# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:26:01 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (3E)-2,6-dioxo-6-phenylhex-3-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-]C(=O)C(=O)/C=C/CC(=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
 HPK  HPK  (3E)-2,6-dioxo-6-phenylhex-3-enoate  ligand  25  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HPK
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
 HPK  CB3   C  CR16   0  -0.237   4.5276  -1.4585   0.4271
 HPK  CB4   C  CR16   0  -0.247   5.4428  -0.6282  -0.2050
 HPK  CB5   C  CR16   0  -0.240   5.0221   0.5773  -0.7553
 HPK  CB6   C  CR16   0  -0.262   3.6918   0.9507  -0.6710
 HPK  CB1   C  CR6    0  -0.009   2.7630   0.1228  -0.0366
 HPK  CB2   C  CR16   0  -0.290   3.1941  -1.0860   0.5100
 HPK  CA6   C  C      0   0.380   1.3413   0.5575   0.0311
 HPK  OA4   O  O      0  -0.387   0.9910   1.6236  -0.4266
 HPK  CA5   C  CH2    0  -0.672   0.3394  -0.3752   0.6781
 HPK  CA4   C  C1     0  -0.103  -1.0267   0.2133   0.7498
 HPK  CA3   C  C1     0  -0.367  -2.0995  -0.3260   0.1702
 HPK  CA2   C  C      0   0.188  -3.4436   0.2783   0.2989
 HPK  OA3   O  O      0  -0.401  -3.6351   1.2995   0.9255
 HPK  CA1   C  C      0   0.348  -4.6259  -0.4492  -0.4048
 HPK  OA2   O  OC    -1  -0.574  -4.3291  -1.4808  -1.0330
 HPK  OA1   O  O      0  -0.583  -5.7369   0.0773  -0.2610
 HPK  HB3   H  HCR6   0   0.267   4.8506  -2.3972   0.8567
 HPK  HB4   H  HCR6   0   0.268   6.4833  -0.9191  -0.2687
 HPK  HB5   H  HCR6   0   0.265   5.7333   1.2256  -1.2497
 HPK  HB6   H  HCR6   0   0.264   3.3704   1.8903  -1.1001
 HPK  HB2   H  HCR6   0   0.267   2.4998  -1.7490   1.0089
 HPK  HA51  H  HCH2   0   0.300   0.3323  -1.3219   0.1299
 HPK  HA52  H  HCH2   0   0.296   0.6881  -0.6131   1.6892
 HPK  HA4   H  H      0   0.267  -1.1343   1.1208   1.3359
 HPK  HA3   H  H      0   0.259  -2.0104  -1.2315  -0.4151

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
 HPK  CB3  CB2   aromatic  1.387  0.020  1.387
 HPK  CB3  CB4   aromatic  1.388  0.020  1.388
 HPK  CB3  HB3   single    0.930  0.020  1.080
 HPK  CB4  CB5   aromatic  1.390  0.020  1.390
 HPK  CB4  HB4   single    0.930  0.020  1.080
 HPK  CB5  CB6   aromatic  1.384  0.020  1.384
 HPK  CB5  HB5   single    0.930  0.020  1.080
 HPK  CB6  CB1   aromatic  1.397  0.020  1.397
 HPK  CB6  HB6   single    0.930  0.020  1.080
 HPK  CB1  CA6   single    1.488  0.020  1.488
 HPK  CB1  CB2   aromatic  1.395  0.020  1.395
 HPK  CB2  HB2   single    0.930  0.020  1.080
 HPK  CA6  OA4   double    1.212  0.020  1.212
 HPK  CA6  CA5   single    1.514  0.020  1.514
 HPK  CA5  CA4   single    1.489  0.020  1.489
 HPK  CA5  HA51  single    0.970  0.020  1.090
 HPK  CA5  HA52  single    0.970  0.020  1.090
 HPK  CA4  CA3   double    1.333  0.020  1.333
 HPK  CA4  HA4   single    0.930  0.020  1.080
 HPK  CA3  CA2   single    1.479  0.020  1.479
 HPK  CA3  HA3   single    0.930  0.020  1.080
 HPK  CA2  CA1   single    1.556  0.020  1.556
 HPK  CA2  OA3   double    1.213  0.020  1.213
 HPK  CA1  OA1   double    1.238  0.020  1.238
 HPK  CA1  OA2   single    1.244  0.020  1.244

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
 HPK  HB3   CB3  CB2   119.76  3.000
