# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:02:51 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 5-chloro-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2[nH]cnc2c1
#
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
 ES9  ES9  5-chloro-1H-benzimidazole  ligand  15  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ES9
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
 ES9  C10   C   CR16  0  -0.288  -0.4256   1.0038   0.0242
 ES9  CL01  CL  CL    0  -0.138  -3.0363   0.3438   0.0131
 ES9  C02   C   CR6   0  -0.050  -1.3383  -0.0306   0.0141
 ES9  C03   C   CR16  0  -0.240  -0.9585  -1.3797   0.0041
 ES9  C04   C   CR16  0  -0.298   0.3779  -1.7325   0.0035
 ES9  C05   C   CR56  0   0.341   1.3058  -0.6982   0.0131
 ES9  N06   N   NR15  0  -0.658   2.6728  -0.6702   0.0160
 ES9  C07   C   CR15  0   0.108   3.0439   0.6308   0.0276
 ES9  N08   N   N     0  -0.461   2.0375   1.4597   0.0325
 ES9  C09   C   CR56  0   0.132   0.9249   0.6546   0.0236
 ES9  H10   H   HCR6  0   0.278  -0.7371   2.0398   0.0334
 ES9  H03   H   HCR6  0   0.279  -1.7175  -2.1494  -0.0029
 ES9  H04   H   HCR6  0   0.279   0.6757  -2.7724  -0.0048
 ES9  HN06  H   HNR5  0   0.426   3.2975  -1.4608   0.0109
 ES9  H07   H   HCR5  0   0.291   4.0853   0.9154   0.0319

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
 ES9  C10   C02   aromatic  1.380  0.020  1.380
 ES9  C10   C09   aromatic  1.395  0.020  1.395
 ES9  CL01  C02   single    1.739  0.020  1.739
 ES9  C02   C03   aromatic  1.402  0.020  1.402
 ES9  C03   C04   aromatic  1.382  0.020  1.382
 ES9  C04   C05   aromatic  1.390  0.020  1.390
 ES9  C05   N06   aromatic  1.367  0.020  1.367
 ES9  C05   C09   aromatic  1.405  0.020  1.405
 ES9  N06   C07   aromatic  1.353  0.020  1.353
 ES9  C07   N08   aromatic  1.304  0.020  1.304
 ES9  N08   C09   aromatic  1.373  0.020  1.373
 ES9  C10   H10   single    0.930  0.020  1.080
 ES9  C03   H03   single    0.930  0.020  1.080
 ES9  C04   H04   single    0.930  0.020  1.080
 ES9  N06   HN06  single    0.860  0.020  1.020
 ES9  C07   H07   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
 ES9  H10   C10  C09   121.23  3.000
 ES9  H10   C10  C02   121.84  3.000
 ES9  C09   C10  C02   116.93  3.000
 ES9  C03   C02  CL01  118.16  3.000
 ES9  C03   C02  C10   122.85  3.000
 ES9  CL01  C02  C10   118.99  3.000
 ES9  H03   C03  C04   119.81  3.000
 ES9  H03   C03  C02   119.67  3.000
 ES9  C04   C03  C02   120.51  3.000
 ES9  H04   C04  C05   122.12  3.000
 ES9  H04   C04  C03   120.77  3.000
 ES9  C05   C04  C03   117.11  3.000
 ES9  C09   C05  N06   104.55  3.000
 ES9  C09   C05  C04   122.38  3.000
 ES9  N06   C05  C04   133.07  3.000
 ES9  HN06  N06  C07   125.77  3.000
 ES9  HN06  N06  C05   127.14  3.000
 ES9  C07   N06  C05   107.09  3.000
 ES9  H07   C07  N08   125.23  3.000
 ES9  H07   C07  N06   121.21  3.000
 ES9  N08   C07  N06   113.56  3.000
 ES9  C09   N08  C07   104.63  3.000
 ES9  N08   C09  C05   110.16  3.000
 ES9  N08   C09  C10   129.61  3.000
 ES9  C05   C09  C10   120.22  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
 ES9  CONST_01  C04   C03  C02  C10     0.00  0.0  0
 ES9  CONST_02  C04   C05  C09  C10     0.00  0.0  0
 ES9  CONST_03  N06   C05  C09  C10   180.00  0.0  0
 ES9  CONST_04  C07   N08  C09  C10   180.00  0.0  0
 ES9  CONST_05  C05   C09  C10  C02     0.00  0.0  0
 ES9  CONST_06  N08   C09  C10  C02   180.00  0.0  0
 ES9  CONST_07  C05   C04  C03  C02     0.00  0.0  0
 ES9  CONST_08  C09   C10  C02  C03     0.00  0.0  0
 ES9  CONST_09  N06   C05  C04  C03   180.00  0.0  0
 ES9  CONST_10  C09   C05  C04  C03     0.00  0.0  0
 ES9  CONST_11  C07   N06  C05  C04   180.00  0.0  0
 ES9  CONST_12  N08   C09  C05  C04   180.00  0.0  0
 ES9  CONST_13  N08   C07  N06  C05     0.00  0.0  0
 ES9  CONST_14  C07   N08  C09  C05     0.00  0.0  0
 ES9  CONST_15  N08   C09  C05  N06     0.00  0.0  0
 ES9  CONST_16  C09   N08  C07  N06     0.00  0.0  0
 ES9  CONST_17  C09   C05  N06  C07     0.00  0.0  0
 ES9  CONST_18  C09   C10  C02  CL01  180.00  0.0  0
 ES9  CONST_19  C04   C03  C02  CL01  180.00  0.0  0
 ES9  CONST_20  H03   C03  C02  C10   180.00  0.0  0
 ES9  CONST_21  H04   C04  C03  C02   180.00  0.0  0
 ES9  CONST_22  H10   C10  C02  C03   180.00  0.0  0
 ES9  CONST_23  HN06  N06  C05  C04     0.00  0.0  0
 ES9  CONST_24  H07   C07  N06  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
 ES9  plan-1  C10   0.020
 ES9  plan-1  CL01  0.020
 ES9  plan-1  C02   0.020
 ES9  plan-1  C03   0.020
 ES9  plan-1  C04   0.020
 ES9  plan-1  C05   0.020
 ES9  plan-1  N06   0.020
 ES9  plan-1  C07   0.020
 ES9  plan-1  N08   0.020
 ES9  plan-1  C09   0.020
 ES9  plan-1  H10   0.020
 ES9  plan-1  H03   0.020
 ES9  plan-1  H04   0.020
 ES9  plan-1  HN06  0.020
 ES9  plan-1  H07   0.020

