# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:50:29 2022
#   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  16  11  .  2022-03-18  2022-03-18
;
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  -0.504  -2.2460  -1.7148   0.3795
 DOR  C2   C  C      0   0.655  -1.4163  -0.9116  -0.0109
 DOR  N1   N  NH1    0  -0.614  -0.4472  -1.1771  -0.9050
 DOR  N3   N  NH1    0  -0.687  -1.4712   0.4108   0.4247
 DOR  C4   C  C      0   0.528  -0.7043   1.4571  -0.0099
 DOR  O4   O  O      0  -0.449  -0.8532   2.5746   0.4390
 DOR  C5   C  CH2    0  -0.572   0.2772   1.1077  -1.0932
 DOR  C6   C  CH1    0  -0.254   0.7306  -0.3414  -0.9809
 DOR  C7   C  C      0   0.419   1.6855  -0.5143   0.2339
 DOR  O72  O  OC    -1  -0.604   2.7969   0.0300   0.1024
 DOR  O71  O  O      0  -0.585   1.2497  -1.1407   1.2134
 DOR  HN1  H  HNH1   0   0.400  -0.3232  -2.1580  -1.1039
 DOR  HN3  H  HNH1   0   0.411  -2.1881   0.6132   1.1089
 DOR  H51  H  HCH2   0   0.283   1.1257   1.7869  -1.0427
 DOR  H52  H  HCH2   0   0.294  -0.2197   1.2800  -2.0537
 DOR  H6   H  HCH1   0   0.278   1.2672  -0.6077  -1.8921

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  1.219  0.020  1.219
 DOR  C2  N1   single  1.345  0.020  1.345
 DOR  C2  N3   single  1.393  0.020  1.393
 DOR  N1  C6   single  1.446  0.020  1.446
 DOR  N1  HN1  single  0.890  0.020  1.040
 DOR  N3  C4   single  1.368  0.020  1.368
 DOR  N3  HN3  single  0.860  0.020  1.020
 DOR  C4  O4   double  1.213  0.020  1.213
 DOR  C4  C5   single  1.503  0.020  1.503
 DOR  C5  C6   single  1.523  0.020  1.523
 DOR  C5  H51  single  0.970  0.020  1.090
 DOR  C5  H52  single  0.970  0.020  1.090
 DOR  C6  C7   single  1.555  0.020  1.555
 DOR  C6  H6   single  0.970  0.020  1.090
 DOR  C7  O72  deloc   1.245  0.020  1.245
 DOR  C7  O71  deloc   1.242  0.020  1.242

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   115.06  3.000
 DOR  N3   C2  O2   119.89  3.000
 DOR  N1   C2  O2   124.98  3.000
 DOR  HN1  N1  C6   116.84  3.000
 DOR  HN1  N1  C2   114.31  3.000
 DOR  C6   N1  C2   120.51  3.000
 DOR  HN3  N3  C4   117.34  3.000
 DOR  HN3  N3  C2   115.42  3.000
 DOR  C4   N3  C2   127.19  3.000
 DOR  C5   C4  O4   124.12  3.000
 DOR  C5   C4  N3   114.66  3.000
 DOR  O4   C4  N3   121.19  3.000
 DOR  H52  C5  H51  107.24  3.000
 DOR  H52  C5  C6   110.46  3.000
 DOR  H51  C5  C6   111.00  3.000
 DOR  H52  C5  C4   107.42  3.000
 DOR  H51  C5  C4   109.31  3.000
 DOR  C6   C5  C4   111.26  3.000
 DOR  H6   C6  C7   108.88  3.000
 DOR  H6   C6  C5   108.50  3.000
 DOR  C7   C6  C5   110.26  3.000
 DOR  H6   C6  N1   107.67  3.000
 DOR  C7   C6  N1   113.26  3.000
 DOR  C5   C6  N1   108.14  3.000
 DOR  O71  C7  O72  128.12  3.000
 DOR  O71  C7  C6   117.19  3.000
 DOR  O72  C7  C6   114.66  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_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  Var_01    H51  C5  C4  N3  -152.65  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

