# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:22:47 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-(trifluoromethyl)-1H-benzimidazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2[nH]c(nc2c1)C(F)(F)F
#
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
 71N  71N  2-(trifluoromethyl)-1H-benzimidazol-5-amine  ligand  20  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_71N
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
 71N  F3   F  F     0  -0.297   3.0149  -1.2428  -0.5360
 71N  F1   F  F     0  -0.309   3.0775  -0.1159   1.2936
 71N  F2   F  F     0  -0.307   3.1824   0.9105  -0.5943
 71N  C12  C  CR56  0   0.152  -0.9370  -0.4927   0.0693
 71N  C11  C  CR16  0  -0.423  -2.1758  -1.1359   0.1113
 71N  C8   C  CR16  0  -0.296  -1.9971   1.7009  -0.0321
 71N  C7   C  CR56  0   0.320  -0.8566   0.9048  -0.0003
 71N  C9   C  CR16  0  -0.332  -3.2136   1.0562   0.0155
 71N  C10  C  CR6   0   0.301  -3.3241  -0.3556   0.0897
 71N  C4   C  CR5   0   0.174   1.1210  -0.0041   0.0115
 71N  C1   C  CT    0   1.063   2.6094  -0.1158   0.0403
 71N  N5   N  NR15  0  -0.697   0.4855   1.1855  -0.0336
 71N  N6   N  N     0  -0.462   0.3256  -1.0322   0.0743
 71N  H1   H  HCR6  0   0.258  -2.2354  -2.2165   0.1597
 71N  H2   H  HCR6  0   0.272  -1.9430   2.7797  -0.0906
 71N  H3   H  HCR6  0   0.264  -4.1210   1.6478  -0.0030
 71N  H4   H  HNR5  0   0.430   0.9054   2.1005  -0.0994
 71N  H6   H  HNH2  0   0.376  -4.6327  -1.8975  -0.0657
 71N  H7   H  HNH2  0   0.376  -5.3255  -0.3986  -0.2364
 71N  N13  N  NH2   0  -0.863  -4.5823  -0.9253   0.1947

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
 71N  F2   C1   single    1.336  0.020  1.336
 71N  F3   C1   single    1.329  0.020  1.329
 71N  C1   F1   single    1.338  0.020  1.338
 71N  C1   C4   single    1.493  0.020  1.493
 71N  C4   N5   aromatic  1.349  0.020  1.349
 71N  C4   N6   aromatic  1.301  0.020  1.301
 71N  N5   C7   aromatic  1.372  0.020  1.372
 71N  N6   C12  aromatic  1.373  0.020  1.373
 71N  C7   C12  aromatic  1.402  0.020  1.402
 71N  C7   C8   aromatic  1.391  0.020  1.391
 71N  C12  C11  aromatic  1.396  0.020  1.396
 71N  C8   C9   aromatic  1.378  0.020  1.378
 71N  C11  C10  aromatic  1.389  0.020  1.389
 71N  C9   C10  aromatic  1.418  0.020  1.418
 71N  C10  N13  single    1.385  0.020  1.385
 71N  C11  H1   single    0.930  0.020  1.080
 71N  C8   H2   single    0.930  0.020  1.080
 71N  C9   H3   single    0.930  0.020  1.080
 71N  N5   H4   single    0.860  0.020  1.020
 71N  N13  H6   single    0.890  0.020  1.040
 71N  N13  H7   single    0.890  0.020  1.040

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
 71N  N6   C12  C7   109.83  3.000
 71N  C7   C12  C11  120.77  3.000
 71N  N6   C12  C11  129.40  3.000
 71N  H1   C11  C10  121.05  3.000
 71N  H1   C11  C12  120.63  3.000
 71N  C10  C11  C12  118.32  3.000
 71N  H2   C8   C9   120.85  3.000
