# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:59:15 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (4S)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1NC(=O)NC=C1
#
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
 HPY  HPY  (4S)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one  ligand  14  8  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HPY
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
 HPY  N1   N  NH1   0  -0.733   1.0109  -0.3393  -1.0417
 HPY  C2   C  C     0   0.637  -0.3152  -0.0176  -1.1735
 HPY  O2   O  O     0  -0.386  -0.9220  -0.1734  -2.2182
 HPY  N3   N  NH1   0  -0.687  -0.8722   0.5363  -0.0609
 HPY  C4   C  CH1   0   0.251  -0.3471   0.4578   1.2690
 HPY  O4   O  OH1   0  -0.671  -0.9305  -0.6695   1.9010
 HPY  C5   C  C1    0  -0.430   1.1434   0.3603   1.2111
 HPY  C6   C  C1    0   0.022   1.7340  -0.0676   0.0993
 HPY  H1   H  HNH1  0   0.392   1.4841  -0.6617  -1.8690
 HPY  H3   H  HNH1  0   0.406  -1.8534   0.7524  -0.1502
 HPY  H4   H  HCH1  0   0.211  -0.6518   1.3675   1.7994
 HPY  HO4  H  HOH1  0   0.424  -0.6674  -0.6670   2.8271
 HPY  H5   H  H     0   0.270   1.7127   0.5717   2.1043
 HPY  H6   H  H     0   0.293   2.8011  -0.2160   0.0153

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
 HPY  N1  C2   single  1.371  0.020  1.371
 HPY  N1  C6   single  1.378  0.020  1.378
 HPY  N1  H1   single  0.860  0.020  1.020
 HPY  C2  O2   double  1.218  0.020  1.218
 HPY  C2  N3   single  1.362  0.020  1.362
 HPY  N3  C4   single  1.432  0.020  1.432
 HPY  N3  H3   single  0.890  0.020  1.040
 HPY  C4  O4   single  1.418  0.020  1.418
 HPY  C4  C5   single  1.495  0.020  1.495
 HPY  C4  H4   single  0.970  0.020  1.090
 HPY  O4  HO4  single  0.850  0.020  0.980
 HPY  C5  C6   double  1.330  0.020  1.330
 HPY  C5  H5   single  0.930  0.020  1.080
 HPY  C6  H6   single  0.930  0.020  1.080

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
 HPY  H1   N1  C6  119.82  3.000
 HPY  H1   N1  C2  116.81  3.000
 HPY  C6   N1  C2  122.75  3.000
 HPY  N3   C2  O2  123.29  3.000
 HPY  N3   C2  N1  114.36  3.000
 HPY  O2   C2  N1  122.30  3.000
 HPY  H3   N3  C4  116.78  3.000
 HPY  H3   N3  C2  114.38  3.000
 HPY  C4   N3  C2  125.90  3.000
 HPY  H4   C4  C5  110.49  3.000
 HPY  H4   C4  O4  109.25  3.000
 HPY  C5   C4  O4  112.07  3.000
 HPY  H4   C4  N3  107.57  3.000
 HPY  C5   C4  N3  109.47  3.000
 HPY  O4   C4  N3  107.86  3.000
 HPY  HO4  O4  C4  108.32  3.000
 HPY  H5   C5  C6  121.35  3.000
 HPY  H5   C5  C4  118.74  3.000
 HPY  C6   C5  C4  119.75  3.000
 HPY  H6   C6  C5  123.21  3.000
 HPY  H6   C6  N1  115.27  3.000
 HPY  C5   C6  N1  121.52  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
 HPY  CONST_02  C6  N1  C2  N3    0.00   0.0  0
 HPY  CONST_03  C6  N1  C2  O2  180.00   0.0  0
 HPY  CONST_05  H3  N3  C2  N1  180.00   0.0  0
 HPY  CONST_06  H1  N1  C2  N3  180.00   0.0  0
 HPY  Var_01    C4  C5  C6  N1    4.54  30.0  1
 HPY  Var_02    C5  C6  N1  C2    9.29  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
 HPY  chir_01  C4  N3  O4  C5  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
 HPY  plan-1  N1  0.020
 HPY  plan-1  C2  0.020
 HPY  plan-1  O2  0.020
 HPY  plan-1  N3  0.020
 HPY  plan-1  C4  0.020
 HPY  plan-1  C6  0.020
 HPY  plan-1  H1  0.020
 HPY  plan-1  H3  0.020

