# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:32:48 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  51  22  .  2021-08-05  2021-08-05  
;
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  -7.9006   4.8708   0.6698
 6OC  C17   C  CH2    0  -0.419  -7.6205   3.6628  -0.2132
 6OC  C16   C  CH2    0  -0.408  -6.8069   2.5887   0.4983
 6OC  C15   C  CH2    0  -0.415  -6.4981   1.3861  -0.3833
 6OC  C14   C  CH2    0  -0.488  -5.7091   0.3017   0.3513
 6OC  C13   C  C1     0  -0.202  -5.4071  -0.8713  -0.5270
 6OC  C12   C  C1     0  -0.218  -4.2178  -1.4107  -0.7900
 6OC  C11   C  CH2    0  -0.579  -2.8890  -0.9958  -0.2265
 6OC  C10   C  C1     0  -0.190  -2.4080  -2.0003   0.7822
 6OC  C9    C  C1     0  -0.253  -1.2332  -2.6241   0.8167
 6OC  C8    C  CH1    0  -0.023  -0.0850  -2.4518  -0.1361
 6OC  C7    C  CH2    0  -0.598   1.0479  -1.6972   0.5504
 6OC  C6    C  C      0   0.426   2.2042  -1.3256  -0.3494
 6OC  O3    O  O      0  -0.410   2.0801  -1.2272  -1.5492
 6OC  C5    C  CH2    0  -0.566   3.5035  -1.0504   0.3590
 6OC  C4    C  CH2    0  -0.413   4.5475  -0.2995  -0.4501
 6OC  C3    C  CH2    0  -0.405   5.8284  -0.0712   0.3449
 6OC  C2    C  CH2    0  -0.583   6.8632   0.7254  -0.4312
 6OC  C1    C  C      0   0.411   8.2003   0.9767   0.2888
 6OC  O1    O  O      0  -0.610   8.3888   0.4082   1.3824
 6OC  O2    O  OC    -1  -0.634   9.0036   1.7321  -0.2990
 6OC  OXT   O  OH1    0  -0.665   0.3576  -3.6983  -0.6382
 6OC  H181  H  HCH3   0   0.226  -8.4846   5.6273   0.1446
 6OC  H182  H  HCH3   0   0.216  -8.4593   4.5841   1.5630
 6OC  H183  H  HCH3   0   0.216  -6.9720   5.3399   1.0010
 6OC  H171  H  HCH2   0   0.211  -8.5658   3.2310  -0.5563
 6OC  H172  H  HCH2   0   0.211  -7.0882   3.9803  -1.1152
 6OC  H161  H  HCH2   0   0.209  -5.8680   3.0240   0.8585
 6OC  H162  H  HCH2   0   0.208  -7.3484   2.2583   1.3918
 6OC  H151  H  HCH2   0   0.214  -7.4331   0.9597  -0.7626
 6OC  H152  H  HCH2   0   0.216  -5.9333   1.7114  -1.2630
 6OC  H141  H  HCH2   0   0.230  -4.7953   0.7338   0.7658
 6OC  H142  H  HCH2   0   0.231  -6.3002  -0.0369   1.2101
 6OC  H13   H  H      0   0.231  -6.2739  -1.3179  -1.0083
 6OC  H12   H  H      0   0.237  -4.1846  -2.2671  -1.4571
 6OC  H111  H  HCH2   0   0.254  -2.1679  -0.8834  -1.0394
 6OC  H112  H  HCH2   0   0.256  -2.9604  -0.0184   0.2570
 6OC  H10   H  H      0   0.244  -3.1222  -2.2248   1.5692
 6OC  H9    H  H      0   0.246  -1.0519  -3.3189   1.6343
 6OC  H8    H  HCH1   0   0.243  -0.4033  -1.8820  -1.0105
 6OC  H7C1  H  HCH2   0   0.289   0.6689  -0.7533   0.9602
 6OC  H7C2  H  HCH2   0   0.265   1.4143  -2.2555   1.4190
