# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:50:17 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3Z)-5-(2-methylpropyl)-3-(sulfanylmethylidene)pyrazine-2,6(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC1=N\C(=C/S)C(=O)NC1=O
#
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
 22Q  22Q  (3Z)-5-(2-methylpropyl)-3-(sulfanylmethylidene)pyrazine-2,6(1H,3H)-dione  ligand  26  14  .  2022-07-22  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_22Q
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
 22Q  C    C  C1    0  -0.444  -2.0932  -1.4652   0.2125
 22Q  N    N  N     0  -0.381  -0.0713  -0.2841   0.1698
 22Q  S    S  S2    0  -0.052  -1.2387  -2.9410   0.4107
 22Q  C1   C  CR6   0   0.094   0.6070   0.7895   0.0747
 22Q  N1   N  NR16  0  -0.711  -1.4242   2.0814  -0.1563
 22Q  C2   C  CR6   0   0.550  -2.2140   0.9560  -0.0674
 22Q  O2   O  O     0  -0.434  -3.4239   1.0290  -0.1340
 22Q  C4   C  CH2   0  -0.480   2.0991   0.7823   0.1680
 22Q  C5   C  CR6   0   0.550  -0.0543   2.1182  -0.0985
 22Q  C6   C  CH1   0  -0.233   2.7533  -0.5937   0.0592
 22Q  C7   C  CH3   0  -0.653   2.6201  -1.1727  -1.3457
 22Q  C8   C  CH3   0  -0.653   4.2217  -0.4918   0.4593
 22Q  CA   C  CR6   0   0.148  -1.4466  -0.2817   0.1088
 22Q  H    H  H     0   0.339  -3.1735  -1.5102   0.1725
 22Q  HS   H  HSH1  0   0.259  -2.3159  -3.7315   0.4629
 22Q  HN1  H  HNR6  0   0.425  -1.9018   2.9677  -0.2806
 22Q  H4   H  HCH2  0   0.254   2.5108   1.4503  -0.5951
 22Q  H4A  H  HCH2  0   0.270   2.3668   1.2459   1.1257
 22Q  H6   H  HCH1  0   0.226   2.2521  -1.2703   0.7573
 22Q  H7   H  HCH3  0   0.211   3.1244  -0.5376  -2.0784
 22Q  H7A  H  HCH3  0   0.225   3.0758  -2.1627  -1.4000
 22Q  H7B  H  HCH3  0   0.233   1.5783  -1.2750  -1.6474
 22Q  H8   H  HCH3  0   0.226   4.3344  -0.1258   1.4814
 22Q  H8A  H  HCH3  0   0.228   4.7123  -1.4644   0.3997
 22Q  H8B  H  HCH3  0   0.214   4.7626   0.1916  -0.1998
 22Q  O3   O  O     0  -0.412   0.5612   3.1578  -0.1816

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
 22Q  C   S    single  1.717  0.020  1.717
 22Q  C   CA   double  1.353  0.020  1.353
 22Q  C   H    single  0.930  0.020  1.080
 22Q  N   C1   double  1.273  0.020  1.273
 22Q  N   CA   single  1.377  0.020  1.377
 22Q  S   HS   single  1.200  0.020  1.300
 22Q  C1  C4   single  1.495  0.020  1.495
 22Q  C1  C5   single  1.494  0.020  1.494
 22Q  N1  C2   single  1.378  0.020  1.378
 22Q  N1  C5   single  1.372  0.020  1.372
 22Q  N1  HN1  single  0.860  0.020  1.020
 22Q  C2  O2   double  1.214  0.020  1.214
 22Q  C2  CA   single  1.467  0.020  1.467
 22Q  O3  C5   double  1.211  0.020  1.211
 22Q  C4  C6   single  1.527  0.020  1.527
