# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 20:57:32 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2n(cnc2c1)C3CCCCC3
#
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
 Q8G  Q8G  '1-cyclohexyl-1H-benzimidazole-5-carboxylic acid'  ligand  33  18  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q8G
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
 Q8G  C05  C  CR56   0   0.140  -28.7127  -72.2962  33.2453
 Q8G  C06  C  C      0   0.397  -26.0496  -72.2840  30.5306
 Q8G  C18  C  CH2    0  -0.451  -34.7839  -74.0264  32.5549
 Q8G  C17  C  CH2    0  -0.449  -33.6554  -74.9205  32.0574
 Q8G  C16  C  CH2    0  -0.432  -34.4722  -72.5472  32.2754
 Q8G  C15  C  CH2    0  -0.458  -32.9633  -72.2641  32.2400
 Q8G  C11  C  CR16   0  -0.307  -28.5252  -72.8696  30.5565
 Q8G  C02  C  CR15   0   0.095  -30.3196  -72.3774  34.6226
 Q8G  C04  C  CR56   0   0.326  -29.8355  -72.7377  32.5238
 Q8G  N01  N  NR5    0  -0.519  -30.8564  -72.7809  33.4419
 Q8G  N03  N  N      0  -0.473  -29.0545  -72.0790  34.5612
 Q8G  C07  C  CR6    0  -0.121  -27.3841  -72.4328  31.2562
 Q8G  C08  C  CR16   0  -0.376  -27.4826  -72.1444  32.6085
 Q8G  C09  C  CR16   0  -0.291  -29.7557  -73.0316  31.1640
 Q8G  C10  C  CH1    0  -0.086  -32.2434  -73.1680  33.2362
 Q8G  O12  O  O      0  -0.591  -26.0467  -72.5345  29.3091
 Q8G  O13  O  OC    -1  -0.589  -25.0760  -71.9269  31.2225
 Q8G  C14  C  CH2    0  -0.438  -32.3656  -74.6499  32.8402
 Q8G  H3   H  HCH2   0   0.237  -33.9248  -75.9743  32.1464
 Q8G  H4   H  HCH2   0   0.224  -33.4917  -74.7367  30.9915
 Q8G  H5   H  HCH2   0   0.230  -34.9075  -72.2495  31.3197
 Q8G  H6   H  HCH2   0   0.229  -34.9453  -71.9231  33.0364
 Q8G  H7   H  HCH2   0   0.237  -32.5747  -72.4342  31.2332
 Q8G  H8   H  HCH2   0   0.248  -32.7688  -71.2167  32.4770
 Q8G  H9   H  HCR6   0   0.238  -28.4317  -73.0888  29.5017
 Q8G  H10  H  HCR5   0   0.282  -30.9291  -72.3243  35.5144
 Q8G  H11  H  HCR6   0   0.237  -26.6164  -71.8071  33.1628
 Q8G  H12  H  HCR6   0   0.260  -30.6088  -73.3747  30.5943
 Q8G  H13  H  HCH1   0   0.266  -32.7202  -73.0244  34.2097
 Q8G  H15  H  HCH2   0   0.240  -32.3402  -75.2574  33.7475
 Q8G  H16  H  HCH2   0   0.242  -31.5034  -74.9526  32.2432
 Q8G  H1   H  HCH2   0   0.236  -35.7314  -74.3038  32.0897
 Q8G  H2   H  HCH2   0   0.222  -34.9153  -74.1870  33.6292

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
 Q8G  O12  C06  deloc     1.247  0.020  1.247
 Q8G  C06  C07  single    1.526  0.020  1.526
 Q8G  C06  O13  deloc     1.247  0.020  1.247
 Q8G  C11  C07  aromatic  1.408  0.020  1.408
 Q8G  C11  C09  aromatic  1.382  0.020  1.382
 Q8G  C07  C08  aromatic  1.386  0.020  1.386
 Q8G  C09  C04  aromatic  1.394  0.020  1.394
 Q8G  C17  C18  single    1.523  0.020  1.523
 Q8G  C17  C14  single    1.533  0.020  1.533
 Q8G  C18  C16  single    1.537  0.020  1.537
