# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:15:24 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C/C=C\[C@H](O)CC(=O)CCCCC(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
 6OC  6OC  '(8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid'  ligand  52  22  .  2021-08-05  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6OC
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
 6OC  C18   C  CH3   0  -0.662  -7.8615   4.8351   0.7419
 6OC  C17   C  CH2   0  -0.419  -7.5924   3.6325  -0.1519
 6OC  C16   C  CH2   0  -0.408  -6.7858   2.5462   0.5491
 6OC  C15   C  CH2   0  -0.415  -6.4837   1.3512  -0.3450
 6OC  C14   C  CH2   0  -0.489  -5.7061   0.2520   0.3796
 6OC  C13   C  C1    0  -0.202  -5.4098  -0.9126  -0.5116
 6OC  C12   C  C1    0  -0.218  -4.2225  -1.4496  -0.7876
 6OC  C11   C  CH2   0  -0.578  -2.8905  -1.0389  -0.2287
 6OC  C10   C  C1    0  -0.190  -2.4013  -2.0504   0.7690
 6OC  C9    C  C1    0  -0.254  -1.2195  -2.6613   0.7988
 6OC  C8    C  CH1   0  -0.022  -0.0724  -2.4665  -0.1507
 6OC  C7    C  CH2   0  -0.598   1.0502  -1.7038   0.5445
 6OC  C6    C  C     0   0.427   2.2032  -1.3138  -0.3503
 6OC  O3    O  O     0  -0.408   2.0841  -1.2191  -1.5507
 6OC  C5    C  CH2   0  -0.567   3.4955  -1.0129   0.3619
 6OC  C4    C  CH2   0  -0.418   4.5200  -0.2438  -0.4546
 6OC  C3    C  CH2   0  -0.421   5.7869   0.0308   0.3470
 6OC  C2    C  CH2   0  -0.581   6.7904   0.8371  -0.4596
 6OC  C1    C  C     0   0.551   8.0603   1.1474   0.2822
 6OC  O1    O  O     0  -0.446   8.3129   0.7992   1.4089
 6OC  O2    O  OH1   0  -0.598   8.8999   1.8684  -0.4565
 6OC  OXT   O  OH1   0  -0.665   0.3863  -3.7025  -0.6635
 6OC  H181  H  HCH3  0   0.226  -8.4412   5.6002   0.2244
 6OC  H182  H  HCH3  0   0.216  -8.4206   4.5446   1.6336
 6OC  H183  H  HCH3  0   0.216  -6.9289   5.2946   1.0751
 6OC  H171  H  HCH2  0   0.211  -8.5418   3.2107  -0.4961
 6OC  H172  H  HCH2  0   0.211  -7.0598   3.9530  -1.0525
 6OC  H161  H  HCH2  0   0.209  -5.8447   2.9721   0.9147
 6OC  H162  H  HCH2  0   0.208  -7.3303   2.2100   1.4387
 6OC  H151  H  HCH2  0   0.214  -7.4206   0.9371  -0.7331
 6OC  H152  H  HCH2  0   0.216  -5.9126   1.6821  -1.2186
 6OC  H141  H  HCH2  0   0.230  -4.7906   0.6718   0.8030
 6OC  H142  H  HCH2  0   0.231  -6.3029  -0.0927   1.2319
 6OC  H13   H  H     0   0.231  -6.2798  -1.3540  -0.9920
 6OC  H12   H  H     0   0.238  -4.1938  -2.2998  -1.4626
 6OC  H111  H  HCH2  0   0.254  -2.1740  -0.9190  -1.0445
 6OC  H112  H  HCH2  0   0.256  -2.9600  -0.0657   0.2635
 6OC  H10   H  H     0   0.245  -3.1134  -2.2912   1.5532
 6OC  H9    H  H     0   0.247  -1.0308  -3.3615   1.6103
 6OC  H8    H  HCH1  0   0.244  -0.3959  -1.8924  -1.0204
