# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:49:31 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2E,5R)-5-hydroxy-2-methylhept-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](O)C\C=C(C)\C(O)=O
#
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
 7OD  7OD  '(2E,5R)-5-hydroxy-2-methylhept-2-enoic acid'  ligand  25  11  .  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_7OD
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
 7OD  OAB  O  O     0  -0.455   2.8310  -1.5236   0.5815
 7OD  CAA  C  C     0   0.519   2.6987  -0.4216   0.0971
 7OD  OAI  O  OH1   0  -0.600   3.6754   0.1697  -0.5841
 7OD  CAC  C  C     0  -0.093   1.4667   0.4046   0.1849
 7OD  CAK  C  CH3   0  -0.737   1.4130   1.7782  -0.4298
 7OD  CAD  C  C1    0  -0.156   0.4260  -0.1449   0.8216
 7OD  CAE  C  CH2   0  -0.521  -0.9172   0.4681   1.0059
 7OD  CAF  C  CH1   0   0.042  -1.9794  -0.2424   0.1538
 7OD  OAH  O  OH1   0  -0.662  -1.6533  -0.1907  -1.2189
 7OD  CAG  C  CH2   0  -0.453  -3.3709   0.3107   0.4428
 7OD  CAJ  C  CH3   0  -0.662  -4.4744  -0.3824  -0.3435
 7OD  H1   H  HOH1  0   0.481   4.4499  -0.4114  -0.6088
 7OD  HAM  H  HCH3  0   0.259   2.3784   2.1185  -0.7911
 7OD  HAN  H  HCH3  0   0.245   0.7214   1.8013  -1.2732
 7OD  HAO  H  HCH3  0   0.248   1.0635   2.5161   0.2926
 7OD  HAD  H  H     0   0.260   0.5395  -1.1440   1.2301
 7OD  HAF  H  HCH2  0   0.255  -1.2045   0.3730   2.0574
 7OD  HAE  H  HCH2  0   0.246  -0.9201   1.5356   0.7705
 7OD  HAG  H  HCH1  0   0.226  -1.9713  -1.3075   0.4105
 7OD  HAP  H  HOH1  0   0.441  -1.7359   0.7223  -1.5151
 7OD  HAH  H  HCH2  0   0.227  -3.5624   0.2066   1.5143
 7OD  HAI  H  HCH2  0   0.220  -3.3834   1.3871   0.2367
 7OD  HAK  H  HCH3  0   0.230  -5.4536   0.0048  -0.0614
 7OD  HAL  H  HCH3  0   0.222  -4.3594  -0.2334  -1.4170
 7OD  HAJ  H  HCH3  0   0.219  -4.4784  -1.4577  -0.1558

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
 7OD  CAJ  CAG  single  1.522  0.020  1.522
 7OD  CAG  CAF  single  1.525  0.020  1.525
 7OD  CAF  OAH  single  1.412  0.020  1.412
 7OD  CAF  CAE  single  1.536  0.020  1.536
 7OD  CAE  CAD  single  1.488  0.020  1.488
 7OD  CAD  CAC  double  1.338  0.020  1.338
 7OD  CAC  CAK  single  1.506  0.020  1.506
 7OD  CAC  CAA  single  1.486  0.020  1.486
 7OD  OAB  CAA  double  1.211  0.020  1.211
 7OD  CAA  OAI  single  1.329  0.020  1.329
 7OD  OAI  H1   single  0.850  0.020  0.980
 7OD  CAK  HAM  single  0.970  0.020  1.090
 7OD  CAK  HAN  single  0.970  0.020  1.090
 7OD  CAK  HAO  single  0.970  0.020  1.090
 7OD  CAD  HAD  single  0.930  0.020  1.080
 7OD  CAE  HAF  single  0.970  0.020  1.090
 7OD  CAE  HAE  single  0.970  0.020  1.090
 7OD  CAF  HAG  single  0.970  0.020  1.090
 7OD  OAH  HAP  single  0.850  0.020  0.980
 7OD  CAG  HAH  single  0.970  0.020  1.090
 7OD  CAG  HAI  single  0.970  0.020  1.090
 7OD  CAJ  HAK  single  0.970  0.020  1.090
 7OD  CAJ  HAL  single  0.970  0.020  1.090
 7OD  CAJ  HAJ  single  0.970  0.020  1.090

