# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:39:50 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 6-amino-5-bromopyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(Br)C(=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
 JFD  JFD  6-amino-5-bromopyrimidine-2,4(1H,3H)-dione  ligand  14  10  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JFD
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
 JFD  BR    BR  BR    0  -0.025  -2.0473   0.1238   0.0314
 JFD  C5    C   CR6   0  -0.434  -0.1782   0.0478   0.0228
 JFD  C4    C   CR6   0   0.586   0.5276   1.2876   0.0463
 JFD  O8    O   O     0  -0.469   0.0263   2.3990   0.0720
 JFD  N3    N   NR16  0  -0.721   1.9142   1.1560   0.0391
 JFD  C2    C   CR6   0   0.681   2.6280  -0.0039   0.0093
 JFD  O9    O   O     0  -0.474   3.8402  -0.0474   0.0008
 JFD  N1    N   NR16  0  -0.731   1.8568  -1.1393  -0.0111
 JFD  C6    C   CR6   0   0.696   0.4892  -1.1592  -0.0044
 JFD  N7    N   NH2   0  -0.829  -0.0819  -2.3589  -0.0341
 JFD  HN3   H   HNR6  0   0.428   2.4525   2.0125   0.0555
 JFD  HN1   H   HNR6  0   0.439   2.3615  -2.0143  -0.0460
 JFD  HN7   H   HNH2  0   0.426  -1.0811  -2.4649   0.0028
 JFD  HN7A  H   HNH2  0   0.427   0.4645  -3.2033   0.0056

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
 JFD  BR  C5    single  1.871  0.020  1.871
 JFD  C5  C4    single  1.427  0.020  1.427
 JFD  C5  C6    double  1.379  0.020  1.379
 JFD  C4  O8    double  1.220  0.020  1.220
 JFD  C4  N3    single  1.393  0.020  1.393
 JFD  N3  C2    single  1.362  0.020  1.362
 JFD  C2  O9    double  1.213  0.020  1.213
 JFD  C2  N1    single  1.373  0.020  1.373
 JFD  N1  C6    single  1.368  0.020  1.368
 JFD  C6  N7    single  1.329  0.020  1.329
 JFD  N3  HN3   single  0.860  0.020  1.020
 JFD  N1  HN1   single  0.860  0.020  1.020
 JFD  N7  HN7   single  0.860  0.020  1.020
 JFD  N7  HN7A  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
 JFD  C6    C5  C4   121.42  3.000
 JFD  C6    C5  BR   121.27  3.000
 JFD  C4    C5  BR   117.31  3.000
 JFD  N3    C4  O8   119.70  3.000
 JFD  N3    C4  C5   114.22  3.000
 JFD  O8    C4  C5   126.08  3.000
 JFD  HN3   N3  C2   116.26  3.000
 JFD  HN3   N3  C4   116.71  3.000
 JFD  C2    N3  C4   127.03  3.000
 JFD  N1    C2  O9   122.12  3.000
 JFD  N1    C2  N3   114.21  3.000
 JFD  O9    C2  N3   123.66  3.000
 JFD  HN1   N1  C6   119.13  3.000
 JFD  HN1   N1  C2   115.85  3.000
 JFD  C6    N1  C2   125.01  3.000
 JFD  N7    C6  N1   116.28  3.000
 JFD  N7    C6  C5   125.62  3.000
 JFD  N1    C6  C5   118.11  3.000
 JFD  HN7A  N7  HN7  116.71  3.000
 JFD  HN7A  N7  C6   121.55  3.000
 JFD  HN7   N7  C6   121.42  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
 JFD  CONST_01  C2    N3  C4  C5    0.00  0.0  0
 JFD  CONST_02  C2    N1  C6  C5    0.00  0.0  0
 JFD  CONST_03  N1    C2  N3  C4    0.00  0.0  0
 JFD  CONST_04  C6    N1  C2  N3    0.00  0.0  0
 JFD  CONST_05  O9    C2  N3  C4  180.00  0.0  0
 JFD  CONST_06  C2    N3  C4  O8  180.00  0.0  0
 JFD  CONST_07  N7    C6  N1  C2  180.00  0.0  0
 JFD  CONST_08  C6    N1  C2  O9  180.00  0.0  0
 JFD  CONST_09  HN3   N3  C4  C5  180.00  0.0  0
 JFD  CONST_10  HN1   N1  C6  C5  180.00  0.0  0
 JFD  CONST_11  HN7   N7  C6  C5    0.00  0.0  0
 JFD  CONST_12  HN7A  N7  C6  C5  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
 JFD  plan-1  BR    0.020
 JFD  plan-1  C5    0.020
 JFD  plan-1  C4    0.020
 JFD  plan-1  O8    0.020
 JFD  plan-1  N3    0.020
 JFD  plan-1  C2    0.020
 JFD  plan-1  O9    0.020
 JFD  plan-1  N1    0.020
 JFD  plan-1  C6    0.020
 JFD  plan-1  N7    0.020
 JFD  plan-1  HN3   0.020
 JFD  plan-1  HN1   0.020
 JFD  plan-1  HN7   0.020
 JFD  plan-1  HN7A  0.020

