# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:11:59 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (9E,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
 HO2  HO2  '(9E,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid'  ligand  52  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HO2
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
 HO2  C18   C  CH3    0  -0.662   -9.6648   3.4488  -0.2479
 HO2  C17   C  CH2    0  -0.418   -9.2237   2.0389   0.1198
 HO2  C16   C  CH2    0  -0.407   -7.7915   1.7356  -0.3049
 HO2  C15   C  CH2    0  -0.411   -7.3352   0.3302   0.0660
 HO2  C14   C  CH2    0  -0.462   -5.9005   0.0528  -0.3668
 HO2  C13   C  CH1    0   0.006   -5.3944  -1.3461  -0.0035
 HO2  O21   O  OH1    0  -0.662   -5.4646  -1.5964   1.3807
 HO2  C12   C  C1     0  -0.268   -4.0223  -1.5581  -0.5760
 HO2  C11   C  C1     0  -0.250   -2.9166  -1.8186   0.1254
 HO2  C10   C  C1     0  -0.243   -1.5969  -1.9705  -0.4643
 HO2  C09   C  C1     0  -0.217   -0.4873  -2.1792   0.2506
 HO2  C08   C  CH2    0  -0.483    0.8901  -2.3101  -0.3095
 HO2  C07   C  CH2    0  -0.414    1.8049  -1.1621   0.1246
 HO2  C06   C  CH2    0  -0.413    3.2492  -1.3526  -0.3197
 HO2  C05   C  CH2    0  -0.410    4.1556  -0.1928   0.0736
 HO2  C04   C  CH2    0  -0.409    5.6106  -0.4048  -0.3247
 HO2  C03   C  CH2    0  -0.403    6.5156   0.7667   0.0382
 HO2  C02   C  CH2    0  -0.578    7.9662   0.5298  -0.3491
 HO2  C01   C  C      0   0.408    8.9471   1.6703  -0.0271
 HO2  O20   O  O      0  -0.611    8.5725   2.5503   0.7734
 HO2  O19   O  OC    -1  -0.633   10.0639   1.6091  -0.5848
 HO2  H18   H  HCH3   0   0.226  -10.6970   3.6360   0.0501
 HO2  H18A  H  HCH3   0   0.216   -9.0400   4.1992   0.2401
 HO2  H18B  H  HCH3   0   0.216   -9.5981   3.6150  -1.3248
 HO2  H17   H  HCH2   0   0.210   -9.3188   1.8960   1.2007
 HO2  H17A  H  HCH2   0   0.210   -9.8998   1.3123  -0.3413
 HO2  H16   H  HCH2   0   0.207   -7.6981   1.8754  -1.3876
 HO2  H16A  H  HCH2   0   0.207   -7.1167   2.4669   0.1537
 HO2  H15   H  HCH2   0   0.214   -7.4300   0.1934   1.1467
 HO2  H15A  H  HCH2   0   0.210   -8.0027  -0.4045  -0.3975
 HO2  H14   H  HCH2   0   0.228   -5.8174   0.1770  -1.4510
 HO2  H14A  H  HCH2   0   0.223   -5.2268   0.7984   0.0730
 HO2  H13   H  HCH1   0   0.234   -6.0698  -2.0762  -0.4676
 HO2  HO21  H  HOH1   0   0.445   -4.9953  -0.8922   1.8419
 HO2  H12   H  H      0   0.245   -3.9541  -1.4607  -1.6572
 HO2  H11   H  H      0   0.235   -2.9743  -1.9243   1.2052
 HO2  H10   H  H      0   0.235   -1.5259  -1.9007  -1.5476
 HO2  H09   H  H      0   0.236   -0.5699  -2.2369   1.3344
 HO2  H08   H  HCH2   0   0.228    1.3283  -3.2554   0.0304
