# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:50:37 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCc1[nH]c2cc(ccc2n1)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
 6DH  6DH  3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol  ligand  28  17  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6DH
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
 6DH  F01  F  F     0  -0.318   4.2702   0.7116   1.1169
 6DH  F02  F  F     0  -0.316   4.0775   1.1211  -0.9813
 6DH  F    F  F     0  -0.303   4.6272  -0.8503  -0.3172
 6DH  C01  C  CT    0   1.046   3.8357   0.1916  -0.0439
 6DH  O    O  OH1   0  -0.674  -6.7464  -0.5177  -0.7740
 6DH  C02  C  CH2   0  -0.140  -5.8837   0.3084  -0.0239
 6DH  C03  C  CH2   0  -0.458  -4.4524  -0.1156  -0.2879
 6DH  N01  N  NR15  0  -0.708  -1.0305   1.2030   0.2604
 6DH  C05  C  CR5   0   0.494  -2.0581   0.3189   0.3350
 6DH  C06  C  CR16  0  -0.296   1.9955  -1.5225   0.0508
 6DH  N    N  N     0  -0.475  -1.6538  -0.9245   0.3019
 6DH  C07  C  CR6   0  -0.225   2.3886  -0.1768   0.0203
 6DH  C08  C  CR16  0  -0.326   1.4592   0.8539   0.0843
 6DH  C09  C  CR16  0  -0.325   0.6613  -1.8758   0.1413
 6DH  C10  C  CR56  0   0.355   0.1297   0.4834   0.1783
 6DH  C    C  CR56  0   0.148  -0.2878  -0.8596   0.2062
 6DH  H1   H  HOH1  0   0.454  -7.6510  -0.2420  -0.6021
 6DH  H2   H  HCH2  0   0.192  -6.0071   1.3661  -0.2929
 6DH  H3   H  HCH2  0   0.192  -6.0879   0.2318   1.0528
 6DH  H4   H  HCH2  0   0.239  -4.3169  -1.1575   0.0092
 6DH  H5   H  HCH2  0   0.237  -4.2410  -0.0550  -1.3588
 6DH  H6   H  HCH2  0   0.263  -3.5563   1.8045   0.1507
 6DH  H7   H  HCH2  0   0.273  -3.7221   0.7625   1.5433
 6DH  H8   H  HNR5  0   0.422  -1.1159   2.2075   0.2598
 6DH  H9   H  HCR6  0   0.267   2.7372  -2.3070   0.0037
 6DH  H11  H  HCR6  0   0.283   1.7511   1.8961   0.0604
 6DH  H12  H  HCR6  0   0.262   0.3664  -2.9166   0.1640
 6DH  C04  C  CH2   0  -0.561  -3.4711   0.7654   0.4769

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
 6DH  O    C02  single    1.410  0.020  1.410
 6DH  C02  C03  single    1.516  0.020  1.516
 6DH  C03  C04  single    1.525  0.020  1.525
 6DH  C04  C05  single    1.489  0.020  1.489
 6DH  C05  N    aromatic  1.308  0.020  1.308
 6DH  C05  N01  aromatic  1.358  0.020  1.358
 6DH  N    C    aromatic  1.371  0.020  1.371
 6DH  N01  C10  aromatic  1.368  0.020  1.368
 6DH  C    C09  aromatic  1.392  0.020  1.392
 6DH  C    C10  aromatic  1.407  0.020  1.407
 6DH  C09  C06  aromatic  1.383  0.020  1.383
 6DH  C10  C08  aromatic  1.383  0.020  1.383
 6DH  C06  C07  aromatic  1.402  0.020  1.402
 6DH  C08  C07  aromatic  1.389  0.020  1.389
 6DH  C07  C01  single    1.495  0.020  1.495
 6DH  C01  F    single    1.337  0.020  1.337
 6DH  C01  F02  single    1.342  0.020  1.342
 6DH  C01  F01  single    1.344  0.020  1.344
 6DH  O    H1   single    0.850  0.020  0.980
 6DH  C02  H2   single    0.970  0.020  1.090
 6DH  C02  H3   single    0.970  0.020  1.090
 6DH  C03  H4   single    0.970  0.020  1.090
 6DH  C03  H5   single    0.970  0.020  1.090
 6DH  C04  H6   single    0.970  0.020  1.090
 6DH  C04  H7   single    0.970  0.020  1.090
 6DH  N01  H8   single    0.860  0.020  1.020
 6DH  C06  H9   single    0.930  0.020  1.080
 6DH  C08  H11  single    0.930  0.020  1.080
 6DH  C09  H12  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
 6DH  C07  C01  F    112.95  3.000
 6DH  F    C01  F02  106.88  3.000
 6DH  C07  C01  F02  112.03  3.000
 6DH  F02  C01  F01  106.08  3.000
 6DH  F    C01  F01  106.66  3.000
