# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:30:38 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-oxidanylidene-6-phenyl-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCC(=O)c1ccccc1
#
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
 5VO  5VO  '6-oxidanylidene-6-phenyl-hexanoic acid'  ligand  28  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5VO
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
 5VO  C21  C  C      0   0.411  -5.0120  -0.3504  -0.0024
 5VO  O2   O  O      0  -0.610  -4.8622  -1.5853  -0.0861
 5VO  C22  C  CH2    0  -0.583  -3.7511   0.5320  -0.0233
 5VO  C23  C  CH2    0  -0.405  -2.4221  -0.2046  -0.0233
 5VO  C24  C  CH2    0  -0.409  -1.2284   0.7444  -0.0303
 5VO  C25  C  CH2    0  -0.586   0.0905  -0.0116  -0.0256
 5VO  C26  C  C      0   0.380   1.3186   0.8626  -0.0212
 5VO  O3   O  O      0  -0.400   1.2362   2.0733  -0.0186
 5VO  C27  C  CR6    0  -0.006   2.6586   0.2021  -0.0182
 5VO  C28  C  CR16   0  -0.296   2.8015  -1.1854  -0.0122
 5VO  C29  C  CR16   0  -0.238   4.0627  -1.7638  -0.0077
 5VO  C30  C  CR16   0  -0.249   5.1955  -0.9620  -0.0098
 5VO  C31  C  CR16   0  -0.241   5.0640   0.4220  -0.0163
 5VO  C32  C  CR16   0  -0.264   3.8053   0.9991  -0.0202
 5VO  OXT  O  OC    -1  -0.634  -6.1007   0.2556   0.0926
 5VO  H1   H  HCH2   0   0.219  -3.8081   1.1838  -0.9039
 5VO  H2   H  HCH2   0   0.215  -3.7955   1.2144   0.8335
 5VO  H3   H  HCH2   0   0.204  -2.3593  -0.8564   0.8536
 5VO  H4   H  HCH2   0   0.205  -2.3641  -0.8664  -0.8922
 5VO  H5   H  HCH2   0   0.218  -1.2827   1.3929  -0.9092
 5VO  H6   H  HCH2   0   0.218  -1.2814   1.4044   0.8399
 5VO  H7   H  HCH2   0   0.266   0.1391  -0.6754   0.8452
 5VO  H8   H  HCH2   0   0.266   0.1459  -0.6788  -0.8932
 5VO  H9   H  HCR6   0   0.265   1.9349  -1.8323  -0.0105
 5VO  H10  H  HCR6   0   0.265   4.1593  -2.8414  -0.0029
 5VO  H11  H  HCR6   0   0.266   6.1794  -1.4132  -0.0063
 5VO  H12  H  HCR6   0   0.263   5.9440   1.0515  -0.0177
 5VO  H13  H  HCR6   0   0.260   3.7102   2.0767  -0.0250

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
 5VO  O2   C21  deloc     1.247  0.020  1.247
 5VO  C21  OXT  deloc     1.250  0.020  1.250
 5VO  C21  C22  single    1.539  0.020  1.539
 5VO  C22  C23  single    1.519  0.020  1.519
 5VO  C23  C24  single    1.525  0.020  1.525
 5VO  C24  C25  single    1.520  0.020  1.520
 5VO  C25  C26  single    1.507  0.020  1.507
 5VO  C26  O3   double    1.213  0.020  1.213
 5VO  C26  C27  single    1.494  0.020  1.494
 5VO  C28  C27  aromatic  1.395  0.020  1.395
 5VO  C28  C29  aromatic  1.387  0.020  1.387
 5VO  C27  C32  aromatic  1.396  0.020  1.396
 5VO  C29  C30  aromatic  1.388  0.020  1.388
 5VO  C32  C31  aromatic  1.385  0.020  1.385
 5VO  C30  C31  aromatic  1.390  0.020  1.390
 5VO  C22  H1   single    0.970  0.020  1.090
 5VO  C22  H2   single    0.970  0.020  1.090
 5VO  C23  H3   single    0.970  0.020  1.090
 5VO  C23  H4   single    0.970  0.020  1.090
 5VO  C24  H5   single    0.970  0.020  1.090
 5VO  C24  H6   single    0.970  0.020  1.090
 5VO  C25  H7   single    0.970  0.020  1.090
 5VO  C25  H8   single    0.970  0.020  1.090
 5VO  C28  H9   single    0.930  0.020  1.080
 5VO  C29  H10  single    0.930  0.020  1.080
 5VO  C30  H11  single    0.930  0.020  1.080
 5VO  C31  H12  single    0.930  0.020  1.080
