# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:19:07 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: 1-(2,4-dimethyl-1H-imidazol-5-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(CN)c(C)n1
#
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
 WUG  WUG  1-(2,4-dimethyl-1H-imidazol-5-yl)methanamine  ligand  20  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WUG
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
 WUG  C01  C  CH3   0  -0.744  4.9919  -75.2107  20.4915
 WUG  C02  C  CR5   0   0.073  6.0680  -76.1183  20.0029
 WUG  C03  C  CR5   0   0.263  6.3469  -77.3992  20.3939
 WUG  C04  C  CH2   0  -0.373  5.7347  -78.3117  21.3991
 WUG  N05  N  NH2   0  -0.800  5.6623  -79.6721  20.8837
 WUG  N06  N  NR15  0  -0.623  7.4327  -77.7701  19.6439
 WUG  C07  C  CR5   0   0.399  7.7656  -76.7383  18.8406
 WUG  C08  C  CH3   0  -0.744  8.8940  -76.7893  17.8737
 WUG  N09  N  N     0  -0.479  6.9617  -75.7221  19.0383
 WUG  H1   H  HCH3  0   0.236  4.4533  -74.7542  19.6599
 WUG  H2   H  HCH3  0   0.234  4.2654  -75.7473  21.1012
 WUG  H3   H  HCH3  0   0.236  5.3901  -74.3969  21.1017
 WUG  H4   H  HCH2  0   0.240  6.3517  -78.3363  22.3029
 WUG  H5   H  HCH2  0   0.218  4.7687  -77.8899  21.7048
 WUG  H6   H  HNH2  0   0.356  5.3343  -80.2883  21.6163
 WUG  H7   H  HNH2  0   0.345  4.9709  -79.7198  20.1457
 WUG  H9   H  HNR5  0   0.403  7.8549  -78.6852  19.6579
 WUG  H10  H  HCH3  0   0.254  8.9064  -75.8796  17.2780
 WUG  H11  H  HCH3  0   0.253  9.8567  -76.8749  18.3809
 WUG  H12  H  HCH3  0   0.252  8.8047  -77.6400  17.1971

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
 WUG  C08  C07  single    1.487  0.020  1.487
 WUG  C07  N09  aromatic  1.311  0.020  1.311
 WUG  C07  N06  aromatic  1.349  0.020  1.349
 WUG  N09  C02  aromatic  1.373  0.020  1.373
 WUG  N06  C03  aromatic  1.371  0.020  1.371
 WUG  C02  C03  aromatic  1.368  0.020  1.368
 WUG  C02  C01  single    1.490  0.020  1.490
 WUG  C03  C04  single    1.489  0.020  1.489
 WUG  N05  C04  single    1.457  0.020  1.457
 WUG  C01  H1   single    0.970  0.020  1.090
 WUG  C01  H2   single    0.970  0.020  1.090
 WUG  C01  H3   single    0.970  0.020  1.090
 WUG  C04  H4   single    0.970  0.020  1.090
 WUG  C04  H5   single    0.970  0.020  1.090
 WUG  N05  H6   single    0.890  0.020  1.040
 WUG  N05  H7   single    0.890  0.020  1.040
 WUG  N06  H9   single    0.860  0.020  1.020
 WUG  C08  H10  single    0.970  0.020  1.090
 WUG  C08  H11  single    0.970  0.020  1.090
 WUG  C08  H12  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
 WUG  H3   C01  H2   107.30  3.000
 WUG  H3   C01  H1   107.10  3.000
 WUG  H2   C01  H1   107.66  3.000
 WUG  H3   C01  C02  111.94  3.000
 WUG  H2   C01  C02  111.41  3.000
 WUG  H1   C01  C02  111.19  3.000
 WUG  N09  C02  C03  109.77  3.000
 WUG  C03  C02  C01  128.59  3.000
 WUG  N09  C02  C01  121.63  3.000
 WUG  N06  C03  C04  121.95  3.000
 WUG  C04  C03  C02  133.07  3.000
 WUG  N06  C03  C02  104.98  3.000
 WUG  H5   C04  H4   105.95  3.000
 WUG  H5   C04  N05  114.44  3.000
 WUG  H4   C04  N05  107.42  3.000
 WUG  H5   C04  C03  108.32  3.000
 WUG  H4   C04  C03  109.84  3.000
 WUG  N05  C04  C03  110.72  3.000
 WUG  H7   N05  H6   106.13  3.000
 WUG  H7   N05  C04  109.63  3.000
 WUG  H6   N05  C04  109.18  3.000
 WUG  H9   N06  C07  126.82  3.000
 WUG  H9   N06  C03  124.74  3.000
 WUG  C07  N06  C03  108.31  3.000
 WUG  N09  C07  C08  126.17  3.000
 WUG  N09  C07  N06  110.60  3.000
 WUG  C08  C07  N06  123.24  3.000
 WUG  H12  C08  H11  107.42  3.000
 WUG  H12  C08  H10  108.28  3.000
 WUG  H11  C08  H10  108.07  3.000
 WUG  H12  C08  C07  111.59  3.000
 WUG  H11  C08  C07  111.71  3.000
 WUG  H10  C08  C07  109.65  3.000
 WUG  C07  N09  C02  106.34  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
 WUG  CONST_01  N06  C07  N09  C02     0.00   0.0  0
 WUG  CONST_02  C07  N06  C03  C02     0.00   0.0  0
 WUG  CONST_03  N09  C07  N06  C03     0.00   0.0  0
 WUG  CONST_04  C07  N09  C02  C03     0.00   0.0  0
 WUG  CONST_05  N09  C02  C03  N06     0.00   0.0  0
 WUG  CONST_06  C07  N09  C02  C01   180.00   0.0  0
 WUG  CONST_07  N06  C03  C02  C01   180.00   0.0  0
 WUG  CONST_08  C08  C07  N09  C02   180.00   0.0  0
 WUG  CONST_09  C08  C07  N06  C03   180.00   0.0  0
 WUG  CONST_10  C07  N06  C03  C04   180.00   0.0  0
 WUG  CONST_11  N09  C02  C03  C04   180.00   0.0  0
 WUG  CONST_12  H9   N06  C03  C02   180.00   0.0  0
 WUG  Var_01    N05  C04  C03  C02   139.76  30.0  2
 WUG  Var_02    H1   C01  C02  C03  -131.71  30.0  2
 WUG  Var_03    H10  C08  C07  N06   174.70  30.0  2
 WUG  Var_04    H6   N05  C04  C03   174.13  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
 WUG  plan-1  C01  0.020
 WUG  plan-1  C02  0.020
 WUG  plan-1  C03  0.020
 WUG  plan-1  C04  0.020
 WUG  plan-1  N06  0.020
 WUG  plan-1  C07  0.020
 WUG  plan-1  C08  0.020
 WUG  plan-1  N09  0.020
 WUG  plan-1  H9   0.020

