# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 00:25:36 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)\C=C\C=C/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
 13H  13H  '(9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid'  ligand  52  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13H
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
 13H  C18   C  CH3    0  -0.662  10.2443   2.1354   0.0901
 13H  C17   C  CH2    0  -0.419   8.7763   2.3087  -0.2738
 13H  C16   C  CH2    0  -0.408   7.9443   1.0664   0.0197
 13H  C15   C  CH2    0  -0.413   6.4772   1.2236  -0.3589
 13H  C14   C  CH2    0  -0.462   5.6603  -0.0320  -0.0831
 13H  C13   C  CH1    0   0.009   4.2091   0.0643  -0.5596
 13H  O3    O  OH1    0  -0.661   3.5175   1.1363   0.0371
 13H  C12   C  C1     0  -0.263   3.5094  -1.2537  -0.3963
 13H  C11   C  C1     0  -0.263   2.3147  -1.4397   0.1721
 13H  C10   C  C1     0  -0.246   1.6942  -2.7487   0.2946
 13H  C9    C  C1     0  -0.221   0.4794  -3.0094   0.7932
 13H  C8    C  CH2    0  -0.491  -0.5246  -2.0298   1.3099
 13H  C7    C  CH2    0  -0.413  -1.7258  -1.8958   0.3691
 13H  C6    C  CH2    0  -0.412  -2.8160  -0.9909   0.9282
 13H  C5    C  CH2    0  -0.411  -4.0048  -0.8326  -0.0118
 13H  C4    C  CH2    0  -0.409  -5.1105   0.0440   0.5630
 13H  C3    C  CH2    0  -0.402  -6.3004   0.2120  -0.3750
 13H  C2    C  CH2    0  -0.581  -7.3948   1.0825   0.2205
 13H  C1    C  C      0   0.409  -8.6377   1.3116  -0.6569
 13H  O1    O  OC    -1  -0.635  -9.4925   2.0998  -0.1980
 13H  O2    O  O      0  -0.610  -8.7080   0.7036  -1.7432
 13H  H118  H  HCH3   0   0.216  10.3647   1.9200   1.1535
 13H  H218  H  HCH3   0   0.216  10.6906   1.3075  -0.4642
 13H  H318  H  HCH3   0   0.226  10.8231   3.0322  -0.1340
 13H  H117  H  HCH2   0   0.211   8.3594   3.1615   0.2708
 13H  H217  H  HCH2   0   0.210   8.6895   2.5572  -1.3362
 13H  H116  H  HCH2   0   0.207   8.3697   0.2121  -0.5192
 13H  H216  H  HCH2   0   0.208   8.0234   0.8200   1.0845
 13H  H115  H  HCH2   0   0.215   6.0513   2.0730   0.1825
 13H  H215  H  HCH2   0   0.210   6.4047   1.4726  -1.4238
 13H  H114  H  HCH2   0   0.226   6.1282  -0.8852  -0.5846
 13H  H214  H  HCH2   0   0.225   5.6770  -0.2661   0.9883
 13H  H13   H  HCH1   0   0.236   4.2343   0.2967  -1.6326
 13H  H3    H  HOH1   0   0.444   3.5452   1.0168   0.9933
 13H  H12   H  H      0   0.245   4.0470  -2.1116  -0.7942
 13H  H11   H  H      0   0.240   1.7708  -0.5824   0.5545
 13H  H10   H  H      0   0.235   2.2825  -3.5878  -0.0661
 13H  H9    H  H      0   0.236   0.1572  -4.0468   0.8005
 13H  H18C  H  HCH2   0   0.232  -0.8817  -2.3703   2.2877
 13H  H28C  H  HCH2   0   0.233  -0.0817  -1.0444   1.4708
 13H  H17C  H  HCH2   0   0.217  -1.3828  -1.5086  -0.5955
 13H  H27C  H  HCH2   0   0.215  -2.1444  -2.8878   0.1687
 13H  H16C  H  HCH2   0   0.208  -3.1619  -1.3938   1.8868
 13H  H26C  H  HCH2   0   0.209  -2.3937  -0.0043   1.1494
 13H  H15C  H  HCH2   0   0.206  -3.6639  -0.4097  -0.9635
 13H  H25C  H  HCH2   0   0.205  -4.4135  -1.8212  -0.2496
 13H  H14C  H  HCH2   0   0.202  -5.4514  -0.3849   1.5125
 13H  H24C  H  HCH2   0   0.202  -4.6990   1.0294   0.8107
 13H  H13C  H  HCH2   0   0.199  -5.9569   0.6446  -1.3198
 13H  H23C  H  HCH2   0   0.200  -6.7037  -0.7733  -0.6256
 13H  H12C  H  HCH2   0   0.217  -7.7260   0.6500   1.1728
 13H  H22C  H  HCH2   0   0.213  -6.9798   2.0612   0.4884

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
 13H  C18  C17   single  1.522  0.020  1.522
