# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 09:32:08 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: [3-(2-methylimidazol-1-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nccn1c2cccc(CN)c2
#
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
 QT5  QT5  '[3-(2-methylimidazol-1-yl)phenyl]methanamine'  ligand  27  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QT5
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
 QT5  C1   C  CH3   0  -0.751  24.4311  33.0320  35.2992
 QT5  C2   C  CR5   0   0.413  25.6986  33.6405  34.8166
 QT5  N1   N  N     0  -0.457  26.6662  34.0819  35.5792
 QT5  C3   C  CR15  0  -0.219  27.6426  34.5346  34.7355
 QT5  C4   C  CR15  0  -0.118  27.2650  34.3594  33.4408
 QT5  N2   N  NR5   0  -0.539  26.0146  33.7918  33.4990
 QT5  C5   C  CR6   0   0.328  25.2390  33.4062  32.3801
 QT5  C6   C  CR16  0  -0.289  23.9583  33.9083  32.2108
 QT5  C7   C  CR16  0  -0.240  23.2164  33.5074  31.1069
 QT5  C8   C  CR16  0  -0.280  23.7542  32.6315  30.1780
 QT5  C9   C  CR6   0   0.116  25.0503  32.1410  30.3326
 QT5  C10  C  CR16  0  -0.341  25.7813  32.5273  31.4479
 QT5  C11  C  CH2   0  -0.356  25.6438  31.2026  29.3134
 QT5  N3   N  NH2   0  -0.788  24.7735  30.0612  29.0788
 QT5  H1   H  HCH3  0   0.265  24.5373  32.7811  36.3521
 QT5  H2   H  HCH3  0   0.259  23.5852  33.7141  35.2031
 QT5  H3   H  HCH3  0   0.256  24.1808  32.1223  34.7530
 QT5  H4   H  HCR5  0   0.248  28.5620  34.9629  35.1038
 QT5  H5   H  HCR5  0   0.290  27.7423  34.5931  32.5038
 QT5  H6   H  HCR6  0   0.273  23.5451  34.6118  32.9218
 QT5  H7   H  HCR6  0   0.260  22.2152  33.8942  30.9690
 QT5  H8   H  HCR6  0   0.251  23.1667  32.3258  29.3218
 QT5  H9   H  HCR6  0   0.266  26.7798  32.1349  31.6037
 QT5  H10  H  HCH2  0   0.219  26.6601  30.9332  29.6293
 QT5  H11  H  HCH2  0   0.241  25.7529  31.7394  28.3672
 QT5  H12  H  HNH2  0   0.352  25.1429  29.5098  28.3149
 QT5  H13  H  HNH2  0   0.343  24.7837  29.4576  29.8914

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
 QT5  N3   C11  single    1.454  0.020  1.454
 QT5  C11  C9   single    1.507  0.020  1.507
 QT5  C8   C9   aromatic  1.394  0.020  1.394
 QT5  C8   C7   aromatic  1.385  0.020  1.385
 QT5  C9   C10  aromatic  1.388  0.020  1.388
 QT5  C7   C6   aromatic  1.389  0.020  1.389
 QT5  C10  C5   aromatic  1.391  0.020  1.391
 QT5  C6   C5   aromatic  1.386  0.020  1.386
 QT5  C5   N2   single    1.415  0.020  1.415
 QT5  C4   N2   aromatic  1.374  0.020  1.374
 QT5  C4   C3   aromatic  1.360  0.020  1.360
 QT5  N2   C2   aromatic  1.363  0.020  1.363
 QT5  C3   N1   aromatic  1.368  0.020  1.368
 QT5  C2   C1   single    1.487  0.020  1.487
 QT5  C2   N1   aromatic  1.309  0.020  1.309
 QT5  C1   H1   single    0.970  0.020  1.090
 QT5  C1   H2   single    0.970  0.020  1.090
 QT5  C1   H3   single    0.970  0.020  1.090
 QT5  C3   H4   single    0.930  0.020  1.080
 QT5  C4   H5   single    0.930  0.020  1.080
 QT5  C6   H6   single    0.930  0.020  1.080
 QT5  C7   H7   single    0.930  0.020  1.080
 QT5  C8   H8   single    0.930  0.020  1.080
 QT5  C10  H9   single    0.930  0.020  1.080
 QT5  C11  H10  single    0.970  0.020  1.090
 QT5  C11  H11  single    0.970  0.020  1.090
 QT5  N3   H12  single    0.890  0.020  1.040
 QT5  N3   H13  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
 QT5  H3   C1   H2   107.44  3.000
 QT5  H3   C1   H1   108.36  3.000
 QT5  H2   C1   H1   107.77  3.000
 QT5  H3   C1   C2   112.00  3.000
 QT5  H2   C1   C2   112.12  3.000