 HPK  HB3   CB3  CB4   120.21  3.000
 HPK  CB2   CB3  CB4   120.03  3.000
 HPK  HB4   CB4  CB5   120.05  3.000
 HPK  HB4   CB4  CB3   119.99  3.000
 HPK  CB5   CB4  CB3   119.96  3.000
 HPK  HB5   CB5  CB6   119.86  3.000
 HPK  HB5   CB5  CB4   120.10  3.000
 HPK  CB6   CB5  CB4   120.04  3.000
 HPK  HB6   CB6  CB1   119.83  3.000
 HPK  HB6   CB6  CB5   119.71  3.000
 HPK  CB1   CB6  CB5   120.45  3.000
 HPK  CA6   CB1  CB2   122.04  3.000
 HPK  CB2   CB1  CB6   119.09  3.000
 HPK  CA6   CB1  CB6   118.87  3.000
 HPK  HB2   CB2  CB1   120.89  3.000
 HPK  HB2   CB2  CB3   118.69  3.000
 HPK  CB1   CB2  CB3   120.42  3.000
 HPK  CA5   CA6  OA4   120.79  3.000
 HPK  CA5   CA6  CB1   118.15  3.000
 HPK  OA4   CA6  CB1   121.06  3.000
 HPK  HA52  CA5  HA51  106.05  3.000
 HPK  HA52  CA5  CA4   109.47  3.000
 HPK  HA51  CA5  CA4   111.11  3.000
 HPK  HA52  CA5  CA6   108.51  3.000
 HPK  HA51  CA5  CA6   108.86  3.000
 HPK  CA4   CA5  CA6   112.59  3.000
 HPK  HA4   CA4  CA3   119.54  3.000
 HPK  HA4   CA4  CA5   116.56  3.000
 HPK  CA3   CA4  CA5   123.87  3.000
 HPK  HA3   CA3  CA2   117.63  3.000
 HPK  HA3   CA3  CA4   120.49  3.000
 HPK  CA2   CA3  CA4   121.87  3.000
 HPK  CA1   CA2  OA3   120.46  3.000
 HPK  OA3   CA2  CA3   122.15  3.000
 HPK  CA1   CA2  CA3   117.38  3.000
 HPK  OA1   CA1  OA2   128.73  3.000
 HPK  OA2   CA1  CA2   115.77  3.000
 HPK  OA1   CA1  CA2   115.50  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
 HPK  CONST_01  CB6  CB1  CB2  CB3     0.00   0.0  0
 HPK  CONST_02  CB6  CB5  CB4  CB3     0.00   0.0  0
 HPK  CONST_03  CB1  CB2  CB3  CB4     0.00   0.0  0
 HPK  CONST_04  CB1  CB6  CB5  CB4     0.00   0.0  0
 HPK  CONST_05  CB2  CB3  CB4  CB5     0.00   0.0  0
 HPK  CONST_06  CB2  CB1  CB6  CB5     0.00   0.0  0
 HPK  CONST_07  CA6  CB1  CB2  CB3   180.00   0.0  0
 HPK  CONST_08  CA6  CB1  CB6  CB5   180.00   0.0  0
 HPK  CONST_09  HB5  CB5  CB4  CB3   180.00   0.0  0
 HPK  CONST_10  HB2  CB2  CB3  CB4   180.00   0.0  0
 HPK  CONST_11  HB6  CB6  CB5  CB4   180.00   0.0  0
 HPK  CONST_12  HB3  CB3  CB4  CB5   180.00   0.0  0
 HPK  CONST_13  HB4  CB4  CB5  CB6   180.00   0.0  0
 HPK  Var_01    OA4  CA6  CB1  CB6    -1.67  30.0  2
 HPK  Var_02    CA4  CA5  CA6  CB1   176.70  30.0  3
 HPK  Var_03    CA2  CA3  CA4  CA5   178.41   0.0  2
 HPK  Var_04    CA3  CA4  CA5  CA6   119.87  30.0  3
 HPK  Var_05    CA1  CA2  CA3  CA4  -179.18  30.0  2
 HPK  Var_06    OA1  CA1  CA2  CA3   179.15  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
 HPK  plan-1  CB3  0.020
 HPK  plan-1  CB4  0.020
 HPK  plan-1  CB5  0.020
 HPK  plan-1  CB6  0.020
 HPK  plan-1  CB1  0.020
 HPK  plan-1  CB2  0.020
 HPK  plan-1  CA6  0.020
 HPK  plan-1  HB3  0.020
 HPK  plan-1  HB4  0.020
 HPK  plan-1  HB5  0.020
 HPK  plan-1  HB6  0.020
 HPK  plan-1  HB2  0.020
 HPK  plan-2  CB1  0.020
 HPK  plan-2  CA6  0.020
 HPK  plan-2  OA4  0.020
 HPK  plan-2  CA5  0.020
 HPK  plan-3  CA3  0.020
 HPK  plan-3  CA2  0.020
 HPK  plan-3  OA3  0.020
 HPK  plan-3  CA1  0.020
 HPK  plan-4  CA2  0.020
 HPK  plan-4  CA1  0.020
 HPK  plan-4  OA2  0.020
 HPK  plan-4  OA1  0.020
 HPK  plan-5  CA5  0.020
 HPK  plan-5  CA4  0.020
 HPK  plan-5  CA3  0.020
 HPK  plan-5  CA2  0.020
 HPK  plan-5  HA4  0.020
 HPK  plan-5  HA3  0.020

