# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:37:46 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: dihydropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCNC(=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
 DUC  DUC  dihydropyrimidine-2,4(1H,3H)-dione  ligand  14  8  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DUC
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
 DUC  N3   N  NH1   0  -0.698  -0.9341   0.1134  -0.0243
 DUC  C2   C  C     0   0.670  -0.3221  -0.0226   1.2220
 DUC  O2   O  O     0  -0.498  -0.9978  -0.0771   2.2339
 DUC  N1   N  NH1   0  -0.637   1.0180  -0.0952   1.1880
 DUC  C6   C  CH2   0  -0.289   1.7803   0.2428   0.0047
 DUC  C5   C  CH2   0  -0.593   1.1154  -0.3683  -1.2125
 DUC  C4   C  C     0   0.542  -0.3522  -0.0464  -1.2552
 DUC  O4   O  O     0  -0.442  -1.0030   0.0374  -2.2741
 DUC  HN3  H  HNH1  0   0.417  -1.9386   0.2325  -0.0007
 DUC  HN1  H  HNH1  0   0.414   1.4872  -0.1006   2.0799
 DUC  H61  H  HCH2  0   0.278   2.7873  -0.1500   0.1215
 DUC  H62  H  HCH2  0   0.252   1.8615   1.3278  -0.1128
 DUC  H51  H  HCH2  0   0.290   1.5849  -0.0177  -2.1299
 DUC  H52  H  HCH2  0   0.294   1.2121  -1.4583  -1.1885

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
 DUC  N3  C2   single  1.395  0.020  1.395
 DUC  N3  C4   single  1.371  0.020  1.371
 DUC  N3  HN3  single  0.860  0.020  1.020
 DUC  C2  O2   double  1.218  0.020  1.218
 DUC  C2  N1   single  1.343  0.020  1.343
 DUC  N1  C6   single  1.448  0.020  1.448
 DUC  N1  HN1  single  0.860  0.020  1.020
 DUC  C6  C5   single  1.516  0.020  1.516
 DUC  C6  H61  single  0.970  0.020  1.090
 DUC  C6  H62  single  0.970  0.020  1.090
 DUC  C5  C4   single  1.503  0.020  1.503
 DUC  C5  H51  single  0.970  0.020  1.090
 DUC  C5  H52  single  0.970  0.020  1.090
 DUC  C4  O4   double  1.212  0.020  1.212

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
 DUC  HN3  N3  C4   117.14  3.000
 DUC  HN3  N3  C2   115.22  3.000
 DUC  C4   N3  C2   127.19  3.000
 DUC  N1   C2  O2   124.92  3.000
 DUC  N1   C2  N3   114.87  3.000
 DUC  O2   C2  N3   120.21  3.000
 DUC  HN1  N1  C6   118.66  3.000
 DUC  HN1  N1  C2   116.26  3.000
 DUC  C6   N1  C2   122.26  3.000
 DUC  H62  C6  H61  107.52  3.000
 DUC  H62  C6  C5   110.24  3.000
 DUC  H61  C6  C5   110.30  3.000
 DUC  H62  C6  N1   111.00  3.000
 DUC  H61  C6  N1   108.40  3.000
 DUC  C5   C6  N1   109.35  3.000
 DUC  H52  C5  H51  107.53  3.000
 DUC  H52  C5  C4   107.46  3.000
 DUC  H51  C5  C4   109.16  3.000
 DUC  H52  C5  C6   110.19  3.000
 DUC  H51  C5  C6   110.97  3.000
 DUC  C4   C5  C6   111.39  3.000
 DUC  O4   C4  C5   124.26  3.000
 DUC  O4   C4  N3   121.26  3.000
 DUC  C5   C4  N3   114.46  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
 DUC  CONST_01  C6   N1  C2  N3    0.00   0.0  0
 DUC  CONST_02  C4   N3  C2  N1    0.00   0.0  0
 DUC  CONST_03  C4   N3  C2  O2  180.00   0.0  0
 DUC  CONST_04  C6   N1  C2  O2  180.00   0.0  0
 DUC  CONST_05  HN1  N1  C2  N3  180.00   0.0  0
 DUC  CONST_06  HN3  N3  C2  N1  180.00   0.0  0
 DUC  Var_01    C6   C5  C4  N3  -30.15  30.0  1
 DUC  Var_02    C5   C4  N3  C2   -1.68  30.0  1
 DUC  Var_03    C5   C6  N1  C2  -44.14  30.0  1
 DUC  Var_04    C4   C5  C6  N1   50.24  30.0  1

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
 DUC  plan-1  N3   0.020
 DUC  plan-1  C5   0.020
 DUC  plan-1  C4   0.020
 DUC  plan-1  O4   0.020
 DUC  plan-2  N3   0.020
 DUC  plan-2  C2   0.020
 DUC  plan-2  O2   0.020
 DUC  plan-2  N1   0.020
 DUC  plan-2  C6   0.020
 DUC  plan-2  C4   0.020
 DUC  plan-2  HN3  0.020
 DUC  plan-2  HN1  0.020

