# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 06:34:04 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC(=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
 BR8  BR8  pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  13  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BR8
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
 BR8  N1    N  NH1   0  -0.704   1.1711  -0.6171   0.0260
 BR8  C2    C  C     0   0.710   0.0189  -1.3672   0.0028
 BR8  O2    O  O     0  -0.441   0.0389  -2.5737  -0.0073
 BR8  N3    N  NH1   0  -0.704  -1.1576  -0.6554  -0.0062
 BR8  C4    C  C     0   0.580  -1.3001   0.7066   0.0047
 BR8  O4    O  O     0  -0.424  -2.3910   1.2248   0.0019
 BR8  C5    C  CH2   0  -0.734  -0.0287   1.5042   0.0174
 BR8  C6    C  C     0   0.580   1.2682   0.7490   0.0381
 BR8  O8    O  O     0  -0.424   2.3412   1.3027   0.0622
 BR8  H1    H  HNH1  0   0.435   2.0353  -1.1454   0.0364
 BR8  H3    H  HNH1  0   0.435  -2.0038  -1.2120  -0.0212
 BR8  H51C  H  HCH2  0   0.345  -0.0281   2.1569  -0.8598
 BR8  H52C  H  HCH2  0   0.344  -0.0509   2.1710   0.8830

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
 BR8  N1  C2    single  1.375  0.020  1.375
 BR8  N1  C6    single  1.370  0.020  1.370
 BR8  C2  O2    double  1.207  0.020  1.207
 BR8  C2  N3    single  1.375  0.020  1.375
 BR8  N3  C4    single  1.369  0.020  1.369
 BR8  C4  O4    double  1.208  0.020  1.208
 BR8  C4  C5    single  1.501  0.020  1.501
 BR8  C5  C6    single  1.501  0.020  1.501
 BR8  C6  O8    double  1.208  0.020  1.208
 BR8  N1  H1    single  0.860  0.020  1.020
 BR8  N3  H3    single  0.860  0.020  1.020
 BR8  C5  H51C  single  0.970  0.020  1.090
 BR8  C5  H52C  single  0.970  0.020  1.090

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
 BR8  H1    N1  C6    117.36  3.000
 BR8  H1    N1  C2    115.50  3.000
 BR8  C6    N1  C2    127.14  3.000
 BR8  N3    C2  O2    122.12  3.000
 BR8  N3    C2  N1    115.76  3.000
 BR8  O2    C2  N1    122.12  3.000
 BR8  H3    N3  C4    117.37  3.000
 BR8  H3    N3  C2    115.49  3.000
 BR8  C4    N3  C2    127.14  3.000
 BR8  C5    C4  O4    122.49  3.000
 BR8  C5    C4  N3    116.13  3.000
 BR8  O4    C4  N3    121.38  3.000
 BR8  H52C  C5  H51C  105.73  3.000
 BR8  H52C  C5  C6    108.28  3.000
 BR8  H51C  C5  C6    108.12  3.000
 BR8  H52C  C5  C4    108.28  3.000
 BR8  H51C  C5  C4    108.11  3.000
 BR8  C6    C5  C4    117.69  3.000
 BR8  O8    C6  C5    122.50  3.000
 BR8  O8    C6  N1    121.37  3.000
 BR8  C5    C6  N1    116.13  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
 BR8  CONST_01  C4  N3  C2  N1    0.00   0.0  0
 BR8  CONST_02  C5  C4  N3  C2    0.00   0.0  0
 BR8  CONST_03  C6  N1  C2  N3    0.00   0.0  0
 BR8  CONST_04  O4  C4  N3  C2  180.00   0.0  0
 BR8  CONST_05  C6  N1  C2  O2  180.00   0.0  0
 BR8  CONST_06  C4  N3  C2  O2  180.00   0.0  0
 BR8  CONST_07  H3  N3  C2  N1  180.00   0.0  0
 BR8  CONST_08  H1  N1  C2  N3  180.00   0.0  0
 BR8  Var_01    O8  C6  N1  C2  179.80  30.0  1

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
 BR8  plan-1  N1  0.020
 BR8  plan-1  C5  0.020
 BR8  plan-1  C6  0.020
 BR8  plan-1  O8  0.020
 BR8  plan-2  N1  0.020
 BR8  plan-2  C2  0.020
 BR8  plan-2  O2  0.020
 BR8  plan-2  N3  0.020
 BR8  plan-2  C4  0.020
 BR8  plan-2  O4  0.020
 BR8  plan-2  C5  0.020
 BR8  plan-2  C6  0.020
 BR8  plan-2  H1  0.020
 BR8  plan-2  H3  0.020

