# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:23:35 2021
#   Inital geometry file: a 43 line input string
#   Ligand name: pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccncc1
#
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
 S3V  S3V  'pyridine-4-carboxylic acid'  ligand  14  9  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S3V
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
 S3V  C4  C  CR6   0   0.018  -12.4927  78.3474  122.0778
 S3V  C5  C  C     0   0.543  -12.2660  77.5484  123.3156
 S3V  N   N  N     0  -0.392  -12.9041  79.7563  119.7135
 S3V  C   C  CR16  0  -0.327  -12.3748  77.7192  120.8444
 S3V  O   O  O     0  -0.424  -11.9597  76.3827  123.3016
 S3V  C1  C  CR16  0  -0.054  -12.5905  78.4662  119.6972
 S3V  C2  C  CR16  0  -0.053  -13.0140  80.3509  120.8943
 S3V  C3  C  CR16  0  -0.332  -12.8219  79.6973  122.1030
 S3V  O1  O  OH1   0  -0.586  -12.4393  78.2546  124.4186
 S3V  H1  H  HCR6  0   0.282  -12.1213  76.6713  120.7669
 S3V  H2  H  HCR6  0   0.274  -12.5050  77.9981  118.7235
 S3V  H3  H  HCR6  0   0.275  -13.2694  81.4042  120.8870
 S3V  H4  H  HCR6  0   0.284  -12.9310  80.2468  123.0270
 S3V  H5  H  HOH1  0   0.493  -12.2895  77.7005  125.1997

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
 S3V  N   C1  aromatic  1.328  0.020  1.328
 S3V  N   C2  aromatic  1.327  0.020  1.327
 S3V  C1  C   aromatic  1.386  0.020  1.386
 S3V  C2  C3  aromatic  1.387  0.020  1.387
 S3V  C   C4  aromatic  1.389  0.020  1.389
 S3V  C3  C4  aromatic  1.390  0.020  1.390
 S3V  C4  C5  single    1.491  0.020  1.491
 S3V  O   C5  double    1.205  0.020  1.205
 S3V  C5  O1  single    1.321  0.020  1.321
 S3V  C   H1  single    0.930  0.020  1.080
 S3V  C1  H2  single    0.930  0.020  1.080
 S3V  C2  H3  single    0.930  0.020  1.080
 S3V  C3  H4  single    0.930  0.020  1.080
 S3V  O1  H5  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
 S3V  C3  C4  C   118.39  3.000
 S3V  C3  C4  C5  122.79  3.000
 S3V  C   C4  C5  118.82  3.000
 S3V  O1  C5  O   124.06  3.000
 S3V  O1  C5  C4  112.76  3.000
 S3V  O   C5  C4  123.18  3.000
 S3V  C2  N   C1  117.77  3.000
 S3V  H1  C   C1  119.98  3.000
 S3V  H1  C   C4  121.46  3.000
 S3V  C1  C   C4  118.56  3.000
 S3V  H2  C1  C   119.91  3.000
 S3V  H2  C1  N   116.70  3.000
 S3V  C   C1  N   123.39  3.000
 S3V  H3  C2  C3  119.76  3.000
 S3V  H3  C2  N   116.68  3.000
 S3V  C3  C2  N   123.56  3.000
 S3V  H4  C3  C2  119.44  3.000
 S3V  H4  C3  C4  122.23  3.000
 S3V  C2  C3  C4  118.33  3.000
 S3V  H5  O1  C5  110.30  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
 S3V  CONST_01  N   C1  C   C4    0.00   0.0  0
 S3V  CONST_02  N   C2  C3  C4    0.00   0.0  0
 S3V  CONST_03  C2  N   C1  C     0.00   0.0  0
 S3V  CONST_04  C2  C3  C4  C     0.00   0.0  0
 S3V  CONST_05  C3  C2  N   C1    0.00   0.0  0
 S3V  CONST_06  C3  C4  C   C1    0.00   0.0  0
 S3V  CONST_07  C1  C   C4  C5  180.00   0.0  0
 S3V  CONST_08  C2  C3  C4  C5  180.00   0.0  0
 S3V  CONST_09  H2  C1  C   C4  180.00   0.0  0
 S3V  CONST_10  H3  C2  C3  C4  180.00   0.0  0
 S3V  CONST_11  H1  C   C1  N   180.00   0.0  0
 S3V  CONST_12  H4  C3  C2  N   180.00   0.0  0
 S3V  CONST_13  H5  O1  C5  C4  180.00   0.0  0
 S3V  Var_01    O   C5  C4  C     1.39  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
 S3V  plan-1  C4  0.020
 S3V  plan-1  C5  0.020
 S3V  plan-1  N   0.020
 S3V  plan-1  C   0.020
 S3V  plan-1  C1  0.020
 S3V  plan-1  C2  0.020
 S3V  plan-1  C3  0.020
 S3V  plan-1  H1  0.020
 S3V  plan-1  H2  0.020
 S3V  plan-1  H3  0.020
 S3V  plan-1  H4  0.020
 S3V  plan-2  C4  0.020
 S3V  plan-2  C5  0.020
 S3V  plan-2  O   0.020
 S3V  plan-2  O1  0.020
 S3V  plan-2  H5  0.020

