# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:24:57 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-pyridin-2-ylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccccn2
#
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
 AVA  AVA  '3-pyridin-2-ylbenzoic acid'  ligand  24  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AVA
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
 AVA  C1   C  CR6   0  -0.061   2.0345  -0.1167  -0.0347
 AVA  C2   C  CR16  0  -0.302   0.7121   0.3128  -0.0488
 AVA  C3   C  CR6   0   0.098  -0.3371  -0.5931   0.0766
 AVA  C4   C  CR6   0   0.230  -1.7363  -0.1100   0.0511
 AVA  C5   C  CR16  0  -0.336  -2.7948  -0.9418  -0.3134
 AVA  C6   C  CR16  0  -0.150  -4.0818  -0.4299  -0.3125
 AVA  O1   O  OH1   0  -0.594   4.3203   0.3886  -0.1649
 AVA  N    N  N     0  -0.428  -1.9305   1.1663   0.3805
 AVA  C    C  C     0   0.537   3.1008   0.9060  -0.1883
 AVA  O    O  O     0  -0.437   2.8856   2.0869  -0.3216
 AVA  C10  C  CR16  0  -0.223   1.2846  -2.3784   0.2551
 AVA  C11  C  CR16  0  -0.270   2.3233  -1.4720   0.1187
 AVA  C7   C  CR16  0  -0.325  -4.2791   0.8952   0.0424
 AVA  C8   C  CR16  0  -0.072  -3.1637   1.6500   0.3745
 AVA  C9   C  CR16  0  -0.310  -0.0324  -1.9458   0.2337
 AVA  H    H  HCR6  0   0.261   0.4923   1.3650  -0.1658
 AVA  H1   H  HCR6  0   0.272  -2.6224  -1.9671  -0.6097
 AVA  H2   H  HCR6  0   0.277  -4.9177  -1.0578  -0.5913
 AVA  H8   H  HOH1  0   0.489   4.9803   1.0898  -0.2718
 AVA  H6   H  HCR6  0   0.270   1.5008  -3.4301   0.3849
 AVA  H7   H  HCR6  0   0.271   3.3442  -1.8269   0.1374
 AVA  H3   H  HCR6  0   0.273  -5.2656   1.3369   0.0586
 AVA  H4   H  HCR6  0   0.264  -3.2730   2.6930   0.6508
 AVA  H5   H  HCR6  0   0.265  -0.8217  -2.6751   0.3602

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
 AVA  O    C    double    1.208  0.020  1.208
 AVA  C    O1   single    1.325  0.020  1.325
 AVA  C    C1   single    1.485  0.020  1.485
 AVA  C11  C10  aromatic  1.385  0.020  1.385
 AVA  C11  C1   aromatic  1.394  0.020  1.394
 AVA  C10  C9   aromatic  1.386  0.020  1.386
 AVA  C1   C2   aromatic  1.390  0.020  1.390
 AVA  C9   C3   aromatic  1.395  0.020  1.395
 AVA  C2   C3   aromatic  1.392  0.020  1.392
 AVA  C3   C4   single    1.480  0.020  1.480
 AVA  C4   C5   aromatic  1.395  0.020  1.395
 AVA  C4   N    aromatic  1.332  0.020  1.332
 AVA  C5   C6   aromatic  1.385  0.020  1.385
 AVA  N    C8   aromatic  1.325  0.020  1.325
 AVA  C6   C7   aromatic  1.386  0.020  1.386
 AVA  C8   C7   aromatic  1.387  0.020  1.387
 AVA  C2   H    single    0.930  0.020  1.080
 AVA  C5   H1   single    0.930  0.020  1.080
 AVA  C6   H2   single    0.930  0.020  1.080
 AVA  O1   H8   single    0.850  0.020  0.980
 AVA  C10  H6   single    0.930  0.020  1.080
 AVA  C11  H7   single    0.930  0.020  1.080
 AVA  C7   H3   single    0.930  0.020  1.080
 AVA  C8   H4   single    0.930  0.020  1.080
 AVA  C9   H5   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
 AVA  C11  C1   C    122.14  3.000
 AVA  C11  C1   C2   119.89  3.000
 AVA  C    C1   C2   117.97  3.000
 AVA  H    C2   C3   119.33  3.000
 AVA  H    C2   C1   119.67  3.000
 AVA  C3   C2   C1   120.99  3.000
 AVA  C9   C3   C4   121.65  3.000
 AVA  C4   C3   C2   119.90  3.000
