# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:28:10 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C=C/[C@@H](O)CCCCCCCC(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
 9HO  9HO  '(9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid'  ligand  52  21  .  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_9HO
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
 9HO  O2    O  O      0  -0.610    9.1924  -1.0426   0.9301
 9HO  C1    C  C      0   0.410    9.2169  -0.1818   0.0284
 9HO  O1    O  OC    -1  -0.635   10.2374   0.2496  -0.5505
 9HO  C2    C  CH2    0  -0.582    7.8784   0.4241  -0.4286
 9HO  C3    C  CH2    0  -0.402    6.6273  -0.1157   0.2446
 9HO  C4    C  CH2    0  -0.409    5.3550   0.5497  -0.2666
 9HO  C5    C  CH2    0  -0.410    4.0858   0.0311   0.3974
 9HO  C6    C  CH2    0  -0.412    2.8241   0.7207  -0.1062
 9HO  C7    C  CH2    0  -0.414    1.5493   0.2098   0.5537
 9HO  C8    C  CH2    0  -0.462    0.3080   0.9490   0.0713
 9HO  C9    C  CH1    0   0.008   -0.9889   0.4909   0.7441
 9HO  C10   C  C1     0  -0.261   -2.1252   1.3903   0.3532
 9HO  C11   C  C1     0  -0.266   -3.3081   0.9990  -0.1288
 9HO  C12   C  C1     0  -0.247   -4.3546   1.9406  -0.4946
 9HO  C13   C  C1     0  -0.220   -5.5777   1.6397  -0.9478
 9HO  C14   C  CH2    0  -0.490   -6.1628   0.2813  -1.1612
 9HO  C15   C  CH2    0  -0.413   -7.3174   0.0014  -0.1959
 9HO  C16   C  CH2    0  -0.408   -7.9830  -1.3459  -0.4442
 9HO  C17   C  CH2    0  -0.420   -9.1277  -1.6340   0.5196
 9HO  C18   C  CH3    0  -0.662   -9.7909  -2.9801   0.2618
 9HO  O3    O  OH1    0  -0.661   -1.2578  -0.8732   0.5202
 9HO  H12C  H  HCH2   0   0.216    7.9305   1.5103  -0.2844
 9HO  H22C  H  HCH2   0   0.215    7.7972   0.2914  -1.5139
 9HO  H13C  H  HCH2   0   0.200    6.5575  -1.1966   0.0882
 9HO  H23C  H  HCH2   0   0.200    6.6978   0.0255   1.3273
 9HO  H14C  H  HCH2   0   0.202    5.4245   1.6328  -0.1123
 9HO  H24C  H  HCH2   0   0.202    5.2795   0.4077  -1.3508
 9HO  H15C  H  HCH2   0   0.205    4.0024  -1.0489   0.2320
 9HO  H25C  H  HCH2   0   0.205    4.1631   0.1652   1.4822
 9HO  H16C  H  HCH2   0   0.206    2.9116   1.7999   0.0617
 9HO  H26C  H  HCH2   0   0.208    2.7481   0.5901  -1.1915
 9HO  H17C  H  HCH2   0   0.215    1.4459  -0.8618   0.3622
 9HO  H27C  H  HCH2   0   0.210    1.6343   0.3205   1.6406
 9HO  H18C  H  HCH2   0   0.226    0.4310   2.0201   0.2600
 9HO  H28C  H  HCH2   0   0.225    0.2054   0.8448  -1.0157
 9HO  H9    H  HCH1   0   0.236   -0.8469   0.5858   1.8289
 9HO  H10   H  H      0   0.245   -1.9355   2.4531   0.4857
 9HO  H3    H  HOH1   0   0.444   -1.2981  -1.0189  -0.4318
