# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 14:07:46 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (4Z)-6-oxo-6-phenylhex-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC\C=C/C(=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
 YAC  YAC  '(4Z)-6-oxo-6-phenylhex-4-enoic acid'  ligand  27  15  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YAC
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
 YAC  C21  C  C     0   0.556  -4.3126   0.1672  -0.5298
 YAC  O2   O  O     0  -0.442  -4.5731   1.0678   0.2280
 YAC  C22  C  CH2   0  -0.586  -3.1364  -0.7612  -0.4022
 YAC  C23  C  CH2   0  -0.502  -2.1837  -0.3727   0.7225
 YAC  C24  C  C1    0  -0.136  -1.0988  -1.3894   0.8472
 YAC  C25  C  C1    0  -0.375   0.2263  -1.2175   0.8844
 YAC  C26  C  C     0   0.334   0.9301   0.0807   0.8725
 YAC  O3   O  O     0  -0.403   0.4461   1.0874   1.3578
 YAC  C27  C  CR6   0  -0.010   2.2871   0.1214   0.2584
 YAC  C28  C  CR16  0  -0.285   2.7190  -0.8634  -0.6302
 YAC  C29  C  CR16  0  -0.241   3.9732  -0.7786  -1.2174
 YAC  C30  C  CR16  0  -0.247   4.8127   0.2833  -0.9105
 YAC  C31  C  CR16  0  -0.242   4.3916   1.2674  -0.0228
 YAC  C32  C  CR16  0  -0.267   3.1336   1.1926   0.5505
 YAC  H29  H  HCH2  0   0.287  -3.5252  -1.7734  -0.2496
 YAC  H30  H  HCH2  0   0.288  -2.6089  -0.7903  -1.3595
 YAC  H31  H  HCH2  0   0.263  -1.7902   0.6277   0.5626
 YAC  H32  H  HCH2  0   0.263  -2.7329  -0.3489   1.6692
 YAC  H33  H  H     0   0.264  -1.4475  -2.4186   0.8810
 YAC  H34  H  H     0   0.276   0.8482  -2.1037   0.9246
 YAC  H35  H  HCR6  0   0.264   2.0729  -1.6933  -0.8869
 YAC  H36  H  HCR6  0   0.265   4.2938  -1.5421  -1.9138
 YAC  H37  H  HCR6  0   0.267   5.7943   0.3457  -1.3616
 YAC  H38  H  HCR6  0   0.264   5.0476   2.0926   0.2213
 YAC  H39  H  HCR6  0   0.263   2.8099   1.9638   1.2371
 YAC  OXT  O  OH1   0  -0.595  -5.0558  -0.1272  -1.5913
 YAC  HXT  H  HOH1  0   0.480  -5.8122   0.4758  -1.6432

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
 YAC  C21  O2   double    1.205  0.020  1.205
 YAC  C21  C22  single    1.504  0.020  1.504
 YAC  C22  C23  single    1.524  0.020  1.524
 YAC  C23  C24  single    1.492  0.020  1.492
 YAC  C24  C25  double    1.337  0.020  1.337
 YAC  C25  C26  single    1.477  0.020  1.477
 YAC  C26  O3   double    1.218  0.020  1.218
 YAC  C26  C27  single    1.490  0.020  1.490
 YAC  C27  C32  aromatic  1.396  0.020  1.396
 YAC  C27  C28  aromatic  1.395  0.020  1.395
 YAC  C28  C29  aromatic  1.387  0.020  1.387
 YAC  C29  C30  aromatic  1.388  0.020  1.388
 YAC  C30  C31  aromatic  1.391  0.020  1.391
 YAC  C31  C32  aromatic  1.385  0.020  1.385
 YAC  C22  H29  single    0.970  0.020  1.090
 YAC  C22  H30  single    0.970  0.020  1.090
 YAC  C23  H31  single    0.970  0.020  1.090
 YAC  C23  H32  single    0.970  0.020  1.090
 YAC  C24  H33  single    0.930  0.020  1.080
 YAC  C25  H34  single    0.930  0.020  1.080
 YAC  C28  H35  single    0.930  0.020  1.080
 YAC  C29  H36  single    0.930  0.020  1.080
 YAC  C30  H37  single    0.930  0.020  1.080
 YAC  C31  H38  single    0.930  0.020  1.080
 YAC  C32  H39  single    0.930  0.020  1.080
 YAC  C21  OXT  single    1.329  0.020  1.329
 YAC  OXT  HXT  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
 YAC  OXT  C21  C22  111.62  3.000
