# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:50:11 2021
#   Inital geometry file: a 50 line input string
#   Ligand name: (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC(=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
 DOR  DOR  '(4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid'  ligand  17  11  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DOR
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
 DOR  O2   O  O     0  -0.485  25.0097  37.3199  72.8225
 DOR  C2   C  C     0   0.681  25.7079  38.3069  72.6956
 DOR  N1   N  NH1   0  -0.654  25.2408  39.5685  72.6459
 DOR  N3   N  NH1   0  -0.701  27.0900  38.1859  72.5779
 DOR  C4   C  C     0   0.558  27.9692  39.1640  72.1969
 DOR  O4   O  O     0  -0.432  29.1484  38.9335  72.0500
 DOR  C5   C  CH2   0  -0.599  27.3477  40.5105  71.9394
 DOR  C6   C  CH1   0  -0.187  26.1047  40.7111  72.7973
 DOR  C7   C  C     0   0.560  25.3450  41.9656  72.4162
 DOR  O72  O  OH1   0  -0.582  26.1261  43.0276  72.4718
 DOR  O71  O  O     0  -0.423  24.1782  41.9866  72.1258
 DOR  HN1  H  HNH1  0   0.415  24.2522  39.6844  72.8120
 DOR  HN3  H  HNH1  0   0.423  27.4549  37.2467  72.6764
 DOR  H51  H  HCH2  0   0.310  27.0863  40.5541  70.8769
 DOR  H52  H  HCH2  0   0.306  28.0927  41.2793  72.1305
 DOR  H6   H  HCH1  0   0.316  26.4128  40.8327  73.8452
 DOR  H72  H  HOH1  0   0.494  25.6262  43.8286  72.2513

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
 DOR  O2   C2   double  1.216  0.020  1.216
 DOR  C2   N1   single  1.346  0.020  1.346
 DOR  C2   N3   single  1.392  0.020  1.392
 DOR  N1   C6   single  1.440  0.020  1.440
 DOR  N1   HN1  single  0.890  0.020  1.040
 DOR  N3   C4   single  1.369  0.020  1.369
 DOR  N3   HN3  single  0.860  0.020  1.020
 DOR  C4   O4   double  1.210  0.020  1.210
 DOR  C4   C5   single  1.505  0.020  1.505
 DOR  C5   C6   single  1.524  0.020  1.524
 DOR  C5   H51  single  0.970  0.020  1.090
 DOR  C5   H52  single  0.970  0.020  1.090
 DOR  C6   C7   single  1.515  0.020  1.515
 DOR  C6   H6   single  0.970  0.020  1.090
 DOR  C7   O72  single  1.320  0.020  1.320
 DOR  C7   O71  double  1.203  0.020  1.203
 DOR  O72  H72  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
 DOR  N3   C2   N1   115.00  3.000
 DOR  N3   C2   O2   120.56  3.000
 DOR  N1   C2   O2   124.43  3.000
 DOR  HN1  N1   C6   118.63  3.000
 DOR  HN1  N1   C2   116.20  3.000
 DOR  C6   N1   C2   122.11  3.000
 DOR  HN3  N3   C4   117.28  3.000
 DOR  HN3  N3   C2   115.47  3.000
 DOR  C4   N3   C2   126.79  3.000
 DOR  C5   C4   O4   123.49  3.000
 DOR  C5   C4   N3   114.93  3.000
 DOR  O4   C4   N3   121.56  3.000
 DOR  H52  C5   H51  107.81  3.000
 DOR  H52  C5   C6   111.52  3.000
 DOR  H51  C5   C6   110.26  3.000
 DOR  H52  C5   C4   108.64  3.000
 DOR  H51  C5   C4   107.47  3.000
 DOR  C6   C5   C4   111.00  3.000
 DOR  H6   C6   C7   106.78  3.000
 DOR  H6   C6   C5   108.83  3.000
 DOR  C7   C6   C5   112.12  3.000
 DOR  H6   C6   N1   110.86  3.000
 DOR  C7   C6   N1   109.25  3.000
 DOR  C5   C6   N1   109.00  3.000
 DOR  O71  C7   O72  124.79  3.000
 DOR  O71  C7   C6   124.17  3.000
 DOR  O72  C7   C6   111.03  3.000
 DOR  H72  O72  C7   110.49  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
 DOR  CONST_01  C5   C4   N3  C2    0.00   0.0  0
 DOR  CONST_02  C4   N3   C2  N1    0.00   0.0  0
 DOR  CONST_03  C6   N1   C2  N3    0.00   0.0  0
 DOR  CONST_04  C6   N1   C2  O2  180.00   0.0  0
 DOR  CONST_05  C4   N3   C2  O2  180.00   0.0  0
 DOR  CONST_06  O4   C4   N3  C2  180.00   0.0  0
 DOR  CONST_07  HN3  N3   C2  N1  180.00   0.0  0
 DOR  CONST_08  HN1  N1   C2  N3  180.00   0.0  0
 DOR  CONST_09  H72  O72  C7  C6  180.00   0.0  0
 DOR  Var_01    H51  C5   C4  N3  -91.24  30.0  1

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
 DOR  chir_01  C6  N1  C5  C7  negativ

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
 DOR  plan-1  O2   0.020
 DOR  plan-1  C2   0.020
 DOR  plan-1  N1   0.020
 DOR  plan-1  N3   0.020
 DOR  plan-1  C4   0.020
 DOR  plan-1  O4   0.020
 DOR  plan-1  C5   0.020
 DOR  plan-1  C6   0.020
 DOR  plan-1  HN1  0.020
 DOR  plan-1  HN3  0.020
 DOR  plan-2  C6   0.020
 DOR  plan-2  C7   0.020
 DOR  plan-2  O72  0.020
 DOR  plan-2  O71  0.020
 DOR  plan-2  H72  0.020

