# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 02:03:52 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CC1=CNC(=O)NC1=O
#
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
 FYU  FYU  2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde  ligand  14  10  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_FYU
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
 FYU  N1   N  NR16  0  -0.663   1.4228   1.2067  -0.0103
 FYU  N3   N  NR16  0  -0.720   0.9769  -1.0511  -0.0147
 FYU  C4   C  CR6   0   0.583  -0.4050  -0.8954  -0.0033
 FYU  C5   C  CR6   0  -0.288  -0.8364   0.4943   0.0052
 FYU  C6   C  CR16  0   0.110   0.1106   1.4697   0.0010
 FYU  O4   O  O     0  -0.426  -1.1249  -1.8693  -0.0011
 FYU  C2   C  CR6   0   0.701   1.9367  -0.0762  -0.0194
 FYU  O2   O  O     0  -0.451   3.1238  -0.2996  -0.0300
 FYU  CM5  C  C1    0   0.124  -2.2327   0.9038   0.0174
 FYU  O3   O  O     0  -0.388  -3.1933   0.1691   0.0231
 FYU  H1   H  HNR6  0   0.434   1.3210  -2.0045  -0.0220
 FYU  H3   H  HCR6  0   0.342  -0.1542   2.5189   0.0069
 FYU  H4   H  H     0   0.193  -2.3610   2.0018   0.0216
 FYU  H5   H  HNR6  0   0.450   2.0870   1.9685  -0.0132

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
 FYU  CM5  O3  double  1.209  0.020  1.209
 FYU  CM5  C5  single  1.455  0.020  1.455
 FYU  O4   C4  double  1.211  0.020  1.211
 FYU  C5   C4  single  1.455  0.020  1.455
 FYU  C5   C6  double  1.360  0.020  1.360
 FYU  C4   N3  single  1.391  0.020  1.391
 FYU  C6   N1  single  1.338  0.020  1.338
 FYU  N3   C2  single  1.368  0.020  1.368
 FYU  N1   C2  single  1.382  0.020  1.382
 FYU  C2   O2  double  1.208  0.020  1.208
 FYU  N3   H1  single  0.860  0.020  1.020
 FYU  C6   H3  single  0.930  0.020  1.080
 FYU  CM5  H4  single  0.930  0.020  1.080
 FYU  N1   H5  single  0.860  0.020  1.020

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
 FYU  H5   N1   C2  117.08  3.000
 FYU  H5   N1   C6  119.75  3.000
 FYU  C2   N1   C6  123.16  3.000
 FYU  H1   N3   C2  115.60  3.000
 FYU  H1   N3   C4  116.27  3.000
 FYU  C2   N3   C4  128.12  3.000
 FYU  O4   C4   C5  126.28  3.000
 FYU  C5   C4   N3  113.67  3.000
 FYU  O4   C4   N3  120.04  3.000
 FYU  CM5  C5   C6  117.81  3.000
 FYU  C6   C5   C4  118.60  3.000
 FYU  CM5  C5   C4  123.59  3.000
 FYU  H3   C6   C5  121.68  3.000
 FYU  H3   C6   N1  115.50  3.000
 FYU  C5   C6   N1  122.82  3.000
 FYU  O2   C2   N3  123.89  3.000
 FYU  O2   C2   N1  122.49  3.000
 FYU  N3   C2   N1  113.62  3.000
 FYU  H4   CM5  O3  120.74  3.000
 FYU  H4   CM5  C5  113.01  3.000
 FYU  O3   CM5  C5  126.25  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
 FYU  CONST_01  C4  N3   C2  N1    0.00   0.0  0
 FYU  CONST_02  C6  N1   C2  N3    0.00   0.0  0
 FYU  CONST_03  C2  N3   C4  C5    0.00   0.0  0
 FYU  CONST_04  O2  C2   N3  C4  180.00   0.0  0
 FYU  CONST_05  O2  C2   N1  C6  180.00   0.0  0
 FYU  CONST_06  C2  N3   C4  O4  180.00   0.0  0
 FYU  CONST_07  H1  N3   C2  N1  180.00   0.0  0
 FYU  CONST_08  H5  N1   C2  N3  180.00   0.0  0
 FYU  Var_01    O3  CM5  C5  C4    0.07  30.0  2

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
 FYU  plan-1  N1   0.020
 FYU  plan-1  N3   0.020
 FYU  plan-1  C4   0.020
 FYU  plan-1  C5   0.020
 FYU  plan-1  C6   0.020
 FYU  plan-1  O4   0.020
 FYU  plan-1  C2   0.020
 FYU  plan-1  O2   0.020
 FYU  plan-1  CM5  0.020
 FYU  plan-1  H1   0.020
 FYU  plan-1  H3   0.020
 FYU  plan-1  H5   0.020
 FYU  plan-2  C5   0.020
 FYU  plan-2  CM5  0.020
 FYU  plan-2  O3   0.020
 FYU  plan-2  H4   0.020

