# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 09:43:08 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 1,3-diazinane-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C1NCCCN1
#
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
 93B  93B  '1,3-diazinane-2-thione   '  ligand  15  7  .  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_93B
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
 93B  C2  C  CH2   0  -0.500   2.1892   0.0101  -0.4412
 93B  C3  C  CH2   0  -0.269   1.5456   1.2330   0.1826
 93B  N1  N  NH1   0  -0.601   0.1016   1.1283   0.0787
 93B  C   C  C     0   0.382  -0.5769  -0.0193   0.0228
 93B  C1  C  CH2   0  -0.269   1.5651  -1.2422   0.1428
 93B  N   N  NH1   0  -0.601   0.1196  -1.1572   0.0418
 93B  H1  H  HCH2  0   0.252   2.0486   0.0264  -1.5241
 93B  H2  H  HCH2  0   0.265   3.2612   0.0156  -0.2484
 93B  H3  H  HCH2  0   0.244   1.8452   1.3301   1.2302
 93B  H4  H  HCH2  0   0.267   1.8571   2.1417  -0.3306
 93B  H5  H  HNH1  0   0.406  -0.4462   1.9722   0.0756
 93B  H6  H  HCH2  0   0.267   1.8910  -2.1290  -0.3990
 93B  H7  H  HCH2  0   0.244   1.8666  -1.3679   1.1869
 93B  H8  H  HNH1  0   0.406  -0.4145  -2.0091   0.0069
 93B  S   S  S1    0  -0.492  -2.2691  -0.0310  -0.0798

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
 93B  N1  C3  single  1.452  0.020  1.452
 93B  N1  C   single  1.334  0.020  1.334
 93B  C3  C2  single  1.516  0.020  1.516
 93B  S   C   double  1.695  0.020  1.695
 93B  C   N   single  1.334  0.020  1.334
 93B  C2  C1  single  1.516  0.020  1.516
 93B  N   C1  single  1.452  0.020  1.452
 93B  C2  H1  single  0.970  0.020  1.090
 93B  C2  H2  single  0.970  0.020  1.090
 93B  C3  H3  single  0.970  0.020  1.090
 93B  C3  H4  single  0.970  0.020  1.090
 93B  N1  H5  single  0.860  0.020  1.020
 93B  C1  H6  single  0.970  0.020  1.090
 93B  C1  H7  single  0.970  0.020  1.090
 93B  N   H8  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
 93B  H2  C2  H1  107.59  3.000
 93B  H2  C2  C1  109.94  3.000
 93B  H1  C2  C1  109.95  3.000
 93B  H2  C2  C3  109.93  3.000
 93B  H1  C2  C3  109.95  3.000
 93B  C1  C2  C3  109.45  3.000
 93B  H4  C3  H3  107.39  3.000
 93B  H4  C3  N1  108.12  3.000
 93B  H3  C3  N1  110.33  3.000
 93B  H4  C3  C2  110.96  3.000
 93B  H3  C3  C2  110.44  3.000
 93B  N1  C3  C2  109.55  3.000
 93B  H5  N1  C   116.38  3.000
 93B  H5  N1  C3  118.78  3.000
 93B  C   N1  C3  124.81  3.000
 93B  N   C   S   121.06  3.000
 93B  N   C   N1  117.87  3.000
 93B  S   C   N1  121.06  3.000
 93B  H7  C1  H6  107.39  3.000
 93B  H7  C1  N   110.34  3.000
 93B  H6  C1  N   108.12  3.000
 93B  H7  C1  C2  110.43  3.000
 93B  H6  C1  C2  110.96  3.000
 93B  N   C1  C2  109.56  3.000
 93B  H8  N   C1  118.79  3.000
 93B  H8  N   C   116.39  3.000
 93B  C1  N   C   124.80  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
 93B  CONST_01  N   C   N1  C3    0.00   0.0  0
 93B  CONST_02  C1  N   C   N1    0.00   0.0  0
 93B  CONST_03  S   C   N1  C3  180.00   0.0  0
 93B  CONST_04  C1  N   C   S   180.00   0.0  0
 93B  CONST_05  H8  N   C   N1  180.00   0.0  0
 93B  CONST_06  H5  N1  C   N   180.00   0.0  0
 93B  Var_01    C   N1  C3  C2   27.53  30.0  1
 93B  Var_02    C   N   C1  C2  -27.54  30.0  1
 93B  Var_03    N   C1  C2  C3   51.53  30.0  1
 93B  Var_04    C1  C2  C3  N1  -51.52  30.0  1

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
 93B  plan-1  C3  0.020
 93B  plan-1  N1  0.020
 93B  plan-1  C   0.020
 93B  plan-1  C1  0.020
 93B  plan-1  N   0.020
 93B  plan-1  H5  0.020
 93B  plan-1  H8  0.020
 93B  plan-1  S   0.020

