# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 22:05:03 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2-(trifluoromethyl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1[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
 36E  36E  2-(trifluoromethyl)-1H-benzimidazole  ligand  18  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_36E
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
 36E  CAA   C  CR16  0  -0.267   3.6604  -0.7447  -0.0101
 36E  CAB   C  CR16  0  -0.327   2.4721  -1.4465  -0.0113
 36E  FAC   F  F     0  -0.292  -2.7203  -1.2158   0.2868
 36E  CAD   C  CR16  0  -0.271   3.6825   0.6615   0.0051
 36E  CAE   C  CR16  0  -0.301   2.5199   1.4069   0.0191
 36E  CAF   C  CR56  0   0.348   1.3256   0.6916   0.0164
 36E  CAG   C  CR56  0   0.137   1.2846  -0.7119   0.0018
 36E  FAH   F  F     0  -0.307  -2.6958   0.8621   0.8739
 36E  CAJ   C  CR5   0   0.182  -0.7227  -0.0533   0.0215
 36E  NAK   N  NR15  0  -0.702   0.0149   1.0820   0.0286
 36E  NAL   N  N     0  -0.447  -0.0194  -1.1437   0.0058
 36E  FAM   F  F     0  -0.308  -2.6734   0.3330  -1.2097
 36E  HAA   H  HCR6  0   0.259   4.5982  -1.2843  -0.0209
 36E  HAB   H  HCR6  0   0.263   2.4559  -2.5283  -0.0225
 36E  HAD   H  HCR6  0   0.263   4.6362   1.1727   0.0065
 36E  HAE   H  HCR6  0   0.274   2.5399   2.4882   0.0312
 36E  HNAK  H  HNR5  0   0.434  -0.3244   2.0324   0.0441
 36E  CAI   C  CT    0   1.062  -2.2163  -0.0240  -0.0043

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
 36E  CAA  CAB   aromatic  1.380  0.020  1.380
 36E  CAA  CAD   aromatic  1.406  0.020  1.406
 36E  CAB  CAG   aromatic  1.396  0.020  1.396
 36E  FAC  CAI   single    1.326  0.020  1.326
 36E  CAD  CAE   aromatic  1.381  0.020  1.381
 36E  CAE  CAF   aromatic  1.392  0.020  1.392
 36E  CAF  CAG   aromatic  1.404  0.020  1.404
 36E  CAF  NAK   aromatic  1.368  0.020  1.368
 36E  CAG  NAL   aromatic  1.374  0.020  1.374
 36E  FAH  CAI   single    1.336  0.020  1.336
 36E  CAI  CAJ   single    1.494  0.020  1.494
 36E  CAI  FAM   single    1.338  0.020  1.338
 36E  CAJ  NAK   aromatic  1.354  0.020  1.354
 36E  CAJ  NAL   aromatic  1.298  0.020  1.298
 36E  CAA  HAA   single    0.930  0.020  1.080
 36E  CAB  HAB   single    0.930  0.020  1.080
 36E  CAD  HAD   single    0.930  0.020  1.080
 36E  CAE  HAE   single    0.930  0.020  1.080
 36E  NAK  HNAK  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
 36E  HAA   CAA  CAD  119.02  3.000
 36E  HAA   CAA  CAB  119.51  3.000
 36E  CAD   CAA  CAB  121.47  3.000
 36E  HAB   CAB  CAG  120.89  3.000
 36E  HAB   CAB  CAA  121.43  3.000
 36E  CAG   CAB  CAA  117.69  3.000
 36E  HAD   CAD  CAE  119.14  3.000