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
 7OD  CAC  CAA  OAI  113.08  3.000
 7OD  OAI  CAA  OAB  121.96  3.000
 7OD  CAC  CAA  OAB  124.95  3.000
 7OD  H1   OAI  CAA  109.49  3.000
 7OD  CAD  CAC  CAK  122.76  3.000
 7OD  CAK  CAC  CAA  120.84  3.000
 7OD  CAD  CAC  CAA  116.40  3.000
 7OD  HAO  CAK  HAN  107.14  3.000
 7OD  HAO  CAK  HAM  107.06  3.000
 7OD  HAN  CAK  HAM  107.45  3.000
 7OD  HAO  CAK  CAC  111.01  3.000
 7OD  HAN  CAK  CAC  110.95  3.000
 7OD  HAM  CAK  CAC  112.96  3.000
 7OD  HAD  CAD  CAE  115.27  3.000
 7OD  HAD  CAD  CAC  118.41  3.000
 7OD  CAE  CAD  CAC  126.29  3.000
 7OD  HAE  CAE  HAF  106.92  3.000
 7OD  HAE  CAE  CAF  109.30  3.000
 7OD  HAF  CAE  CAF  108.14  3.000
 7OD  HAE  CAE  CAD  112.21  3.000
 7OD  HAF  CAE  CAD  108.68  3.000
 7OD  CAF  CAE  CAD  111.41  3.000
 7OD  HAG  CAF  CAG  108.36  3.000
 7OD  HAG  CAF  OAH  105.17  3.000
 7OD  CAG  CAF  OAH  112.44  3.000
 7OD  HAG  CAF  CAE  108.33  3.000
 7OD  OAH  CAF  CAE  111.26  3.000
 7OD  CAG  CAF  CAE  110.99  3.000
 7OD  HAP  OAH  CAF  108.29  3.000
 7OD  HAI  CAG  HAH  106.00  3.000
 7OD  HAI  CAG  CAJ  109.99  3.000
 7OD  HAH  CAG  CAJ  109.63  3.000
 7OD  HAI  CAG  CAF  109.33  3.000
 7OD  HAH  CAG  CAF  108.12  3.000
 7OD  CAJ  CAG  CAF  113.48  3.000
 7OD  HAJ  CAJ  HAL  107.73  3.000
 7OD  HAJ  CAJ  HAK  107.59  3.000
 7OD  HAL  CAJ  HAK  107.53  3.000
 7OD  HAJ  CAJ  CAG  111.24  3.000
 7OD  HAL  CAJ  CAG  111.72  3.000
 7OD  HAK  CAJ  CAG  110.84  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
 7OD  CONST_01  H1   OAI  CAA  OAB     0.00   0.0  0
 7OD  Var_01    CAE  CAD  CAC  CAA  -178.30   0.0  2
 7OD  Var_02    CAD  CAC  CAA  OAB    -1.84  30.0  2
 7OD  Var_03    CAF  CAE  CAD  CAC   109.29  30.0  1
 7OD  Var_04    HAM  CAK  CAC  CAA    -8.10  30.0  3
 7OD  Var_05    HAK  CAJ  CAG  CAF   176.65  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7OD  chir_01  CAF  CAG  OAH  CAE  negativ

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
 7OD  plan-1  OAB  0.020
 7OD  plan-1  CAA  0.020
 7OD  plan-1  OAI  0.020
 7OD  plan-1  CAC  0.020
 7OD  plan-1  H1   0.020
 7OD  plan-2  CAA  0.020
 7OD  plan-2  CAC  0.020
 7OD  plan-2  CAK  0.020
 7OD  plan-2  CAD  0.020
 7OD  plan-2  CAE  0.020
 7OD  plan-2  HAD  0.020