 22Q  C4  H4   single  0.970  0.020  1.090
 22Q  C4  H4A  single  0.970  0.020  1.090
 22Q  C6  C7   single  1.525  0.020  1.525
 22Q  C6  C8   single  1.525  0.020  1.525
 22Q  C6  H6   single  0.970  0.020  1.090
 22Q  C7  H7   single  0.970  0.020  1.090
 22Q  C7  H7A  single  0.970  0.020  1.090
 22Q  C7  H7B  single  0.970  0.020  1.090
 22Q  C8  H8   single  0.970  0.020  1.090
 22Q  C8  H8A  single  0.970  0.020  1.090
 22Q  C8  H8B  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
 22Q  H    C   CA   120.72  3.000
 22Q  H    C   S    117.74  3.000
 22Q  CA   C   S    121.54  3.000
 22Q  CA   N   C1   121.82  3.000
 22Q  HS   S   C     96.42  3.000
 22Q  C5   C1  C4   116.95  3.000
 22Q  C5   C1  N    121.51  3.000
 22Q  C4   C1  N    121.52  3.000
 22Q  HN1  N1  C5   116.87  3.000
 22Q  HN1  N1  C2   116.86  3.000
 22Q  C5   N1  C2   126.27  3.000
 22Q  CA   C2  O2   125.36  3.000
 22Q  CA   C2  N1   113.40  3.000
 22Q  O2   C2  N1   121.24  3.000
 22Q  H4A  C4  H4   105.00  3.000
 22Q  H4A  C4  C6   109.78  3.000
 22Q  H4   C4  C6   109.82  3.000
 22Q  H4A  C4  C1   107.21  3.000
 22Q  H4   C4  C1   109.20  3.000
 22Q  C6   C4  C1   115.30  3.000
 22Q  O3   C5  N1   121.85  3.000
 22Q  O3   C5  C1   123.12  3.000
 22Q  N1   C5  C1   115.03  3.000
 22Q  H6   C6  C8   108.36  3.000
 22Q  H6   C6  C7   108.25  3.000
 22Q  C8   C6  C7   110.55  3.000
 22Q  H6   C6  C4   108.39  3.000
 22Q  C8   C6  C4   109.48  3.000
 22Q  C7   C6  C4   111.73  3.000
 22Q  H7B  C7  H7A  107.48  3.000
 22Q  H7B  C7  H7   108.07  3.000
 22Q  H7A  C7  H7   107.52  3.000
 22Q  H7B  C7  C6   111.98  3.000
 22Q  H7A  C7  C6   110.72  3.000
 22Q  H7   C7  C6   110.89  3.000
 22Q  H8B  C8  H8A  107.58  3.000
 22Q  H8B  C8  H8   107.69  3.000
 22Q  H8A  C8  H8   107.68  3.000
 22Q  H8B  C8  C6   111.10  3.000
 22Q  H8A  C8  C6   111.04  3.000
 22Q  H8   C8  C6   111.56  3.000
 22Q  C2   CA  N    121.97  3.000
 22Q  C2   CA  C    119.83  3.000
 22Q  N    CA  C    118.20  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
 22Q  CONST_01  CA   C2  N1  C5    0.00   0.0  0
 22Q  CONST_02  C5   N1  C2  O2  180.00   0.0  0
 22Q  CONST_03  HN1  N1  C2  CA  180.00   0.0  0
 22Q  Var_01    C6   C4  C1  N    13.48  30.0  3
 22Q  Var_02    S    C   CA  N    -0.18  30.0  2
 22Q  Var_03    C7   C6  C4  C1   69.00  30.0  3
 22Q  Var_04    H7   C7  C6  C4   61.80  30.0  3
 22Q  Var_05    H8   C8  C6  C4   59.34  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
 22Q  plan-1  C    0.020
 22Q  plan-1  N    0.020
 22Q  plan-1  C1   0.020
 22Q  plan-1  N1   0.020
 22Q  plan-1  C2   0.020
 22Q  plan-1  O2   0.020
 22Q  plan-1  C4   0.020
 22Q  plan-1  C5   0.020
 22Q  plan-1  CA   0.020
 22Q  plan-1  HN1  0.020
 22Q  plan-1  O3   0.020