 YAC  OXT  C21  O2   123.15  3.000
 YAC  C22  C21  O2   125.23  3.000
 YAC  H30  C22  H29  105.59  3.000
 YAC  H30  C22  C23  110.56  3.000
 YAC  H29  C22  C23  110.77  3.000
 YAC  H30  C22  C21  108.63  3.000
 YAC  H29  C22  C21  107.75  3.000
 YAC  C23  C22  C21  113.21  3.000
 YAC  H32  C23  H31  106.79  3.000
 YAC  H32  C23  C24  107.90  3.000
 YAC  H31  C23  C24  112.10  3.000
 YAC  H32  C23  C22  109.27  3.000
 YAC  H31  C23  C22  110.63  3.000
 YAC  C24  C23  C22  110.03  3.000
 YAC  H33  C24  C25  116.02  3.000
 YAC  H33  C24  C23  114.48  3.000
 YAC  C25  C24  C23  129.46  3.000
 YAC  H34  C25  C26  116.47  3.000
 YAC  H34  C25  C24  117.71  3.000
 YAC  C26  C25  C24  125.82  3.000
 YAC  C27  C26  O3   120.24  3.000
 YAC  C27  C26  C25  117.47  3.000
 YAC  O3   C26  C25  122.28  3.000
 YAC  C32  C27  C28  119.16  3.000
 YAC  C28  C27  C26  121.68  3.000
 YAC  C32  C27  C26  119.13  3.000
 YAC  H35  C28  C29  119.07  3.000
 YAC  H35  C28  C27  120.50  3.000
 YAC  C29  C28  C27  120.42  3.000
 YAC  H36  C29  C30  120.20  3.000
 YAC  H36  C29  C28  119.81  3.000
 YAC  C30  C29  C28  119.99  3.000
 YAC  H37  C30  C31  120.00  3.000
 YAC  H37  C30  C29  120.04  3.000
 YAC  C31  C30  C29  119.97  3.000
 YAC  H38  C31  C32  119.91  3.000
 YAC  H38  C31  C30  120.01  3.000
 YAC  C32  C31  C30  120.08  3.000
 YAC  H39  C32  C31  119.73  3.000
 YAC  H39  C32  C27  119.89  3.000
 YAC  C31  C32  C27  120.38  3.000
 YAC  HXT  OXT  C21  109.97  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
 YAC  CONST_01  C30  C31  C32  C27     0.00   0.0  0
 YAC  CONST_02  C30  C29  C28  C27     0.00   0.0  0
 YAC  CONST_03  C31  C32  C27  C28     0.00   0.0  0
 YAC  CONST_04  C31  C30  C29  C28     0.00   0.0  0
 YAC  CONST_05  C32  C27  C28  C29     0.00   0.0  0
 YAC  CONST_06  C32  C31  C30  C29     0.00   0.0  0
 YAC  CONST_07  C31  C32  C27  C26   180.00   0.0  0
 YAC  CONST_08  C29  C28  C27  C26   180.00   0.0  0
 YAC  CONST_09  H38  C31  C32  C27   180.00   0.0  0
 YAC  CONST_10  H36  C29  C28  C27   180.00   0.0  0
 YAC  CONST_11  H39  C32  C27  C28   180.00   0.0  0
 YAC  CONST_12  H37  C30  C29  C28   180.00   0.0  0
 YAC  CONST_13  H35  C28  C29  C30   180.00   0.0  0
 YAC  CONST_14  HXT  OXT  C21  O2      0.00   0.0  0
 YAC  Var_01    C32  C27  C26  C25  -162.02  30.0  2
 YAC  Var_02    C27  C26  C25  C24  -150.29  30.0  2
 YAC  Var_03    C26  C25  C24  C23     3.18   0.0  2
 YAC  Var_04    C24  C23  C22  C21   176.08  30.0  3
 YAC  Var_05    C23  C22  C21  O2     -6.08  30.0  3
 YAC  Var_06    C25  C24  C23  C22   128.87  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
 YAC  plan-1  C26  0.020
 YAC  plan-1  C27  0.020
 YAC  plan-1  C28  0.020
 YAC  plan-1  C29  0.020
 YAC  plan-1  C30  0.020
 YAC  plan-1  C31  0.020
 YAC  plan-1  C32  0.020
 YAC  plan-1  H35  0.020
 YAC  plan-1  H36  0.020
 YAC  plan-1  H37  0.020
 YAC  plan-1  H38  0.020
 YAC  plan-1  H39  0.020
 YAC  plan-2  C25  0.020
 YAC  plan-2  C26  0.020
 YAC  plan-2  O3   0.020
 YAC  plan-2  C27  0.020
 YAC  plan-3  C21  0.020
 YAC  plan-3  O2   0.020
 YAC  plan-3  C22  0.020
 YAC  plan-3  OXT  0.020
 YAC  plan-3  HXT  0.020
 YAC  plan-4  C23  0.020
 YAC  plan-4  C24  0.020
 YAC  plan-4  C25  0.020
 YAC  plan-4  C26  0.020
 YAC  plan-4  H33  0.020
 YAC  plan-4  H34  0.020