 9HO  H11   H  H      0   0.241   -3.5105  -0.0601  -0.2508
 9HO  H12   H  H      0   0.235   -4.1037   2.9912  -0.3776
 9HO  H13   H  H      0   0.236   -6.2469   2.4682  -1.1632
 9HO  H114  H  HCH2   0   0.232   -6.5418   0.2150  -2.1872
 9HO  H214  H  HCH2   0   0.233   -5.4080  -0.5014  -1.0623
 9HO  H115  H  HCH2   0   0.217   -6.9435   0.0424   0.8320
 9HO  H215  H  HCH2   0   0.215   -8.0630   0.7989  -0.2820
 9HO  H116  H  HCH2   0   0.209   -8.3566  -1.3818  -1.4737
 9HO  H216  H  HCH2   0   0.209   -7.2346  -2.1422  -0.3655
 9HO  H117  H  HCH2   0   0.211   -8.7518  -1.6004   1.5470
 9HO  H217  H  HCH2   0   0.211   -9.8736  -0.8369   0.4436
 9HO  H118  H  HCH3   0   0.226  -10.6042  -3.1687   0.9635
 9HO  H218  H  HCH3   0   0.216  -10.2064  -3.0267  -0.7467
 9HO  H318  H  HCH3   0   0.216   -9.0740  -3.7977   0.3594

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
 9HO  O2   C1    deloc   1.247  0.020  1.247
 9HO  C1   O1    deloc   1.250  0.020  1.250
 9HO  C1   C2    single  1.539  0.020  1.539
 9HO  C2   C3    single  1.520  0.020  1.520
 9HO  C3   C4    single  1.524  0.020  1.524
 9HO  C4   C5    single  1.523  0.020  1.523
 9HO  C5   C6    single  1.524  0.020  1.524
 9HO  C6   C7    single  1.524  0.020  1.524
 9HO  C7   C8    single  1.523  0.020  1.523
 9HO  C8   C9    single  1.531  0.020  1.531
 9HO  C9   C10   single  1.501  0.020  1.501
 9HO  C9   O3    single  1.408  0.020  1.408
 9HO  C10  C11   double  1.336  0.020  1.336
 9HO  C11  C12   single  1.455  0.020  1.455
 9HO  C12  C13   double  1.339  0.020  1.339
 9HO  C13  C14   single  1.494  0.020  1.494
 9HO  C14  C15   single  1.531  0.020  1.531
 9HO  C15  C16   single  1.523  0.020  1.523
 9HO  C16  C17   single  1.524  0.020  1.524
 9HO  C17  C18   single  1.523  0.020  1.523
 9HO  C2   H12C  single  0.970  0.020  1.090
 9HO  C2   H22C  single  0.970  0.020  1.090
 9HO  C3   H13C  single  0.970  0.020  1.090
 9HO  C3   H23C  single  0.970  0.020  1.090
 9HO  C4   H14C  single  0.970  0.020  1.090
 9HO  C4   H24C  single  0.970  0.020  1.090
 9HO  C5   H15C  single  0.970  0.020  1.090
 9HO  C5   H25C  single  0.970  0.020  1.090
 9HO  C6   H16C  single  0.970  0.020  1.090
 9HO  C6   H26C  single  0.970  0.020  1.090
 9HO  C7   H17C  single  0.970  0.020  1.090
 9HO  C7   H27C  single  0.970  0.020  1.090
 9HO  C8   H18C  single  0.970  0.020  1.090
 9HO  C8   H28C  single  0.970  0.020  1.090
 9HO  C9   H9    single  0.970  0.020  1.090
 9HO  C10  H10   single  0.930  0.020  1.080
 9HO  O3   H3    single  0.850  0.020  0.980
 9HO  C11  H11   single  0.930  0.020  1.080
 9HO  C12  H12   single  0.930  0.020  1.080
 9HO  C13  H13   single  0.930  0.020  1.080