 HO2  H08A  H  HCH2   0   0.230    0.8519  -2.3569  -1.4015
 HO2  H07   H  HCH2   0   0.216    1.4132  -0.2228  -0.2786
 HO2  H07A  H  HCH2   0   0.215    1.7710  -1.0627   1.2147
 HO2  H06   H  HCH2   0   0.209    3.6389  -2.2812   0.1121
 HO2  H06A  H  HCH2   0   0.209    3.2839  -1.4871  -1.4066
 HO2  H05   H  HCH2   0   0.206    3.7825   0.7297  -0.3852
 HO2  H05A  H  HCH2   0   0.205    4.0960  -0.0360   1.1566
 HO2  H04   H  HCH2   0   0.202    5.9861  -1.3166   0.1543
 HO2  H04A  H  HCH2   0   0.202    5.6678  -0.5895  -1.4037
 HO2  H03   H  HCH2   0   0.199    6.1436   1.6723  -0.4523
 HO2  H03A  H  HCH2   0   0.201    6.4464   0.9591   1.1125
 HO2  H02   H  HCH2   0   0.219    8.3310  -0.3735   0.1573
 HO2  H02A  H  HCH2   0   0.208    8.0334   0.2985  -1.4176

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
 HO2  C17  C18   single  1.522  0.020  1.522
 HO2  C18  H18   single  0.970  0.020  1.090
 HO2  C18  H18A  single  0.970  0.020  1.090
 HO2  C18  H18B  single  0.970  0.020  1.090
 HO2  C17  C16   single  1.524  0.020  1.524
 HO2  C17  H17   single  0.970  0.020  1.090
 HO2  C17  H17A  single  0.970  0.020  1.090
 HO2  C15  C16   single  1.523  0.020  1.523
 HO2  C16  H16   single  0.970  0.020  1.090
 HO2  C16  H16A  single  0.970  0.020  1.090
 HO2  C15  C14   single  1.524  0.020  1.524
 HO2  C15  H15   single  0.970  0.020  1.090
 HO2  C15  H15A  single  0.970  0.020  1.090
 HO2  C13  C14   single  1.531  0.020  1.531
 HO2  C14  H14   single  0.970  0.020  1.090
 HO2  C14  H14A  single  0.970  0.020  1.090
 HO2  C12  C13   single  1.502  0.020  1.502
 HO2  C13  O21   single  1.408  0.020  1.408
 HO2  C13  H13   single  0.970  0.020  1.090
 HO2  O21  HO21  single  0.850  0.020  0.980
 HO2  C11  C12   double  1.335  0.020  1.335
 HO2  C12  H12   single  0.930  0.020  1.080
 HO2  C10  C11   single  1.453  0.020  1.453
 HO2  C11  H11   single  0.930  0.020  1.080
 HO2  C09  C10   double  1.336  0.020  1.336
 HO2  C10  H10   single  0.930  0.020  1.080
 HO2  C08  C09   single  1.493  0.020  1.493
 HO2  C09  H09   single  0.930  0.020  1.080
 HO2  C07  C08   single  1.531  0.020  1.531
 HO2  C08  H08   single  0.970  0.020  1.090
 HO2  C08  H08A  single  0.970  0.020  1.090
 HO2  C06  C07   single  1.523  0.020  1.523
 HO2  C07  H07   single  0.970  0.020  1.090
 HO2  C07  H07A  single  0.970  0.020  1.090
 HO2  C05  C06   single  1.524  0.020  1.524
 HO2  C06  H06   single  0.970  0.020  1.090
 HO2  C06  H06A  single  0.970  0.020  1.090
 HO2  C04  C05   single  1.523  0.020  1.523
 HO2  C05  H05   single  0.970  0.020  1.090
 HO2  C05  H05A  single  0.970  0.020  1.090
