# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 23:21:29 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  17  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.419   2.5852   1.8069  -0.0069
 PD2  C41  C  C     0   0.549   2.5333   0.6037  -0.0102
 PD2  O41  O  OH1   0  -0.585   3.5885  -0.1889  -0.0185
 PD2  C4   C  CR6   0   0.031   1.2485  -0.1551  -0.0055
 PD2  C5   C  CR16  0  -0.313   1.1933  -1.5411  -0.0094
 PD2  C6   C  CR16  0  -0.064  -0.0552  -2.1521  -0.0039
 PD2  C3   C  CR16  0  -0.299   0.0563   0.5569   0.0031
 PD2  C2   C  CR6   0   0.105  -1.1345  -0.1529   0.0082
 PD2  N1   N  N     0  -0.389  -1.1926  -1.4792   0.0048
 PD2  C21  C  C     0   0.533  -2.4221   0.6069   0.0187
 PD2  O21  O  O     0  -0.425  -2.4680   1.8121   0.0135
 PD2  O22  O  OH1   0  -0.579  -3.4804  -0.1789   0.0352
 PD2  H41  H  HOH1  0   0.496   4.4049   0.3339  -0.0226
 PD2  H5   H  HCR6  0   0.293   2.0825  -2.1545  -0.0153
 PD2  H6   H  HCR6  0   0.284  -0.1280  -3.2329  -0.0066
 PD2  H3   H  HCR6  0   0.291   0.0545   1.6375   0.0060
 PD2  H22  H  HOH1  0   0.490  -4.2870   0.3586   0.0422

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  double    1.204  0.020  1.204
 PD2  C41  O41  single    1.320  0.020  1.320
 PD2  C41  C4   single    1.492  0.020  1.492
 PD2  O41  H41  single    0.850  0.020  0.980
 PD2  C4   C5   aromatic  1.387  0.020  1.387
 PD2  C4   C3   aromatic  1.389  0.020  1.389
 PD2  C5   C6   aromatic  1.390  0.020  1.390
 PD2  C5   H5   single    0.930  0.020  1.080
 PD2  C6   N1   aromatic  1.322  0.020  1.322
 PD2  C6   H6   single    0.930  0.020  1.080
 PD2  C3   C2   aromatic  1.386  0.020  1.386
 PD2  C3   H3   single    0.930  0.020  1.080
 PD2  C2   N1   aromatic  1.328  0.020  1.328
 PD2  C2   C21  single    1.495  0.020  1.495
 PD2  C21  O21  double    1.206  0.020  1.206
 PD2  C21  O22  single    1.318  0.020  1.318
 PD2  O22  H22  single    0.850  0.020  0.980

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  112.52  3.000
 PD2  C4   C41  O42  123.04  3.000
 PD2  O41  C41  O42  124.44  3.000
 PD2  H41  O41  C41  110.45  3.000
 PD2  C3   C4   C5   118.56  3.000
 PD2  C3   C4   C41  118.59  3.000
 PD2  C5   C4   C41  122.85  3.000
 PD2  H5   C5   C6   119.32  3.000
 PD2  H5   C5   C4   122.32  3.000
 PD2  C6   C5   C4   118.36  3.000
 PD2  H6   C6   N1   116.76  3.000
 PD2  H6   C6   C5   119.93  3.000
 PD2  N1   C6   C5   123.31  3.000
 PD2  H3   C3   C2   120.70  3.000
 PD2  H3   C3   C4   120.94  3.000
 PD2  C2   C3   C4   118.36  3.000
 PD2  C21  C2   N1   118.04  3.000
 PD2  C21  C2   C3   118.66  3.000
 PD2  N1   C2   C3   123.31  3.000
 PD2  C2   N1   C6   118.10  3.000
 PD2  O22  C21  O21  124.41  3.000
 PD2  O22  C21  C2   112.86  3.000
 PD2  O21  C21  C2   122.72  3.000
 PD2  H22  O22  C21  109.73  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  CONST_14  H41  O41  C41  C4    180.00   0.0  0
 PD2  CONST_15  H22  O22  C21  C2    180.00   0.0  0
 PD2  Var_01    C5   C4   C41  O42  -180.00  30.0  2
 PD2  Var_02    O21  C21  C2   C3      0.53  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-2  H41  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
 PD2  plan-3  H22  0.020