 6OC  H7C1  H  HCH2  0   0.290   0.6595  -0.7667   0.9590
 6OC  H7C2  H  HCH2  0   0.266   1.4203  -2.2632   1.4107
 6OC  H5C1  H  HCH2  0   0.261   3.2624  -0.4846   1.2926
 6OC  H5C2  H  HCH2  0   0.274   3.9058  -1.9780   0.6859
 6OC  H4C1  H  HCH2  0   0.229   4.7735  -0.8002  -1.3603
 6OC  H4C2  H  HCH2  0   0.227   4.0868   0.7041  -0.7872
 6OC  H3C1  H  HCH2  0   0.229   5.5289   0.5694   1.2627
 6OC  H3C2  H  HCH2  0   0.230   6.2336  -0.9164   0.6608
 6OC  H2C1  H  HCH2  0   0.277   7.0553   0.3096  -1.3817
 6OC  H2C2  H  HCH2  0   0.277   6.3474   1.7839  -0.7850
 6OC  H2    H  HOH1  0   0.478   9.7075   2.0524   0.0457
 6OC  HOT1  H  HOH1  0   0.443   0.6814  -4.2475   0.0743

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
 6OC  C18  C17   single  1.522  0.020  1.522
 6OC  C17  C16   single  1.524  0.020  1.524
 6OC  C16  C15   single  1.523  0.020  1.523
 6OC  C15  C14   single  1.529  0.020  1.529
 6OC  C14  C13   single  1.496  0.020  1.496
 6OC  C13  C12   double  1.332  0.020  1.332
 6OC  C12  C11   single  1.502  0.020  1.502
 6OC  C11  C10   single  1.503  0.020  1.503
 6OC  C10  C9    double  1.331  0.020  1.331
 6OC  C9   C8    single  1.502  0.020  1.502
 6OC  C8   C7    single  1.525  0.020  1.525
 6OC  C7   C6    single  1.511  0.020  1.511
 6OC  C6   O3    double  1.210  0.020  1.210
 6OC  C6   C5    single  1.506  0.020  1.506
 6OC  C5   C4    single  1.519  0.020  1.519
 6OC  C4   C3    single  1.524  0.020  1.524
 6OC  C3   C2    single  1.519  0.020  1.519
 6OC  C2   C1    single  1.503  0.020  1.503
 6OC  C1   O1    double  1.206  0.020  1.206
 6OC  C1   O2    single  1.331  0.020  1.331
 6OC  C18  H181  single  0.970  0.020  1.090
 6OC  C18  H182  single  0.970  0.020  1.090
 6OC  C18  H183  single  0.970  0.020  1.090
 6OC  C17  H171  single  0.970  0.020  1.090
 6OC  C17  H172  single  0.970  0.020  1.090
 6OC  C16  H161  single  0.970  0.020  1.090
 6OC  C16  H162  single  0.970  0.020  1.090
 6OC  C15  H151  single  0.970  0.020  1.090
 6OC  C15  H152  single  0.970  0.020  1.090
 6OC  C14  H141  single  0.970  0.020  1.090
 6OC  C14  H142  single  0.970  0.020  1.090
 6OC  C13  H13   single  0.930  0.020  1.080
 6OC  C12  H12   single  0.930  0.020  1.080
 6OC  C11  H111  single  0.970  0.020  1.090
 6OC  C11  H112  single  0.970  0.020  1.090
 6OC  C10  H10   single  0.930  0.020  1.080
 6OC  C9   H9    single  0.930  0.020  1.080
 6OC  C8   H8    single  0.970  0.020  1.090
 6OC  C7   H7C1  single  0.970  0.020  1.090
 6OC  C7   H7C2  single  0.970  0.020  1.090
 6OC  C5   H5C1  single  0.970  0.020  1.090
 6OC  C5   H5C2  single  0.970  0.020  1.090
 6OC  C4   H4C1  single  0.970  0.020  1.090