 Q8G  C16  C15  single    1.536  0.020  1.536
 Q8G  C15  C10  single    1.526  0.020  1.526
 Q8G  C04  C05  aromatic  1.406  0.020  1.406
 Q8G  C04  N01  aromatic  1.374  0.020  1.374
 Q8G  C08  C05  aromatic  1.393  0.020  1.393
 Q8G  C14  C10  single    1.539  0.020  1.539
 Q8G  C05  N03  aromatic  1.377  0.020  1.377
 Q8G  C10  N01  single    1.455  0.020  1.455
 Q8G  N01  C02  aromatic  1.358  0.020  1.358
 Q8G  N03  C02  aromatic  1.301  0.020  1.301
 Q8G  C18  H1   single    0.970  0.020  1.090
 Q8G  C18  H2   single    0.970  0.020  1.090
 Q8G  C17  H3   single    0.970  0.020  1.090
 Q8G  C17  H4   single    0.970  0.020  1.090
 Q8G  C16  H5   single    0.970  0.020  1.090
 Q8G  C16  H6   single    0.970  0.020  1.090
 Q8G  C15  H7   single    0.970  0.020  1.090
 Q8G  C15  H8   single    0.970  0.020  1.090
 Q8G  C11  H9   single    0.930  0.020  1.080
 Q8G  C02  H10  single    0.930  0.020  1.080
 Q8G  C08  H11  single    0.930  0.020  1.080
 Q8G  C09  H12  single    0.930  0.020  1.080
 Q8G  C10  H13  single    0.970  0.020  1.090
 Q8G  C14  H15  single    0.970  0.020  1.090
 Q8G  C14  H16  single    0.970  0.020  1.090

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
 Q8G  C08  C05  N03  129.69  3.000
 Q8G  N03  C05  C04  109.99  3.000
 Q8G  C08  C05  C04  120.32  3.000
 Q8G  O13  C06  O12  126.82  3.000
 Q8G  O13  C06  C07  116.55  3.000
 Q8G  O12  C06  C07  116.63  3.000
 Q8G  H2   C18  H1   106.08  3.000
 Q8G  H2   C18  C16  110.13  3.000
 Q8G  H1   C18  C16  110.06  3.000
 Q8G  H2   C18  C17  108.87  3.000
 Q8G  H1   C18  C17  110.78  3.000
 Q8G  C16  C18  C17  110.81  3.000
 Q8G  H4   C17  H3   106.18  3.000
 Q8G  H4   C17  C14  110.00  3.000
 Q8G  H3   C17  C14  109.66  3.000
 Q8G  H4   C17  C18  109.30  3.000
 Q8G  H3   C17  C18  110.94  3.000
 Q8G  C14  C17  C18  110.67  3.000
 Q8G  H6   C16  H5   106.35  3.000
 Q8G  H6   C16  C15  109.66  3.000
 Q8G  H5   C16  C15  108.75  3.000
 Q8G  H6   C16  C18  109.59  3.000
 Q8G  H5   C16  C18  109.92  3.000
 Q8G  C15  C16  C18  112.38  3.000
 Q8G  H8   C15  H7   106.63  3.000
 Q8G  H8   C15  C10  110.04  3.000
 Q8G  H7   C15  C10  109.98  3.000
 Q8G  H8   C15  C16  110.31  3.000
 Q8G  H7   C15  C16  110.00  3.000
 Q8G  C10  C15  C16  109.84  3.000
 Q8G  H9   C11  C09  118.82  3.000
 Q8G  H9   C11  C07  118.53  3.000
 Q8G  C09  C11  C07  122.66  3.000
 Q8G  H10  C02  N03  125.13  3.000
 Q8G  H10  C02  N01  120.58  3.000
 Q8G  N03  C02  N01  114.29  3.000
 Q8G  C09  C04  N01  133.48  3.000
 Q8G  N01  C04  C05  105.10  3.000
 Q8G  C09  C04  C05  121.42  3.000
 Q8G  C10  N01  C04  128.50  3.000
 Q8G  C10  N01  C02  125.36  3.000
 Q8G  C04  N01  C02  106.13  3.000
 Q8G  C02  N03  C05  104.49  3.000
 Q8G  C08  C07  C11  119.45  3.000
 Q8G  C08  C07  C06  120.37  3.000
 Q8G  C11  C07  C06  120.17  3.000
 Q8G  H11  C08  C07  120.50  3.000
