# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:50:11 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (5,6-dichloro-1H-benzimidazol-2-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1[nH]c2cc(Cl)c(Cl)cc2n1
#
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
 6B1  6B1  (5,6-dichloro-1H-benzimidazol-2-yl)methanol  ligand  19  13  .  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_6B1
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
 6B1  C12  C   CR6   0  -0.044   1.4354  -0.7608  -0.0089
 6B1  C11  C   CR16  0  -0.281   0.1966  -1.3447  -0.1012
 6B1  C10  C   CR56  0   0.274  -0.9081  -0.5264  -0.1036
 6B1  CL2  CL  CL    0  -0.079   2.8058  -1.8185   0.0229
 6B1  C02  C   CR6   0   0.015   1.5656   0.6245   0.0793
 6B1  CL1  CL  CL    0  -0.136   3.1482   1.2738   0.2471
 6B1  C04  C   CR56  0   0.213  -0.7861   0.8795  -0.0609
 6B1  C03  C   CR16  0  -0.270   0.4763   1.4814   0.0311
 6B1  N09  N   NR15  0  -0.650  -2.2716  -0.8018  -0.1323
 6B1  C06  C   CR5   0   0.362  -2.8879   0.3852  -0.0926
 6B1  N05  N   N     0  -0.455  -2.0591   1.4007  -0.0904
 6B1  C07  C   CH2   0  -0.201  -4.3551   0.4772  -0.1426
 6B1  O08  O   OH1   0  -0.656  -4.9155  -0.7883   0.0323
 6B1  H1   H   HCR6  0   0.270   0.1015  -2.4254  -0.1448
 6B1  H2   H   HCR6  0   0.277   0.6001   2.5550   0.1029
 6B1  H3   H   HNR5  0   0.421  -2.7306  -1.6927  -0.1505
 6B1  H5   H   HCH2  0   0.241  -4.6820   1.2137   0.5856
 6B1  H6   H   HCH2  0   0.255  -4.6625   0.8904  -1.1098
 6B1  H7   H   HOH1  0   0.444  -5.1433  -0.8718   0.9751

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
 6B1  CL2  C12  single    1.731  0.020  1.731
 6B1  C12  C11  aromatic  1.373  0.020  1.373
 6B1  C12  C02  aromatic  1.394  0.020  1.394
 6B1  C11  C10  aromatic  1.375  0.020  1.375
 6B1  CL1  C02  single    1.719  0.020  1.719
 6B1  C02  C03  aromatic  1.387  0.020  1.387
 6B1  C10  N09  aromatic  1.391  0.020  1.391
 6B1  C10  C04  aromatic  1.412  0.020  1.412
 6B1  N09  C06  aromatic  1.338  0.020  1.338
 6B1  C03  C04  aromatic  1.402  0.020  1.402
 6B1  C04  N05  aromatic  1.376  0.020  1.376
 6B1  C06  N05  aromatic  1.311  0.020  1.311
 6B1  C06  C07  single    1.471  0.020  1.471
 6B1  C07  O08  single    1.395  0.020  1.395
 6B1  C11  H1   single    0.930  0.020  1.080
 6B1  C03  H2   single    0.930  0.020  1.080
 6B1  N09  H3   single    0.860  0.020  1.020
 6B1  C07  H5   single    0.970  0.020  1.090
 6B1  C07  H6   single    0.970  0.020  1.090
 6B1  O08  H7   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
 6B1  C02  C12  CL2  122.14  3.000
 6B1  C02  C12  C11  120.74  3.000
 6B1  CL2  C12  C11  117.11  3.000
 6B1  H1   C11  C10  121.47  3.000
 6B1  H1   C11  C12  120.34  3.000
 6B1  C10  C11  C12  118.18  3.000
