# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 16:02:44 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc(c1)c2cc(ccc2O)C#N
#
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
 VAO  VAO  '2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid'  ligand  26  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VAO
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
 VAO  N1   N  NS    0  -0.260  -4.0352  -3.3235   0.0456
 VAO  C    C  CSP   0   0.046  -3.5890  -2.2603   0.0258
 VAO  C1   C  CR6   0   0.012  -3.0489  -0.9440   0.0011
 VAO  C6   C  CR16  0  -0.345  -1.6732  -0.7593  -0.0061
 VAO  C5   C  CR6   0  -0.084  -1.1056   0.5111  -0.0297
 VAO  C4   C  CR6   0   0.389  -1.9778   1.6292  -0.0486
 VAO  O2   O  OH1   0  -0.615  -1.5480   2.8789  -0.0728
 VAO  C3   C  CR16  0  -0.339  -3.3655   1.4303  -0.0402
 VAO  C2   C  CR16  0  -0.237  -3.9003   0.1667  -0.0158
 VAO  C7   C  CR6   0   0.431   0.3605   0.6835  -0.0344
 VAO  N    N  N     0  -0.571   0.8143   1.9395  -0.0719
 VAO  C11  C  CR16  0  -0.006   2.1155   2.1872  -0.0793
 VAO  C10  C  CR16  0  -0.363   3.0666   1.1849  -0.0487
 VAO  C9   C  CR6   0   0.053   2.6171  -0.1305  -0.0078
 VAO  C8   C  CR16  0  -0.369   1.2566  -0.3853  -0.0005
 VAO  C12  C  C     0   0.555   3.5514  -1.2965   0.0307
 VAO  O1   O  O     0  -0.419   3.1760  -2.4406   0.0595
 VAO  O    O  OH1   0  -0.584   4.8178  -0.9272   0.0307
 VAO  H6   H  HCR6  0   0.285  -1.0419  -1.6363   0.0067
 VAO  H2   H  HCR6  0   0.286  -4.9733   0.0322  -0.0095
 VAO  H3   H  HCR6  0   0.282  -4.0139   2.2963  -0.0536
 VAO  H8   H  HCR6  0   0.289   0.9125  -1.4081   0.0338
 VAO  H11  H  HCR6  0   0.292   2.4082   3.2285  -0.1107
 VAO  H10  H  HCR6  0   0.290   4.1156   1.4400  -0.0570
 VAO  H    H  HOH1  0   0.496   5.3980  -1.7035   0.0589
 VAO  H21  H  HOH1  0   0.484  -0.5488   2.8546  -0.0799

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
 VAO  N1   C    triple    1.153  0.020  1.153
 VAO  C    C1   single    1.423  0.020  1.423
 VAO  C1   C6   aromatic  1.388  0.020  1.388
 VAO  C1   C2   aromatic  1.400  0.020  1.400
 VAO  C6   C5   aromatic  1.392  0.020  1.392
 VAO  C5   C4   aromatic  1.418  0.020  1.418
 VAO  C5   C7   single    1.476  0.020  1.476
 VAO  C4   O2   single    1.322  0.020  1.322
 VAO  C4   C3   aromatic  1.402  0.020  1.402
 VAO  C3   C2   aromatic  1.372  0.020  1.372
 VAO  C7   N    aromatic  1.336  0.020  1.336
 VAO  C7   C8   aromatic  1.395  0.020  1.395
 VAO  N    C11  aromatic  1.325  0.020  1.325
 VAO  C11  C10  aromatic  1.382  0.020  1.382
 VAO  C10  C9   aromatic  1.391  0.020  1.391
 VAO  C9   C8   aromatic  1.384  0.020  1.384
 VAO  C9   C12  single    1.495  0.020  1.495
 VAO  C12  O1   double    1.204  0.020  1.204
 VAO  C12  O    single    1.319  0.020  1.319
 VAO  C6   H6   single    0.930  0.020  1.080
 VAO  C2   H2   single    0.930  0.020  1.080
 VAO  C3   H3   single    0.930  0.020  1.080
 VAO  C8   H8   single    0.930  0.020  1.080
 VAO  C11  H11  single    0.930  0.020  1.080
 VAO  C10  H10  single    0.930  0.020  1.080
 VAO  O    H    single    0.850  0.020  0.980
 VAO  O2   H21  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
 VAO  C1   C    N1   180.00  3.000
 VAO  C2   C1   C6   119.82  3.000
 VAO  C2   C1   C    120.22  3.000
 VAO  C6   C1   C    119.96  3.000
 VAO  H6   C6   C5   120.19  3.000
 VAO  H6   C6   C1   118.09  3.000
 VAO  C5   C6   C1   121.72  3.000
 VAO  C7   C5   C4   121.24  3.000
 VAO  C7   C5   C6   120.78  3.000
 VAO  C4   C5   C6   117.97  3.000
 VAO  C3   C4   O2   117.14  3.000
 VAO  C3   C4   C5   119.79  3.000
 VAO  O2   C4   C5   123.07  3.000
