# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:39:12 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: [3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(c1c2ccncc2)c3c(C)cc(CN)cc3C
#
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
 EHH  EHH  '[3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)phenyl]methanamine'  ligand  42  22  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EHH
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
 EHH  N1   N  NR5   0  -0.457  -2.6916   1.6898   0.0359
 EHH  C5   C  CR15  0   0.080  -2.0487   2.8707  -0.0179
 EHH  C6   C  CH3   0  -0.543  -4.1303   1.5329   0.0524
 EHH  C7   C  CR6   0   0.125  -1.9822  -0.7232   0.0395
 EHH  C8   C  CR6   0  -0.050   0.8329   0.8147  -0.1203
 EHH  C10  C  CR16  0  -0.059  -1.4450  -2.9572  -0.6485
 EHH  C13  C  CR16  0  -0.367  -2.9495  -1.2972   0.8650
 EHH  C15  C  CR16  0  -0.383   2.8611   0.3794  -1.3369
 EHH  C17  C  CR16  0  -0.378   2.6715  -0.3282   0.9356
 EHH  C12  C  CR16  0  -0.060  -3.1045  -2.6742   0.8680
 EHH  C14  C  CR6   0   0.111   1.5769   0.9073  -1.3046
 EHH  C16  C  CR6   0   0.108   3.4225  -0.2466  -0.2285
 EHH  C18  C  CR6   0   0.107   1.3828   0.1962   1.0077
 EHH  C19  C  CH3   0  -0.745   0.9929   1.5393  -2.5357
 EHH  C2   C  CR5   0   0.308  -1.7271   0.7102  -0.0044
 EHH  C3   C  CR5   0   0.043  -0.5270   1.3840  -0.0730
 EHH  C9   C  CR16  0  -0.374  -1.2153  -1.5951  -0.7350
 EHH  N11  N  N     0  -0.409  -2.3729  -3.5019   0.1318
 EHH  N22  N  NH2   0  -0.796   5.4477  -0.9974   0.9617
 EHH  N4   N  N     0  -0.439  -0.7489   2.7283  -0.0784
 EHH  H1   H  HCR5  0   0.284  -2.5831   3.8094  -0.0206
 EHH  H2   H  HCH3  0   0.268  -4.4337   0.7398  -0.6266
 EHH  H3   H  HCH3  0   0.263  -4.4970   1.3083   1.0520
 EHH  H4   H  HCH3  0   0.277  -4.5849   2.4623  -0.2801
 EHH  H5   H  HCR6  0   0.265  -0.8530  -3.6396  -1.2480
 EHH  H6   H  HCR6  0   0.268  -3.5640  -0.6971   1.5211
 EHH  H7   H  HCR6  0   0.235   3.4388   0.4533  -2.2528
 EHH  H8   H  HCR6  0   0.238   3.1019  -0.8031   1.8088
 EHH  H9   H  HCH3  0   0.242   0.1415   1.0302   2.5677
 EHH  H10  H  HCH3  0   0.245  -0.1932  -0.6535   2.2098
 EHH  H11  H  HCH3  0   0.248   1.2534  -0.2262   3.1104
 EHH  H12  H  HCH2  0   0.242   4.7245  -1.8286  -0.7868
 EHH  H13  H  HCH2  0   0.213   5.3874  -0.2328  -1.0416
 EHH  H14  H  HCR6  0   0.265  -3.8550  -3.1268   1.5066
 EHH  H15  H  HCH3  0   0.239   0.0684   1.0405  -2.8347
 EHH  H16  H  HCH3  0   0.247   0.7439   2.5883  -2.3755
 EHH  H17  H  HCH3  0   0.246   1.6882   1.4814  -3.3722
 EHH  H18  H  HCR6  0   0.269  -0.4539  -1.2208  -1.4050
 EHH  H19  H  HNH2  0   0.355   6.3263  -1.4828   0.8369
 EHH  H20  H  HNH2  0   0.344   5.6821  -0.0882   1.3403
