   C6   C7     0.00   0.0  0
 XVD  CONST_35  O1   C13  N1   C10  180.00   0.0  0
 XVD  CONST_36  O2   C5   C6   C1   180.00   0.0  0
 XVD  CONST_37  CL1  C1   C2   C3   180.00   0.0  0
 XVD  CONST_38  O2   C5   C4   C3   180.00   0.0  0
 XVD  CONST_39  O1   C13  N2   C9   180.00   0.0  0
 XVD  CONST_40  H4   C11  C10  N1     0.00   0.0  0
 XVD  CONST_41  H8   N2   C13  N1   180.00   0.0  0
 XVD  CONST_42  H6   C2   C3   C4   180.00   0.0  0
 XVD  CONST_43  H7   C3   C4   C5   180.00   0.0  0
 XVD  CONST_44  H5   C12  C7   C6     0.00   0.0  0
 XVD  CONST_45  H3   C8   C7   C6     0.00   0.0  0
 XVD  CONST_46  H2   C4   C5   C6   180.00   0.0  0
 XVD  Var_01    F3   C14  O2   C5    52.12  30.0  3

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
 XVD  plan-1  C4   0.020
 XVD  plan-1  C5   0.020
 XVD  plan-1  C6   0.020
 XVD  plan-1  C7   0.020
 XVD  plan-1  C1   0.020
 XVD  plan-1  C2   0.020
 XVD  plan-1  C3   0.020
 XVD  plan-1  CL1  0.020
 XVD  plan-1  H2   0.020
 XVD  plan-1  H6   0.020
 XVD  plan-1  H7   0.020
 XVD  plan-1  O2   0.020
 XVD  plan-2  N1   0.020
 XVD  plan-2  C6   0.020
 XVD  plan-2  C7   0.020
 XVD  plan-2  C8   0.020
 XVD  plan-2  C10  0.020
 XVD  plan-2  C13  0.020
 XVD  plan-2  C11  0.020
 XVD  plan-2  C12  0.020
 XVD  plan-2  C9   0.020
 XVD  plan-2  N2   0.020
 XVD  plan-2  O1   0.020
 XVD  plan-2  H3   0.020
 XVD  plan-2  H4   0.020
 XVD  plan-2  H5   0.020
 XVD  plan-2  H8   0.020