 VAO  H21  O2   C4   107.59  3.000
 VAO  H3   C3   C2   120.24  3.000
 VAO  H3   C3   C4   118.66  3.000
 VAO  C2   C3   C4   121.10  3.000
 VAO  H2   C2   C3   120.09  3.000
 VAO  H2   C2   C1   120.32  3.000
 VAO  C3   C2   C1   119.59  3.000
 VAO  C8   C7   N    120.18  3.000
 VAO  C8   C7   C5   123.26  3.000
 VAO  N    C7   C5   116.57  3.000
 VAO  C11  N    C7   120.64  3.000
 VAO  H11  C11  C10  120.82  3.000
 VAO  H11  C11  N    116.48  3.000
 VAO  C10  C11  N    122.70  3.000
 VAO  H10  C10  C9   122.53  3.000
 VAO  H10  C10  C11  119.81  3.000
 VAO  C9   C10  C11  117.66  3.000
 VAO  C12  C9   C8   118.08  3.000
 VAO  C12  C9   C10  122.46  3.000
 VAO  C8   C9   C10  119.47  3.000
 VAO  H8   C8   C9   119.20  3.000
 VAO  H8   C8   C7   121.45  3.000
 VAO  C9   C8   C7   119.35  3.000
 VAO  O    C12  O1   124.41  3.000
 VAO  O    C12  C9   112.44  3.000
 VAO  O1   C12  C9   123.15  3.000
 VAO  H    O    C12  110.51  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
 VAO  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 VAO  CONST_02  C7   C5   C6   C1    180.00   0.0  0
 VAO  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 VAO  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 VAO  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 VAO  CONST_06  N    C7   C5   C6    180.00   0.0  0
 VAO  CONST_07  C8   C7   C5   C6      0.00   0.0  0
 VAO  CONST_08  C2   C1   C6   C5      0.00   0.0  0
 VAO  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 VAO  CONST_10  C11  N    C7   C5    180.00   0.0  0
 VAO  CONST_11  C9   C8   C7   C5    180.00   0.0  0
 VAO  CONST_12  N    C7   C5   C4      0.00   0.0  0
 VAO  CONST_13  C8   C7   C5   C4    180.00   0.0  0
 VAO  CONST_14  C7   C5   C4   C3    180.00   0.0  0
 VAO  CONST_15  C10  C11  N    C7      0.00   0.0  0
 VAO  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 VAO  CONST_17  C9   C8   C7   N       0.00   0.0  0
 VAO  CONST_18  C9   C10  C11  N       0.00   0.0  0
 VAO  CONST_19  C8   C7   N    C11     0.00   0.0  0
 VAO  CONST_20  C8   C9   C10  C11     0.00   0.0  0
 VAO  CONST_21  C5   C6   C1   C     180.00   0.0  0
 VAO  CONST_22  C3   C2   C1   C     180.00   0.0  0
 VAO  CONST_23  O2   C4   C5   C6    180.00   0.0  0
 VAO  CONST_24  C7   C5   C4   O2      0.00   0.0  0
 VAO  CONST_25  C2   C3   C4   O2    180.00   0.0  0
 VAO  CONST_26  C12  C9   C8   C7    180.00   0.0  0
 VAO  CONST_27  C12  C9   C10  C11   180.00   0.0  0
 VAO  CONST_28  H3   C3   C2   C1    180.00   0.0  0
 VAO  CONST_29  H2   C2   C1   C6    180.00   0.0  0
 VAO  CONST_30  H8   C8   C7   C5      0.00   0.0  0
 VAO  CONST_31  H6   C6   C5   C4    180.00   0.0  0
 VAO  CONST_32  H11  C11  N    C7    180.00   0.0  0
 VAO  CONST_33  H10  C10  C11  N     180.00   0.0  0
 VAO  CONST_34  H    O    C12  C9    180.00   0.0  0
 VAO  Var_01    O1   C12  C9   C10  -179.61  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
 VAO  plan-1  N1   0.020
 VAO  plan-1  C    0.020
 VAO  plan-1  C1   0.020
 VAO  plan-1  C6   0.020
 VAO  plan-1  C5   0.020
 VAO  plan-1  C4   0.020
 VAO  plan-1  O2   0.020
 VAO  plan-1  C3   0.020
 VAO  plan-1  C2   0.020
 VAO  plan-1  C7   0.020
 VAO  plan-1  H6   0.020
 VAO  plan-1  H2   0.020
 VAO  plan-1  H3   0.020
 VAO  plan-2  C5   0.020
 VAO  plan-2  C7   0.020
 VAO  plan-2  N    0.020
 VAO  plan-2  C11  0.020
 VAO  plan-2  C10  0.020
 VAO  plan-2  C9   0.020
 VAO  plan-2  C8   0.020
 VAO  plan-2  C12  0.020
 VAO  plan-2  H8   0.020
 VAO  plan-2  H11  0.020
 VAO  plan-2  H10  0.020
 VAO  plan-3  C9   0.020
 VAO  plan-3  C12  0.020
 VAO  plan-3  O1   0.020
 VAO  plan-3  O    0.020
 VAO  plan-3  H    0.020

