# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 07:17:54 2021
#   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  34  18  .  2022-03-23  2022-11-17
;
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   0.144  -28.7023  -72.2926  33.1875
 Q8G  C06  C  C     0   0.535  -26.1144  -72.3604  30.4626
 Q8G  C18  C  C     0  -0.455  -34.7940  -73.9946  32.5891
 Q8G  C17  C  C     0  -0.451  -33.6885  -74.9212  32.0990
 Q8G  C16  C  C     0  -0.434  -34.4691  -72.5294  32.2535
 Q8G  C15  C  C     0  -0.458  -32.9570  -72.2694  32.1779
 Q8G  C11  C  CR16  0  -0.278  -28.5175  -72.9409  30.5092
 Q8G  C02  C  CR15  0   0.109  -30.3102  -72.3336  34.5576
 Q8G  C04  C  CR56  0   0.353  -29.8242  -72.7533  32.4723
 Q8G  N01  N  NR5   0  -0.523  -30.8443  -72.7687  33.3844
 Q8G  N03  N  N     0  -0.466  -29.0456  -72.0400  34.4933
 Q8G  C07  C  CR6   0  -0.110  -27.3858  -72.4802  31.2104
 Q8G  C08  C  CR16  0  -0.335  -27.4718  -72.1534  32.5576
 Q8G  C09  C  CR16  0  -0.283  -29.7442  -73.0852  31.1202
 Q8G  C10  C  CR16  0  -0.089  -32.2372  -73.1505  33.1935
 Q8G  O12  O  O     0  -0.445  -25.9920  -72.6262  29.2893
 Q8G  O13  O  OH1   0  -0.597  -25.1065  -71.9284  31.2110
 Q8G  C14  C  C     0  -0.440  -32.3762  -74.6403  32.8409
 Q8G  H2   H  H     0   0.224  -34.9059  -74.1179  33.6709
 Q8G  H3   H  H     0   0.240  -33.9676  -75.9671  32.2370
 Q8G  H4   H  H     0   0.225  -33.5493  -74.7821  31.0232
 Q8G  H5   H  H     0   0.233  -34.9192  -72.2560  31.2974
 Q8G  H6   H  H     0   0.232  -34.9167  -71.8736  33.0033
 Q8G  H7   H  H     0   0.234  -32.5926  -72.4841  31.1702
 Q8G  H8   H  H     0   0.254  -32.7409  -71.2173  32.3717
 Q8G  H9   H  HCR6  0   0.265  -28.4225  -73.1889  29.4612
 Q8G  H10  H  HCR5  0   0.293  -30.9224  -72.2558  35.4453
 Q8G  H11  H  HCR6  0   0.268  -26.6172  -71.7997  33.1181
 Q8G  H12  H  HCR6  0   0.272  -30.5943  -73.4445  30.5575
 Q8G  H13  H  HCR6  0   0.271  -32.7028  -72.9716  34.1657
 Q8G  H14  H  HOH1  0   0.486  -24.3010  -71.8729  30.6762
 Q8G  H15  H  H     0   0.245  -32.3327  -75.2252  33.7621
 Q8G  H16  H  H     0   0.243  -31.5322  -74.9667  32.2304
 Q8G  H1   H  H     0   0.238  -35.7541  -74.2744  32.1523

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  double    1.209  0.020  1.209
 Q8G  C06  C07  single    1.480  0.020  1.480
 Q8G  C06  O13  single    1.328  0.020  1.328
 Q8G  C11  C07  aromatic  1.409  0.020  1.409
 Q8G  C11  C09  aromatic  1.378  0.020  1.378
 Q8G  C07  C08  aromatic  1.389  0.020  1.389
 Q8G  C09  C04  aromatic  1.395  0.020  1.395
 Q8G  C17  C18  single    1.524  0.020  1.524
 Q8G  C17  C14  single    1.533  0.020  1.533
 Q8G  C18  C16  single    1.538  0.020  1.538
 Q8G  C16  C15  single    1.536  0.020  1.536
 Q8G  C15  C10  single    1.525  0.020  1.525
 Q8G  C04  C05  aromatic  1.408  0.020  1.408
 Q8G  C04  N01  aromatic  1.368  0.020  1.368
 Q8G  C08  C05  aromatic  1.389  0.020  1.389
 Q8G  C14  C10  single    1.537  0.020  1.537
 Q8G  C05  N03  aromatic  1.374  0.020  1.374
