# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 02:13:41 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](OO)\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
 13S  13S  '(9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoic acid'  ligand  53  22  .  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_13S
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
 13S  C1    C  C      0   0.410   0.7088  -0.4041   -9.3164
 13S  C2    C  CH2    0  -0.580   0.8670   0.1921   -7.9067
 13S  C3    C  CH2    0  -0.401  -0.1700  -0.2256   -6.8771
 13S  C4    C  CH2    0  -0.408   0.0423   0.4447   -5.5246
 13S  C5    C  CH2    0  -0.410  -0.9892   0.0411   -4.4784
 13S  C6    C  CH2    0  -0.411  -0.7926   0.7434   -3.1405
 13S  C7    C  CH2    0  -0.415  -1.8169   0.3336   -2.0904
 13S  C8    C  CH2    0  -0.488  -1.6418   1.0815   -0.7672
 13S  C9    C  C1     0  -0.214  -2.6886   0.7059    0.2307
 13S  C10   C  C1     0  -0.251  -2.5118   0.2509    1.4773
 13S  C11   C  C1     0  -0.253  -1.2407   0.0442    2.1527
 13S  C12   C  C1     0  -0.281  -1.1674  -0.4086    3.4076
 13S  C13   C  CH1    0   0.041   0.0738  -0.6361    4.2157
 13S  C14   C  CH2    0  -0.444  -0.0730   0.0114    5.5943
 13S  C15   C  CH2    0  -0.443   1.0975  -0.1880    6.5514
 13S  C16   C  CH2    0  -0.405   0.7618   0.2786    7.9634
 13S  C17   C  CH2    0  -0.419   1.9168   0.1167    8.9435
 13S  C18   C  CH3    0  -0.663   1.5623   0.5739   10.3517
 13S  O19   O  O      0  -0.610  -0.2555  -1.1664   -9.5254
 13S  O20   O  OC    -1  -0.636   1.5747  -0.0642  -10.1516
 13S  O21   O  O2     0  -0.311   1.1790  -0.1218    3.4830
 13S  O22   O  OH1    0  -0.452   2.3257  -0.8969    3.7303
 13S  H21   H  HCH2   0   0.215   0.8690   1.2848   -8.0009
 13S  H22   H  HCH2   0   0.215   1.8705  -0.0581   -7.5421
 13S  H31   H  HCH2   0   0.199  -0.1502  -1.3121   -6.7488
 13S  H32   H  HCH2   0   0.199  -1.1723   0.0155   -7.2442
 13S  H41   H  HCH2   0   0.201   0.0195   1.5330   -5.6525
 13S  H42   H  HCH2   0   0.201   1.0456   0.2075   -5.1520
 13S  H51   H  HCH2   0   0.205  -0.9510  -1.0437   -4.3293
 13S  H52   H  HCH2   0   0.204  -1.9942   0.2600   -4.8563
 13S  H61   H  HCH2   0   0.208  -0.8431   1.8274   -3.2913
 13S  H62   H  HCH2   0   0.208   0.2155   0.5357   -2.7649
 13S  H71   H  HCH2   0   0.218  -1.7484  -0.7438   -1.9096
 13S  H72   H  HCH2   0   0.214  -2.8262   0.5162   -2.4746
 13S  H81   H  HCH2   0   0.234  -1.7130   2.1573   -0.9663
 13S  H82   H  HCH2   0   0.234  -0.6364   0.9076   -0.3777
 13S  H91   H  H      0   0.236  -3.7129   0.8127   -0.1159
 13S  H101  H  H      0   0.237  -3.3993   0.0177    2.0588
 13S  H111  H  H      0   0.249  -0.3323   0.2758    1.6092
 13S  H121  H  H      0   0.258  -2.0884  -0.6369    3.9383
 13S  H131  H  HCH1   0   0.241   0.2076  -1.7184    4.3480
 13S  H141  H  HCH2   0   0.228  -0.9732  -0.4132    6.0506
 13S  H142  H  HCH2   0   0.232  -0.2715   1.0803    5.4683
 13S  H151  H  HCH2   0   0.211   1.9742   0.3707    6.2067
 13S  H152  H  HCH2   0   0.220   1.3845  -1.2443    6.5774
 13S  H161  H  HCH2   0   0.211  -0.1069  -0.2794    8.3300
 13S  H162  H  HCH2   0   0.211   0.4553   1.3299    7.9350
 13S  H171  H  HCH2   0   0.212   2.7824   0.6797    8.5808
 13S  H172  H  HCH2   0   0.212   2.2268  -0.9325    8.9662
 13S  H181  H  HCH3   0   0.227   2.4004   0.4476   11.0377
 13S  H182  H  HCH3   0   0.216   1.2796   1.6282   10.3656
 13S  H183  H  HCH3   0   0.216   0.7209   0.0034   10.7495
 13S  H221  H  HOH1   0   0.472   2.7893  -0.3935    4.4141

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
 13S  C1   C2    single  1.539  0.020  1.539
 13S  C1   O19   deloc   1.247  0.020  1.247
 13S  C1   O20   deloc   1.250  0.020  1.250
 13S  C2   C3    single  1.520  0.020  1.520
 13S  C2   H21   single  0.970  0.020  1.090
 13S  C2   H22   single  0.970  0.020  1.090
