# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:08:52 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 5-bromopyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: BrC1=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
 URB  URB  5-bromopyrimidine-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_URB
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
 URB  O4   O   O     0  -0.434  -0.0049  -2.1768   0.0178
 URB  C4   C   CR6   0   0.605  -0.5251  -1.0818   0.0134
 URB  C5   C   CR6   0  -0.357   0.1786   0.1884   0.0040
 URB  BR   BR  BR    0   0.006   2.0431   0.1493  -0.0003
 URB  C6   C   CR16  0   0.113  -0.5131   1.3427  -0.0018
 URB  N1   N   NR16  0  -0.668  -1.8687   1.3535   0.0019
 URB  C2   C   CR6   0   0.696  -2.6370   0.2181   0.0127
 URB  O2   O   O     0  -0.466  -3.8477   0.2360   0.0178
 URB  N3   N   NR16  0  -0.718  -1.9024  -0.9418   0.0170
 URB  H6   H   HCR6  0   0.342  -0.0406   2.3146  -0.0099
 URB  HN1  H   HNR6  0   0.447  -2.3525   2.2404   0.0018
 URB  HN3  H   HNR6  0   0.435  -2.4408  -1.7999   0.0257

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
 URB  O4  C4   double  1.212  0.020  1.212
 URB  C4  C5   single  1.452  0.020  1.452
 URB  C4  N3   single  1.384  0.020  1.384
 URB  C5  BR   single  1.865  0.020  1.865
 URB  C5  C6   double  1.346  0.020  1.346
 URB  C6  N1   single  1.356  0.020  1.356
 URB  N1  C2   single  1.371  0.020  1.371
 URB  C2  O2   double  1.211  0.020  1.211
 URB  C2  N3   single  1.373  0.020  1.373
 URB  C6  H6   single  0.930  0.020  1.080
 URB  N1  HN1  single  0.860  0.020  1.020
 URB  N3  HN3  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
 URB  N3   C4  C5  113.18  3.000
 URB  N3   C4  O4  121.22  3.000
 URB  C5   C4  O4  125.60  3.000
 URB  C6   C5  BR  122.13  3.000
 URB  C6   C5  C4  120.08  3.000
 URB  BR   C5  C4  117.78  3.000
 URB  H6   C6  N1  115.47  3.000
 URB  H6   C6  C5  123.14  3.000
 URB  N1   C6  C5  121.39  3.000
 URB  HN1  N1  C2  117.30  3.000
 URB  HN1  N1  C6  119.07  3.000
 URB  C2   N1  C6  123.63  3.000
 URB  N3   C2  O2  123.19  3.000
 URB  N3   C2  N1  113.57  3.000
 URB  O2   C2  N1  123.24  3.000
 URB  HN3  N3  C2  115.55  3.000
 URB  HN3  N3  C4  116.30  3.000
 URB  C2   N3  C4  128.15  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
 URB  CONST_01  N1   C2  N3  C4    0.00  0.0  0
 URB  CONST_02  C2   N3  C4  C5    0.00  0.0  0
 URB  CONST_03  N3   C2  N1  C6    0.00  0.0  0
 URB  CONST_04  C2   N3  C4  O4  180.00  0.0  0
 URB  CONST_05  O2   C2  N3  C4  180.00  0.0  0
 URB  CONST_06  O2   C2  N1  C6  180.00  0.0  0
 URB  CONST_07  HN3  N3  C4  C5  180.00  0.0  0
 URB  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
 URB  plan-1  O4   0.020
 URB  plan-1  C4   0.020
 URB  plan-1  C5   0.020
 URB  plan-1  BR   0.020
 URB  plan-1  C6   0.020
 URB  plan-1  N1   0.020
 URB  plan-1  C2   0.020
 URB  plan-1  O2   0.020
 URB  plan-1  N3   0.020
 URB  plan-1  H6   0.020
 URB  plan-1  HN1  0.020
 URB  plan-1  HN3  0.020

