# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:05:49 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: 4-amino-5-fluoropyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=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
 1LD  1LD  4-amino-5-fluoropyrimidin-2(1H)-one  ligand  13  9  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1LD
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
 1LD  N1  N  NR16  0  -0.655   1.2053   1.1712   0.0213
 1LD  C6  C  CR16  0  -0.054  -0.1021   1.5138   0.0381
 1LD  C2  C  CR6   0   0.563   1.6411  -0.1467  -0.0006
 1LD  O2  O  O     0  -0.518   2.8414  -0.3851  -0.0125
 1LD  N3  N  N     0  -0.528   0.6923  -1.1131  -0.0075
 1LD  C4  C  CR6   0   0.409  -0.5905  -0.8190   0.0094
 1LD  N4  N  NH2   0  -0.805  -1.4873  -1.8011   0.0044
 1LD  C5  C  CR6   0   0.300  -1.0273   0.5424   0.0320
 1LD  F   F  F     0  -0.303  -2.3419   0.8145   0.0489
 1LD  H1  H  HNR6  0   0.428   1.9015   1.9018   0.0293
 1LD  H2  H  HCR6  0   0.335  -0.3460   2.5664   0.0561
 1LD  H3  H  HNH2  0   0.410  -1.1749  -2.7578  -0.0036
 1LD  H4  H  HNH2  0   0.418  -2.4773  -1.6294   0.0230

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
 1LD  F   C5  single  1.343  0.020  1.343
 1LD  N4  C4  single  1.330  0.020  1.330
 1LD  C5  C4  single  1.430  0.020  1.430
 1LD  C5  C6  double  1.341  0.020  1.341
 1LD  C4  N3  double  1.316  0.020  1.316
 1LD  C6  N1  single  1.352  0.020  1.352
 1LD  N3  C2  single  1.354  0.020  1.354
 1LD  N1  C2  single  1.388  0.020  1.388
 1LD  C2  O2  double  1.224  0.020  1.224
 1LD  N1  H1  single  0.860  0.020  1.020
 1LD  C6  H2  single  0.930  0.020  1.080
 1LD  N4  H3  single  0.860  0.020  1.020
 1LD  N4  H4  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
 1LD  H1  N1  C2  118.09  3.000
 1LD  H1  N1  C6  118.92  3.000
 1LD  C2  N1  C6  122.99  3.000
 1LD  H2  C6  C5  123.35  3.000
 1LD  H2  C6  N1  117.74  3.000
 1LD  C5  C6  N1  118.92  3.000
 1LD  N3  C2  O2  123.23  3.000
 1LD  O2  C2  N1  119.54  3.000
 1LD  N3  C2  N1  117.23  3.000
 1LD  C4  N3  C2  121.55  3.000
 1LD  C5  C4  N4  119.82  3.000
 1LD  C5  C4  N3  120.71  3.000
 1LD  N4  C4  N3  119.48  3.000
 1LD  H4  N4  H3  117.92  3.000
 1LD  H4  N4  C4  122.55  3.000
 1LD  H3  N4  C4  119.52  3.000
 1LD  F   C5  C4  119.49  3.000
 1LD  C4  C5  C6  118.61  3.000
 1LD  F   C5  C6  121.91  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
 1LD  CONST_01  C4  N3  C2  N1    0.00  0.0  0
 1LD  CONST_02  N3  C2  N1  C6    0.00  0.0  0
 1LD  CONST_03  C5  C4  N3  C2    0.00  0.0  0
 1LD  CONST_04  O2  C2  N1  C6  180.00  0.0  0
 1LD  CONST_05  N4  C4  N3  C2  180.00  0.0  0
 1LD  CONST_06  C4  N3  C2  O2  180.00  0.0  0
 1LD  CONST_07  H1  N1  C2  N3  180.00  0.0  0
 1LD  CONST_08  H3  N4  C4  N3    0.00  0.0  0
 1LD  CONST_09  H4  N4  C4  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
 1LD  plan-1  N1  0.020
 1LD  plan-1  C6  0.020
 1LD  plan-1  C2  0.020
 1LD  plan-1  O2  0.020
 1LD  plan-1  N3  0.020
 1LD  plan-1  C4  0.020
 1LD  plan-1  N4  0.020
 1LD  plan-1  C5  0.020
 1LD  plan-1  F   0.020
 1LD  plan-1  H1  0.020
 1LD  plan-1  H2  0.020
 1LD  plan-1  H3  0.020
 1LD  plan-1  H4  0.020

