# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:59:57 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=S)NC2=C1NC(=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
 5JL  5JL  2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one  ligand  16  12  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5JL
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
 5JL  C4  C  CR56  0   0.641  -0.1601   0.6131  -0.0013
 5JL  C5  C  CR56  0   0.110  -0.3611  -0.7312   0.0001
 5JL  C6  C  CR6   0   0.547   0.7351  -1.6409   0.0068
 5JL  C8  C  CR5   0   0.343  -2.3659   0.2672  -0.0076
 5JL  N1  N  NR16  0  -0.684   1.9528  -0.9459   0.0081
 5JL  N3  N  NR16  0  -0.674   1.0692   1.1755   0.0026
 5JL  O6  O  O     0  -0.437   0.6962  -2.8528   0.0106
 5JL  N7  N  NR15  0  -0.650  -1.7268  -0.9165  -0.0034
 5JL  S8  S  S1    0  -0.374  -4.0013   0.5601  -0.0132
 5JL  N9  N  NR15  0  -0.658  -1.3704   1.2144  -0.0065
 5JL  C2  C  CR6   0   0.365   2.1800   0.3936   0.0081
 5JL  S2  S  S1    0  -0.314   3.7064   1.0415   0.0146
 5JL  H1  H  HNR6  0   0.441   2.7853  -1.5230   0.0122
 5JL  H2  H  HNR6  0   0.454   1.1933   2.1788   0.0045
 5JL  H3  H  HNR5  0   0.441  -2.2022  -1.8062  -0.0050
 5JL  H4  H  HNR5  0   0.449  -1.5523   2.2078  -0.0079

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
 5JL  O6  C6  double  1.213  0.020  1.213
 5JL  N7  C5  single  1.378  0.020  1.378
 5JL  N7  C8  single  1.345  0.020  1.345
 5JL  C6  C5  single  1.424  0.020  1.424
 5JL  C6  N1  single  1.402  0.020  1.402
 5JL  S8  C8  double  1.661  0.020  1.661
 5JL  C5  C4  double  1.359  0.020  1.359
 5JL  C8  N9  single  1.374  0.020  1.374
 5JL  N1  C2  single  1.359  0.020  1.359
 5JL  C4  N9  single  1.351  0.020  1.351
 5JL  C4  N3  single  1.352  0.020  1.352
 5JL  C2  N3  single  1.358  0.020  1.358
 5JL  C2  S2  double  1.658  0.020  1.658
 5JL  N1  H1  single  0.860  0.020  1.020
 5JL  N3  H2  single  0.860  0.020  1.020
 5JL  N7  H3  single  0.860  0.020  1.020
 5JL  N9  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
 5JL  N9  C4  N3  129.00  3.000
 5JL  N3  C4  C5  123.08  3.000
 5JL  N9  C4  C5  107.92  3.000
 5JL  N7  C5  C6  132.59  3.000
 5JL  C6  C5  C4  121.18  3.000
 5JL  N7  C5  C4  106.23  3.000
 5JL  O6  C6  N1  121.55  3.000
 5JL  N1  C6  C5  110.60  3.000
 5JL  O6  C6  C5  127.85  3.000
 5JL  N9  C8  S8  126.27  3.000
 5JL  N9  C8  N7  105.21  3.000
 5JL  S8  C8  N7  128.52  3.000
 5JL  H1  N1  C2  115.10  3.000
 5JL  H1  N1  C6  115.56  3.000
 5JL  C2  N1  C6  129.34  3.000
 5JL  H2  N3  C2  118.09  3.000
 5JL  H2  N3  C4  121.63  3.000
 5JL  C2  N3  C4  120.28  3.000
 5JL  H3  N7  C8  123.52  3.000
 5JL  H3  N7  C5  125.84  3.000
 5JL  C8  N7  C5  110.64  3.000
 5JL  H4  N9  C8  123.20  3.000
 5JL  H4  N9  C4  126.80  3.000
 5JL  C8  N9  C4  110.00  3.000
 5JL  S2  C2  N3  121.86  3.000
 5JL  S2  C2  N1  122.63  3.000
 5JL  N3  C2  N1  115.52  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
 5JL  CONST_01  C8  N7  C5  C4    0.00  0.0  0
 5JL  CONST_02  N7  C8  N9  C4    0.00  0.0  0
 5JL  CONST_03  N1  C2  N3  C4    0.00  0.0  0
 5JL  CONST_04  N9  C8  N7  C5    0.00  0.0  0
 5JL  CONST_05  C2  N1  C6  C5    0.00  0.0  0
 5JL  CONST_06  C8  N9  C4  C5    0.00  0.0  0
 5JL  CONST_07  C2  N3  C4  C5    0.00  0.0  0
 5JL  CONST_08  N3  C2  N1  C6    0.00  0.0  0
 5JL  CONST_09  N3  C4  N9  C8  180.00  0.0  0
 5JL  CONST_10  N9  C4  C5  N7    0.00  0.0  0
 5JL  CONST_11  C2  N3  C4  N9  180.00  0.0  0
 5JL  CONST_12  S8  C8  N9  C4  180.00  0.0  0
 5JL  CONST_13  S2  C2  N3  C4  180.00  0.0  0
 5JL  CONST_14  S8  C8  N7  C5  180.00  0.0  0
 5JL  CONST_15  S2  C2  N1  C6  180.00  0.0  0
 5JL  CONST_16  C2  N1  C6  O6  180.00  0.0  0
 5JL  CONST_17  H3  N7  C5  C4  180.00  0.0  0
 5JL  CONST_18  H1  N1  C6  C5  180.00  0.0  0
 5JL  CONST_19  H4  N9  C4  C5  180.00  0.0  0
 5JL  CONST_20  H2  N3  C4  C5  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
 5JL  plan-1  C4  0.020
 5JL  plan-1  C5  0.020
 5JL  plan-1  C6  0.020
 5JL  plan-1  C8  0.020
 5JL  plan-1  N1  0.020
 5JL  plan-1  N3  0.020
 5JL  plan-1  O6  0.020
 5JL  plan-1  N7  0.020
 5JL  plan-1  S8  0.020
 5JL  plan-1  N9  0.020
 5JL  plan-1  C2  0.020
 5JL  plan-1  S2  0.020
 5JL  plan-1  H1  0.020
 5JL  plan-1  H2  0.020
 5JL  plan-1  H3  0.020
 5JL  plan-1  H4  0.020

