# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:14:37 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 5-fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(F)C(=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
 FOT  FOT  '5-fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  15  12  .  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_FOT
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
 FOT  C2    C  CR6   0   0.685  -1.4359  -1.3930  0.0352
 FOT  C6    C  CR6   0   0.500  -1.4453   1.0758  0.0559
 FOT  C5    C  CR6   0   0.347   0.0131   1.0072  0.0443
 FOT  O2    O  O     0  -0.463  -2.0581  -2.4314  0.0315
 FOT  N3    N  NR16  0  -0.727  -0.0724  -1.3352  0.0235
 FOT  N1    N  NR16  0  -0.719  -2.0480  -0.1586  0.0508
 FOT  O6    O  O     0  -0.428  -2.0678   2.1135  0.0697
 FOT  F5    F  F     0  -0.265   0.6288   2.1768  0.0513
 FOT  C4    C  CR6   0   0.087   0.6563  -0.1712  0.0307
 FOT  C41   C  C     0   0.573   2.1461  -0.2758  0.0225
 FOT  O42   O  O     0  -0.393   2.8787   0.6739  0.0195
 FOT  O41   O  OH1   0  -0.593   2.5290  -1.5373  0.0202
 FOT  HN3   H  HNR6  0   0.447   0.4153  -2.2206  0.0154
 FOT  HN1   H  HNR6  0   0.441  -3.0612  -0.1681  0.0591
 FOT  HO41  H  HOH1  0   0.507   3.4968  -1.6081  0.0163

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
 FOT  C2   O2    double  1.211  0.020  1.211
 FOT  C2   N3    single  1.365  0.020  1.365
 FOT  C2   N1    single  1.378  0.020  1.378
 FOT  C6   C5    single  1.460  0.020  1.460
 FOT  C6   N1    single  1.374  0.020  1.374
 FOT  C6   O6    double  1.210  0.020  1.210
 FOT  C5   F5    single  1.322  0.020  1.322
 FOT  C5   C4    double  1.343  0.020  1.343
 FOT  N3   C4    single  1.373  0.020  1.373
 FOT  N3   HN3   single  0.860  0.020  1.020
 FOT  N1   HN1   single  0.860  0.020  1.020
 FOT  C4   C41   single  1.494  0.020  1.494
 FOT  C41  O42   double  1.199  0.020  1.199
 FOT  C41  O41   single  1.318  0.020  1.318
 FOT  O41  HO41  single  0.850  0.020  0.980

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
 FOT  N1    C2   N3   113.95  3.000
 FOT  N1    C2   O2   122.70  3.000
 FOT  N3    C2   O2   123.35  3.000
 FOT  O6    C6   N1   123.01  3.000
 FOT  O6    C6   C5   123.65  3.000
 FOT  N1    C6   C5   113.33  3.000
 FOT  C4    C5   F5   123.61  3.000
 FOT  C4    C5   C6   121.32  3.000
 FOT  F5    C5   C6   115.07  3.000
 FOT  HN3   N3   C4   119.11  3.000
 FOT  HN3   N3   C2   116.42  3.000
 FOT  C4    N3   C2   124.47  3.000
 FOT  HN1   N1   C6   116.56  3.000
 FOT  HN1   N1   C2   115.84  3.000
 FOT  C6    N1   C2   127.60  3.000
 FOT  C41   C4   N3   118.03  3.000
 FOT  C41   C4   C5   122.64  3.000
 FOT  N3    C4   C5   119.33  3.000
 FOT  O41   C41  O42  125.47  3.000
 FOT  O41   C41  C4   110.90  3.000
 FOT  O42   C41  C4   123.63  3.000
 FOT  HO41  O41  C41  111.07  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
 FOT  CONST_01  C5    C6   N1   C2    0.00   0.0  0
 FOT  CONST_02  N3    C2   N1   C6    0.00   0.0  0
 FOT  CONST_03  C4    N3   C2   N1    0.00   0.0  0
 FOT  CONST_04  O6    C6   N1   C2  180.00   0.0  0
 FOT  CONST_05  O2    C2   N1   C6  180.00   0.0  0
 FOT  CONST_06  C4    N3   C2   O2  180.00   0.0  0
 FOT  CONST_07  HN1   N1   C6   C5  180.00   0.0  0
 FOT  CONST_08  HN3   N3   C2   N1  180.00   0.0  0
 FOT  CONST_09  HO41  O41  C41  C4  180.00   0.0  0
 FOT  Var_01    O42   C41  C4   C5   -0.45  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
 FOT  plan-1  C2    0.020
 FOT  plan-1  C6    0.020
 FOT  plan-1  C5    0.020
 FOT  plan-1  O2    0.020
 FOT  plan-1  N3    0.020
 FOT  plan-1  N1    0.020
 FOT  plan-1  O6    0.020
 FOT  plan-1  F5    0.020
 FOT  plan-1  C4    0.020
 FOT  plan-1  C41   0.020
 FOT  plan-1  HN3   0.020
 FOT  plan-1  HN1   0.020
 FOT  plan-2  C4    0.020
 FOT  plan-2  C41   0.020
 FOT  plan-2  O42   0.020
 FOT  plan-2  O41   0.020
 FOT  plan-2  HO41  0.020