 13H  C17  C16   single  1.524  0.020  1.524
 13H  C16  C15   single  1.523  0.020  1.523
 13H  C15  C14   single  1.523  0.020  1.523
 13H  C14  C13   single  1.530  0.020  1.530
 13H  C13  O3    single  1.408  0.020  1.408
 13H  C13  C12   single  1.501  0.020  1.501
 13H  C12  C11   double  1.336  0.020  1.336
 13H  C11  C10   single  1.454  0.020  1.454
 13H  C10  C9    double  1.339  0.020  1.339
 13H  C9   C8    single  1.495  0.020  1.495
 13H  C8   C7    single  1.532  0.020  1.532
 13H  C7   C6    single  1.523  0.020  1.523
 13H  C6   C5    single  1.524  0.020  1.524
 13H  C5   C4    single  1.524  0.020  1.524
 13H  C4   C3    single  1.524  0.020  1.524
 13H  C3   C2    single  1.520  0.020  1.520
 13H  C2   C1    single  1.539  0.020  1.539
 13H  C1   O1    deloc   1.250  0.020  1.250
 13H  C1   O2    deloc   1.247  0.020  1.247
 13H  C18  H118  single  0.970  0.020  1.090
 13H  C18  H218  single  0.970  0.020  1.090
 13H  C18  H318  single  0.970  0.020  1.090
 13H  C17  H117  single  0.970  0.020  1.090
 13H  C17  H217  single  0.970  0.020  1.090
 13H  C16  H116  single  0.970  0.020  1.090
 13H  C16  H216  single  0.970  0.020  1.090
 13H  C15  H115  single  0.970  0.020  1.090
 13H  C15  H215  single  0.970  0.020  1.090
 13H  C14  H114  single  0.970  0.020  1.090
 13H  C14  H214  single  0.970  0.020  1.090
 13H  C13  H13   single  0.970  0.020  1.090
 13H  O3   H3    single  0.850  0.020  0.980
 13H  C12  H12   single  0.930  0.020  1.080
 13H  C11  H11   single  0.930  0.020  1.080
 13H  C10  H10   single  0.930  0.020  1.080
 13H  C9   H9    single  0.930  0.020  1.080
 13H  C8   H18C  single  0.970  0.020  1.090
 13H  C8   H28C  single  0.970  0.020  1.090
 13H  C7   H17C  single  0.970  0.020  1.090
 13H  C7   H27C  single  0.970  0.020  1.090
 13H  C6   H16C  single  0.970  0.020  1.090
 13H  C6   H26C  single  0.970  0.020  1.090
 13H  C5   H15C  single  0.970  0.020  1.090
 13H  C5   H25C  single  0.970  0.020  1.090
 13H  C4   H14C  single  0.970  0.020  1.090
 13H  C4   H24C  single  0.970  0.020  1.090
 13H  C3   H13C  single  0.970  0.020  1.090
 13H  C3   H23C  single  0.970  0.020  1.090
 13H  C2   H12C  single  0.970  0.020  1.090
 13H  C2   H22C  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
 13H  H318  C18  H218  107.60  3.000
 13H  H318  C18  H118  107.69  3.000
 13H  H218  C18  H118  107.45  3.000
 13H  H318  C18  C17   111.66  3.000
 13H  H218  C18  C17   111.05  3.000
 13H  H118  C18  C17   111.20  3.000
 13H  H217  C17  H117  106.01  3.000
 13H  H217  C17  C16   109.19  3.000
 13H  H117  C17  C16   109.36  3.000
 13H  H217  C17  C18   109.53  3.000
 13H  H117  C17  C18   109.70  3.000
 13H  C16   C17  C18   112.81  3.000
 13H  H216  C16  H116  105.93  3.000
 13H  H216  C16  C15   109.52  3.000
 13H  H116  C16  C15   109.39  3.000
 13H  H216  C16  C17   109.33  3.000
 13H  H116  C16  C17   109.20  3.000
 13H  C15   C16  C17   113.20  3.000
 13H  H215  C15  H115  106.18  3.000
 13H  H215  C15  C14   109.13  3.000
 13H  H115  C15  C14   109.98  3.000
 13H  H215  C15  C16   109.19  3.000
 13H  H115  C15  C16   109.40  3.000
 13H  C14   C15  C16   112.73  3.000
 13H  H214  C14  H114  105.94  3.000
 13H  H214  C14  C13   109.39  3.000
 13H  H114  C14  C13   108.16  3.000
 13H  H214  C14  C15   110.16  3.000
 13H  H114  C14  C15   109.29  3.000
 13H  C13   C14  C15   113.60  3.000
 13H  H13   C13  C12   107.63  3.000
 13H  H13   C13  O3    105.31  3.000
 13H  C12   C13  O3    113.16  3.000
 13H  H13   C13  C14   107.20  3.000
 13H  C12   C13  C14   110.66  3.000
