# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:10:46 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 4,6-dioxo-1,3,5-triazinane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1NC(=O)NC(=O)N1
#
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
 OXC  OXC  '4,6-dioxo-1,3,5-triazinane-2-carboxylic acid'  ligand  15  11  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OXC
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
 OXC  N1   N  NH1    0  -0.718  -0.1806   0.1990  -1.9091
 OXC  C2   C  C      0   0.654  -1.3457  -0.0122  -1.1795
 OXC  O2   O  O      0  -0.502  -2.4109  -0.2219  -1.7329
 OXC  N3   N  NH1    0  -0.650  -1.1515   0.0170   0.1501
 OXC  C4   C  CH1    0  -0.014   0.0541   0.5798   0.6996
 OXC  N5   N  NH1    0  -0.650   1.1608   0.0670  -0.0650
 OXC  C6   C  C      0   0.655   1.1063   0.0368  -1.4076
 OXC  O6   O  O      0  -0.502   2.0585  -0.1359  -2.1482
 OXC  CG   C  C      0   0.422   0.2025   0.2307   2.2014
 OXC  OD1  O  OC    -1  -0.587  -0.8608   0.0954   2.8254
 OXC  OD2  O  O      0  -0.588   1.3683   0.1702   2.6206
 OXC  HN1  H  HNH1   0   0.417  -0.2726   0.1259  -2.9121
 OXC  HN3  H  HNH1   0   0.402  -1.9437  -0.0755   0.7676
 OXC  H4   H  HCH1   0   0.258   0.0233   1.6790   0.6203
 OXC  HN5  H  HNH1   0   0.402   2.0572   0.0110   0.3944

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
 OXC  N1  C2   single  1.391  0.020  1.391
 OXC  N1  C6   single  1.391  0.020  1.391
 OXC  N1  HN1  single  0.890  0.020  1.040
 OXC  C2  O2   double  1.219  0.020  1.219
 OXC  C2  N3   single  1.344  0.020  1.344
 OXC  N3  C4   single  1.439  0.020  1.439
 OXC  N3  HN3  single  0.860  0.020  1.020
 OXC  C4  N5   single  1.440  0.020  1.440
 OXC  C4  CG   single  1.549  0.020  1.549
 OXC  C4  H4   single  0.970  0.020  1.090
 OXC  N5  C6   single  1.344  0.020  1.344
 OXC  N5  HN5  single  0.860  0.020  1.020
 OXC  C6  O6   double  1.219  0.020  1.219
 OXC  CG  OD1  deloc   1.240  0.020  1.240
 OXC  CG  OD2  deloc   1.240  0.020  1.240

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
 OXC  HN1  N1  C6   115.72  3.000
 OXC  HN1  N1  C2   115.70  3.000
 OXC  C6   N1  C2   124.64  3.000
 OXC  N3   C2  O2   125.40  3.000
 OXC  N3   C2  N1   113.24  3.000
 OXC  O2   C2  N1   121.35  3.000
 OXC  HN3  N3  C4   117.39  3.000
 OXC  HN3  N3  C2   119.34  3.000
 OXC  C4   N3  C2   120.47  3.000
 OXC  H4   C4  CG   107.29  3.000
 OXC  H4   C4  N5   109.78  3.000
 OXC  CG   C4  N5   111.17  3.000
 OXC  H4   C4  N3   109.81  3.000
 OXC  CG   C4  N3   111.24  3.000
 OXC  N5   C4  N3   107.57  3.000
 OXC  HN5  N5  C6   119.32  3.000
 OXC  HN5  N5  C4   117.45  3.000
 OXC  C6   N5  C4   120.50  3.000
 OXC  O6   C6  N5   125.35  3.000
 OXC  O6   C6  N1   121.36  3.000
 OXC  N5   C6  N1   113.27  3.000
 OXC  OD2  CG  OD1  129.08  3.000
 OXC  OD2  CG  C4   115.39  3.000
 OXC  OD1  CG  C4   115.49  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
 OXC  CONST_07  C4   N3  C2  O2  180.00  0.0  0
 OXC  CONST_08  O6   C6  N5  C4  180.00  0.0  0
 OXC  CONST_09  HN3  N3  C2  N1  180.00  0.0  0
 OXC  CONST_10  HN5  N5  C6  N1  180.00  0.0  0
 OXC  CONST_11  HN1  N1  C2  N3  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OXC  chir_01  C4  N3  N5  CG  positiv

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
 OXC  plan-1  N1   0.020
 OXC  plan-1  C2   0.020
 OXC  plan-1  O2   0.020
 OXC  plan-1  N3   0.020
 OXC  plan-1  C4   0.020
 OXC  plan-1  N5   0.020
 OXC  plan-1  C6   0.020
 OXC  plan-1  O6   0.020
 OXC  plan-1  HN1  0.020
 OXC  plan-1  HN3  0.020
 OXC  plan-1  HN5  0.020
 OXC  plan-2  C4   0.020
 OXC  plan-2  CG   0.020
 OXC  plan-2  OD1  0.020
 OXC  plan-2  OD2  0.020

