# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:11:36 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-thioxo-2,3,7,9-tetrahydro-1H-purine-6,8-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC2=C(N1)C(=O)NC(=S)N2
#
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
 5JQ  5JQ  2-thioxo-2,3,7,9-tetrahydro-1H-purine-6,8-dione  ligand  16  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5JQ
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
 5JQ  C2  C  CR5   0   0.634  -0.5028   0.7048  -0.0279
 5JQ  C3  C  CR5   0   0.634  -2.7419   0.5232  -0.0333
 5JQ  C4  C  C     0   0.364   1.8177   0.3175  -0.0123
 5JQ  C5  C  C     0   0.542   0.2253  -1.6018   0.0053
 5JQ  O2  O  O     0  -0.452   0.1048  -2.8113   0.0228
 5JQ  N4  N  NH1   0  -0.681   1.4945  -0.9992   0.0012
 5JQ  S1  S  S1    0  -0.331   3.3896   0.8563  -0.0105
 5JQ  N3  N  NH1   0  -0.668   0.7661   1.1747  -0.0276
 5JQ  C1  C  CR5   0   0.119  -0.7997  -0.6216  -0.0136
 5JQ  N2  N  NR15  0  -0.723  -2.1796  -0.7180  -0.0163
 5JQ  O1  O  O     0  -0.482  -3.9161   0.8290  -0.0414
 5JQ  N1  N  NR15  0  -0.718  -1.6583   1.4037  -0.0405
 5JQ  H1  H  HNH1  0   0.437   2.2811  -1.6367   0.0126
 5JQ  H2  H  HNH1  0   0.451   0.9611   2.1666  -0.0370
 5JQ  H3  H  HNR5  0   0.432  -2.7119  -1.5735  -0.0115
 5JQ  H4  H  HNR5  0   0.443  -1.7574   2.4084  -0.0481

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
 5JQ  O2  C5  double  1.216  0.020  1.216
 5JQ  N2  C1  single  1.383  0.020  1.383
 5JQ  N2  C3  single  1.363  0.020  1.363
 5JQ  C5  C1  single  1.418  0.020  1.418
 5JQ  C5  N4  single  1.405  0.020  1.405
 5JQ  O1  C3  double  1.213  0.020  1.213
 5JQ  C1  C2  double  1.359  0.020  1.359
 5JQ  C3  N1  single  1.396  0.020  1.396
 5JQ  N4  C4  single  1.356  0.020  1.356
 5JQ  C2  N1  single  1.350  0.020  1.350
 5JQ  C2  N3  single  1.353  0.020  1.353
 5JQ  C4  N3  single  1.357  0.020  1.357
 5JQ  C4  S1  double  1.662  0.020  1.662
 5JQ  N4  H1  single  0.860  0.020  1.020
 5JQ  N3  H2  single  0.860  0.020  1.020
 5JQ  N2  H3  single  0.860  0.020  1.020
 5JQ  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
 5JQ  N1  C2  C1  108.56  3.000
 5JQ  N1  C2  N3  128.51  3.000
 5JQ  C1  C2  N3  122.93  3.000
 5JQ  N1  C3  O1  126.30  3.000
 5JQ  N1  C3  N2  104.72  3.000
 5JQ  O1  C3  N2  128.97  3.000
 5JQ  N3  C4  S1  121.89  3.000
 5JQ  S1  C4  N4  122.71  3.000
 5JQ  N3  C4  N4  115.40  3.000
 5JQ  C1  C5  N4  110.88  3.000
 5JQ  N4  C5  O2  121.08  3.000
 5JQ  C1  C5  O2  128.04  3.000
 5JQ  H1  N4  C5  115.58  3.000
 5JQ  H1  N4  C4  115.23  3.000
 5JQ  C5  N4  C4  129.19  3.000
 5JQ  H2  N3  C4  118.07  3.000
 5JQ  H2  N3  C2  121.44  3.000
 5JQ  C4  N3  C2  120.49  3.000
 5JQ  N2  C1  C5  132.28  3.000
 5JQ  C5  C1  C2  121.11  3.000
 5JQ  N2  C1  C2  106.61  3.000
 5JQ  H3  N2  C1  125.89  3.000
 5JQ  H3  N2  C3  123.73  3.000
 5JQ  C1  N2  C3  110.37  3.000
 5JQ  H4  N1  C3  123.46  3.000
 5JQ  H4  N1  C2  126.81  3.000
 5JQ  C3  N1  C2  109.73  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
 5JQ  CONST_01  C3  N2  C1  C2    0.00  0.0  0
 5JQ  CONST_02  N2  C3  N1  C2    0.00  0.0  0
 5JQ  CONST_03  N4  C4  N3  C2    0.00  0.0  0
 5JQ  CONST_04  C1  C2  N1  C3    0.00  0.0  0
 5JQ  CONST_05  N3  C2  N1  C3  180.00  0.0  0
 5JQ  CONST_06  C1  C5  N4  C4    0.00  0.0  0
 5JQ  CONST_07  C1  C2  N3  C4    0.00  0.0  0
 5JQ  CONST_08  N1  C2  N3  C4  180.00  0.0  0
 5JQ  CONST_09  N3  C4  N4  C5    0.00  0.0  0
 5JQ  CONST_10  N1  C3  N2  C1    0.00  0.0  0
 5JQ  CONST_11  N1  C2  C1  N2    0.00  0.0  0
 5JQ  CONST_12  O1  C3  N1  C2  180.00  0.0  0
 5JQ  CONST_13  S1  C4  N3  C2  180.00  0.0  0
 5JQ  CONST_14  O2  C5  N4  C4  180.00  0.0  0
 5JQ  CONST_15  S1  C4  N4  C5  180.00  0.0  0
 5JQ  CONST_16  O1  C3  N2  C1  180.00  0.0  0
 5JQ  CONST_17  H3  N2  C1  C2  180.00  0.0  0
 5JQ  CONST_18  H2  N3  C4  N4  180.00  0.0  0
 5JQ  CONST_19  H4  N1  C2  N3    0.00  0.0  0
 5JQ  CONST_20  H1  N4  C4  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
 5JQ  plan-1  C2  0.020
 5JQ  plan-1  C3  0.020
 5JQ  plan-1  C4  0.020
 5JQ  plan-1  C5  0.020
 5JQ  plan-1  O2  0.020
 5JQ  plan-1  N4  0.020
 5JQ  plan-1  S1  0.020
 5JQ  plan-1  N3  0.020
 5JQ  plan-1  C1  0.020
 5JQ  plan-1  N2  0.020
 5JQ  plan-1  O1  0.020
 5JQ  plan-1  N1  0.020
 5JQ  plan-1  H1  0.020
 5JQ  plan-1  H2  0.020
 5JQ  plan-1  H3  0.020
 5JQ  plan-1  H4  0.020

