# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:25:12 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: 2-chloranyl-1~{H}-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1[nH]c2ccccc2n1
#
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
 98K  98K  2-chloranyl-1~{H}-benzimidazole  ligand  15  10  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_98K
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
 98K  CL   CL  CL    0  -0.072  185.4600  283.2973  106.9935
 98K  C02  C   CR5   0   0.366  185.7010  283.9614  108.5393
 98K  N03  N   NR15  0  -0.665  185.2616  285.2067  108.8286
 98K  C04  C   CR56  0   0.354  185.6088  285.4408  110.1353
 98K  C05  C   CR16  0  -0.300  185.4247  286.5313  110.9758
 98K  C06  C   CR16  0  -0.274  185.9196  286.4089  112.2624
 98K  C07  C   CR16  0  -0.266  186.5722  285.2432  112.6916
 98K  C08  C   CR16  0  -0.329  186.7505  284.1623  111.8475
 98K  C09  C   CR56  0   0.148  186.2582  284.2658  110.5479
 98K  N10  N   N     0  -0.434  186.2962  283.3555  109.5136
 98K  H1   H   HNR5  0   0.431  184.7807  285.8337  108.2009
 98K  H2   H   HCR6  0   0.270  184.9218  287.4302  110.6451
 98K  H3   H   HCR6  0   0.258  185.8007  287.2322  112.9545
 98K  H4   H   HCR6  0   0.255  186.9434  285.1925  113.7068
 98K  H5   H   HCR6  0   0.258  187.2547  283.2643  112.1802

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
 98K  CL   C02  single    1.700  0.020  1.700
 98K  C02  N03  aromatic  1.352  0.020  1.352
 98K  C02  N10  aromatic  1.292  0.020  1.292
 98K  N03  C04  aromatic  1.372  0.020  1.372
 98K  N10  C09  aromatic  1.378  0.020  1.378
 98K  C04  C09  aromatic  1.405  0.020  1.405
 98K  C04  C05  aromatic  1.389  0.020  1.389
 98K  C09  C08  aromatic  1.394  0.020  1.394
 98K  C05  C06  aromatic  1.384  0.020  1.384
 98K  C08  C07  aromatic  1.383  0.020  1.383
 98K  C06  C07  aromatic  1.403  0.020  1.403
 98K  N03  H1   single    0.860  0.020  1.020
 98K  C05  H2   single    0.930  0.020  1.080
 98K  C06  H3   single    0.930  0.020  1.080
 98K  C07  H4   single    0.930  0.020  1.080
 98K  C08  H5   single    0.930  0.020  1.080

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
 98K  N10  C02  N03  114.85  3.000
 98K  N10  C02  CL   124.59  3.000
 98K  N03  C02  CL   120.56  3.000
 98K  H1   N03  C04  127.36  3.000
 98K  H1   N03  C02  126.45  3.000
 98K  C04  N03  C02  106.18  3.000
 98K  C09  C04  C05  122.71  3.000
 98K  C05  C04  N03  132.58  3.000
 98K  C09  C04  N03  104.71  3.000
 98K  H2   C05  C06  121.59  3.000
 98K  H2   C05  C04  121.94  3.000
 98K  C06  C05  C04  116.47  3.000
 98K  H3   C06  C07  119.18  3.000
 98K  H3   C06  C05  119.21  3.000
 98K  C07  C06  C05  121.61  3.000
 98K  H4   C07  C08  119.45  3.000
 98K  H4   C07  C06  119.04  3.000
 98K  C08  C07  C06  121.51  3.000
 98K  H5   C08  C09  120.85  3.000
 98K  H5   C08  C07  121.40  3.000
 98K  C09  C08  C07  117.75  3.000
 98K  N10  C09  C08  129.87  3.000
 98K  C08  C09  C04  119.96  3.000
 98K  N10  C09  C04  110.17  3.000
 98K  C09  N10  C02  104.09  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
 98K  CONST_01  C09  C04  N03  C02    0.00  0.0  0
 98K  CONST_02  C05  C04  N03  C02  180.00  0.0  0
 98K  CONST_03  C04  C09  N10  C02    0.00  0.0  0
 98K  CONST_04  C08  C09  N10  C02  180.00  0.0  0
 98K  CONST_05  C09  N10  C02  N03    0.00  0.0  0
 98K  CONST_06  N10  C09  C04  N03    0.00  0.0  0
 98K  CONST_07  C08  C09  C04  N03  180.00  0.0  0
 98K  CONST_08  C06  C05  C04  N03  180.00  0.0  0
 98K  CONST_09  N10  C02  N03  C04    0.00  0.0  0
 98K  CONST_10  C07  C08  C09  C04    0.00  0.0  0
 98K  CONST_11  C07  C06  C05  C04    0.00  0.0  0
 98K  CONST_12  N10  C09  C04  C05  180.00  0.0  0
 98K  CONST_13  C08  C09  C04  C05    0.00  0.0  0
 98K  CONST_14  C08  C07  C06  C05    0.00  0.0  0
 98K  CONST_15  C09  C04  C05  C06    0.00  0.0  0
 98K  CONST_16  C09  C08  C07  C06    0.00  0.0  0
 98K  CONST_17  N10  C09  C08  C07  180.00  0.0  0
 98K  CONST_18  C04  N03  C02  CL   180.00  0.0  0
 98K  CONST_19  C09  N10  C02  CL   180.00  0.0  0
 98K  CONST_20  H2   C05  C04  N03    0.00  0.0  0
 98K  CONST_21  H5   C08  C09  C04  180.00  0.0  0
 98K  CONST_22  H3   C06  C05  C04  180.00  0.0  0
 98K  CONST_23  H1   N03  C04  C05    0.00  0.0  0
 98K  CONST_24  H4   C07  C06  C05  180.00  0.0  0

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
 98K  plan-1  CL   0.020
 98K  plan-1  C02  0.020
 98K  plan-1  N03  0.020
 98K  plan-1  C04  0.020
 98K  plan-1  C05  0.020
 98K  plan-1  C06  0.020
 98K  plan-1  C07  0.020
 98K  plan-1  C08  0.020
 98K  plan-1  C09  0.020
 98K  plan-1  N10  0.020
 98K  plan-1  H1   0.020
 98K  plan-1  H2   0.020
 98K  plan-1  H3   0.020
 98K  plan-1  H4   0.020
 98K  plan-1  H5   0.020