 71N  H2   C8   C7   122.07  3.000
 71N  C9   C8   C7   117.08  3.000
 71N  N5   C7   C8   133.20  3.000
 71N  C8   C7   C12  121.65  3.000
 71N  N5   C7   C12  105.15  3.000
 71N  H3   C9   C10  118.64  3.000
 71N  H3   C9   C8   118.91  3.000
 71N  C10  C9   C8   122.45  3.000
 71N  N13  C10  C9   118.96  3.000
 71N  N13  C10  C11  121.26  3.000
 71N  C9   C10  C11  119.73  3.000
 71N  N6   C4   N5   114.22  3.000
 71N  N6   C4   C1   123.32  3.000
 71N  N5   C4   C1   122.43  3.000
 71N  C4   C1   F2   111.16  3.000
 71N  C4   C1   F1   111.52  3.000
 71N  F2   C1   F1   107.16  3.000
 71N  C4   C1   F3   111.06  3.000
 71N  F1   C1   F3   107.42  3.000
 71N  F2   C1   F3   108.34  3.000
 71N  H4   N5   C4   127.27  3.000
 71N  H4   N5   C7   126.47  3.000
 71N  C4   N5   C7   106.24  3.000
 71N  C4   N6   C12  104.56  3.000
 71N  H7   N13  H6   110.90  3.000
 71N  H7   N13  C10  114.99  3.000
 71N  H6   N13  C10  115.00  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
 71N  CONST_01  N5   C4   N6   C12     0.00   0.0  0
 71N  CONST_02  C4   N5   C7   C12     0.00   0.0  0
 71N  CONST_03  C9   C8   C7   C12     0.00   0.0  0
 71N  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 71N  CONST_05  C4   N6   C12  C11   180.00   0.0  0
 71N  CONST_06  N5   C7   C12  C11   180.00   0.0  0
 71N  CONST_07  C8   C7   C12  C11     0.00   0.0  0
 71N  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 71N  CONST_09  C4   N5   C7   C8    180.00   0.0  0
 71N  CONST_10  N6   C12  C7   C8    180.00   0.0  0
 71N  CONST_11  N6   C4   N5   C7      0.00   0.0  0
 71N  CONST_12  C4   N6   C12  C7      0.00   0.0  0
 71N  CONST_13  C10  C11  C12  C7      0.00   0.0  0
 71N  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 71N  CONST_15  N5   C7   C8   C9    180.00   0.0  0
 71N  CONST_16  N6   C12  C11  C10   180.00   0.0  0
 71N  CONST_17  N6   C12  C7   N5      0.00   0.0  0
 71N  CONST_18  C1   C4   N6   C12   180.00   0.0  0
 71N  CONST_19  N13  C10  C11  C12   180.00   0.0  0
 71N  CONST_20  N13  C10  C9   C8    180.00   0.0  0
 71N  CONST_21  C1   C4   N5   C7    180.00   0.0  0
 71N  CONST_22  H4   N5   C7   C12   180.00   0.0  0
 71N  CONST_23  H2   C8   C7   C12   180.00   0.0  0
 71N  CONST_24  H3   C9   C10  C11   180.00   0.0  0
 71N  CONST_25  H1   C11  C12  C7    180.00   0.0  0
 71N  Var_01    N5   C4   C1   F3   -150.26  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
 71N  plan-1  C12  0.020
 71N  plan-1  C11  0.020
 71N  plan-1  C8   0.020
 71N  plan-1  C7   0.020
 71N  plan-1  C9   0.020
 71N  plan-1  C10  0.020
 71N  plan-1  C4   0.020
 71N  plan-1  C1   0.020
 71N  plan-1  N5   0.020
 71N  plan-1  N6   0.020
 71N  plan-1  H1   0.020
 71N  plan-1  H2   0.020
 71N  plan-1  H3   0.020
 71N  plan-1  H4   0.020
 71N  plan-1  N13  0.020
 71N  plan-2  C10  0.020
 71N  plan-2  H6   0.020
 71N  plan-2  H7   0.020
 71N  plan-2  N13  0.020