 AVA  C9   C3   C2   118.45  3.000
 AVA  N    C4   C5   121.69  3.000
 AVA  N    C4   C3   116.49  3.000
 AVA  C5   C4   C3   121.81  3.000
 AVA  H1   C5   C6   119.93  3.000
 AVA  H1   C5   C4   121.08  3.000
 AVA  C6   C5   C4   118.99  3.000
 AVA  H2   C6   C7   120.72  3.000
 AVA  H2   C6   C5   120.21  3.000
 AVA  C7   C6   C5   119.07  3.000
 AVA  H8   O1   C    110.02  3.000
 AVA  C8   N    C4   118.97  3.000
 AVA  O    C    O1   123.22  3.000
 AVA  O1   C    C1   112.96  3.000
 AVA  O    C    C1   123.82  3.000
 AVA  H6   C10  C9   119.68  3.000
 AVA  H6   C10  C11  119.88  3.000
 AVA  C9   C10  C11  120.44  3.000
 AVA  H7   C11  C10  119.45  3.000
 AVA  H7   C11  C1   121.11  3.000
 AVA  C10  C11  C1   119.44  3.000
 AVA  H3   C7   C8   120.53  3.000
 AVA  H3   C7   C6   121.63  3.000
 AVA  C8   C7   C6   117.85  3.000
 AVA  H4   C8   C7   120.22  3.000
 AVA  H4   C8   N    116.35  3.000
 AVA  C7   C8   N    123.43  3.000
 AVA  H5   C9   C10  118.74  3.000
 AVA  H5   C9   C3   120.48  3.000
 AVA  C10  C9   C3   120.77  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
 AVA  CONST_01  C9   C10  C11  C1    0.00   0.0  0
 AVA  CONST_02  C9   C3   C2   C1    0.00   0.0  0
 AVA  CONST_03  C4   C3   C2   C1  180.00   0.0  0
 AVA  CONST_04  C10  C11  C1   C2    0.00   0.0  0
 AVA  CONST_05  C10  C9   C3   C2    0.00   0.0  0
 AVA  CONST_08  C11  C10  C9   C3    0.00   0.0  0
 AVA  CONST_09  C11  C1   C2   C3    0.00   0.0  0
 AVA  CONST_10  C6   C5   C4   C3  180.00   0.0  0
 AVA  CONST_11  C8   N    C4   C3  180.00   0.0  0
 AVA  CONST_12  C10  C9   C3   C4  180.00   0.0  0
 AVA  CONST_13  C7   C6   C5   C4    0.00   0.0  0
 AVA  CONST_14  C7   C8   N    C4    0.00   0.0  0
 AVA  CONST_16  C8   N    C4   C5    0.00   0.0  0
 AVA  CONST_17  C8   C7   C6   C5    0.00   0.0  0
 AVA  CONST_18  N    C4   C5   C6    0.00   0.0  0
 AVA  CONST_19  N    C8   C7   C6    0.00   0.0  0
 AVA  CONST_21  C    C1   C2   C3  180.00   0.0  0
 AVA  CONST_22  C10  C11  C1   C   180.00   0.0  0
 AVA  CONST_23  H6   C10  C11  C1  180.00   0.0  0
 AVA  CONST_24  H7   C11  C1   C2  180.00   0.0  0
 AVA  CONST_25  H5   C9   C3   C2  180.00   0.0  0
 AVA  CONST_26  H1   C5   C4   C3    0.00   0.0  0
 AVA  CONST_27  H    C2   C3   C4    0.00   0.0  0
 AVA  CONST_28  H2   C6   C5   C4  180.00   0.0  0
 AVA  CONST_29  H4   C8   N    C4  180.00   0.0  0
 AVA  CONST_30  H3   C7   C6   C5  180.00   0.0  0
 AVA  CONST_31  H8   O1   C    C1  180.00   0.0  0
 AVA  Var_01    O    C    C1   C2    0.17  30.0  3

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
 AVA  plan-1  C3   0.020
 AVA  plan-1  C4   0.020
 AVA  plan-1  C5   0.020
 AVA  plan-1  C6   0.020
 AVA  plan-1  N    0.020
 AVA  plan-1  C7   0.020
 AVA  plan-1  C8   0.020
 AVA  plan-1  H1   0.020
 AVA  plan-1  H2   0.020
 AVA  plan-1  H3   0.020
 AVA  plan-1  H4   0.020
 AVA  plan-2  C1   0.020
 AVA  plan-2  C2   0.020
 AVA  plan-2  C3   0.020
 AVA  plan-2  C4   0.020
 AVA  plan-2  C    0.020
 AVA  plan-2  C10  0.020
 AVA  plan-2  C11  0.020
 AVA  plan-2  C9   0.020
 AVA  plan-2  H    0.020
 AVA  plan-2  H6   0.020
 AVA  plan-2  H7   0.020
 AVA  plan-2  H5   0.020
 AVA  plan-3  C1   0.020
 AVA  plan-3  O1   0.020
 AVA  plan-3  C    0.020
 AVA  plan-3  O    0.020
 AVA  plan-3  H8   0.020

