# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:24:06 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(CN2CCc3[nH]cnc3C2)c1
#
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
 I9O  I9O  "5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine"
  ligand  34  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_I9O
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
 I9O  C2   C  CT    0   1.050  27.2434   9.1187  22.8717
 I9O  C11  C  CR16  0  -0.220  25.8744   9.8532  19.4268
 I9O  C13  C  CR16  0  -0.303  26.1245   9.1871  20.6196
 I9O  C15  C  CH2   0  -0.310  27.7808  13.1042  19.9316
 I9O  C19  C  CH2   0  -0.299  29.2239  12.6764  18.0506
 I9O  C22  C  CH2   0  -0.503  29.2872  12.7015  16.5233
 I9O  C25  C  CR5   0   0.295  29.0424  14.1029  16.1037
 I9O  C27  C  CR15  0   0.064  28.8844  15.9992  15.0231
 I9O  F1   F  F     0  -0.302  26.5683   7.9787  23.0401
 I9O  F3   F  F     0  -0.316  28.5482   8.8223  22.9785
 I9O  F4   F  F     0  -0.315  26.9505   9.9025  23.9201
 I9O  C5   C  CR6   0  -0.173  26.9323   9.7910  21.5723
 I9O  C6   C  CR16  0  -0.336  27.4891  11.0430  21.3287
 I9O  C8   C  CR6   0   0.101  27.2316  11.7158  20.1427
 I9O  C9   C  CR16  0  -0.280  26.4167  11.1057  19.1912
 I9O  N18  N  NT    0  -0.436  28.0594  13.3999  18.5451
 I9O  N26  N  NR15  0  -0.626  29.2542  14.7056  14.8970
 I9O  N29  N  N     0  -0.459  28.4468  16.2648  16.2292
 I9O  C31  C  CR5   0   0.072  28.5417  15.0821  16.9064
 I9O  C32  C  CH2   0  -0.333  28.1614  14.8364  18.3255
 I9O  H1   H  HCR6  0   0.263  25.2472   9.3876  18.6781
 I9O  H2   H  HCR6  0   0.268  25.6891   8.2118  20.7873
 I9O  H3   H  HCH2  0   0.220  28.6609  13.2498  20.5794
 I9O  H4   H  HCH2  0   0.262  27.0301  13.8194  20.2830
 I9O  H6   H  HCH2  0   0.212  30.1575  13.0914  18.4643
 I9O  H7   H  HCH2  0   0.246  28.5368  12.0244  16.1041
 I9O  H8   H  HCH2  0   0.251  30.2633  12.3385  16.1927
 I9O  H9   H  HCR5  0   0.270  28.9540  16.6997  14.2050
 I9O  H10  H  HCR6  0   0.266  28.1304  11.5108  22.0676
 I9O  H11  H  HCR6  0   0.255  26.2147  11.6155  18.2580
 I9O  H13  H  HNR5  0   0.412  29.6216  14.2733  14.0636
 I9O  H15  H  HCH2  0   0.207  28.8950  15.3047  19.0051
 I9O  H16  H  HCH2  0   0.246  27.1941  15.2943  18.5516
 I9O  H5   H  HCH2  0   0.250  29.1621  11.6413  18.3889

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
 I9O  N26  C27  aromatic  1.351  0.020  1.351
 I9O  N26  C25  aromatic  1.365  0.020  1.365
 I9O  C27  N29  aromatic  1.310  0.020  1.310
 I9O  N29  C31  aromatic  1.366  0.020  1.366
 I9O  C25  C22  single    1.483  0.020  1.483
 I9O  C25  C31  aromatic  1.362  0.020  1.362
 I9O  C22  C19  single    1.529  0.020  1.529
 I9O  C31  C32  single    1.490  0.020  1.490