 6B1  N09  C10  C04  106.40  3.000
 6B1  C04  C10  C11  121.55  3.000
 6B1  N09  C10  C11  132.04  3.000
 6B1  C03  C02  CL1  119.55  3.000
 6B1  C03  C02  C12  122.57  3.000
 6B1  CL1  C02  C12  117.87  3.000
 6B1  N05  C04  C03  132.23  3.000
 6B1  N05  C04  C10  107.26  3.000
 6B1  C03  C04  C10  120.49  3.000
 6B1  H2   C03  C04  122.21  3.000
 6B1  H2   C03  C02  121.36  3.000
 6B1  C04  C03  C02  116.39  3.000
 6B1  H3   N09  C06  125.32  3.000
 6B1  H3   N09  C10  128.68  3.000
 6B1  C06  N09  C10  105.97  3.000
 6B1  C07  C06  N05  125.61  3.000
 6B1  C07  C06  N09  120.92  3.000
 6B1  N05  C06  N09  113.34  3.000
 6B1  C06  N05  C04  106.95  3.000
 6B1  H6   C07  H5   104.57  3.000
 6B1  H6   C07  O08  109.88  3.000
 6B1  H5   C07  O08  114.22  3.000
 6B1  H6   C07  C06  109.48  3.000
 6B1  H5   C07  C06  108.65  3.000
 6B1  O08  C07  C06  109.86  3.000
 6B1  H7   O08  C07  107.05  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
 6B1  CONST_01  N09  C10  C11  C12  180.00   0.0  0
 6B1  CONST_02  C04  C10  C11  C12    0.00   0.0  0
 6B1  CONST_03  C04  C03  C02  C12    0.00   0.0  0
 6B1  CONST_04  C03  C02  C12  C11    0.00   0.0  0
 6B1  CONST_05  C06  N09  C10  C11  180.00   0.0  0
 6B1  CONST_06  C03  C04  C10  C11    0.00   0.0  0
 6B1  CONST_07  N05  C04  C10  C11  180.00   0.0  0
 6B1  CONST_08  C02  C12  C11  C10    0.00   0.0  0
 6B1  CONST_09  N05  C06  N09  C10    0.00   0.0  0
 6B1  CONST_10  C02  C03  C04  C10    0.00   0.0  0
 6B1  CONST_11  C06  N05  C04  C10    0.00   0.0  0
 6B1  CONST_12  N05  C04  C03  C02  180.00   0.0  0
 6B1  CONST_13  C06  N09  C10  C04    0.00   0.0  0
 6B1  CONST_14  N09  C06  N05  C04    0.00   0.0  0
 6B1  CONST_15  N09  C10  C04  C03  180.00   0.0  0
 6B1  CONST_16  C06  N05  C04  C03  180.00   0.0  0
 6B1  CONST_17  N05  C04  C10  N09    0.00   0.0  0
 6B1  CONST_18  CL1  C02  C12  C11  180.00   0.0  0
 6B1  CONST_19  CL2  C12  C11  C10  180.00   0.0  0
 6B1  CONST_20  C07  C06  N09  C10  180.00   0.0  0
 6B1  CONST_21  C03  C02  C12  CL2  180.00   0.0  0
 6B1  CONST_22  C04  C03  C02  CL1  180.00   0.0  0
 6B1  CONST_23  C07  C06  N05  C04  180.00   0.0  0
 6B1  CONST_24  H2   C03  C02  C12  180.00   0.0  0
 6B1  CONST_25  H3   N09  C10  C11    0.00   0.0  0
 6B1  CONST_26  H1   C11  C12  C02  180.00   0.0  0
 6B1  Var_01    O08  C07  C06  N09   11.53  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
 6B1  plan-1  C12  0.020
 6B1  plan-1  C11  0.020
 6B1  plan-1  C10  0.020
 6B1  plan-1  CL2  0.020
 6B1  plan-1  C02  0.020
 6B1  plan-1  CL1  0.020
 6B1  plan-1  C04  0.020
 6B1  plan-1  C03  0.020
 6B1  plan-1  N09  0.020
 6B1  plan-1  C06  0.020
 6B1  plan-1  N05  0.020
 6B1  plan-1  C07  0.020
 6B1  plan-1  H1   0.020
 6B1  plan-1  H2   0.020
 6B1  plan-1  H3   0.020

