# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 06:24:31 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 6-methyl-5-sulfanylidene-2~{H}-1,2,4-triazin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NNC(=O)NC1=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
 V8Q  V8Q  "6-methyl-5-sulfanylidene-2H-1,2,4-triazin-3-one"
  ligand  14  9  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V8Q
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
 V8Q  C01  C  CR6   0   0.708  -1.6410  -7.2304  -15.5113
 V8Q  C02  C  CR6   0   0.179  -0.0016  -5.8934  -16.7229
 V8Q  C03  C  CR6   0   0.180  -0.0479  -6.9219  -17.7601
 V8Q  C04  C  CH3   0  -0.718   0.8038  -6.7983  -18.9744
 V8Q  N01  N  NR16  0  -0.660  -0.8172  -6.1348  -15.6671
 V8Q  N02  N  N     0  -0.163  -0.8128  -7.9480  -17.6489
 V8Q  N03  N  NR16  0  -0.504  -1.5756  -8.0875  -16.5706
 V8Q  O01  O  O     0  -0.451  -2.3398  -7.4043  -14.5409
 V8Q  S01  S  S1    0  -0.233   0.9490  -4.5555  -16.8075
 V8Q  H1   H  HCH3  0   0.262   0.6295  -7.6416  -19.6383
 V8Q  H2   H  HCH3  0   0.259   0.5881  -5.8742  -19.5101
 V8Q  H3   H  HCH3  0   0.259   1.8602  -6.7734  -18.7057
 V8Q  H4   H  HNR6  0   0.439  -0.8285  -5.4578  -14.9118
 V8Q  H5   H  HNR6  0   0.443  -2.1494  -8.9190  -16.5531

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
 V8Q  C04  C03  single  1.488  0.020  1.488
 V8Q  C03  N02  double  1.285  0.020  1.285
 V8Q  C03  C02  single  1.461  0.020  1.461
 V8Q  N02  N03  single  1.328  0.020  1.328
 V8Q  S01  C02  double  1.643  0.020  1.643
 V8Q  C02  N01  single  1.356  0.020  1.356
 V8Q  N03  C01  single  1.364  0.020  1.364
 V8Q  N01  C01  single  1.380  0.020  1.380
 V8Q  C01  O01  double  1.208  0.020  1.208
 V8Q  C04  H1   single  0.970  0.020  1.090
 V8Q  C04  H2   single  0.970  0.020  1.090
 V8Q  C04  H3   single  0.970  0.020  1.090
 V8Q  N01  H4   single  0.860  0.020  1.020
 V8Q  N03  H5   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
 V8Q  O01  C01  N03  124.12  3.000
 V8Q  O01  C01  N01  123.39  3.000
 V8Q  N03  C01  N01  112.50  3.000
 V8Q  S01  C02  N01  122.21  3.000
 V8Q  N01  C02  C03  114.10  3.000
 V8Q  S01  C02  C03  123.69  3.000
 V8Q  N02  C03  C04  118.53  3.000
 V8Q  N02  C03  C02  121.30  3.000
 V8Q  C04  C03  C02  120.16  3.000
 V8Q  H3   C04  H2   107.07  3.000
 V8Q  H3   C04  H1   108.88  3.000
 V8Q  H2   C04  H1   109.01  3.000
 V8Q  H3   C04  C03  110.81  3.000
 V8Q  H2   C04  C03  110.99  3.000
 V8Q  H1   C04  C03  110.00  3.000
 V8Q  H4   N01  C02  117.89  3.000
 V8Q  H4   N01  C01  116.06  3.000
 V8Q  C02  N01  C01  126.05  3.000
 V8Q  N03  N02  C03  119.74  3.000
 V8Q  H5   N03  N02  115.26  3.000
 V8Q  H5   N03  C01  118.45  3.000
 V8Q  N02  N03  C01  126.30  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
 V8Q  CONST_01  N03  C01  N01  C02     0.00   0.0  0
 V8Q  CONST_02  N02  N03  C01  N01     0.00   0.0  0
 V8Q  CONST_03  O01  C01  N01  C02   180.00   0.0  0
 V8Q  CONST_04  O01  C01  N03  N02   180.00   0.0  0
 V8Q  CONST_05  H5   N03  C01  N01   180.00   0.0  0
 V8Q  CONST_06  H4   N01  C01  N03   180.00   0.0  0
 V8Q  CONST_07  H5   N03  C01  O01     0.00   0.0  0
 V8Q  CONST_08  H4   N01  C01  O01     0.00   0.0  0
 V8Q  Var_01    C03  N02  N03  C01    -0.37  30.0  1
 V8Q  Var_02    C03  C02  N01  C01     0.24  30.0  1
 V8Q  Var_03    N03  N02  C03  C02    -0.30  30.0  1
 V8Q  Var_04    N02  C03  C02  N01     0.35  30.0  1
 V8Q  Var_05    S01  C02  N01  C01  -179.68  30.0  1
 V8Q  Var_06    N03  N02  C03  C04   179.50  30.0  1
 V8Q  Var_07    N01  C02  C03  C04  -179.44  30.0  1
 V8Q  Var_08    S01  C02  C03  N02  -179.73  30.0  1
 V8Q  Var_09    H5   N03  N02  C03  -179.95  30.0  1
 V8Q  Var_10    H4   N01  C02  C03   179.85  30.0  1
 V8Q  Var_11    S01  C02  C03  C04     0.48  30.0  1
 V8Q  Var_12    H1   C04  C03  C02  -179.24  30.0  3
 V8Q  Var_13    H2   C04  C03  C02   -58.51  30.0  3
 V8Q  Var_14    H3   C04  C03  C02    60.32  30.0  3
 V8Q  Var_15    H1   C04  C03  N02     0.97  30.0  3
 V8Q  Var_16    H2   C04  C03  N02   121.69  30.0  3
 V8Q  Var_17    H3   C04  C03  N02  -119.48  30.0  3
 V8Q  Var_18    H4   N01  C02  S01    -0.07  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
 V8Q  plan-1  C01  0.020
 V8Q  plan-1  C02  0.020
 V8Q  plan-1  N01  0.020
 V8Q  plan-1  N02  0.020
 V8Q  plan-1  N03  0.020
 V8Q  plan-1  O01  0.020
 V8Q  plan-1  H4   0.020
 V8Q  plan-1  H5   0.020
 V8Q  plan-2  C02  0.020
 V8Q  plan-2  C03  0.020
 V8Q  plan-2  N01  0.020
 V8Q  plan-2  S01  0.020