 Q8G  H11  C08  C05  120.42  3.000
 Q8G  C07  C08  C05  119.07  3.000
 Q8G  H12  C09  C04  122.39  3.000
 Q8G  H12  C09  C11  120.52  3.000
 Q8G  C04  C09  C11  117.08  3.000
 Q8G  H13  C10  C14  108.72  3.000
 Q8G  H13  C10  N01  104.77  3.000
 Q8G  C14  C10  N01  111.62  3.000
 Q8G  H13  C10  C15  107.32  3.000
 Q8G  N01  C10  C15  112.62  3.000
 Q8G  C14  C10  C15  111.41  3.000
 Q8G  H16  C14  H15  106.37  3.000
 Q8G  H16  C14  C10  110.18  3.000
 Q8G  H15  C14  C10  108.66  3.000
 Q8G  H16  C14  C17  109.66  3.000
 Q8G  H15  C14  C17  110.22  3.000
 Q8G  C10  C14  C17  111.61  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
 Q8G  CONST_01  C11  C09  C04  C05    0.00   0.0  0
 Q8G  CONST_02  C02  N01  C04  C05    0.00   0.0  0
 Q8G  CONST_03  C11  C07  C08  C05    0.00   0.0  0
 Q8G  CONST_04  N01  C02  N03  C05    0.00   0.0  0
 Q8G  CONST_05  N01  C04  C09  C11  180.00   0.0  0
 Q8G  CONST_06  C09  C04  N01  C02  180.00   0.0  0
 Q8G  CONST_07  C04  C05  N03  C02    0.00   0.0  0
 Q8G  CONST_08  C08  C05  N03  C02  180.00   0.0  0
 Q8G  CONST_09  C07  C11  C09  C04    0.00   0.0  0
 Q8G  CONST_10  C07  C08  C05  C04    0.00   0.0  0
 Q8G  CONST_11  N03  C02  N01  C04    0.00   0.0  0
 Q8G  CONST_12  C08  C05  C04  N01  180.00   0.0  0
 Q8G  CONST_13  N03  C05  C04  N01    0.00   0.0  0
 Q8G  CONST_14  C09  C04  C05  N03  180.00   0.0  0
 Q8G  CONST_15  C07  C08  C05  N03  180.00   0.0  0
 Q8G  CONST_16  C09  C11  C07  C08    0.00   0.0  0
 Q8G  CONST_17  C09  C04  C05  C08    0.00   0.0  0
 Q8G  CONST_18  C10  N01  C04  C05  180.00   0.0  0
 Q8G  CONST_19  C10  N01  C02  N03  180.00   0.0  0
 Q8G  CONST_20  C10  N01  C04  C09    0.00   0.0  0
 Q8G  CONST_21  C06  C07  C08  C05  180.00   0.0  0
 Q8G  CONST_22  C09  C11  C07  C06  180.00   0.0  0
 Q8G  CONST_23  H12  C09  C04  C05  180.00   0.0  0
 Q8G  CONST_24  H10  C02  N03  C05  180.00   0.0  0
 Q8G  CONST_25  H11  C08  C07  C11  180.00   0.0  0
 Q8G  CONST_26  H9   C11  C09  C04  180.00   0.0  0
 Q8G  Var_01    C10  C14  C17  C18  -34.08  30.0  1
 Q8G  Var_02    C10  C15  C16  C18  -33.85  30.0  1
 Q8G  Var_03    C15  C16  C18  C17  -28.10  30.0  1
 Q8G  Var_04    C14  C17  C18  C16   64.76  30.0  1
 Q8G  Var_05    O12  C06  C07  C11    1.72  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
 Q8G  chir_01  C10  C15  C14  N01  negativ

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
 Q8G  plan-1  C05  0.020
 Q8G  plan-1  C06  0.020
 Q8G  plan-1  C11  0.020
 Q8G  plan-1  C02  0.020
 Q8G  plan-1  C04  0.020
 Q8G  plan-1  N01  0.020
 Q8G  plan-1  N03  0.020
 Q8G  plan-1  C07  0.020
 Q8G  plan-1  C08  0.020
 Q8G  plan-1  C09  0.020
 Q8G  plan-1  C10  0.020
 Q8G  plan-1  H9   0.020
 Q8G  plan-1  H10  0.020
 Q8G  plan-1  H11  0.020
 Q8G  plan-1  H12  0.020
 Q8G  plan-2  C06  0.020
 Q8G  plan-2  C07  0.020
 Q8G  plan-2  O12  0.020
 Q8G  plan-2  O13  0.020