 6OC  C4   H4C2  single  0.970  0.020  1.090
 6OC  C3   H3C1  single  0.970  0.020  1.090
 6OC  C3   H3C2  single  0.970  0.020  1.090
 6OC  C2   H2C1  single  0.970  0.020  1.090
 6OC  C2   H2C2  single  0.970  0.020  1.090
 6OC  O2   H2    single  0.850  0.020  0.980
 6OC  OXT  HOT1  single  0.850  0.020  0.980
 6OC  OXT  C8    single  1.415  0.020  1.415

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
 6OC  H183  C18  H182  107.47  3.000
 6OC  H183  C18  H181  107.67  3.000
 6OC  H182  C18  H181  107.58  3.000
 6OC  H183  C18  C17   111.14  3.000
 6OC  H182  C18  C17   111.09  3.000
 6OC  H181  C18  C17   111.69  3.000
 6OC  H172  C17  H171  106.03  3.000
 6OC  H172  C17  C16   109.25  3.000
 6OC  H171  C17  C16   109.22  3.000
 6OC  H172  C17  C18   109.75  3.000
 6OC  H171  C17  C18   109.62  3.000
 6OC  C16   C17  C18   112.75  3.000
 6OC  H162  C16  H161  105.97  3.000
 6OC  H162  C16  C15   109.54  3.000
 6OC  H161  C16  C15   109.30  3.000
 6OC  H162  C16  C17   109.22  3.000
 6OC  H161  C16  C17   109.33  3.000
 6OC  C15   C16  C17   113.23  3.000
 6OC  H152  C15  H151  106.12  3.000
 6OC  H152  C15  C14   109.28  3.000
 6OC  H151  C15  C14   109.34  3.000
 6OC  H152  C15  C16   109.56  3.000
 6OC  H151  C15  C16   109.57  3.000
 6OC  C14   C15  C16   112.76  3.000
 6OC  H142  C14  H141  106.01  3.000
 6OC  H142  C14  C13   109.04  3.000
 6OC  H141  C14  C13   111.35  3.000
 6OC  H142  C14  C15   108.52  3.000
 6OC  H141  C14  C15   109.48  3.000
 6OC  C13   C14  C15   112.21  3.000
 6OC  H13   C13  C12   117.26  3.000
 6OC  H13   C13  C14   114.88  3.000
 6OC  C12   C13  C14   127.86  3.000
 6OC  H12   C12  C11   114.96  3.000
 6OC  H12   C12  C13   117.90  3.000
 6OC  C11   C12  C13   127.11  3.000
 6OC  H112  C11  H111  106.27  3.000
 6OC  H112  C11  C10   108.73  3.000
 6OC  H111  C11  C10   110.87  3.000
 6OC  H112  C11  C12   110.78  3.000
 6OC  H111  C11  C12   109.51  3.000
 6OC  C10   C11  C12   110.60  3.000
 6OC  H10   C10  C9    117.66  3.000
 6OC  H10   C10  C11   114.53  3.000
 6OC  C9    C10  C11   127.81  3.000
 6OC  H9    C9   C8    114.99  3.000
 6OC  H9    C9   C10   117.78  3.000
 6OC  C8    C9   C10   127.20  3.000
 6OC  H8    C8   OXT   105.48  3.000
 6OC  OXT   C8   C7    111.32  3.000
 6OC  H8    C8   C7    108.57  3.000
 6OC  OXT   C8   C9    111.32  3.000
 6OC  H8    C8   C9    110.23  3.000
 6OC  C7    C8   C9    109.81  3.000
 6OC  H7C2  C7   H7C1  104.94  3.000
 6OC  H7C2  C7   C6    110.02  3.000
 6OC  H7C1  C7   C6    105.97  3.000
 6OC  H7C2  C7   C8    110.72  3.000
 6OC  H7C1  C7   C8    109.72  3.000
 6OC  C6    C7   C8    114.89  3.000
 6OC  C5    C6   O3    122.55  3.000