 I9O  C32  N18  single    1.457  0.020  1.457
 I9O  C19  N18  single    1.457  0.020  1.457
 I9O  N18  C15  single    1.445  0.020  1.445
 I9O  C9   C11  aromatic  1.385  0.020  1.385
 I9O  C9   C8   aromatic  1.393  0.020  1.393
 I9O  C15  C8   single    1.508  0.020  1.508
 I9O  C11  C13  aromatic  1.389  0.020  1.389
 I9O  C8   C6   aromatic  1.388  0.020  1.388
 I9O  C13  C5   aromatic  1.387  0.020  1.387
 I9O  C6   C5   aromatic  1.392  0.020  1.392
 I9O  C5   C2   single    1.496  0.020  1.496
 I9O  F3   C2   single    1.342  0.020  1.342
 I9O  F1   C2   single    1.336  0.020  1.336
 I9O  C2   F4   single    1.341  0.020  1.341
 I9O  C11  H1   single    0.930  0.020  1.080
 I9O  C13  H2   single    0.930  0.020  1.080
 I9O  C15  H3   single    0.970  0.020  1.090
 I9O  C15  H4   single    0.970  0.020  1.090
 I9O  C19  H5   single    0.970  0.020  1.090
 I9O  C19  H6   single    0.970  0.020  1.090
 I9O  C22  H7   single    0.970  0.020  1.090
 I9O  C22  H8   single    0.970  0.020  1.090
 I9O  C27  H9   single    0.930  0.020  1.080
 I9O  C6   H10  single    0.930  0.020  1.080
 I9O  C9   H11  single    0.930  0.020  1.080
 I9O  N26  H13  single    0.860  0.020  1.020
 I9O  C32  H15  single    0.970  0.020  1.090
 I9O  C32  H16  single    0.970  0.020  1.090

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
 I9O  C5   C2   F4   111.77  3.000
 I9O  F4   C2   F3   106.20  3.000
 I9O  C5   C2   F3   111.75  3.000
 I9O  F4   C2   F1   106.85  3.000
 I9O  F3   C2   F1   107.03  3.000
 I9O  C5   C2   F1   112.84  3.000
 I9O  H1   C11  C9   119.89  3.000
 I9O  H1   C11  C13  119.49  3.000
 I9O  C9   C11  C13  120.61  3.000
 I9O  H2   C13  C5   121.37  3.000
 I9O  H2   C13  C11  119.56  3.000
 I9O  C5   C13  C11  119.07  3.000
 I9O  H4   C15  H3   105.81  3.000
 I9O  H4   C15  N18  107.85  3.000
 I9O  H3   C15  N18  112.52  3.000
 I9O  H4   C15  C8   107.86  3.000
 I9O  H3   C15  C8   109.28  3.000
 I9O  N18  C15  C8   113.14  3.000
 I9O  H6   C19  H5   106.79  3.000
 I9O  H6   C19  N18  111.25  3.000
 I9O  H5   C19  N18  108.70  3.000
 I9O  H6   C19  C22  109.49  3.000
 I9O  H5   C19  C22  109.14  3.000
 I9O  N18  C19  C22  111.34  3.000
 I9O  H8   C22  H7   106.93  3.000
 I9O  H8   C22  C25  112.07  3.000
 I9O  H7   C22  C25  111.29  3.000
 I9O  H8   C22  C19  109.50  3.000
 I9O  H7   C22  C19  110.13  3.000
 I9O  C25  C22  C19  106.93  3.000
 I9O  C31  C25  N26  105.10  3.000
 I9O  C31  C25  C22  124.99  3.000
 I9O  N26  C25  C22  129.90  3.000
 I9O  H9   C27  N29  126.00  3.000
 I9O  H9   C27  N26  122.20  3.000
 I9O  N29  C27  N26  111.80  3.000
 I9O  C6   C5   C13  120.28  3.000
 I9O  C6   C5   C2   118.25  3.000
 I9O  C13  C5   C2   121.46  3.000
