# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:43:53 2020
#   Inital geometry file: a 34 line input string
#   Ligand name: 1,3-dihydroimidazole-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C1NC=CN1
#
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
 MZY  MZY  1,3-dihydroimidazole-2-thione  ligand  10  6  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MZY
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
 MZY  S2   S  S1    0  -0.467  -1.9184   0.0544  0.0181
 MZY  C2   C  CR5   0   0.354  -0.2367   0.0405  0.0130
 MZY  N3   N  NR15  0  -0.587   0.5979   1.0989  0.0089
 MZY  C3A  C  CR15  0  -0.092   1.9146   0.6969  0.0058
 MZY  C1A  C  CR15  0  -0.092   1.9037  -0.6506  0.0077
 MZY  N1   N  NR15  0  -0.587   0.5808  -1.0315  0.0119
 MZY  H1   H  HCR5  0   0.307   2.7321   1.3954  0.0035
 MZY  H2   H  HCR5  0   0.307   2.7096  -1.3623  0.0075
 MZY  H3   H  HNR5  0   0.429   0.2780   2.0543  0.0095
 MZY  H4   H  HNR5  0   0.429   0.2461  -1.9818  0.0163

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
 MZY  S2   C2   double  1.682  0.020  1.682
 MZY  C2   N3   single  1.348  0.020  1.348
 MZY  C2   N1   single  1.348  0.020  1.348
 MZY  N3   C3A  single  1.377  0.020  1.377
 MZY  N1   C1A  single  1.377  0.020  1.377
 MZY  C3A  C1A  double  1.348  0.020  1.348
 MZY  C3A  H1   single  0.930  0.020  1.080
 MZY  C1A  H2   single  0.930  0.020  1.080
 MZY  N3   H3   single  0.860  0.020  1.020
 MZY  N1   H4   single  0.860  0.020  1.020

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
 MZY  N1   C2   N3   104.42  3.000
 MZY  N1   C2   S2   127.80  3.000
 MZY  N3   C2   S2   127.78  3.000
 MZY  H3   N3   C3A  125.49  3.000
 MZY  H3   N3   C2   123.23  3.000
 MZY  C3A  N3   C2   111.28  3.000
 MZY  H1   C3A  C1A  130.97  3.000
 MZY  H1   C3A  N3   122.51  3.000
 MZY  C1A  C3A  N3   106.51  3.000
 MZY  H2   C1A  N1   122.49  3.000
 MZY  H2   C1A  C3A  130.99  3.000
 MZY  N1   C1A  C3A  106.52  3.000
 MZY  H4   N1   C1A  125.46  3.000
 MZY  H4   N1   C2   123.27  3.000
 MZY  C1A  N1   C2   111.27  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
 MZY  CONST_01  C1A  C3A  N3   C2     0.00  0.0  0
 MZY  CONST_02  C3A  C1A  N1   C2     0.00  0.0  0
 MZY  CONST_03  C1A  N1   C2   N3     0.00  0.0  0
 MZY  CONST_04  N1   C1A  C3A  N3     0.00  0.0  0
 MZY  CONST_05  N1   C2   N3   C3A    0.00  0.0  0
 MZY  CONST_06  C3A  N3   C2   S2   180.00  0.0  0
 MZY  CONST_07  C1A  N1   C2   S2   180.00  0.0  0
 MZY  CONST_08  H4   N1   C2   N3   180.00  0.0  0
 MZY  CONST_09  H3   N3   C3A  C1A  180.00  0.0  0

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
 MZY  plan-1  S2   0.020
 MZY  plan-1  C2   0.020
 MZY  plan-1  N3   0.020
 MZY  plan-1  C3A  0.020
 MZY  plan-1  C1A  0.020
 MZY  plan-1  N1   0.020
 MZY  plan-1  H1   0.020
 MZY  plan-1  H2   0.020
 MZY  plan-1  H3   0.020
 MZY  plan-1  H4   0.020

