# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:47:50 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: 1-methyl-1,3-dihydro-2H-imidazole-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=CNC1=S
#
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
 MMZ  MMZ  1-methyl-1,3-dihydro-2H-imidazole-2-thione  ligand  13  7  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MMZ
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
 MMZ  N1   N  NR15  0  -0.601   0.4981  -1.3916  -0.0687
 MMZ  C1A  C  CR15  0  -0.094   1.8216  -1.0357   0.0309
 MMZ  C2   C  CR5   0   0.380  -0.2973  -0.3032  -0.0836
 MMZ  S2   S  S1    0  -0.464  -1.9743  -0.2569  -0.1937
 MMZ  N3   N  NR5   0  -0.427   0.5449   0.7494   0.0102
 MMZ  C3A  C  CR15  0  -0.107   1.8509   0.3107   0.0796
 MMZ  C4   C  CH3   0  -0.510   0.1149   2.1277   0.0187
 MMZ  HN1  H  HNR5  0   0.427   0.1466  -2.3342  -0.1213
 MMZ  H1A  H  HCR5  0   0.306   2.6156  -1.7601   0.0589
 MMZ  H3A  H  HCR5  0   0.309   2.6802   0.9919   0.1563
 MMZ  H41  H  HCH3  0   0.259  -0.3473   2.3913  -0.9308
 MMZ  H42  H  HCH3  0   0.259  -0.6065   2.2939   0.8157
 MMZ  H43  H  HCH3  0   0.262   0.9805   2.7627   0.1813

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
 MMZ  N1   C1A  aromatic  1.374  0.020  1.374
 MMZ  N1   C2   aromatic  1.348  0.020  1.348
 MMZ  N1   HN1  single    0.860  0.020  1.020
 MMZ  C1A  C3A  aromatic  1.348  0.020  1.348
 MMZ  C1A  H1A  single    0.930  0.020  1.080
 MMZ  C2   S2   double    1.681  0.020  1.681
 MMZ  C2   N3   aromatic  1.351  0.020  1.351
 MMZ  N3   C3A  aromatic  1.379  0.020  1.379
 MMZ  N3   C4   single    1.444  0.020  1.444
 MMZ  C3A  H3A  single    0.930  0.020  1.080
 MMZ  C4   H41  single    0.970  0.020  1.090
 MMZ  C4   H42  single    0.970  0.020  1.090
 MMZ  C4   H43  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
 MMZ  HN1  N1   C2   123.29  3.000
 MMZ  HN1  N1   C1A  125.61  3.000
 MMZ  C2   N1   C1A  111.10  3.000
 MMZ  H1A  C1A  C3A  131.01  3.000
 MMZ  H1A  C1A  N1   122.60  3.000
 MMZ  C3A  C1A  N1   106.40  3.000
 MMZ  N3   C2   S2   127.21  3.000
 MMZ  N3   C2   N1   105.09  3.000
 MMZ  S2   C2   N1   127.70  3.000
 MMZ  C4   N3   C3A  125.82  3.000
 MMZ  C4   N3   C2   123.95  3.000
 MMZ  C3A  N3   C2   110.23  3.000
 MMZ  H3A  C3A  N3   122.14  3.000
 MMZ  H3A  C3A  C1A  130.68  3.000
 MMZ  N3   C3A  C1A  107.18  3.000
 MMZ  H43  C4   H42  109.25  3.000
 MMZ  H43  C4   H41  109.12  3.000
 MMZ  H42  C4   H41  108.70  3.000
 MMZ  H43  C4   N3   108.77  3.000
 MMZ  H42  C4   N3   110.34  3.000
 MMZ  H41  C4   N3   110.64  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
 MMZ  CONST_01  N3   C3A  C1A  N1     0.00   0.0  0
 MMZ  CONST_02  C3A  N3   C2   N1     0.00   0.0  0
 MMZ  CONST_03  N3   C2   N1   C1A    0.00   0.0  0
 MMZ  CONST_04  C2   N3   C3A  C1A    0.00   0.0  0
 MMZ  CONST_05  C3A  C1A  N1   C2     0.00   0.0  0
 MMZ  CONST_06  C4   N3   C2   N1   180.00   0.0  0
 MMZ  CONST_07  S2   C2   N1   C1A  180.00   0.0  0
 MMZ  CONST_08  C4   N3   C3A  C1A  180.00   0.0  0
 MMZ  CONST_09  C3A  N3   C2   S2   180.00   0.0  0
 MMZ  CONST_10  H3A  C3A  C1A  N1   180.00   0.0  0
 MMZ  CONST_11  H1A  C1A  N1   C2   180.00   0.0  0
 MMZ  CONST_12  HN1  N1   C2   N3   180.00   0.0  0
 MMZ  Var_01    H41  C4   N3   C2   -64.57  30.0  2

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
 MMZ  plan-1  N1   0.020
 MMZ  plan-1  C1A  0.020
 MMZ  plan-1  C2   0.020
 MMZ  plan-1  S2   0.020
 MMZ  plan-1  N3   0.020
 MMZ  plan-1  C3A  0.020
 MMZ  plan-1  C4   0.020
 MMZ  plan-1  HN1  0.020
 MMZ  plan-1  H1A  0.020
 MMZ  plan-1  H3A  0.020

