# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:59:49 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 5-chloropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ClC1=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
 5UC  5UC  5-chloropyrimidine-2,4(1H,3H)-dione  ligand  12  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5UC
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
 5UC  O2   O   O     0  -0.467  -3.2063  -0.0480   0.0060
 5UC  C2   C   CR6   0   0.693  -1.9973  -0.1207   0.0079
 5UC  N3   N   NR16  0  -0.720  -1.1784   0.9818  -0.0093
 5UC  C4   C   CR6   0   0.614   0.2050   1.0183  -0.0087
 5UC  O4   O   O     0  -0.434   0.8106   2.0681  -0.0250
 5UC  N1   N   NR16  0  -0.673  -1.3161  -1.3097   0.0272
 5UC  C6   C   CR16  0   0.125   0.0375  -1.3996   0.0289
 5UC  C5   C   CR6   0  -0.278   0.8111  -0.3005   0.0120
 5UC  CL5  CL  CL    0  -0.083   2.5229  -0.3910   0.0139
 5UC  H1   H   HNR6  0   0.435  -1.6508   1.8779  -0.0232
 5UC  H2   H   HCR6  0   0.343   0.4435  -2.4005   0.0445
 5UC  H4   H   HNR6  0   0.446  -1.8646  -2.1576   0.0418

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
 5UC  CL5  C5  single  1.714  0.020  1.714
 5UC  O4   C4  double  1.212  0.020  1.212
 5UC  C5   C4  single  1.452  0.020  1.452
 5UC  C5   C6  double  1.344  0.020  1.344
 5UC  C4   N3  single  1.384  0.020  1.384
 5UC  C6   N1  single  1.357  0.020  1.357
 5UC  N3   C2  single  1.374  0.020  1.374
 5UC  N1   C2  single  1.370  0.020  1.370
 5UC  C2   O2  double  1.211  0.020  1.211
 5UC  N3   H1  single  0.860  0.020  1.020
 5UC  C6   H2  single  0.930  0.020  1.080
 5UC  N1   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
 5UC  N1   C2  N3  113.59  3.000
 5UC  N1   C2  O2  123.25  3.000
 5UC  N3   C2  O2  123.16  3.000
 5UC  H1   N3  C4  116.28  3.000
 5UC  H1   N3  C2  115.61  3.000
 5UC  C4   N3  C2  128.11  3.000
 5UC  C5   C4  O4  125.35  3.000
 5UC  C5   C4  N3  113.17  3.000
 5UC  O4   C4  N3  121.49  3.000
 5UC  H4   N1  C6  119.09  3.000
 5UC  H4   N1  C2  117.30  3.000
 5UC  C6   N1  C2  123.61  3.000
 5UC  H2   C6  C5  122.79  3.000
 5UC  H2   C6  N1  115.88  3.000
 5UC  C5   C6  N1  121.34  3.000
 5UC  CL5  C5  C6  122.11  3.000
 5UC  C6   C5  C4  120.19  3.000
 5UC  CL5  C5  C4  117.70  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
 5UC  CONST_01  C6  N1  C2  N3    0.00  0.0  0
 5UC  CONST_02  N1  C2  N3  C4    0.00  0.0  0
 5UC  CONST_03  C4  N3  C2  O2  180.00  0.0  0
 5UC  CONST_04  C6  N1  C2  O2  180.00  0.0  0
 5UC  CONST_05  H4  N1  C2  N3  180.00  0.0  0
 5UC  CONST_06  H1  N3  C2  N1  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
 5UC  plan-1  O2   0.020
 5UC  plan-1  C2   0.020
 5UC  plan-1  N3   0.020
 5UC  plan-1  C4   0.020
 5UC  plan-1  O4   0.020
 5UC  plan-1  N1   0.020
 5UC  plan-1  C6   0.020
 5UC  plan-1  C5   0.020
 5UC  plan-1  CL5  0.020
 5UC  plan-1  H1   0.020
 5UC  plan-1  H2   0.020
 5UC  plan-1  H4   0.020