 EHH  C20  C  CH3   0  -0.747   0.6076   0.0843   2.2899
 EHH  C21  C  CH2   0  -0.330   4.8073  -0.8371  -0.3304

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
 EHH  N22  C21  single    1.451  0.020  1.451
 EHH  C21  C16  single    1.509  0.020  1.509
 EHH  C16  C15  aromatic  1.391  0.020  1.391
 EHH  C16  C17  aromatic  1.388  0.020  1.388
 EHH  C15  C14  aromatic  1.389  0.020  1.389
 EHH  C17  C18  aromatic  1.393  0.020  1.393
 EHH  C14  C19  single    1.502  0.020  1.502
 EHH  C14  C8   aromatic  1.402  0.020  1.402
 EHH  C18  C8   aromatic  1.399  0.020  1.399
 EHH  C18  C20  single    1.502  0.020  1.502
 EHH  C8   C3   single    1.475  0.020  1.475
 EHH  C3   N4   aromatic  1.362  0.020  1.362
 EHH  C3   C2   aromatic  1.378  0.020  1.378
 EHH  N4   C5   aromatic  1.309  0.020  1.309
 EHH  C9   C10  aromatic  1.384  0.020  1.384
 EHH  C9   C7   aromatic  1.396  0.020  1.396
 EHH  C10  N11  aromatic  1.329  0.020  1.329
 EHH  C2   C7   single    1.457  0.020  1.457
 EHH  C2   N1   aromatic  1.375  0.020  1.375
 EHH  C7   C13  aromatic  1.395  0.020  1.395
 EHH  N11  C12  aromatic  1.328  0.020  1.328
 EHH  C13  C12  aromatic  1.386  0.020  1.386
 EHH  C5   N1   aromatic  1.346  0.020  1.346
 EHH  N1   C6   single    1.447  0.020  1.447
 EHH  C5   H1   single    0.930  0.020  1.080
 EHH  C6   H2   single    0.970  0.020  1.090
 EHH  C6   H3   single    0.970  0.020  1.090
 EHH  C6   H4   single    0.970  0.020  1.090
 EHH  C10  H5   single    0.930  0.020  1.080
 EHH  C13  H6   single    0.930  0.020  1.080
 EHH  C15  H7   single    0.930  0.020  1.080
 EHH  C17  H8   single    0.930  0.020  1.080
 EHH  C20  H9   single    0.970  0.020  1.090
 EHH  C20  H10  single    0.970  0.020  1.090
 EHH  C20  H11  single    0.970  0.020  1.090
 EHH  C21  H12  single    0.970  0.020  1.090
 EHH  C21  H13  single    0.970  0.020  1.090
 EHH  C12  H14  single    0.930  0.020  1.080
 EHH  C19  H15  single    0.970  0.020  1.090
 EHH  C19  H16  single    0.970  0.020  1.090
 EHH  C19  H17  single    0.970  0.020  1.090
 EHH  C9   H18  single    0.930  0.020  1.080
 EHH  N22  H19  single    0.890  0.020  1.040
 EHH  N22  H20  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
 EHH  C2   N1   C6   128.33  3.000
 EHH  C6   N1   C5   124.79  3.000
 EHH  C2   N1   C5   106.79  3.000
 EHH  H1   C5   N4   125.86  3.000
 EHH  H1   C5   N1   121.76  3.000
 EHH  N4   C5   N1   112.38  3.000
 EHH  H4   C6   H3   108.46  3.000
 EHH  H4   C6   H2   108.43  3.000
 EHH  H3   C6   H2   109.21  3.000
 EHH  H4   C6   N1   108.64  3.000
 EHH  H3   C6   N1   111.58  3.000
 EHH  H2   C6   N1   110.44  3.000
 EHH  C9   C7   C2   120.12  3.000
 EHH  C2   C7   C13  122.96  3.000
 EHH  C9   C7   C13  116.89  3.000