 I9O  H10  C6   C8   118.87  3.000
 I9O  H10  C6   C5   120.35  3.000
 I9O  C8   C6   C5   120.77  3.000
 I9O  C9   C8   C6   118.68  3.000
 I9O  C6   C8   C15  119.90  3.000
 I9O  C9   C8   C15  121.37  3.000
 I9O  H11  C9   C8   119.45  3.000
 I9O  H11  C9   C11  119.97  3.000
 I9O  C8   C9   C11  120.58  3.000
 I9O  C32  N18  C19  112.48  3.000
 I9O  C19  N18  C15  112.21  3.000
 I9O  C32  N18  C15  111.10  3.000
 I9O  H13  N26  C27  125.97  3.000
 I9O  H13  N26  C25  126.71  3.000
 I9O  C27  N26  C25  107.31  3.000
 I9O  C31  N29  C27  104.93  3.000
 I9O  C32  C31  N29  126.68  3.000
 I9O  C32  C31  C25  122.47  3.000
 I9O  N29  C31  C25  110.85  3.000
 I9O  H16  C32  H15  106.42  3.000
 I9O  H16  C32  C31  110.71  3.000
 I9O  H15  C32  C31  110.29  3.000
 I9O  H16  C32  N18  108.65  3.000
 I9O  H15  C32  N18  111.84  3.000
 I9O  C31  C32  N18  108.91  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
 I9O  CONST_01  C6   C8   C9   C11     0.00   0.0  0
 I9O  CONST_02  C6   C5   C13  C11     0.00   0.0  0
 I9O  CONST_03  C8   C9   C11  C13     0.00   0.0  0
 I9O  CONST_04  C8   C6   C5   C13     0.00   0.0  0
 I9O  CONST_05  N29  C27  N26  C25     0.00   0.0  0
 I9O  CONST_06  C27  N29  C31  C25     0.00   0.0  0
 I9O  CONST_07  C31  C25  N26  C27     0.00   0.0  0
 I9O  CONST_08  C9   C11  C13  C5      0.00   0.0  0
 I9O  CONST_09  C9   C8   C6   C5      0.00   0.0  0
 I9O  CONST_10  C31  N29  C27  N26     0.00   0.0  0
 I9O  CONST_11  N29  C31  C25  N26     0.00   0.0  0
 I9O  CONST_12  C11  C13  C5   C2    180.00   0.0  0
 I9O  CONST_13  C8   C6   C5   C2    180.00   0.0  0
 I9O  CONST_14  C15  C8   C9   C11   180.00   0.0  0
 I9O  CONST_15  C5   C6   C8   C15   180.00   0.0  0
 I9O  CONST_16  H11  C9   C11  C13   180.00   0.0  0
 I9O  CONST_17  H10  C6   C5   C13   180.00   0.0  0
 I9O  CONST_18  H13  N26  C25  C22     0.00   0.0  0
 I9O  CONST_19  H9   C27  N26  C25   180.00   0.0  0
 I9O  CONST_20  H1   C11  C13  C5    180.00   0.0  0
 I9O  CONST_21  H11  C9   C8   C6    180.00   0.0  0
 I9O  CONST_22  H2   C13  C5   C6    180.00   0.0  0
 I9O  CONST_23  H1   C11  C9   C8    180.00   0.0  0
 I9O  CONST_24  H2   C13  C11  C9    180.00   0.0  0
 I9O  CONST_25  H10  C6   C8   C9    180.00   0.0  0
 I9O  CONST_26  H13  N26  C27  N29   180.00   0.0  0
 I9O  CONST_27  H9   C27  N29  C31   180.00   0.0  0
 I9O  CONST_28  H13  N26  C25  C31   180.00   0.0  0
 I9O  Var_01    N26  C25  C22  C19   165.26  30.0  1
 I9O  Var_02    C31  C25  C22  C19   -14.31  30.0  1
 I9O  Var_03    C31  C32  N18  C19    49.36  30.0  1
 I9O  Var_04    C32  N18  C19  C22   -68.97  30.0  1
 I9O  Var_05    N18  C19  C22  C25    46.71  30.0  1
 I9O  Var_06    N18  C32  C31  C25   -15.63  30.0  1