 36E  HAD   CAD  CAA  119.09  3.000
 36E  CAE   CAD  CAA  121.77  3.000
 36E  HAE   CAE  CAF  121.98  3.000
 36E  HAE   CAE  CAD  121.61  3.000
 36E  CAF   CAE  CAD  116.41  3.000
 36E  NAK   CAF  CAG  104.92  3.000
 36E  NAK   CAF  CAE  132.49  3.000
 36E  CAG   CAF  CAE  122.59  3.000
 36E  NAL   CAG  CAF  109.99  3.000
 36E  NAL   CAG  CAB  129.94  3.000
 36E  CAF   CAG  CAB  120.07  3.000
 36E  NAL   CAJ  NAK  114.17  3.000
 36E  NAL   CAJ  CAI  123.92  3.000
 36E  NAK   CAJ  CAI  121.89  3.000
 36E  HNAK  NAK  CAJ  127.34  3.000
 36E  HNAK  NAK  CAF  126.24  3.000
 36E  CAJ   NAK  CAF  106.42  3.000
 36E  CAJ   NAL  CAG  104.50  3.000
 36E  FAM   CAI  CAJ  111.24  3.000
 36E  FAM   CAI  FAH  107.01  3.000
 36E  CAJ   CAI  FAH  111.12  3.000
 36E  FAM   CAI  FAC  107.92  3.000
 36E  CAJ   CAI  FAC  111.01  3.000
 36E  FAH   CAI  FAC  108.37  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
 36E  CONST_01  CAF   CAG  CAB  CAA     0.00   0.0  0
 36E  CONST_02  NAL   CAG  CAB  CAA   180.00   0.0  0
 36E  CONST_03  CAF   CAE  CAD  CAA     0.00   0.0  0
 36E  CONST_04  CAE   CAD  CAA  CAB     0.00   0.0  0
 36E  CONST_05  CAE   CAF  CAG  CAB     0.00   0.0  0
 36E  CONST_06  NAK   CAF  CAG  CAB   180.00   0.0  0
 36E  CONST_07  CAJ   NAL  CAG  CAB   180.00   0.0  0
 36E  CONST_08  CAG   CAB  CAA  CAD     0.00   0.0  0
 36E  CONST_09  CAG   CAF  CAE  CAD     0.00   0.0  0
 36E  CONST_10  NAK   CAF  CAE  CAD   180.00   0.0  0
 36E  CONST_11  NAL   CAG  CAF  CAE   180.00   0.0  0
 36E  CONST_12  CAJ   NAK  CAF  CAE   180.00   0.0  0
 36E  CONST_13  CAJ   NAL  CAG  CAF     0.00   0.0  0
 36E  CONST_14  NAL   CAJ  NAK  CAF     0.00   0.0  0
 36E  CONST_15  CAJ   NAK  CAF  CAG     0.00   0.0  0
 36E  CONST_16  NAK   CAJ  NAL  CAG     0.00   0.0  0
 36E  CONST_17  NAL   CAG  CAF  NAK     0.00   0.0  0
 36E  CONST_18  CAI   CAJ  NAK  CAF   180.00   0.0  0
 36E  CONST_19  CAI   CAJ  NAL  CAG   180.00   0.0  0
 36E  CONST_20  HAE   CAE  CAD  CAA   180.00   0.0  0
 36E  CONST_21  HAD   CAD  CAA  CAB   180.00   0.0  0
 36E  CONST_22  HAB   CAB  CAA  CAD   180.00   0.0  0
 36E  CONST_23  HAA   CAA  CAD  CAE   180.00   0.0  0
 36E  CONST_24  HNAK  NAK  CAF  CAE     0.00   0.0  0
 36E  Var_01    NAK   CAJ  CAI  FAC  -166.27  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
 36E  plan-1  CAA   0.020
 36E  plan-1  CAB   0.020
 36E  plan-1  CAD   0.020
 36E  plan-1  CAE   0.020
 36E  plan-1  CAF   0.020
 36E  plan-1  CAG   0.020
 36E  plan-1  CAJ   0.020
 36E  plan-1  NAK   0.020
 36E  plan-1  NAL   0.020
 36E  plan-1  HAA   0.020
 36E  plan-1  HAB   0.020
 36E  plan-1  HAD   0.020
 36E  plan-1  HAE   0.020
 36E  plan-1  HNAK  0.020
 36E  plan-1  CAI   0.020