 Q8G  C10  N01  single    1.457  0.020  1.457
 Q8G  N01  C02  aromatic  1.360  0.020  1.360
 Q8G  N03  C02  aromatic  1.300  0.020  1.300
 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  O13  H14  single    0.850  0.020  0.980
 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  129.34  3.000
 Q8G  N03  C05  C04  110.11  3.000
 Q8G  C08  C05  C04  120.55  3.000
 Q8G  O13  C06  O12  122.79  3.000
 Q8G  O13  C06  C07  113.19  3.000
 Q8G  O12  C06  C07  124.02  3.000
 Q8G  H2   C18  H1   106.07  3.000
 Q8G  H2   C18  C16  110.16  3.000
 Q8G  H1   C18  C16  110.05  3.000
 Q8G  H2   C18  C17  108.88  3.000
 Q8G  H1   C18  C17  110.71  3.000
 Q8G  C16  C18  C17  110.85  3.000
 Q8G  H4   C17  H3   106.19  3.000
 Q8G  H4   C17  C14  110.10  3.000
 Q8G  H3   C17  C14  109.47  3.000
 Q8G  H4   C17  C18  109.35  3.000
 Q8G  H3   C17  C18  110.90  3.000
 Q8G  C14  C17  C18  110.73  3.000
 Q8G  H6   C16  H5   106.38  3.000
 Q8G  H6   C16  C15  109.61  3.000
 Q8G  H5   C16  C15  108.69  3.000
 Q8G  H6   C16  C18  109.61  3.000
 Q8G  H5   C16  C18  110.04  3.000
 Q8G  C15  C16  C18  112.33  3.000
 Q8G  H8   C15  H7   106.69  3.000
 Q8G  H8   C15  C10  110.20  3.000
 Q8G  H7   C15  C10  110.06  3.000
 Q8G  H8   C15  C16  110.45  3.000
 Q8G  H7   C15  C16  109.90  3.000
 Q8G  C10  C15  C16  109.51  3.000
 Q8G  H9   C11  C09  118.94  3.000
 Q8G  H9   C11  C07  119.14  3.000
 Q8G  C09  C11  C07  121.92  3.000
 Q8G  H10  C02  N03  125.11  3.000
 Q8G  H10  C02  N01  120.58  3.000
 Q8G  N03  C02  N01  114.30  3.000
 Q8G  C09  C04  N01  133.34  3.000
 Q8G  N01  C04  C05  105.02  3.000
 Q8G  C09  C04  C05  121.65  3.000
 Q8G  C10  N01  C04  128.92  3.000
 Q8G  C10  N01  C02  124.90  3.000
 Q8G  C04  N01  C02  106.17  3.000
 Q8G  C02  N03  C05  104.40  3.000
 Q8G  C08  C07  C11  120.66  3.000
 Q8G  C08  C07  C06  121.62  3.000
 Q8G  C11  C07  C06  117.72  3.000
 Q8G  H11  C08  C07  122.05  3.000
 Q8G  H11  C08  C05  119.85  3.000
 Q8G  C07  C08  C05  118.10  3.000
 Q8G  H12  C09  C04  122.60  3.000
 Q8G  H12  C09  C11  120.27  3.000
 Q8G  C04  C09  C11  117.13  3.000
 Q8G  H13  C10  C14  108.92  3.000
 Q8G  H13  C10  N01  104.35  3.000
 Q8G  C14  C10  N01  111.75  3.000
 Q8G  H13  C10  C15  107.26  3.000
 Q8G  N01  C10  C15  112.77  3.000
 Q8G  C14  C10  C15  111.38  3.000
 Q8G  H14  O13  C06  109.81  3.000
 Q8G  H16  C14  H15  106.31  3.000
 Q8G  H16  C14  C10  110.37  3.000
 Q8G  H15  C14  C10  108.79  3.000
 Q8G  H16  C14  C17  109.65  3.000
 Q8G  H15  C14  C17  110.12  3.000
 Q8G  C10  C14  C17  111.46  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  CONST_27  H14  O13  C06  C07  180.00   0.0  0
 Q8G  Var_01    C10  C14  C17  C18  -33.34  30.0  1
 Q8G  Var_02    C10  C15  C16  C18  -33.98  30.0  1
 Q8G  Var_03    C15  C16  C18  C17  -28.11  30.0  1
 Q8G  Var_04    C14  C17  C18  C16   64.54  30.0  1
 Q8G  Var_05    O12  C06  C07  C11    0.42  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
 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
 Q8G  plan-2  H14  0.020