 HO2  C03  C04   single  1.524  0.020  1.524
 HO2  C04  H04   single  0.970  0.020  1.090
 HO2  C04  H04A  single  0.970  0.020  1.090
 HO2  C02  C03   single  1.520  0.020  1.520
 HO2  C03  H03   single  0.970  0.020  1.090
 HO2  C03  H03A  single  0.970  0.020  1.090
 HO2  C01  C02   single  1.538  0.020  1.538
 HO2  C02  H02   single  0.970  0.020  1.090
 HO2  C02  H02A  single  0.970  0.020  1.090
 HO2  O20  C01   deloc   1.247  0.020  1.247
 HO2  C01  O19   deloc   1.250  0.020  1.250

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
 HO2  H18B  C18  H18A  107.54  3.000
 HO2  H18B  C18  H18   107.54  3.000
 HO2  H18A  C18  H18   107.55  3.000
 HO2  H18B  C18  C17   111.19  3.000
 HO2  H18A  C18  C17   111.28  3.000
 HO2  H18   C18  C17   111.54  3.000
 HO2  H17A  C17  H17   106.01  3.000
 HO2  H17A  C17  C16   109.33  3.000
 HO2  H17   C17  C16   109.32  3.000
 HO2  H17A  C17  C18   109.52  3.000
 HO2  H17   C17  C18   109.53  3.000
 HO2  C16   C17  C18   112.90  3.000
 HO2  H16A  C16  H16   106.02  3.000
 HO2  H16A  C16  C15   109.23  3.000
 HO2  H16   C16  C15   109.43  3.000
 HO2  H16A  C16  C17   109.22  3.000
 HO2  H16   C16  C17   109.27  3.000
 HO2  C15   C16  C17   113.40  3.000
 HO2  H15A  C15  H15   106.34  3.000
 HO2  H15A  C15  C14   109.35  3.000
 HO2  H15   C15  C14   109.85  3.000
 HO2  H15A  C15  C16   109.46  3.000
 HO2  H15   C15  C16   109.27  3.000
 HO2  C14   C15  C16   112.38  3.000
 HO2  H14A  C14  H14   105.87  3.000
 HO2  H14A  C14  C13   108.84  3.000
 HO2  H14   C14  C13   108.28  3.000
 HO2  H14A  C14  C15   109.91  3.000
 HO2  H14   C14  C15   109.39  3.000
 HO2  C13   C14  C15   114.20  3.000
 HO2  H13   C13  C12   107.89  3.000
 HO2  H13   C13  O21   105.47  3.000
 HO2  C12   C13  O21   113.28  3.000
 HO2  H13   C13  C14   107.70  3.000
 HO2  O21   C13  C14   112.27  3.000
 HO2  C12   C13  C14   109.90  3.000
 HO2  HO21  O21  C13   108.43  3.000
 HO2  H12   C12  C11   119.20  3.000
 HO2  H12   C12  C13   115.06  3.000
 HO2  C11   C12  C13   125.73  3.000
 HO2  H11   C11  C10   116.19  3.000
 HO2  H11   C11  C12   119.81  3.000
 HO2  C10   C11  C12   124.00  3.000
 HO2  H10   C10  C09   119.24  3.000
 HO2  H10   C10  C11   117.17  3.000
 HO2  C09   C10  C11   123.59  3.000
 HO2  H09   C09  C08   116.04  3.000
 HO2  H09   C09  C10   118.55  3.000
 HO2  C08   C09  C10   125.39  3.000
 HO2  H08A  C08  H08   106.66  3.000
 HO2  H08A  C08  C07   109.64  3.000
 HO2  H08   C08  C07   108.66  3.000
 HO2  H08A  C08  C09   110.25  3.000
 HO2  H08   C08  C09   109.16  3.000
 HO2  C07   C08  C09   112.29  3.000
 HO2  H07A  C07  H07   106.12  3.000
 HO2  H07A  C07  C06   109.33  3.000
 HO2  H07   C07  C06   109.83  3.000