 9HO  C14  H114  single  0.970  0.020  1.090
 9HO  C14  H214  single  0.970  0.020  1.090
 9HO  C15  H115  single  0.970  0.020  1.090
 9HO  C15  H215  single  0.970  0.020  1.090
 9HO  C16  H116  single  0.970  0.020  1.090
 9HO  C16  H216  single  0.970  0.020  1.090
 9HO  C17  H117  single  0.970  0.020  1.090
 9HO  C17  H217  single  0.970  0.020  1.090
 9HO  C18  H118  single  0.970  0.020  1.090
 9HO  C18  H218  single  0.970  0.020  1.090
 9HO  C18  H318  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
 9HO  C2    C1   O1    115.89  3.000
 9HO  C2    C1   O2    118.00  3.000
 9HO  O1    C1   O2    126.10  3.000
 9HO  H22C  C2   H12C  104.68  3.000
 9HO  H22C  C2   C3    109.54  3.000
 9HO  H12C  C2   C3    109.43  3.000
 9HO  H22C  C2   C1    108.10  3.000
 9HO  H12C  C2   C1    108.03  3.000
 9HO  C3    C2   C1    116.40  3.000
 9HO  H23C  C3   H13C  105.84  3.000
 9HO  H23C  C3   C4    109.23  3.000
 9HO  H13C  C3   C4    109.27  3.000
 9HO  H23C  C3   C2    109.84  3.000
 9HO  H13C  C3   C2    109.88  3.000
 9HO  C4    C3   C2    112.55  3.000
 9HO  H24C  C4   H14C  105.76  3.000
 9HO  H24C  C4   C5    109.24  3.000
 9HO  H14C  C4   C5    109.14  3.000
 9HO  H24C  C4   C3    109.44  3.000
 9HO  H14C  C4   C3    109.35  3.000
 9HO  C5    C4   C3    113.62  3.000
 9HO  H25C  C5   H15C  105.99  3.000
 9HO  H25C  C5   C6    109.28  3.000
 9HO  H15C  C5   C6    109.46  3.000
 9HO  H25C  C5   C4    109.33  3.000
 9HO  H15C  C5   C4    109.46  3.000
 9HO  C6    C5   C4    113.06  3.000
 9HO  H26C  C6   H16C  105.94  3.000
 9HO  H26C  C6   C7    109.33  3.000
 9HO  H16C  C6   C7    109.31  3.000
 9HO  H26C  C6   C5    109.33  3.000
 9HO  H16C  C6   C5    109.21  3.000
 9HO  C7    C6   C5    113.45  3.000
 9HO  H27C  C7   H17C  106.27  3.000
 9HO  H27C  C7   C8    109.16  3.000
 9HO  H17C  C7   C8    110.07  3.000
 9HO  H27C  C7   C6    109.32  3.000
 9HO  H17C  C7   C6    109.38  3.000
 9HO  C8    C7   C6    112.45  3.000
 9HO  H28C  C8   H18C  105.92  3.000
 9HO  H28C  C8   C9    109.13  3.000
 9HO  H18C  C8   C9    108.20  3.000
 9HO  H28C  C8   C7    110.12  3.000
 9HO  H18C  C8   C7    109.20  3.000
 9HO  C9    C8   C7    113.95  3.000
 9HO  H9    C9   O3    105.39  3.000
 9HO  H9    C9   C10   107.66  3.000
 9HO  O3    C9   C10   113.23  3.000
 9HO  H9    C9   C8    107.38  3.000
 9HO  O3    C9   C8    112.44  3.000
 9HO  C10   C9   C8    110.33  3.000
 9HO  H10   C10  C11   118.98  3.000
 9HO  H10   C10  C9    114.94  3.000
 9HO  C11   C10  C9    126.07  3.000
 9HO  H11   C11  C12   117.99  3.000
 9HO  H11   C11  C10   119.44  3.000
 9HO  C12   C11  C10   122.56  3.000
 9HO  H12   C12  C13   117.70  3.000