 EHH  C3   C8   C18  120.47  3.000
 EHH  C3   C8   C14  119.41  3.000
 EHH  C18  C8   C14  120.12  3.000
 EHH  H5   C10  N11  116.60  3.000
 EHH  H5   C10  C9   119.62  3.000
 EHH  N11  C10  C9   123.77  3.000
 EHH  H6   C13  C12  119.13  3.000
 EHH  H6   C13  C7   121.67  3.000
 EHH  C12  C13  C7   119.18  3.000
 EHH  H7   C15  C16  119.21  3.000
 EHH  H7   C15  C14  119.07  3.000
 EHH  C16  C15  C14  121.71  3.000
 EHH  H8   C17  C18  119.40  3.000
 EHH  H8   C17  C16  119.14  3.000
 EHH  C18  C17  C16  121.46  3.000
 EHH  H14  C12  N11  116.60  3.000
 EHH  H14  C12  C13  119.56  3.000
 EHH  N11  C12  C13  123.83  3.000
 EHH  C19  C14  C15  120.03  3.000
 EHH  C19  C14  C8   120.92  3.000
 EHH  C15  C14  C8   119.04  3.000
 EHH  C21  C16  C17  122.03  3.000
 EHH  C17  C16  C15  118.45  3.000
 EHH  C21  C16  C15  119.51  3.000
 EHH  C20  C18  C17  119.56  3.000
 EHH  C20  C18  C8   121.21  3.000
 EHH  C17  C18  C8   119.22  3.000
 EHH  H17  C19  H16  108.05  3.000
 EHH  H17  C19  H15  107.80  3.000
 EHH  H16  C19  H15  106.65  3.000
 EHH  H17  C19  C14  111.03  3.000
 EHH  H16  C19  C14  111.92  3.000
 EHH  H15  C19  C14  111.18  3.000
 EHH  C3   C2   C7   129.44  3.000
 EHH  C7   C2   N1   125.26  3.000
 EHH  C3   C2   N1   105.30  3.000
 EHH  N4   C3   C2   109.93  3.000
 EHH  C2   C3   C8   128.01  3.000
 EHH  N4   C3   C8   122.06  3.000
 EHH  H18  C9   C10  119.76  3.000
 EHH  H18  C9   C7   120.96  3.000
 EHH  C10  C9   C7   119.27  3.000
 EHH  C12  N11  C10  117.05  3.000
 EHH  H20  N22  H19  106.02  3.000
 EHH  H20  N22  C21  109.64  3.000
 EHH  H19  N22  C21  109.05  3.000
 EHH  C3   N4   C5   105.59  3.000
 EHH  H11  C20  H10  107.31  3.000
 EHH  H11  C20  H9   107.98  3.000
 EHH  H10  C20  H9   106.94  3.000
 EHH  H11  C20  C18  110.98  3.000
 EHH  H10  C20  C18  111.48  3.000
 EHH  H9   C20  C18  111.92  3.000
 EHH  H13  C21  H12  105.56  3.000
 EHH  H13  C21  N22  113.84  3.000
 EHH  H12  C21  N22  107.73  3.000
 EHH  H13  C21  C16  108.24  3.000
 EHH  H12  C21  C16  108.25  3.000
 EHH  N22  C21  C16  112.83  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
 EHH  CONST_01  C8   C3   C2   N1   180.00   0.0  0
 EHH  CONST_02  N4   C3   C2   N1     0.00   0.0  0
 EHH  CONST_05  C3   N4   C5   N1     0.00   0.0  0
 EHH  CONST_06  C8   C3   N4   C5   180.00   0.0  0
 EHH  CONST_07  C2   C3   N4   C5     0.00   0.0  0
 EHH  CONST_08  C3   C2   N1   C5     0.00   0.0  0
 EHH  CONST_09  C7   C2   N1   C5   180.00   0.0  0
 EHH  CONST_10  N11  C10  C9   C7     0.00   0.0  0
 EHH  CONST_11  C8   C3   C2   C7     0.00   0.0  0
 EHH  CONST_12  N4   C3   C2   C7   180.00   0.0  0
 EHH  CONST_13  N11  C12  C13  C7     0.00   0.0  0
 EHH  CONST_14  C16  C15  C14  C8     0.00   0.0  0
