# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:40:01 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-(5-chloro-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cnn(c1)c2[nH]c3cc(F)c(Cl)cc3n2
#
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
 014  014  '1-(5-chloro-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazole-4-carboxylic acid'  ligand  24  19  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_014
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
 014  F    F   F      0  -0.300  -4.9824   1.4507   0.0404
 014  CL   CL  CL     0  -0.098  -5.1988  -1.4168  -0.0145
 014  N1   N   N      0  -0.293   2.5889   1.6131   0.0174
 014  O1   O   OC    -1  -0.596   6.4717   0.0172  -0.0155
 014  C2   C   CR5    0  -0.355   4.1397  -0.0347  -0.0171
 014  N2   N   NR5    0  -0.413   2.0014   0.4058  -0.0045
 014  O2   O   O      0  -0.596   5.4485  -1.9713  -0.0504
 014  C3   C   CR15   0  -0.029   3.8747   1.3560   0.0101
 014  N3   N   NR15   0  -0.723  -0.1440   1.4228   0.0217
 014  C4   C   CR15   0   0.068   2.8986  -0.6119  -0.0256
 014  N4   N   N      0  -0.494  -0.0320  -0.8059  -0.0208
 014  C5   C   CR5    0   0.737   0.6272   0.3112  -0.0018
 014  C6   C   CR56   0   0.371  -1.4414   0.9864   0.0180
 014  C7   C   CR16   0  -0.457  -2.6521   1.6607   0.0355
 014  C8   C   CR6    0   0.593  -3.7790   0.8686   0.0247
 014  C10  C   CR6    0  -0.239  -3.7190  -0.5276  -0.0024
 014  C11  C   CR16   0  -0.292  -2.5054  -1.1894  -0.0195
 014  C12  C   CR56   0   0.160  -1.3503  -0.4160  -0.0089
 014  H3   H   HCR5   0   0.272   4.5887   2.1650   0.0250
 014  H4   H   HCR5   0   0.302   2.5864  -1.6425  -0.0455
 014  H7   H   HCR6   0   0.302  -2.7274   2.7397   0.0560
 014  H11  H   HCR6   0   0.291  -2.4597  -2.2694  -0.0403
 014  HN3  H   HNR5   0   0.434   0.1876   2.3758   0.0391
 014  C1   C   C      0   0.357   5.4724  -0.7263  -0.0288

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
 014  C8   F    single    1.337  0.020  1.337
 014  CL   C10  single    1.726  0.020  1.726
 014  O2   C1   deloc     1.245  0.020  1.245
 014  C1   C2   single    1.502  0.020  1.502
 014  C1   O1   deloc     1.246  0.020  1.246
 014  N2   N1   aromatic  1.343  0.020  1.343
 014  C3   N1   aromatic  1.311  0.020  1.311
 014  C4   C2   aromatic  1.369  0.020  1.369
 014  C2   C3   aromatic  1.416  0.020  1.416
 014  C4   N2   aromatic  1.357  0.020  1.357
 014  C5   N2   single    1.377  0.020  1.377
 014  C3   H3   single    0.930  0.020  1.080
 014  C6   N3   aromatic  1.369  0.020  1.369
 014  C5   N3   aromatic  1.353  0.020  1.353
 014  C4   H4   single    0.930  0.020  1.080
 014  C12  N4   aromatic  1.375  0.020  1.375
 014  N4   C5   aromatic  1.297  0.020  1.297
 014  C12  C6   aromatic  1.406  0.020  1.406
 014  C6   C7   aromatic  1.386  0.020  1.386
 014  C8   C7   aromatic  1.377  0.020  1.377
 014  C7   H7   single    0.930  0.020  1.080
 014  C10  C8   aromatic  1.398  0.020  1.398
 014  C11  C10  aromatic  1.382  0.020  1.382
 014  C11  C12  aromatic  1.390  0.020  1.390
 014  C11  H11  single    0.930  0.020  1.080
 014  N3   HN3  single    0.860  0.020  1.020

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
 014  C3   N1   N2   104.63  3.000
 014  C4   C2   C3   104.16  3.000
 014  C3   C2   C1   128.21  3.000
 014  C4   C2   C1   127.63  3.000
 014  C5   N2   C4   127.45  3.000
 014  C5   N2   N1   119.88  3.000
 014  C4   N2   N1   112.66  3.000
 014  H3   C3   C2   127.79  3.000
 014  H3   C3   N1   120.11  3.000
 014  C2   C3   N1   112.10  3.000
 014  HN3  N3   C6   127.78  3.000
 014  HN3  N3   C5   126.07  3.000
 014  C6   N3   C5   106.15  3.000
 014  H4   C4   N2   121.76  3.000
 014  H4   C4   C2   131.79  3.000
 014  N2   C4   C2   106.45  3.000
 014  C12  N4   C5   104.06  3.000
