# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:55:50 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: pyridine-2,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(n1)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
 PDC  PDC  'pyridine-2,6-dicarboxylic acid'  ligand  15  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDC
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
 PDC  N1  N  N      0  -0.407   0.4489   0.0132   0.0019
 PDC  C2  C  CR6    0   0.021  -0.2157   0.0260   1.1526
 PDC  C3  C  CR16   0  -0.315  -1.6077   0.0481   1.1973
 PDC  C4  C  CR16   0  -0.152  -2.3128   0.0500   0.0054
 PDC  C5  C  CR16   0  -0.315  -1.6111   0.0362  -1.1885
 PDC  C6  C  CR6    0   0.020  -0.2189   0.0206  -1.1468
 PDC  C7  C  C      0   0.381   0.5971   0.0159   2.4501
 PDC  O1  O  O      0  -0.594  -0.0640   0.0865   3.5054
 PDC  O2  O  OC    -1  -0.592   1.8317  -0.0609   2.3400
 PDC  C8  C  C      0   0.381   0.5911   0.0115  -2.4458
 PDC  O3  O  O      0  -0.594  -0.0739   0.0032  -3.5008
 PDC  O4  O  OC    -1  -0.591   1.8280   0.0140  -2.3366
 PDC  H3  H  HCR6   0   0.251  -2.1200   0.0579   2.1483
 PDC  H4  H  HCR6   0   0.258  -3.3957   0.0632   0.0077
 PDC  H5  H  HCR6   0   0.251  -2.1263   0.0385  -2.1380

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
 PDC  N1  C2  aromatic  1.329  0.020  1.329
 PDC  N1  C6  aromatic  1.329  0.020  1.329
 PDC  C2  C3  aromatic  1.393  0.020  1.393
 PDC  C2  C7  single    1.531  0.020  1.531
 PDC  C3  C4  aromatic  1.385  0.020  1.385
 PDC  C3  H3  single    0.930  0.020  1.080
 PDC  C4  C5  aromatic  1.385  0.020  1.385
 PDC  C4  H4  single    0.930  0.020  1.080
 PDC  C5  C6  aromatic  1.393  0.020  1.393
 PDC  C5  H5  single    0.930  0.020  1.080
 PDC  C6  C8  single    1.531  0.020  1.531
 PDC  C7  O1  deloc     1.247  0.020  1.247
 PDC  C7  O2  deloc     1.242  0.020  1.242
 PDC  C8  O3  deloc     1.247  0.020  1.247
 PDC  C8  O4  deloc     1.242  0.020  1.242

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
 PDC  C6  N1  C2  119.82  3.000
 PDC  C7  C2  C3  120.23  3.000
 PDC  C7  C2  N1  117.92  3.000
 PDC  C3  C2  N1  121.85  3.000
 PDC  H3  C3  C4  121.08  3.000
 PDC  H3  C3  C2  120.16  3.000
 PDC  C4  C3  C2  118.77  3.000
 PDC  H4  C4  C5  120.57  3.000
 PDC  H4  C4  C3  120.49  3.000
 PDC  C5  C4  C3  118.94  3.000
 PDC  H5  C5  C6  120.20  3.000
 PDC  H5  C5  C4  121.06  3.000
 PDC  C6  C5  C4  118.73  3.000
 PDC  C8  C6  C5  120.23  3.000
 PDC  C8  C6  N1  117.88  3.000
 PDC  C5  C6  N1  121.89  3.000
 PDC  O2  C7  O1  127.25  3.000
 PDC  O2  C7  C2  116.94  3.000
 PDC  O1  C7  C2  115.80  3.000
 PDC  O4  C8  O3  127.27  3.000
 PDC  O4  C8  C6  116.90  3.000
 PDC  O3  C8  C6  115.83  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
 PDC  CONST_01  C4  C3  C2  N1    0.00   0.0  0
 PDC  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 PDC  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 PDC  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 PDC  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 PDC  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 PDC  CONST_07  C8  C6  N1  C2  180.00   0.0  0
 PDC  CONST_08  C7  C2  C3  C4  180.00   0.0  0
 PDC  CONST_09  C8  C6  C5  C4  180.00   0.0  0
 PDC  CONST_10  C7  C2  N1  C6  180.00   0.0  0
 PDC  CONST_11  H3  C3  C2  N1  180.00   0.0  0
 PDC  CONST_12  H5  C5  C6  N1  180.00   0.0  0
 PDC  CONST_13  H4  C4  C3  C2  180.00   0.0  0
 PDC  Var_01    O1  C7  C2  N1  177.04  30.0  2
 PDC  Var_02    O3  C8  C6  N1  179.20  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
 PDC  plan-1  N1  0.020
 PDC  plan-1  C2  0.020
 PDC  plan-1  C3  0.020
 PDC  plan-1  C4  0.020
 PDC  plan-1  C5  0.020
 PDC  plan-1  C6  0.020
 PDC  plan-1  C7  0.020
 PDC  plan-1  C8  0.020
 PDC  plan-1  H3  0.020
 PDC  plan-1  H4  0.020
 PDC  plan-1  H5  0.020
 PDC  plan-2  C2  0.020
 PDC  plan-2  C7  0.020
 PDC  plan-2  O1  0.020
 PDC  plan-2  O2  0.020
 PDC  plan-3  C6  0.020
 PDC  plan-3  C8  0.020
 PDC  plan-3  O3  0.020
 PDC  plan-3  O4  0.020