 EHH  CONST_15  C16  C17  C18  C8     0.00   0.0  0
 EHH  CONST_16  C2   C7   C9   C10  180.00   0.0  0
 EHH  CONST_17  C13  C7   C9   C10    0.00   0.0  0
 EHH  CONST_18  C13  C12  N11  C10    0.00   0.0  0
 EHH  CONST_20  C18  C17  C16  C15    0.00   0.0  0
 EHH  CONST_21  C18  C8   C14  C15    0.00   0.0  0
 EHH  CONST_22  C3   C8   C14  C15  180.00   0.0  0
 EHH  CONST_23  C14  C15  C16  C17    0.00   0.0  0
 EHH  CONST_24  C14  C8   C18  C17    0.00   0.0  0
 EHH  CONST_25  C3   C8   C18  C17  180.00   0.0  0
 EHH  CONST_26  C9   C10  N11  C12    0.00   0.0  0
 EHH  CONST_27  C9   C7   C13  C12    0.00   0.0  0
 EHH  CONST_28  C2   C7   C13  C12  180.00   0.0  0
 EHH  CONST_33  N4   C5   N1   C2     0.00   0.0  0
 EHH  CONST_35  C3   C2   N1   C6   180.00   0.0  0
 EHH  CONST_36  C7   C2   N1   C6     0.00   0.0  0
 EHH  CONST_37  N4   C5   N1   C6   180.00   0.0  0
 EHH  CONST_38  C16  C17  C18  C20  180.00   0.0  0
 EHH  CONST_39  C14  C8   C18  C20  180.00   0.0  0
 EHH  CONST_40  C3   C8   C18  C20    0.00   0.0  0
 EHH  CONST_41  C14  C15  C16  C21  180.00   0.0  0
 EHH  CONST_42  C18  C17  C16  C21  180.00   0.0  0
 EHH  CONST_43  C19  C14  C15  C16  180.00   0.0  0
 EHH  CONST_44  C19  C14  C8   C18  180.00   0.0  0
 EHH  CONST_45  C3   C8   C14  C19    0.00   0.0  0
 EHH  CONST_46  H5   C10  C9   C7   180.00   0.0  0
 EHH  CONST_47  H14  C12  C13  C7   180.00   0.0  0
 EHH  CONST_48  H7   C15  C14  C8   180.00   0.0  0
 EHH  CONST_49  H8   C17  C18  C8   180.00   0.0  0
 EHH  CONST_50  H18  C9   C7   C13  180.00   0.0  0
 EHH  CONST_51  H6   C13  C7   C2     0.00   0.0  0
 EHH  CONST_52  H1   C5   N1   C2   180.00   0.0  0
 EHH  Var_01    N22  C21  C16  C15  158.47  30.0  2
 EHH  Var_02    H2   C6   N1   C5   135.54  30.0  2
 EHH  Var_03    H15  C19  C14  C8   -57.15  30.0  2
 EHH  Var_04    H9   C20  C18  C8   -47.15  30.0  2
 EHH  Var_05    H19  N22  C21  C16  174.17  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
 EHH  plan-1  N1   0.020
 EHH  plan-1  C5   0.020
 EHH  plan-1  C6   0.020
 EHH  plan-1  C7   0.020
 EHH  plan-1  C8   0.020
 EHH  plan-1  C2   0.020
 EHH  plan-1  C3   0.020
 EHH  plan-1  N4   0.020
 EHH  plan-1  H1   0.020
 EHH  plan-2  C8   0.020
 EHH  plan-2  C15  0.020
 EHH  plan-2  C17  0.020
 EHH  plan-2  C14  0.020
 EHH  plan-2  C16  0.020
 EHH  plan-2  C18  0.020
 EHH  plan-2  C19  0.020
 EHH  plan-2  C3   0.020
 EHH  plan-2  H7   0.020
 EHH  plan-2  H8   0.020
 EHH  plan-2  C20  0.020
 EHH  plan-2  C21  0.020
 EHH  plan-3  C7   0.020
 EHH  plan-3  C10  0.020
 EHH  plan-3  C13  0.020
 EHH  plan-3  C12  0.020
 EHH  plan-3  C2   0.020
 EHH  plan-3  C9   0.020
 EHH  plan-3  N11  0.020
 EHH  plan-3  H5   0.020
 EHH  plan-3  H6   0.020
 EHH  plan-3  H14  0.020
 EHH  plan-3  H18  0.020