 6OC  C5    C6   C7    115.24  3.000
 6OC  O3    C6   C7    122.19  3.000
 6OC  H5C2  C5   H5C1  104.64  3.000
 6OC  H5C2  C5   C4    110.59  3.000
 6OC  H5C1  C5   C4    110.85  3.000
 6OC  H5C2  C5   C6    106.54  3.000
 6OC  H5C1  C5   C6    108.40  3.000
 6OC  C4    C5   C6    115.20  3.000
 6OC  H4C2  C4   H4C1  106.32  3.000
 6OC  H4C2  C4   C3    109.45  3.000
 6OC  H4C1  C4   C3    109.56  3.000
 6OC  H4C2  C4   C5    109.57  3.000
 6OC  H4C1  C4   C5    110.12  3.000
 6OC  C3    C4   C5    111.67  3.000
 6OC  H3C2  C3   H3C1  106.43  3.000
 6OC  H3C2  C3   C2    110.02  3.000
 6OC  H3C1  C3   C2    109.82  3.000
 6OC  H3C2  C3   C4    109.55  3.000
 6OC  H3C1  C3   C4    109.46  3.000
 6OC  C2    C3   C4    111.44  3.000
 6OC  H2C2  C2   H2C1  105.32  3.000
 6OC  H2C2  C2   C1    108.06  3.000
 6OC  H2C1  C2   C1    108.10  3.000
 6OC  H2C2  C2   C3    110.46  3.000
 6OC  H2C1  C2   C3    110.57  3.000
 6OC  C1    C2   C3    113.93  3.000
 6OC  O2    C1   O1    122.89  3.000
 6OC  O2    C1   C2    111.78  3.000
 6OC  O1    C1   C2    125.34  3.000
 6OC  H2    O2   C1    109.95  3.000
 6OC  HOT1  OXT  C8    108.41  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
 6OC  CONST_01  H2    O2   C1   C2    180.00   0.0  0
 6OC  Var_01    C11   C12  C13  C14     2.24   0.0  2
 6OC  Var_02    C8    C9   C10  C11     1.22   0.0  2
 6OC  Var_03    C15   C16  C17  C18  -178.72  30.0  3
 6OC  Var_04    C14   C15  C16  C17  -178.48  30.0  3
 6OC  Var_05    C13   C14  C15  C16  -179.70  30.0  3
 6OC  Var_06    C12   C13  C14  C15   124.40  30.0  3
 6OC  Var_07    C10   C11  C12  C13   106.48  30.0  3
 6OC  Var_08    C9    C10  C11  C12   127.96  30.0  3
 6OC  Var_09    O3    C6   C7   C8     22.38  30.0  3
 6OC  Var_10    C4    C5   C6   C7   -162.89  30.0  3
 6OC  Var_11    C3    C4   C5   C6    179.33  30.0  3
 6OC  Var_12    C2    C3   C4   C5   -178.24  30.0  3
 6OC  Var_13    C1    C2   C3   C4    179.65  30.0  3
 6OC  Var_14    O1    C1   C2   C3      0.76  30.0  3
 6OC  Var_15    H181  C18  C17  C16  -179.87  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
 6OC  chir_01  C8  C9  C7  OXT  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
 6OC  plan-1  C7   0.020
 6OC  plan-1  C6   0.020
 6OC  plan-1  O3   0.020
 6OC  plan-1  C5   0.020
 6OC  plan-2  C2   0.020
 6OC  plan-2  C1   0.020
 6OC  plan-2  O1   0.020
 6OC  plan-2  O2   0.020
 6OC  plan-2  H2   0.020
 6OC  plan-3  C14  0.020
 6OC  plan-3  C13  0.020
 6OC  plan-3  C12  0.020
 6OC  plan-3  C11  0.020
 6OC  plan-3  H13  0.020
 6OC  plan-3  H12  0.020
 6OC  plan-4  C11  0.020
 6OC  plan-4  C10  0.020
 6OC  plan-4  C9   0.020
 6OC  plan-4  C8   0.020
 6OC  plan-4  H10  0.020
 6OC  plan-4  H9   0.020