 014  N4   C5   N3   114.71  3.000
 014  N4   C5   N2   124.48  3.000
 014  N3   C5   N2   120.81  3.000
 014  C12  C6   C7   122.84  3.000
 014  C7   C6   N3   132.28  3.000
 014  C12  C6   N3   104.88  3.000
 014  H7   C7   C8   121.12  3.000
 014  H7   C7   C6   123.11  3.000
 014  C8   C7   C6   115.77  3.000
 014  C10  C8   C7   122.64  3.000
 014  C10  C8   F    118.28  3.000
 014  C7   C8   F    119.07  3.000
 014  C11  C10  C8   121.07  3.000
 014  C11  C10  CL   120.39  3.000
 014  C8   C10  CL   118.54  3.000
 014  H11  C11  C12  121.38  3.000
 014  H11  C11  C10  121.03  3.000
 014  C12  C11  C10  117.58  3.000
 014  C11  C12  C6   120.09  3.000
 014  C11  C12  N4   129.71  3.000
 014  C6   C12  N4   110.20  3.000
 014  O2   C1   C2   116.33  3.000
 014  C2   C1   O1   115.91  3.000
 014  O2   C1   O1   127.76  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
 014  CONST_01  C2   C4   N2   N1     0.00   0.0  0
 014  CONST_02  N3   C5   N2   N1     0.00   0.0  0
 014  CONST_03  N4   C5   N2   N1   180.00   0.0  0
 014  CONST_04  C4   C2   C3   N1     0.00   0.0  0
 014  CONST_05  C5   N2   C4   C2   180.00   0.0  0
 014  CONST_06  N2   N1   C3   C2     0.00   0.0  0
 014  CONST_07  C3   C2   C4   N2     0.00   0.0  0
 014  CONST_08  C6   N3   C5   N2   180.00   0.0  0
 014  CONST_09  C12  N4   C5   N2   180.00   0.0  0
 014  CONST_10  C4   N2   N1   C3     0.00   0.0  0
 014  CONST_11  C5   N2   N1   C3   180.00   0.0  0
 014  CONST_12  N4   C12  C6   N3     0.00   0.0  0
 014  CONST_13  C11  C12  C6   N3   180.00   0.0  0
 014  CONST_14  C8   C7   C6   N3   180.00   0.0  0
 014  CONST_15  C4   N2   C5   N3   180.00   0.0  0
 014  CONST_16  C12  N4   C5   N3     0.00   0.0  0
 014  CONST_17  N4   C5   N2   C4     0.00   0.0  0
 014  CONST_18  C7   C6   C12  N4   180.00   0.0  0
 014  CONST_19  C10  C11  C12  N4   180.00   0.0  0
 014  CONST_20  C6   N3   C5   N4     0.00   0.0  0
 014  CONST_21  C12  C6   N3   C5     0.00   0.0  0
 014  CONST_22  C7   C6   N3   C5   180.00   0.0  0
 014  CONST_23  C6   C12  N4   C5     0.00   0.0  0
 014  CONST_24  C11  C12  N4   C5   180.00   0.0  0
 014  CONST_25  C10  C11  C12  C6     0.00   0.0  0
 014  CONST_26  C10  C8   C7   C6     0.00   0.0  0
 014  CONST_27  C11  C12  C6   C7     0.00   0.0  0
 014  CONST_28  C11  C10  C8   C7     0.00   0.0  0
 014  CONST_29  C12  C6   C7   C8     0.00   0.0  0
 014  CONST_30  C12  C11  C10  C8     0.00   0.0  0
 014  CONST_31  C6   C7   C8   F    180.00   0.0  0
 014  CONST_32  C11  C10  C8   F    180.00   0.0  0
 014  CONST_33  C7   C8   C10  CL   180.00   0.0  0
 014  CONST_34  C12  C11  C10  CL   180.00   0.0  0
 014  CONST_35  N2   C4   C2   C1   180.00   0.0  0
 014  CONST_36  N1   C3   C2   C1   180.00   0.0  0
 014  CONST_37  H4   C4   N2   N1   180.00   0.0  0
 014  CONST_38  H3   C3   N1   N2   180.00   0.0  0
 014  CONST_39  HN3  N3   C5   N2     0.00   0.0  0
 014  CONST_40  H7   C7   C6   N3     0.00   0.0  0
 014  CONST_41  H11  C11  C12  N4     0.00   0.0  0
 014  Var_01    C4   C2   C1   O1  -179.90  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
 014  plan-1  N1   0.020
 014  plan-1  C2   0.020
 014  plan-1  N2   0.020
 014  plan-1  C3   0.020
 014  plan-1  C4   0.020
 014  plan-1  C5   0.020
 014  plan-1  H3   0.020
 014  plan-1  H4   0.020
 014  plan-1  C1   0.020
 014  plan-2  F    0.020
 014  plan-2  CL   0.020
 014  plan-2  N2   0.020
 014  plan-2  N3   0.020
 014  plan-2  N4   0.020
 014  plan-2  C5   0.020
 014  plan-2  C6   0.020
 014  plan-2  C7   0.020
 014  plan-2  C8   0.020
 014  plan-2  C10  0.020
 014  plan-2  C11  0.020
 014  plan-2  C12  0.020
 014  plan-2  H7   0.020
 014  plan-2  H11  0.020
 014  plan-2  HN3  0.020
 014  plan-3  O1   0.020
 014  plan-3  C2   0.020
 014  plan-3  O2   0.020
 014  plan-3  C1   0.020