 6OC  H5C1  H  HCH2   0   0.258   3.2806  -0.5213   1.2921
 6OC  H5C2  H  HCH2   0   0.270   3.8938  -2.0244   0.6824
 6OC  H4C1  H  HCH2   0   0.218   4.7798  -0.8495  -1.3661
 6OC  H4C2  H  HCH2   0   0.216   4.1382   0.6643  -0.7688
 6OC  H3C1  H  HCH2   0   0.203   5.5858   0.4472   1.2778
 6OC  H3C2  H  HCH2   0   0.205   6.2483  -1.0368   0.6398
 6OC  H2C1  H  HCH2   0   0.219   7.0821   0.2168  -1.3784
 6OC  H2C2  H  HCH2   0   0.215   6.4400   1.6928  -0.7244
 6OC  HOT1  H  HOH1   0   0.443   0.6525  -4.2377   0.1038

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  1.512  0.020  1.512
 6OC  C6   O3    double  1.210  0.020  1.210
 6OC  C6   C5    single  1.505  0.020  1.505
 6OC  C5   C4    single  1.519  0.020  1.519
 6OC  C4   C3    single  1.525  0.020  1.525
 6OC  C3   C2    single  1.519  0.020  1.519
 6OC  C2   C1    single  1.539  0.020  1.539
 6OC  C1   O1    deloc   1.247  0.020  1.247
 6OC  C1   O2    deloc   1.250  0.020  1.250
 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  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  107.45  3.000
 6OC  H183  C18  H181  107.67  3.000
 6OC  H182  C18  H181  107.58  3.000
 6OC  H183  C18  C17   111.12  3.000
 6OC  H182  C18  C17   111.12  3.000
 6OC  H181  C18  C17   111.69  3.000
 6OC  H172  C17  H171  106.04  3.000
 6OC  H172  C17  C16   109.25  3.000
 6OC  H171  C17  C16   109.24  3.000
 6OC  H172  C17  C18   109.71  3.000
 6OC  H171  C17  C18   109.63  3.000
 6OC  C16   C17  C18   112.75  3.000
 6OC  H162  C16  H161  105.97  3.000
 6OC  H162  C16  C15   109.52  3.000
 6OC  H161  C16  C15   109.29  3.000
 6OC  H162  C16  C17   109.24  3.000
 6OC  H161  C16  C17   109.33  3.000
 6OC  C15   C16  C17   113.24  3.000
 6OC  H152  C15  H151  106.12  3.000
 6OC  H152  C15  C14   109.30  3.000
 6OC  H151  C15  C14   109.31  3.000
 6OC  H152  C15  C16   109.58  3.000
 6OC  H151  C15  C16   109.56  3.000
 6OC  C14   C15  C16   112.75  3.000
 6OC  H142  C14  H141  106.01  3.000
 6OC  H142  C14  C13   109.06  3.000
 6OC  H141  C14  C13   111.34  3.000
 6OC  H142  C14  C15   108.50  3.000
 6OC  H141  C14  C15   109.47  3.000
 6OC  C13   C14  C15   112.22  3.000
 6OC  H13   C13  C12   117.25  3.000
 6OC  H13   C13  C14   114.89  3.000
 6OC  C12   C13  C14   127.85  3.000
 6OC  H12   C12  C11   114.92  3.000
 6OC  H12   C12  C13   117.89  3.000
 6OC  C11   C12  C13   127.16  3.000
 6OC  H112  C11  H111  106.28  3.000
 6OC  H112  C11  C10   108.77  3.000
 6OC  H111  C11  C10   110.92  3.000
 6OC  H112  C11  C12   110.82  3.000
 6OC  H111  C11  C12   109.47  3.000
 6OC  C10   C11  C12   110.52  3.000
 6OC  H10   C10  C9    117.70  3.000
 6OC  H10   C10  C11   114.46  3.000