 I9O  Var_07    N29  C31  C32  N18   164.16  30.0  1
 I9O  Var_08    C31  C32  N18  C15   176.11  30.0  1
 I9O  Var_09    C22  C19  N18  C15   164.89  30.0  1
 I9O  Var_10    C8   C15  N18  C19   -71.71  30.0  3
 I9O  Var_11    N18  C15  C8   C6    149.63  30.0  2
 I9O  Var_12    C32  N18  C15  C8    161.40  30.0  2
 I9O  Var_13    N18  C15  C8   C9    -33.12  30.0  2
 I9O  Var_14    H15  C32  N18  C19   -72.79  30.0  1
 I9O  Var_15    H16  C32  N18  C19   170.03  30.0  1
 I9O  Var_16    H5   C19  C22  C25   166.71  30.0  1
 I9O  Var_17    H6   C19  C22  C25   -76.73  30.0  1
 I9O  Var_18    H15  C32  C31  C25   107.46  30.0  1
 I9O  Var_19    H16  C32  C31  C25  -135.03  30.0  1
 I9O  Var_20    H7   C22  C19  N18   -74.34  30.0  1
 I9O  Var_21    H8   C22  C19  N18   168.35  30.0  1
 I9O  Var_22    H7   C22  C25  N26   -74.43  30.0  1
 I9O  Var_23    H8   C22  C25  N26    45.26  30.0  1
 I9O  Var_24    H15  C32  C31  N29   -72.75  30.0  1
 I9O  Var_25    H16  C32  C31  N29    44.77  30.0  1
 I9O  Var_26    H7   C22  C25  C31   106.00  30.0  1
 I9O  Var_27    H8   C22  C25  C31  -134.31  30.0  1
 I9O  Var_28    H5   C19  N18  C32   170.77  30.0  1
 I9O  Var_29    H6   C19  N18  C32    53.46  30.0  1
 I9O  Var_30    F3   C2   C5   C13   114.71  30.0  2
 I9O  Var_31    F1   C2   C5   C13    -5.97  30.0  2
 I9O  Var_32    F4   C2   C5   C13  -126.42  30.0  2
 I9O  Var_33    C6   C5   C2   F1    174.78  30.0  3
 I9O  Var_34    C6   C5   C2   F3    -64.55  30.0  3
 I9O  Var_35    C6   C5   C2   F4     54.32  30.0  3
 I9O  Var_36    H15  C32  N18  C15    53.95  30.0  1
 I9O  Var_37    H16  C32  N18  C15   -63.23  30.0  1
 I9O  Var_38    H5   C19  N18  C15    44.63  30.0  1
 I9O  Var_39    H6   C19  N18  C15   -72.68  30.0  1
 I9O  Var_40    H3   C15  N18  C19    52.75  30.0  3
 I9O  Var_41    H4   C15  N18  C19   169.07  30.0  3
 I9O  Var_42    H3   C15  C8   C6     23.42  30.0  2
 I9O  Var_43    H4   C15  C8   C6    -91.16  30.0  2
 I9O  Var_44    H3   C15  C8   C9   -159.33  30.0  2
 I9O  Var_45    H4   C15  C8   C9     86.09  30.0  2
 I9O  Var_46    H3   C15  N18  C32   -74.14  30.0  3
 I9O  Var_47    H4   C15  N18  C32    42.18  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
 I9O  plan-1  C2   0.020
 I9O  plan-1  C11  0.020
 I9O  plan-1  C13  0.020
 I9O  plan-1  C15  0.020
 I9O  plan-1  C5   0.020
 I9O  plan-1  C6   0.020
 I9O  plan-1  C8   0.020
 I9O  plan-1  C9   0.020
 I9O  plan-1  H1   0.020
 I9O  plan-1  H2   0.020
 I9O  plan-1  H10  0.020
 I9O  plan-1  H11  0.020
 I9O  plan-2  C22  0.020
 I9O  plan-2  C25  0.020
 I9O  plan-2  C27  0.020
 I9O  plan-2  N26  0.020
 I9O  plan-2  N29  0.020
 I9O  plan-2  C31  0.020
 I9O  plan-2  C32  0.020
 I9O  plan-2  H9   0.020
 I9O  plan-2  H13  0.020

