# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:24:20 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 5-fluoropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1=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
 URF  URF  5-fluoropyrimidine-2,4(1H,3H)-dione  ligand  12  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_URF
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
 URF  N1   N  NR16  0  -0.666   1.2551  0.0057   1.1002
 URF  C2   C  CR6   0   0.694  -0.0011  0.0114   1.6382
 URF  N3   N  NR16  0  -0.722  -1.0062  0.0159   0.6967
 URF  C4   C  CR6   0   0.480  -0.8845  0.0151  -0.6803
 URF  C5   C  CR6   0   0.274   0.4952  0.0094  -1.1182
 URF  C6   C  CR16  0  -0.066   1.5032  0.0050  -0.2403
 URF  O2   O  O     0  -0.473  -0.2176  0.0123   2.8310
 URF  O4   O  O     0  -0.448  -1.8500  0.0190  -1.4148
 URF  F5   F  F     0  -0.295   0.7095  0.0086  -2.4363
 URF  HN1  H  HNR6  0   0.445   2.0344  0.0025   1.7415
 URF  HN3  H  HNR6  0   0.435  -1.9507  0.0201   1.0640
 URF  H6   H  HCR6  0   0.343   2.5414  0.0007  -0.5388

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
 URF  N1  C2   single  1.367  0.020  1.367
 URF  N1  C6   single  1.363  0.020  1.363
 URF  N1  HN1  single  0.860  0.020  1.020
 URF  C2  N3   single  1.377  0.020  1.377
 URF  C2  O2   double  1.212  0.020  1.212
 URF  N3  C4   single  1.382  0.020  1.382
 URF  N3  HN3  single  0.860  0.020  1.020
 URF  C4  C5   single  1.448  0.020  1.448
 URF  C4  O4   double  1.213  0.020  1.213
 URF  C5  C6   double  1.337  0.020  1.337
 URF  C5  F5   single  1.335  0.020  1.335
 URF  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
 URF  HN1  N1  C6  118.97  3.000
 URF  HN1  N1  C2  117.36  3.000
 URF  C6   N1  C2  123.67  3.000
 URF  O2   C2  N3  122.84  3.000
 URF  O2   C2  N1  123.47  3.000
 URF  N3   C2  N1  113.69  3.000
 URF  HN3  N3  C4  116.29  3.000
 URF  HN3  N3  C2  115.63  3.000
 URF  C4   N3  C2  128.08  3.000
 URF  O4   C4  C5  125.13  3.000
 URF  O4   C4  N3  122.22  3.000
 URF  C5   C4  N3  112.66  3.000
 URF  F5   C5  C6  121.82  3.000
 URF  F5   C5  C4  116.84  3.000
 URF  C6   C5  C4  121.34  3.000
 URF  H6   C6  C5  122.90  3.000
 URF  H6   C6  N1  116.53  3.000
 URF  C5   C6  N1  120.57  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
 URF  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 URF  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 URF  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 URF  CONST_04  O4   C4  N3  C2  180.00  0.0  0
 URF  CONST_05  O2   C2  N3  C4  180.00  0.0  0
 URF  CONST_06  O2   C2  N1  C6  180.00  0.0  0
 URF  CONST_07  HN3  N3  C2  N1  180.00  0.0  0
 URF  CONST_08  HN1  N1  C2  N3  180.00  0.0  0

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
 URF  plan-1  N1   0.020
 URF  plan-1  C2   0.020
 URF  plan-1  N3   0.020
 URF  plan-1  C4   0.020
 URF  plan-1  C5   0.020
 URF  plan-1  C6   0.020
 URF  plan-1  O2   0.020
 URF  plan-1  O4   0.020
 URF  plan-1  F5   0.020
 URF  plan-1  HN1  0.020
 URF  plan-1  HN3  0.020
 URF  plan-1  H6   0.020

