# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:25:30 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (4S)-5-fluoro-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=C1F
#
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
 FPY  FPY  (4S)-5-fluoro-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one  ligand  14  9  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FPY
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
 FPY  N1   N  NH1   0  -0.721  -1.0583   1.2241  -0.3232
 FPY  C2   C  C     0   0.656  -1.5962   0.0107  -0.0094
 FPY  O2   O  O     0  -0.418  -2.7908  -0.2255  -0.1152
 FPY  N3   N  NH1   0  -0.696  -0.7042  -0.8977   0.4773
 FPY  C4   C  CH1   0   0.149   0.7264  -0.8537   0.3636
 FPY  O4   O  OH1   0  -0.641   1.1591  -1.5899  -0.7591
 FPY  C5   C  C     0   0.296   1.1215   0.5757   0.2410
 FPY  F5   F  F     0  -0.305   2.4247   0.8350   0.4549
 FPY  C6   C  C1    0  -0.110   0.2751   1.5291  -0.1145
 FPY  HN1  H  HNH1  0   0.405  -1.6865   1.9489  -0.6295
 FPY  HN3  H  HNH1  0   0.412  -1.1040  -1.7917   0.7212
 FPY  H4   H  HCH1  0   0.201   1.1524  -1.2882   1.2739
 FPY  HO4  H  HOH1  0   0.461   1.8990  -2.1470  -0.4993
 FPY  H6   H  H     0   0.311   0.5636   2.5604  -0.2574

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
 FPY  N1  C2   single  1.364  0.020  1.364
 FPY  N1  C6   single  1.384  0.020  1.384
 FPY  N1  HN1  single  0.860  0.020  1.020
 FPY  C2  O2   double  1.222  0.020  1.222
 FPY  C2  N3   single  1.363  0.020  1.363
 FPY  N3  C4   single  1.436  0.020  1.436
 FPY  N3  HN3  single  0.860  0.020  1.020
 FPY  C4  O4   single  1.411  0.020  1.411
 FPY  C4  C5   single  1.488  0.020  1.488
 FPY  C4  H4   single  0.970  0.020  1.090
 FPY  O4  HO4  single  0.850  0.020  0.980
 FPY  C5  F5   single  1.346  0.020  1.346
 FPY  C5  C6   double  1.324  0.020  1.324
 FPY  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
 FPY  HN1  N1  C6  119.24  3.000
 FPY  HN1  N1  C2  117.67  3.000
 FPY  C6   N1  C2  122.79  3.000
 FPY  N3   C2  O2  122.80  3.000
 FPY  N3   C2  N1  114.64  3.000
 FPY  O2   C2  N1  122.52  3.000
 FPY  HN3  N3  C4  116.17  3.000
 FPY  HN3  N3  C2  114.67  3.000
 FPY  C4   N3  C2  127.11  3.000
 FPY  H4   C4  C5  110.26  3.000
 FPY  H4   C4  O4  109.59  3.000
 FPY  C5   C4  O4  110.75  3.000
 FPY  H4   C4  N3  108.04  3.000
 FPY  C5   C4  N3  107.49  3.000
 FPY  O4   C4  N3  110.66  3.000
 FPY  HO4  O4  C4  108.87  3.000
 FPY  C6   C5  F5  121.54  3.000
 FPY  C6   C5  C4  122.97  3.000
 FPY  F5   C5  C4  115.41  3.000
 FPY  H6   C6  C5  123.53  3.000
 FPY  H6   C6  N1  116.60  3.000
 FPY  C5   C6  N1  119.87  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
 FPY  CONST_02  C6   N1  C2  N3    0.00   0.0  0
 FPY  CONST_03  C6   N1  C2  O2  180.00   0.0  0
 FPY  CONST_05  HN3  N3  C2  N1  180.00   0.0  0
 FPY  CONST_06  HN1  N1  C2  N3  180.00   0.0  0
 FPY  Var_01    C4   C5  C6  N1    3.36  30.0  1
 FPY  Var_02    C5   C6  N1  C2    8.99  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
 FPY  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
 FPY  plan-1  N1   0.020
 FPY  plan-1  C2   0.020
 FPY  plan-1  O2   0.020
 FPY  plan-1  N3   0.020
 FPY  plan-1  C4   0.020
 FPY  plan-1  C6   0.020
 FPY  plan-1  HN1  0.020
 FPY  plan-1  HN3  0.020

