# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:34:35 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 2-thioxo-2,3-dihydropyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=S)NC=C1
#
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
 TUL  TUL  2-thioxo-2,3-dihydropyrimidin-4(1H)-one  ligand  12  8  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TUL
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
 TUL  O4  O  O     0  -0.453   2.3872  -1.4687  0.0079
 TUL  C4  C  CR6   0   0.570   1.5802  -0.5608  0.0093
 TUL  C5  C  CR16  0  -0.474   1.8845   0.8500  0.0101
 TUL  C6  C  CR16  0   0.075   0.8782   1.7403  0.0108
 TUL  N1  N  NR16  0  -0.613  -0.4245   1.3456  0.0113
 TUL  C2  C  CR6   0   0.375  -0.8084   0.0493  0.0103
 TUL  S2  S  S1    0  -0.330  -2.4040  -0.4100  0.0088
 TUL  N3  N  NR16  0  -0.665   0.2125  -0.8395  0.0102
 TUL  H1  H  HCR6  0   0.302   2.9138   1.1729  0.0095
 TUL  H3  H  HCR6  0   0.334   1.0364   2.8084  0.0110
 TUL  H4  H  HNR6  0   0.433  -0.0515  -1.8174  0.0092
 TUL  H2  H  HNR6  0   0.444  -1.1545   2.0426  0.0099

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
 TUL  S2  C2  double  1.660  0.020  1.660
 TUL  N3  C2  single  1.354  0.020  1.354
 TUL  N3  C4  single  1.396  0.020  1.396
 TUL  C2  N1  single  1.352  0.020  1.352
 TUL  O4  C4  double  1.215  0.020  1.215
 TUL  C4  C5  single  1.443  0.020  1.443
 TUL  N1  C6  single  1.361  0.020  1.361
 TUL  C5  C6  double  1.344  0.020  1.344
 TUL  C5  H1  single  0.930  0.020  1.080
 TUL  C6  H3  single  0.930  0.020  1.080
 TUL  N3  H4  single  0.860  0.020  1.020
 TUL  N1  H2  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
 TUL  N3  C4  C5  113.69  3.000
 TUL  C5  C4  O4  126.20  3.000
 TUL  N3  C4  O4  120.12  3.000
 TUL  H1  C5  C6  121.08  3.000
 TUL  H1  C5  C4  119.59  3.000
 TUL  C6  C5  C4  119.33  3.000
 TUL  H3  C6  N1  115.28  3.000
 TUL  H3  C6  C5  123.08  3.000
 TUL  N1  C6  C5  121.64  3.000
 TUL  H2  N1  C2  117.17  3.000
 TUL  H2  N1  C6  119.47  3.000
 TUL  C2  N1  C6  123.36  3.000
 TUL  N3  C2  S2  122.90  3.000
 TUL  N3  C2  N1  114.55  3.000
 TUL  S2  C2  N1  122.56  3.000
 TUL  H4  N3  C2  115.94  3.000
 TUL  H4  N3  C4  116.62  3.000
 TUL  C2  N3  C4  127.44  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
 TUL  CONST_01  N1  C2  N3  C4    0.00  0.0  0
 TUL  CONST_02  C2  N3  C4  C5    0.00  0.0  0
 TUL  CONST_03  N3  C2  N1  C6    0.00  0.0  0
 TUL  CONST_04  C2  N3  C4  O4  180.00  0.0  0
 TUL  CONST_05  S2  C2  N3  C4  180.00  0.0  0
 TUL  CONST_06  S2  C2  N1  C6  180.00  0.0  0
 TUL  CONST_07  H4  N3  C4  C5  180.00  0.0  0
 TUL  CONST_08  H2  N1  C2  N3  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
 TUL  plan-1  O4  0.020
 TUL  plan-1  C4  0.020
 TUL  plan-1  C5  0.020
 TUL  plan-1  C6  0.020
 TUL  plan-1  N1  0.020
 TUL  plan-1  C2  0.020
 TUL  plan-1  S2  0.020
 TUL  plan-1  N3  0.020
 TUL  plan-1  H1  0.020
 TUL  plan-1  H3  0.020
 TUL  plan-1  H4  0.020
 TUL  plan-1  H2  0.020

