# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:19:13 2022
#   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  13  9  .  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_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  -0.002  -12.5055  78.3806  122.0873
 S3V  C5  C  C      0   0.401  -12.2899  77.6321  123.4051
 S3V  N   N  N      0  -0.407  -12.9037  79.7495  119.6701
 S3V  C   C  CR16   0  -0.356  -12.3801  77.7396  120.8600
 S3V  O   O  O      0  -0.578  -11.9512  76.4395  123.3066
 S3V  C1  C  CR16   0  -0.068  -12.5895  78.4585  119.6931
 S3V  C2  C  CR16   0  -0.068  -13.0211  80.3638  120.8427
 S3V  C3  C  CR16   0  -0.356  -12.8373  79.7310  122.0625
 S3V  O1  O  OC    -1  -0.578  -12.4776  78.2900  124.4435
 S3V  H1  H  HCR6   0   0.253  -12.1233  76.6906  120.8084
 S3V  H2  H  HCR6   0   0.253  -12.4981  77.9669  118.7301
 S3V  H3  H  HCR6   0   0.253  -13.2766  81.4179  120.8110
 S3V  H4  H  HCR6   0   0.253  -12.9510  80.2891  122.9816

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  1.329  0.020  1.329
 S3V  N   C2  aromatic  1.329  0.020  1.329
 S3V  C1  C   aromatic  1.386  0.020  1.386
 S3V  C2  C3  aromatic  1.386  0.020  1.386
 S3V  C   C4  aromatic  1.390  0.020  1.390
 S3V  C3  C4  aromatic  1.391  0.020  1.391
 S3V  C4  C5  single    1.531  0.020  1.531
 S3V  O   C5  deloc     1.244  0.020  1.244
 S3V  C5  O1  deloc     1.244  0.020  1.244
 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

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   116.96  3.000
 S3V  C3  C4  C5  121.58  3.000
 S3V  C   C4  C5  121.45  3.000
 S3V  O1  C5  O   127.92  3.000
 S3V  O1  C5  C4  116.04  3.000
 S3V  O   C5  C4  116.04  3.000
 S3V  C2  N   C1  117.04  3.000
 S3V  H1  C   C1  119.92  3.000
 S3V  H1  C   C4  120.72  3.000
 S3V  C1  C   C4  119.36  3.000
 S3V  H2  C1  C   119.96  3.000
 S3V  H2  C1  N   116.40  3.000
 S3V  C   C1  N   123.64  3.000
 S3V  H3  C2  C3  120.02  3.000
 S3V  H3  C2  N   116.36  3.000
 S3V  C3  C2  N   123.62  3.000
 S3V  H4  C3  C2  119.89  3.000
 S3V  H4  C3  C4  120.74  3.000
 S3V  C2  C3  C4  119.37  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  Var_01    O   C5  C4  C     2.51  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