 6OC  C9    C10  C11   127.84  3.000
 6OC  H9    C9   C8    114.99  3.000
 6OC  H9    C9   C10   117.77  3.000
 6OC  C8    C9   C10   127.21  3.000
 6OC  H8    C8   OXT   105.48  3.000
 6OC  OXT   C8   C7    111.31  3.000
 6OC  H8    C8   C7    108.62  3.000
 6OC  OXT   C8   C9    111.29  3.000
 6OC  H8    C8   C9    110.20  3.000
 6OC  C7    C8   C9    109.83  3.000
 6OC  H7C2  C7   H7C1  104.95  3.000
 6OC  H7C2  C7   C6    109.96  3.000
 6OC  H7C1  C7   C6    105.98  3.000
 6OC  H7C2  C7   C8    110.69  3.000
 6OC  H7C1  C7   C8    109.72  3.000
 6OC  C6    C7   C8    114.97  3.000
 6OC  C5    C6   O3    122.70  3.000
 6OC  C5    C6   C7    115.16  3.000
 6OC  O3    C6   C7    122.12  3.000
 6OC  H5C2  C5   H5C1  104.48  3.000
 6OC  H5C2  C5   C4    110.55  3.000
 6OC  H5C1  C5   C4    110.77  3.000
 6OC  H5C2  C5   C6    106.45  3.000
 6OC  H5C1  C5   C6    108.27  3.000
 6OC  C4    C5   C6    115.65  3.000
 6OC  H4C2  C4   H4C1  106.16  3.000
 6OC  H4C2  C4   C3    109.52  3.000
 6OC  H4C1  C4   C3    109.49  3.000
 6OC  H4C2  C4   C5    109.47  3.000
 6OC  H4C1  C4   C5    110.10  3.000
 6OC  C3    C4   C5    111.94  3.000
 6OC  H3C2  C3   H3C1  105.87  3.000
 6OC  H3C2  C3   C2    109.83  3.000
 6OC  H3C1  C3   C2    109.76  3.000
 6OC  H3C2  C3   C4    109.33  3.000
 6OC  H3C1  C3   C4    109.22  3.000
 6OC  C2    C3   C4    112.61  3.000
 6OC  H2C2  C2   H2C1  104.79  3.000
 6OC  H2C2  C2   C1    108.45  3.000
 6OC  H2C1  C2   C1    107.83  3.000
 6OC  H2C2  C2   C3    109.66  3.000
 6OC  H2C1  C2   C3    109.50  3.000
 6OC  C1    C2   C3    116.00  3.000
 6OC  O2    C1   O1    126.23  3.000
 6OC  O2    C1   C2    115.92  3.000
 6OC  O1    C1   C2    117.85  3.000
 6OC  HOT1  OXT  C8    108.40  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  Var_01  C11   C12  C13  C14     2.27   0.0  2
 6OC  Var_02  C8    C9   C10  C11     1.39   0.0  2
 6OC  Var_03  C15   C16  C17  C18  -178.93  30.0  3
 6OC  Var_04  C14   C15  C16  C17  -178.68  30.0  3
 6OC  Var_05  C13   C14  C15  C16  -179.75  30.0  3
 6OC  Var_06  C12   C13  C14  C15   125.16  30.0  3
 6OC  Var_07  C10   C11  C12  C13   106.52  30.0  3
 6OC  Var_08  C9    C10  C11  C12   127.13  30.0  3
 6OC  Var_09  O3    C6   C7   C8     22.98  30.0  3
 6OC  Var_10  C4    C5   C6   C7   -162.96  30.0  3
 6OC  Var_11  C3    C4   C5   C6   -179.80  30.0  3
 6OC  Var_12  C2    C3   C4   C5   -177.79  30.0  3
 6OC  Var_13  C1    C2   C3   C4   -178.79  30.0  3
 6OC  Var_14  O1    C1   C2   C3      6.89  30.0  3
 6OC  Var_15  H181  C18  C17  C16  -179.91  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-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

