# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 02:25:52 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  16  11  .  2021-08-19  2021-08-19  
;
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  -0.0942  -0.5449  -1.4637
 OXC  C2   C  C     0   0.675  -1.3037  -0.0344  -1.0157
 OXC  O2   O  O     0  -0.481  -2.3600  -0.3437  -1.5275
 OXC  N3   N  NH1   0  -0.641  -1.1697   0.8331   0.0119
 OXC  C4   C  CH1   0  -0.060   0.0760   0.9328   0.7233
 OXC  N5   N  NH1   0  -0.630   1.1463   0.9277  -0.2232
 OXC  C6   C  C     0   0.665   1.1518   0.0142  -1.2230
 OXC  O6   O  O     0  -0.480   2.1238  -0.2808  -1.8867
 OXC  CG   C  C     0   0.556   0.2190  -0.2178   1.7359
 OXC  OD1  O  OH1   0  -0.581  -0.7632  -0.1880   2.6166
 OXC  OD2  O  O     0  -0.418   1.1073  -1.0254   1.7137
 OXC  HN1  H  HNH1  0   0.426  -0.1474  -1.1850  -2.2439
 OXC  HN3  H  HNH1  0   0.427  -2.0015   1.2437   0.4061
 OXC  H4   H  HCH1  0   0.346   0.0898   1.8751   1.2717
 OXC  HN5  H  HNH1  0   0.423   2.0364   1.3099   0.0575
 OXC  HD1  H  HOH1  0   0.492  -0.6816  -0.9202   3.2474

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  1.387  0.020  1.387
 OXC  N1   C6   single  1.387  0.020  1.387
 OXC  N1   HN1  single  0.890  0.020  1.040
 OXC  C2   O2   double  1.214  0.020  1.214
 OXC  C2   N3   single  1.352  0.020  1.352
 OXC  N3   C4   single  1.438  0.020  1.438
 OXC  N3   HN3  single  0.860  0.020  1.020
 OXC  C4   N5   single  1.429  0.020  1.429
 OXC  C4   CG   single  1.539  0.020  1.539
 OXC  C4   H4   single  0.970  0.020  1.090
 OXC  N5   C6   single  1.354  0.020  1.354
 OXC  N5   HN5  single  0.890  0.020  1.040
 OXC  C6   O6   double  1.213  0.020  1.213
 OXC  CG   OD1  single  1.320  0.020  1.320
 OXC  CG   OD2  double  1.201  0.020  1.201
 OXC  OD1  HD1  single  0.850  0.020  0.980

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   115.89  3.000
 OXC  HN1  N1   C2   115.88  3.000
 OXC  C6   N1   C2   125.38  3.000
 OXC  N3   C2   O2   124.78  3.000
 OXC  N3   C2   N1   113.29  3.000
 OXC  O2   C2   N1   121.93  3.000
 OXC  HN3  N3   C4   119.55  3.000
 OXC  HN3  N3   C2   118.49  3.000
 OXC  C4   N3   C2   120.43  3.000
 OXC  H4   C4   CG   108.30  3.000
 OXC  H4   C4   N5   109.08  3.000
 OXC  CG   C4   N5   111.31  3.000
 OXC  H4   C4   N3   108.64  3.000
 OXC  CG   C4   N3   110.73  3.000
 OXC  N5   C4   N3   108.72  3.000
 OXC  HN5  N5   C6   117.23  3.000
 OXC  HN5  N5   C4   118.39  3.000
 OXC  C6   N5   C4   119.64  3.000
 OXC  O6   C6   N5   124.82  3.000
 OXC  O6   C6   N1   121.79  3.000
 OXC  N5   C6   N1   113.36  3.000
 OXC  OD2  CG   OD1  125.32  3.000
 OXC  OD2  CG   C4   124.00  3.000
 OXC  OD1  CG   C4   110.67  3.000
 OXC  HD1  OD1  CG   110.76  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_01  C4   N3   C2  N1    0.00  0.0  0
 OXC  CONST_07  C4   N3   C2  O2  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
 OXC  CONST_12  HD1  OD1  CG  C4  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
 OXC  plan-2  HD1  0.020

