# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:21:49 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  25  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 PERFECT
;

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  -0.263  -4.0027  -3.3492   0.0262
 VAO  C    C  CSP    0   0.044  -3.5702  -2.2800   0.0065
 VAO  C1   C  CR6    0   0.010  -3.0422  -0.9591  -0.0193
 VAO  C6   C  CR16   0  -0.347  -1.6666  -0.7626  -0.0187
 VAO  C5   C  CR6    0  -0.087  -1.1090   0.5110  -0.0417
 VAO  C4   C  CR6    0   0.385  -1.9914   1.6215  -0.0666
 VAO  O2   O  OH1    0  -0.620  -1.5655   2.8726  -0.0891
 VAO  C3   C  CR16   0  -0.341  -3.3775   1.4120  -0.0669
 VAO  C2   C  CR16   0  -0.241  -3.9027   0.1435  -0.0439
 VAO  C7   C  CR6    0   0.425   0.3577   0.6982  -0.0395
 VAO  N    N  N      0  -0.584   0.7923   1.9628  -0.0673
 VAO  C11  C  CR16   0  -0.018   2.0947   2.2174  -0.0673
 VAO  C10  C  CR16   0  -0.387   3.0490   1.2194  -0.0397
 VAO  C9   C  CR6    0   0.028   2.6271  -0.1061  -0.0100
 VAO  C8   C  CR16   0  -0.398   1.2649  -0.3600  -0.0099
 VAO  C12  C  C      0   0.418   3.6334  -1.2596   0.0214
 VAO  O1   O  O      0  -0.579   3.1519  -2.4050   0.0497
 VAO  O    O  OC    -1  -0.579   4.8323  -0.9346   0.0149
 VAO  H6   H  HCR6   0   0.282  -1.0262  -1.6331   0.0006
 VAO  H2   H  HCR6   0   0.283  -4.9747   0.0005  -0.0443
 VAO  H3   H  HCR6   0   0.279  -4.0332   2.2726  -0.0864
 VAO  H8   H  HCR6   0   0.267   0.9338  -1.3877   0.0154
 VAO  H11  H  HCR6   0   0.276   2.3781   3.2623  -0.0905
 VAO  H10  H  HCR6   0   0.266   4.1003   1.4693  -0.0414
 VAO  H21  H  HOH1   0   0.480  -0.5601   2.8418  -0.0867

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  1.390  0.020  1.390
 VAO  C1   C2   aromatic  1.399  0.020  1.399
 VAO  C6   C5   aromatic  1.391  0.020  1.391
 VAO  C5   C4   aromatic  1.419  0.020  1.419
 VAO  C5   C7   single    1.479  0.020  1.479
 VAO  C4   O2   single    1.322  0.020  1.322
 VAO  C4   C3   aromatic  1.402  0.020  1.402
 VAO  C3   C2   aromatic  1.373  0.020  1.373
 VAO  C7   N    aromatic  1.337  0.020  1.337
 VAO  C7   C8   aromatic  1.394  0.020  1.394
 VAO  N    C11  aromatic  1.327  0.020  1.327
 VAO  C11  C10  aromatic  1.381  0.020  1.381
 VAO  C10  C9   aromatic  1.391  0.020  1.391
 VAO  C9   C8   aromatic  1.386  0.020  1.386
 VAO  C9   C12  single    1.531  0.020  1.531
 VAO  C12  O1   deloc     1.243  0.020  1.243
 VAO  C12  O    deloc     1.242  0.020  1.242
 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  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   119.83  3.000
 VAO  C2   C1   C    120.26  3.000
 VAO  C6   C1   C    119.91  3.000
 VAO  H6   C6   C5   120.02  3.000
 VAO  H6   C6   C1   118.21  3.000
 VAO  C5   C6   C1   121.77  3.000
 VAO  C7   C5   C4   121.20  3.000
 VAO  C7   C5   C6   120.91  3.000
 VAO  C4   C5   C6   117.89  3.000
 VAO  C3   C4   O2   117.39  3.000
 VAO  C3   C4   C5   119.88  3.000
 VAO  O2   C4   C5   122.74  3.000
 VAO  H21  O2   C4   107.04  3.000
 VAO  H3   C3   C2   120.22  3.000
 VAO  H3   C3   C4   118.71  3.000
 VAO  C2   C3   C4   121.08  3.000
 VAO  H2   C2   C3   120.09  3.000
 VAO  H2   C2   C1   120.36  3.000
 VAO  C3   C2   C1   119.55  3.000
 VAO  C8   C7   N    120.44  3.000
 VAO  C8   C7   C5   123.33  3.000
 VAO  N    C7   C5   116.23  3.000
 VAO  C11  N    C7   120.02  3.000
 VAO  H11  C11  C10  121.12  3.000
 VAO  H11  C11  N    116.23  3.000
 VAO  C10  C11  N    122.65  3.000
 VAO  H10  C10  C9   121.03  3.000
 VAO  H10  C10  C11  120.33  3.000
 VAO  C9   C10  C11  118.64  3.000
 VAO  C12  C9   C8   120.54  3.000
 VAO  C12  C9   C10  121.25  3.000
 VAO  C8   C9   C10  118.21  3.000
 VAO  H8   C8   C9   118.41  3.000
 VAO  H8   C8   C7   121.55  3.000
 VAO  C9   C8   C7   120.04  3.000
 VAO  O    C12  O1   127.96  3.000
 VAO  O    C12  C9   115.92  3.000
 VAO  O1   C12  C9   116.11  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  Var_01    O1   C12  C9   C10  179.84  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