 6DH  C07  C01  F01  111.80  3.000
 6DH  H1   O    C02  108.21  3.000
 6DH  H3   C02  H2   106.64  3.000
 6DH  H3   C02  C03  109.06  3.000
 6DH  H2   C02  C03  109.44  3.000
 6DH  H3   C02  O    111.51  3.000
 6DH  H2   C02  O    111.42  3.000
 6DH  C03  C02  O    108.72  3.000
 6DH  H5   C03  H4   107.19  3.000
 6DH  H5   C03  C04  109.57  3.000
 6DH  H4   C03  C04  109.57  3.000
 6DH  H5   C03  C02  109.73  3.000
 6DH  H4   C03  C02  109.68  3.000
 6DH  C04  C03  C02  111.02  3.000
 6DH  H8   N01  C10  126.58  3.000
 6DH  H8   N01  C05  125.79  3.000
 6DH  C10  N01  C05  107.62  3.000
 6DH  N    C05  N01  112.56  3.000
 6DH  N01  C05  C04  121.89  3.000
 6DH  N    C05  C04  125.52  3.000
 6DH  H9   C06  C09  118.65  3.000
 6DH  H9   C06  C07  120.22  3.000
 6DH  C09  C06  C07  121.13  3.000
 6DH  C    N    C05  105.36  3.000
 6DH  C08  C07  C06  121.56  3.000
 6DH  C08  C07  C01  117.83  3.000
 6DH  C06  C07  C01  120.59  3.000
 6DH  H11  C08  C10  121.23  3.000
 6DH  H11  C08  C07  122.19  3.000
 6DH  C10  C08  C07  116.57  3.000
 6DH  H12  C09  C    121.02  3.000
 6DH  H12  C09  C06  120.66  3.000
 6DH  C    C09  C06  118.32  3.000
 6DH  C    C10  C08  122.84  3.000
 6DH  C08  C10  N01  132.72  3.000
 6DH  C    C10  N01  104.44  3.000
 6DH  C10  C    C09  119.58  3.000
 6DH  C10  C    N    110.02  3.000
 6DH  C09  C    N    130.40  3.000
 6DH  H7   C04  H6   105.99  3.000
 6DH  H7   C04  C05  108.03  3.000
 6DH  H6   C04  C05  109.32  3.000
 6DH  H7   C04  C03  109.83  3.000
 6DH  H6   C04  C03  110.46  3.000
 6DH  C05  C04  C03  112.94  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
 6DH  CONST_01  C    N    C05  N01     0.00   0.0  0
 6DH  CONST_02  N    C    C10  N01     0.00   0.0  0
 6DH  CONST_03  C09  C    C10  N01   180.00   0.0  0
 6DH  CONST_04  C07  C08  C10  N01   180.00   0.0  0
 6DH  CONST_05  C09  C    N    C05   180.00   0.0  0
 6DH  CONST_06  C10  C    N    C05     0.00   0.0  0
 6DH  CONST_07  C    C10  N01  C05     0.00   0.0  0
 6DH  CONST_08  C08  C10  N01  C05   180.00   0.0  0
 6DH  CONST_09  N    C    C09  C06   180.00   0.0  0
 6DH  CONST_10  C10  C    C09  C06     0.00   0.0  0
 6DH  CONST_11  C10  C08  C07  C06     0.00   0.0  0
 6DH  CONST_12  C10  N01  C05  N       0.00   0.0  0
 6DH  CONST_13  C08  C10  C    N     180.00   0.0  0
 6DH  CONST_14  C    C09  C06  C07     0.00   0.0  0
 6DH  CONST_15  C    C10  C08  C07     0.00   0.0  0
 6DH  CONST_16  C09  C    C10  C08     0.00   0.0  0
 6DH  CONST_17  C09  C06  C07  C08     0.00   0.0  0
 6DH  CONST_18  C09  C06  C07  C01   180.00   0.0  0
 6DH  CONST_19  C10  C08  C07  C01   180.00   0.0  0
 6DH  CONST_20  C    N    C05  C04   180.00   0.0  0
 6DH  CONST_21  C10  N01  C05  C04   180.00   0.0  0
 6DH  CONST_22  H11  C08  C10  N01     0.00   0.0  0
 6DH  CONST_23  H8   N01  C05  N     180.00   0.0  0
 6DH  CONST_24  H12  C09  C    N       0.00   0.0  0
 6DH  CONST_25  H9   C06  C07  C08   180.00   0.0  0
 6DH  Var_01    C06  C07  C01  F01  -108.54  30.0  2
 6DH  Var_02    N    C05  C04  C03   -38.13  30.0  2
 6DH  Var_03    C05  C04  C03  C02   175.41  30.0  3
 6DH  Var_04    C04  C03  C02  O     178.80  30.0  3

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
 6DH  plan-1  C01  0.020
 6DH  plan-1  N01  0.020
 6DH  plan-1  C05  0.020
 6DH  plan-1  C06  0.020
 6DH  plan-1  N    0.020
 6DH  plan-1  C07  0.020
 6DH  plan-1  C08  0.020
 6DH  plan-1  C09  0.020
 6DH  plan-1  C10  0.020
 6DH  plan-1  C    0.020
 6DH  plan-1  H8   0.020
 6DH  plan-1  H9   0.020
 6DH  plan-1  H11  0.020
 6DH  plan-1  H12  0.020
 6DH  plan-1  C04  0.020