 HO2  H07A  C07  C08   109.38  3.000
 HO2  H07   C07  C08   108.98  3.000
 HO2  C06   C07  C08   112.97  3.000
 HO2  H06A  C06  H06   106.00  3.000
 HO2  H06A  C06  C05   109.31  3.000
 HO2  H06   C06  C05   109.38  3.000
 HO2  H06A  C06  C07   109.56  3.000
 HO2  H06   C06  C07   109.16  3.000
 HO2  C05   C06  C07   113.18  3.000
 HO2  H05A  C05  H05   105.95  3.000
 HO2  H05A  C05  C04   109.29  3.000
 HO2  H05   C05  C04   109.44  3.000
 HO2  H05A  C05  C06   109.37  3.000
 HO2  H05   C05  C06   109.28  3.000
 HO2  C04   C05  C06   113.25  3.000
 HO2  H04A  C04  H04   105.79  3.000
 HO2  H04A  C04  C03   109.45  3.000
 HO2  H04   C04  C03   109.38  3.000
 HO2  H04A  C04  C05   109.31  3.000
 HO2  H04   C04  C05   109.19  3.000
 HO2  C03   C04  C05   113.45  3.000
 HO2  H03A  C03  H03   105.84  3.000
 HO2  H03A  C03  C02   109.76  3.000
 HO2  H03   C03  C02   109.81  3.000
 HO2  H03A  C03  C04   109.37  3.000
 HO2  H03   C03  C04   109.10  3.000
 HO2  C02   C03  C04   112.72  3.000
 HO2  H02A  C02  H02   104.82  3.000
 HO2  H02A  C02  C01   108.76  3.000
 HO2  H02   C02  C01   107.55  3.000
 HO2  H02A  C02  C03   109.88  3.000
 HO2  H02   C02  C03   109.13  3.000
 HO2  C01   C02  C03   116.08  3.000
 HO2  O19   C01  O20   126.11  3.000
 HO2  O19   C01  C02   116.11  3.000
 HO2  O20   C01  C02   117.77  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
 HO2  Var_01  C10  C11  C12  C13  -177.72   0.0  2
 HO2  Var_02  C08  C09  C10  C11  -178.54   0.0  2
 HO2  Var_03  C15  C16  C17  C18   179.62  30.0  3
 HO2  Var_04  C14  C15  C16  C17  -179.90  30.0  1
 HO2  Var_05  C13  C14  C15  C16   179.51  30.0  3
 HO2  Var_06  C09  C10  C11  C12   177.28  30.0  1
 HO2  Var_07  C07  C08  C09  C10   114.36  30.0  2
 HO2  Var_08  C06  C07  C08  C09   174.15  30.0  1
 HO2  Var_09  C05  C06  C07  C08   178.28  30.0  1
 HO2  Var_10  C04  C05  C06  C07   177.88  30.0  1
 HO2  Var_11  C03  C04  C05  C06   178.68  30.0  1
 HO2  Var_12  C02  C03  C04  C05   179.21  30.0  1
 HO2  Var_13  C01  C02  C03  C04   179.55  30.0  1
 HO2  Var_14  O20  C01  C02  C03    15.72  30.0  2
 HO2  Var_15  H18  C18  C17  C16   179.01  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
 HO2  chir_01  C13  C14  C12  O21  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
 HO2  plan-1  C02  0.020
 HO2  plan-1  C01  0.020
 HO2  plan-1  O20  0.020
 HO2  plan-1  O19  0.020
 HO2  plan-2  C13  0.020
 HO2  plan-2  C12  0.020
 HO2  plan-2  C11  0.020
 HO2  plan-2  C10  0.020
 HO2  plan-2  H12  0.020
 HO2  plan-2  H11  0.020
 HO2  plan-3  C11  0.020
 HO2  plan-3  C10  0.020
 HO2  plan-3  C09  0.020
 HO2  plan-3  C08  0.020
 HO2  plan-3  H10  0.020
 HO2  plan-3  H09  0.020

