# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:17:24 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: pyridine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc(c1)C(O)=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
 PD2  PD2  'pyridine-2,4-dicarboxylic acid'  ligand  15  12  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PD2
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
 PD2  O42  O  O      0  -0.586   2.5039   1.7772   0.0251
 PD2  C41  C  C      0   0.399   2.5465   0.5338   0.0353
 PD2  O41  O  OC    -1  -0.588   3.5610  -0.1866   0.0607
 PD2  C4   C  CR6    0   0.007   1.2036  -0.1927   0.0153
 PD2  C5   C  CR16   0  -0.356   1.1363  -1.5804   0.0060
 PD2  C6   C  CR16   0  -0.090  -0.1101  -2.1874  -0.0095
 PD2  C3   C  CR16   0  -0.361   0.0013   0.5025   0.0062
 PD2  C2   C  CR6    0   0.043  -1.2073  -0.1885  -0.0037
 PD2  N1   N  N      0  -0.410  -1.2561  -1.5195  -0.0117
 PD2  C21  C  C      0   0.385  -2.5352   0.5720  -0.0029
 PD2  O21  O  O      0  -0.592  -2.4513   1.8152  -0.0524
 PD2  O22  O  OC    -1  -0.592  -3.5715  -0.1095   0.0498
 PD2  H5   H  HCR6   0   0.251   2.0337  -2.1833   0.0122
 PD2  H6   H  HCR6   0   0.247  -0.1827  -3.2706  -0.0189
 PD2  H3   H  HCR6   0   0.242  -0.0013   1.5825   0.0099

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
 PD2  O42  C41  deloc     1.244  0.020  1.244
 PD2  C41  O41  deloc     1.245  0.020  1.245
 PD2  C41  C4   single    1.527  0.020  1.527
 PD2  C4   C5   aromatic  1.389  0.020  1.389
 PD2  C4   C3   aromatic  1.389  0.020  1.389
 PD2  C5   C6   aromatic  1.386  0.020  1.386
 PD2  C5   H5   single    0.930  0.020  1.080
 PD2  C6   N1   aromatic  1.326  0.020  1.326
 PD2  C6   H6   single    0.930  0.020  1.080
 PD2  C3   C2   aromatic  1.392  0.020  1.392
 PD2  C3   H3   single    0.930  0.020  1.080
 PD2  C2   N1   aromatic  1.332  0.020  1.332
 PD2  C2   C21  single    1.530  0.020  1.530
 PD2  C21  O21  deloc     1.247  0.020  1.247
 PD2  C21  O22  deloc     1.241  0.020  1.241

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
 PD2  C4   C41  O41  116.22  3.000
 PD2  C4   C41  O42  116.44  3.000
 PD2  O41  C41  O42  127.34  3.000
 PD2  C3   C4   C5   117.25  3.000
 PD2  C3   C4   C41  121.55  3.000
 PD2  C5   C4   C41  121.19  3.000
 PD2  H5   C5   C6   120.14  3.000
 PD2  H5   C5   C4   121.12  3.000
 PD2  C6   C5   C4   118.74  3.000
 PD2  H6   C6   N1   116.40  3.000
 PD2  H6   C6   C5   119.80  3.000
 PD2  N1   C6   C5   123.80  3.000
 PD2  H3   C3   C2   119.62  3.000
 PD2  H3   C3   C4   120.17  3.000
 PD2  C2   C3   C4   120.21  3.000
 PD2  C21  C2   N1   117.70  3.000
 PD2  C21  C2   C3   120.44  3.000
 PD2  N1   C2   C3   121.86  3.000
 PD2  C2   N1   C6   118.13  3.000
 PD2  O22  C21  O21  127.24  3.000
 PD2  O22  C21  C2   116.85  3.000
 PD2  O21  C21  C2   115.91  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
 PD2  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 PD2  CONST_02  N1   C2   C3   C4     0.00   0.0  0
 PD2  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 PD2  CONST_04  C2   N1   C6   C5     0.00   0.0  0
 PD2  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 PD2  CONST_06  C3   C2   N1   C6     0.00   0.0  0
 PD2  CONST_07  C6   C5   C4   C41  180.00   0.0  0
 PD2  CONST_08  C2   C3   C4   C41  180.00   0.0  0
 PD2  CONST_09  C21  C2   C3   C4   180.00   0.0  0
 PD2  CONST_10  C21  C2   N1   C6   180.00   0.0  0
 PD2  CONST_11  H6   C6   C5   C4   180.00   0.0  0
 PD2  CONST_12  H3   C3   C4   C5   180.00   0.0  0
 PD2  CONST_13  H5   C5   C4   C3   180.00   0.0  0
 PD2  Var_01    C5   C4   C41  O42  179.11  30.0  2
 PD2  Var_02    O21  C21  C2   C3     3.04  30.0  2

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
 PD2  plan-1  C41  0.020
 PD2  plan-1  C4   0.020
 PD2  plan-1  C5   0.020
 PD2  plan-1  C6   0.020
 PD2  plan-1  C3   0.020
 PD2  plan-1  C2   0.020
 PD2  plan-1  N1   0.020
 PD2  plan-1  C21  0.020
 PD2  plan-1  H5   0.020
 PD2  plan-1  H6   0.020
 PD2  plan-1  H3   0.020
 PD2  plan-2  O42  0.020
 PD2  plan-2  C41  0.020
 PD2  plan-2  O41  0.020
 PD2  plan-2  C4   0.020
 PD2  plan-3  C2   0.020
 PD2  plan-3  C21  0.020
 PD2  plan-3  O21  0.020
 PD2  plan-3  O22  0.020