 13H  O3    C13  C14   112.44  3.000
 13H  H3    O3   C13   108.16  3.000
 13H  H12   C12  C11   119.19  3.000
 13H  H12   C12  C13   114.98  3.000
 13H  C11   C12  C13   125.82  3.000
 13H  H11   C11  C10   117.89  3.000
 13H  H11   C11  C12   119.23  3.000
 13H  C10   C11  C12   122.87  3.000
 13H  H10   C10  C9    117.68  3.000
 13H  H10   C10  C11   115.87  3.000
 13H  C9    C10  C11   126.44  3.000
 13H  H9    C9   C8    115.11  3.000
 13H  H9    C9   C10   117.24  3.000
 13H  C8    C9   C10   127.63  3.000
 13H  H28C  C8   H18C  106.33  3.000
 13H  H28C  C8   C7    109.24  3.000
 13H  H18C  C8   C7    108.66  3.000
 13H  H28C  C8   C9    111.70  3.000
 13H  H18C  C8   C9    108.89  3.000
 13H  C7    C8   C9    111.82  3.000
 13H  H27C  C7   H17C  106.20  3.000
 13H  H27C  C7   C6    109.37  3.000
 13H  H17C  C7   C6    109.74  3.000
 13H  H27C  C7   C8    109.45  3.000
 13H  H17C  C7   C8    109.05  3.000
 13H  C6    C7   C8    112.82  3.000
 13H  H26C  C6   H16C  106.03  3.000
 13H  H26C  C6   C5    109.37  3.000
 13H  H16C  C6   C5    109.36  3.000
 13H  H26C  C6   C7    109.46  3.000
 13H  H16C  C6   C7    109.18  3.000
 13H  C5    C6   C7    113.18  3.000
 13H  H25C  C5   H15C  106.01  3.000
 13H  H25C  C5   C4    109.29  3.000
 13H  H15C  C5   C4    109.35  3.000
 13H  H25C  C5   C6    109.33  3.000
 13H  H15C  C5   C6    109.46  3.000
 13H  C4    C5   C6    113.15  3.000
 13H  H24C  C4   H14C  105.83  3.000
 13H  H24C  C4   C3    109.45  3.000
 13H  H14C  C4   C3    109.47  3.000
 13H  H24C  C4   C5    109.27  3.000
 13H  H14C  C4   C5    109.11  3.000
 13H  C3    C4   C5    113.44  3.000
 13H  H23C  C3   H13C  105.90  3.000
 13H  H23C  C3   C2    109.88  3.000
 13H  H13C  C3   C2    109.75  3.000
 13H  H23C  C3   C4    109.24  3.000
 13H  H13C  C3   C4    109.26  3.000
 13H  C2    C3   C4    112.59  3.000
 13H  H22C  C2   H12C  104.72  3.000
 13H  H22C  C2   C1    108.20  3.000
 13H  H12C  C2   C1    108.05  3.000
 13H  H22C  C2   C3    109.53  3.000
 13H  H12C  C2   C3    109.37  3.000
 13H  C1    C2   C3    116.33  3.000
 13H  O2    C1   O1    126.07  3.000
 13H  O2    C1   C2    118.02  3.000
 13H  O1    C1   C2    115.91  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
 13H  Var_01  C10   C11  C12  C13   179.89   0.0  2
 13H  Var_02  C8    C9   C10  C11     1.31   0.0  2
 13H  Var_03  C15   C16  C17  C18  -179.21  30.0  3
 13H  Var_04  C14   C15  C16  C17   179.03  30.0  3
 13H  Var_05  C13   C14  C15  C16  -175.35  30.0  3
 13H  Var_06  C9    C10  C11  C12  -176.73  30.0  2
 13H  Var_07  C7    C8   C9   C10   108.96  30.0  3
 13H  Var_08  C6    C7   C8   C9    175.26  30.0  3
 13H  Var_09  C5    C6   C7   C8    179.01  30.0  3
 13H  Var_10  C4    C5   C6   C7    178.54  30.0  3
 13H  Var_11  C3    C4   C5   C6    179.73  30.0  3
 13H  Var_12  C2    C3   C4   C5    179.65  30.0  3
 13H  Var_13  C1    C2   C3   C4    179.89  30.0  3
 13H  Var_14  O1    C1   C2   C3   -175.38  30.0  3
 13H  Var_15  H118  C18  C17  C16   -60.10  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
 13H  chir_01  C13  C14  O3  C12  positiv

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
 13H  plan-1  C2   0.020
 13H  plan-1  C1   0.020
 13H  plan-1  O1   0.020
 13H  plan-1  O2   0.020
 13H  plan-2  C13  0.020
 13H  plan-2  C12  0.020
 13H  plan-2  C11  0.020
 13H  plan-2  C10  0.020
 13H  plan-2  H12  0.020
 13H  plan-2  H11  0.020
 13H  plan-3  C11  0.020
 13H  plan-3  C10  0.020
 13H  plan-3  C9   0.020
 13H  plan-3  C8   0.020
 13H  plan-3  H10  0.020
 13H  plan-3  H9   0.020