 5VO  C32  H13  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
 5VO  OXT  C21  C22  115.90  3.000
 5VO  C22  C21  O2   117.94  3.000
 5VO  OXT  C21  O2   126.16  3.000
 5VO  H2   C22  H1   104.80  3.000
 5VO  H2   C22  C23  109.71  3.000
 5VO  H1   C22  C23  109.48  3.000
 5VO  H2   C22  C21  108.24  3.000
 5VO  H1   C22  C21  107.99  3.000
 5VO  C23  C22  C21  116.02  3.000
 5VO  H4   C23  H3   105.85  3.000
 5VO  H4   C23  C24  109.36  3.000
 5VO  H3   C23  C24  109.23  3.000
 5VO  H4   C23  C22  109.86  3.000
 5VO  H3   C23  C22  109.81  3.000
 5VO  C24  C23  C22  112.52  3.000
 5VO  H6   C24  H5   106.21  3.000
 5VO  H6   C24  C25  109.86  3.000
 5VO  H5   C24  C25  109.90  3.000
 5VO  H6   C24  C23  109.51  3.000
 5VO  H5   C24  C23  109.50  3.000
 5VO  C25  C24  C23  111.69  3.000
 5VO  H8   C25  H7   104.95  3.000
 5VO  H8   C25  C26  108.31  3.000
 5VO  H7   C25  C26  108.23  3.000
 5VO  H8   C25  C24  110.13  3.000
 5VO  H7   C25  C24  110.01  3.000
 5VO  C26  C25  C24  114.74  3.000
 5VO  C27  C26  O3   120.13  3.000
 5VO  C27  C26  C25  118.32  3.000
 5VO  O3   C26  C25  121.55  3.000
 5VO  C32  C27  C28  118.92  3.000
 5VO  C32  C27  C26  118.96  3.000
 5VO  C28  C27  C26  122.12  3.000
 5VO  H9   C28  C29  118.63  3.000
 5VO  H9   C28  C27  120.86  3.000
 5VO  C29  C28  C27  120.52  3.000
 5VO  H10  C29  C30  120.17  3.000
 5VO  H10  C29  C28  119.76  3.000
 5VO  C30  C29  C28  120.07  3.000
 5VO  H11  C30  C31  120.07  3.000
 5VO  H11  C30  C29  120.07  3.000
 5VO  C31  C30  C29  119.86  3.000
 5VO  H12  C31  C32  119.79  3.000
 5VO  H12  C31  C30  120.14  3.000
 5VO  C32  C31  C30  120.06  3.000
 5VO  H13  C32  C31  119.68  3.000
 5VO  H13  C32  C27  119.76  3.000
 5VO  C31  C32  C27  120.57  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
 5VO  CONST_01  C30  C29  C28  C27     0.00   0.0  0
 5VO  CONST_02  C30  C31  C32  C27     0.00   0.0  0
 5VO  CONST_03  C31  C32  C27  C28     0.00   0.0  0
 5VO  CONST_04  C31  C30  C29  C28     0.00   0.0  0
 5VO  CONST_05  C32  C27  C28  C29     0.00   0.0  0
 5VO  CONST_06  C32  C31  C30  C29     0.00   0.0  0
 5VO  CONST_07  C29  C28  C27  C26   180.00   0.0  0
 5VO  CONST_08  C31  C32  C27  C26   180.00   0.0  0
 5VO  CONST_09  H10  C29  C28  C27   180.00   0.0  0
 5VO  CONST_10  H12  C31  C32  C27   180.00   0.0  0
 5VO  CONST_11  H13  C32  C27  C28   180.00   0.0  0
 5VO  CONST_12  H11  C30  C29  C28   180.00   0.0  0
 5VO  CONST_13  H9   C28  C29  C30   180.00   0.0  0
 5VO  Var_01    C28  C27  C26  C25    -0.35  30.0  2
 5VO  Var_02    C27  C26  C25  C24  -179.92  30.0  3
 5VO  Var_03    C24  C23  C22  C21  -179.42  30.0  3
 5VO  Var_04    C23  C22  C21  O2     -5.15  30.0  3
 5VO  Var_05    C25  C24  C23  C22   179.81  30.0  3
 5VO  Var_06    C26  C25  C24  C23  -179.55  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
 5VO  plan-1  C26  0.020
 5VO  plan-1  C27  0.020
 5VO  plan-1  C28  0.020
 5VO  plan-1  C29  0.020
 5VO  plan-1  C30  0.020
 5VO  plan-1  C31  0.020
 5VO  plan-1  C32  0.020
 5VO  plan-1  H9   0.020
 5VO  plan-1  H10  0.020
 5VO  plan-1  H11  0.020
 5VO  plan-1  H12  0.020
 5VO  plan-1  H13  0.020
 5VO  plan-2  C25  0.020
 5VO  plan-2  C26  0.020
 5VO  plan-2  O3   0.020
 5VO  plan-2  C27  0.020
 5VO  plan-3  C21  0.020
 5VO  plan-3  O2   0.020
 5VO  plan-3  C22  0.020
 5VO  plan-3  OXT  0.020