 9HO  H12   C12  C11   115.64  3.000
 9HO  C13   C12  C11   126.66  3.000
 9HO  H13   C13  C14   115.06  3.000
 9HO  H13   C13  C12   117.29  3.000
 9HO  C14   C13  C12   127.62  3.000
 9HO  H214  C14  H114  106.30  3.000
 9HO  H214  C14  C15   109.46  3.000
 9HO  H114  C14  C15   108.57  3.000
 9HO  H214  C14  C13   111.59  3.000
 9HO  H114  C14  C13   108.91  3.000
 9HO  C15   C14  C13   111.81  3.000
 9HO  H215  C15  H115  106.21  3.000
 9HO  H215  C15  C16   109.50  3.000
 9HO  H115  C15  C16   109.60  3.000
 9HO  H215  C15  C14   109.31  3.000
 9HO  H115  C15  C14   109.12  3.000
 9HO  C16   C15  C14   112.86  3.000
 9HO  H216  C16  H116  106.05  3.000
 9HO  H216  C16  C17   109.29  3.000
 9HO  H116  C16  C17   109.38  3.000
 9HO  H216  C16  C15   109.43  3.000
 9HO  H116  C16  C15   109.34  3.000
 9HO  C17   C16  C15   113.11  3.000
 9HO  H217  C17  H117  106.07  3.000
 9HO  H217  C17  C18   109.59  3.000
 9HO  H117  C17  C18   109.61  3.000
 9HO  H217  C17  C16   109.29  3.000
 9HO  H117  C17  C16   109.26  3.000
 9HO  C18   C17  C16   112.79  3.000
 9HO  H318  C18  H218  107.49  3.000
 9HO  H318  C18  H118  107.61  3.000
 9HO  H218  C18  H118  107.65  3.000
 9HO  H318  C18  C17   111.16  3.000
 9HO  H218  C18  C17   111.10  3.000
 9HO  H118  C18  C17   111.64  3.000
 9HO  H3    O3   C9    108.15  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
 9HO  Var_01  C12   C11  C10  C9   -179.47   0.0  2
 9HO  Var_02  C14   C13  C12  C11     1.17   0.0  2
 9HO  Var_03  C3    C2   C1   O2     -1.57  30.0  3
 9HO  Var_04  C4    C3   C2   C1    179.65  30.0  3
 9HO  Var_05  C5    C4   C3   C2   -179.72  30.0  3
 9HO  Var_06  C6    C5   C4   C3    179.05  30.0  3
 9HO  Var_07  C7    C6   C5   C4   -179.92  30.0  3
 9HO  Var_08  C8    C7   C6   C5    177.90  30.0  3
 9HO  Var_09  C9    C8   C7   C6   -178.27  30.0  3
 9HO  Var_10  C13   C12  C11  C10  -178.00  30.0  2
 9HO  Var_11  C15   C14  C13  C12   113.23  30.0  3
 9HO  Var_12  C16   C15  C14  C13   176.76  30.0  3
 9HO  Var_13  C17   C16  C15  C14   179.64  30.0  3
 9HO  Var_14  C18   C17  C16  C15   179.80  30.0  3
 9HO  Var_15  H118  C18  C17  C16   179.79  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
 9HO  chir_01  C9  C8  C10  O3  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
 9HO  plan-1  O2   0.020
 9HO  plan-1  C1   0.020
 9HO  plan-1  O1   0.020
 9HO  plan-1  C2   0.020
 9HO  plan-2  C9   0.020
 9HO  plan-2  C10  0.020
 9HO  plan-2  C11  0.020
 9HO  plan-2  C12  0.020
 9HO  plan-2  H10  0.020
 9HO  plan-2  H11  0.020
 9HO  plan-3  C11  0.020
 9HO  plan-3  C12  0.020
 9HO  plan-3  C13  0.020
 9HO  plan-3  C14  0.020
 9HO  plan-3  H12  0.020
 9HO  plan-3  H13  0.020