 QT5  H1   C1   C2   108.99  3.000
 QT5  N2   C2   N1   110.75  3.000
 QT5  N1   C2   C1   125.40  3.000
 QT5  N2   C2   C1   123.84  3.000
 QT5  C3   N1   C2   106.26  3.000
 QT5  H4   C3   C4   127.78  3.000
 QT5  H4   C3   N1   121.94  3.000
 QT5  C4   C3   N1   110.27  3.000
 QT5  H5   C4   N2   121.98  3.000
 QT5  H5   C4   C3   132.62  3.000
 QT5  N2   C4   C3   105.39  3.000
 QT5  C5   N2   C4   125.29  3.000
 QT5  C4   N2   C2   107.32  3.000
 QT5  C5   N2   C2   127.36  3.000
 QT5  C10  C5   C6   120.48  3.000
 QT5  C6   C5   N2   120.29  3.000
 QT5  C10  C5   N2   119.23  3.000
 QT5  H6   C6   C7   120.39  3.000
 QT5  H6   C6   C5   120.53  3.000
 QT5  C7   C6   C5   119.08  3.000
 QT5  H7   C7   C8   119.98  3.000
 QT5  H7   C7   C6   119.48  3.000
 QT5  C8   C7   C6   120.53  3.000
 QT5  H8   C8   C9   119.52  3.000
 QT5  H8   C8   C7   119.89  3.000
 QT5  C9   C8   C7   120.59  3.000
 QT5  C11  C9   C10  120.61  3.000
 QT5  C10  C9   C8   118.72  3.000
 QT5  C11  C9   C8   120.67  3.000
 QT5  H9   C10  C9   119.98  3.000
 QT5  H9   C10  C5   119.43  3.000
 QT5  C9   C10  C5   120.58  3.000
 QT5  H11  C11  H10  106.09  3.000
 QT5  H11  C11  N3   107.79  3.000
 QT5  H10  C11  N3   114.07  3.000
 QT5  H11  C11  C9   108.59  3.000
 QT5  H10  C11  C9   108.83  3.000
 QT5  N3   C11  C9   111.23  3.000
 QT5  H13  N3   H12  106.11  3.000
 QT5  H13  N3   C11  109.41  3.000
 QT5  H12  N3   C11  109.33  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
 QT5  CONST_03  C3   C4   N2   C2    0.00   0.0  0
 QT5  CONST_04  C4   C3   N1   C2    0.00   0.0  0
 QT5  CONST_05  N2   C4   C3   N1    0.00   0.0  0
 QT5  CONST_06  C5   N2   C2   N1  180.00   0.0  0
 QT5  CONST_07  C4   N2   C2   N1    0.00   0.0  0
 QT5  CONST_08  C5   N2   C4   C3  180.00   0.0  0
 QT5  CONST_09  N2   C2   N1   C3    0.00   0.0  0
 QT5  CONST_12  C9   C10  C5   N2  180.00   0.0  0
 QT5  CONST_13  C7   C6   C5   N2  180.00   0.0  0
 QT5  CONST_14  C8   C9   C10  C5    0.00   0.0  0
 QT5  CONST_15  C8   C7   C6   C5    0.00   0.0  0
 QT5  CONST_16  C9   C8   C7   C6    0.00   0.0  0
 QT5  CONST_17  C9   C10  C5   C6    0.00   0.0  0
 QT5  CONST_18  C10  C9   C8   C7    0.00   0.0  0
 QT5  CONST_19  C10  C5   C6   C7    0.00   0.0  0
 QT5  CONST_20  C5   N2   C2   C1    0.00   0.0  0
 QT5  CONST_21  C4   N2   C2   C1  180.00   0.0  0
 QT5  CONST_22  C3   N1   C2   C1  180.00   0.0  0
 QT5  CONST_23  C11  C9   C10  C5  180.00   0.0  0
 QT5  CONST_24  C11  C9   C8   C7  180.00   0.0  0
 QT5  CONST_25  H5   C4   N2   C2  180.00   0.0  0
 QT5  CONST_26  H4   C3   N1   C2  180.00   0.0  0
 QT5  CONST_27  H9   C10  C5   N2    0.00   0.0  0
 QT5  CONST_28  H6   C6   C5   N2    0.00   0.0  0
 QT5  CONST_29  H7   C7   C6   C5  180.00   0.0  0
 QT5  CONST_30  H8   C8   C7   C6  180.00   0.0  0
 QT5  Var_01    N3   C11  C9   C8  -52.99  30.0  3
 QT5  Var_02    H1   C1   C2   N1  -14.23  30.0  2
 QT5  Var_03    H12  N3   C11  C9  173.31  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
 QT5  plan-1  C1   0.020
 QT5  plan-1  C2   0.020
 QT5  plan-1  N1   0.020
 QT5  plan-1  C3   0.020
 QT5  plan-1  C4   0.020
 QT5  plan-1  N2   0.020
 QT5  plan-1  C5   0.020
 QT5  plan-1  H4   0.020
 QT5  plan-1  H5   0.020
 QT5  plan-2  N2   0.020
 QT5  plan-2  C5   0.020
 QT5  plan-2  C6   0.020
 QT5  plan-2  C7   0.020
 QT5  plan-2  C8   0.020
 QT5  plan-2  C9   0.020
 QT5  plan-2  C10  0.020
 QT5  plan-2  C11  0.020
 QT5  plan-2  H6   0.020
 QT5  plan-2  H7   0.020
 QT5  plan-2  H8   0.020
 QT5  plan-2  H9   0.020