 13S  C3   C4    single  1.524  0.020  1.524
 13S  C3   H31   single  0.970  0.020  1.090
 13S  C3   H32   single  0.970  0.020  1.090
 13S  C4   C5    single  1.524  0.020  1.524
 13S  C4   H41   single  0.970  0.020  1.090
 13S  C4   H42   single  0.970  0.020  1.090
 13S  C5   C6    single  1.524  0.020  1.524
 13S  C5   H51   single  0.970  0.020  1.090
 13S  C5   H52   single  0.970  0.020  1.090
 13S  C6   C7    single  1.523  0.020  1.523
 13S  C6   H61   single  0.970  0.020  1.090
 13S  C6   H62   single  0.970  0.020  1.090
 13S  C7   C8    single  1.530  0.020  1.530
 13S  C7   H71   single  0.970  0.020  1.090
 13S  C7   H72   single  0.970  0.020  1.090
 13S  C8   C9    single  1.494  0.020  1.494
 13S  C8   H81   single  0.970  0.020  1.090
 13S  C8   H82   single  0.970  0.020  1.090
 13S  C9   C10   double  1.339  0.020  1.339
 13S  C9   H91   single  0.930  0.020  1.080
 13S  C10  C11   single  1.454  0.020  1.454
 13S  C10  H101  single  0.930  0.020  1.080
 13S  C11  C12   double  1.336  0.020  1.336
 13S  C11  H111  single  0.930  0.020  1.080
 13S  C12  C13   single  1.498  0.020  1.498
 13S  C12  H121  single  0.930  0.020  1.080
 13S  C13  C14   single  1.530  0.020  1.530
 13S  C13  O21   single  1.422  0.020  1.422
 13S  C13  H131  single  0.970  0.020  1.090
 13S  C14  C15   single  1.525  0.020  1.525
 13S  C14  H141  single  0.970  0.020  1.090
 13S  C14  H142  single  0.970  0.020  1.090
 13S  C15  C16   single  1.525  0.020  1.525
 13S  C15  H151  single  0.970  0.020  1.090
 13S  C15  H152  single  0.970  0.020  1.090
 13S  C16  C17   single  1.523  0.020  1.523
 13S  C16  H161  single  0.970  0.020  1.090
 13S  C16  H162  single  0.970  0.020  1.090
 13S  C17  C18   single  1.522  0.020  1.522
 13S  C17  H171  single  0.970  0.020  1.090
 13S  C17  H172  single  0.970  0.020  1.090
 13S  C18  H181  single  0.970  0.020  1.090
 13S  C18  H182  single  0.970  0.020  1.090
 13S  C18  H183  single  0.970  0.020  1.090
 13S  O21  O22   single  1.406  0.020  1.406
 13S  O22  H221  single  0.850  0.020  0.980

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
 13S  O20   C1   O19   126.15  3.000
 13S  O20   C1   C2    115.82  3.000
 13S  O19   C1   C2    118.03  3.000
 13S  H22   C2   H21   104.73  3.000
 13S  H22   C2   C3    109.66  3.000
 13S  H21   C2   C3    109.46  3.000
 13S  H22   C2   C1    108.08  3.000
 13S  H21   C2   C1    107.91  3.000
 13S  C3    C2   C1    116.36  3.000
 13S  H32   C3   H31   105.94  3.000
 13S  H32   C3   C4    109.17  3.000
 13S  H31   C3   C4    109.27  3.000
 13S  H32   C3   C2    109.71  3.000
 13S  H31   C3   C2    109.87  3.000
 13S  C4    C3   C2    112.66  3.000
 13S  H42   C4   H41   105.88  3.000
 13S  H42   C4   C5    109.20  3.000
 13S  H41   C4   C5    109.21  3.000
 13S  H42   C4   C3    109.51  3.000
 13S  H41   C4   C3    109.28  3.000
 13S  C5    C4   C3    113.48  3.000
 13S  H52   C5   H51   106.06  3.000
 13S  H52   C5   C6    109.21  3.000
 13S  H51   C5   C6    109.41  3.000
 13S  H52   C5   C4    109.34  3.000
 13S  H51   C5   C4    109.40  3.000
 13S  C6    C5   C4    113.17  3.000
 13S  H62   C6   H61   106.09  3.000
 13S  H62   C6   C7    109.35  3.000
 13S  H61   C6   C7    109.27  3.000
 13S  H62   C6   C5    109.41  3.000
 13S  H61   C6   C5    109.22  3.000
 13S  C7    C6   C5    113.24  3.000
 13S  H72   C7   H71   106.25  3.000
 13S  H72   C7   C8    109.10  3.000
 13S  H71   C7   C8    109.34  3.000
 13S  H72   C7   C6    109.45  3.000
 13S  H71   C7   C6    109.67  3.000
 13S  C8    C7   C6    112.81  3.000
 13S  H82   C8   H81   106.31  3.000
 13S  H82   C8   C9    111.51  3.000
 13S  H81   C8   C9    108.81  3.000
 13S  H82   C8   C7    109.63  3.000
 13S  H81   C8   C7    108.37  3.000
 13S  C9    C8   C7    111.99  3.000
 13S  H91   C9   C10   117.06  3.000
 13S  H91   C9   C8    115.00  3.000
 13S  C10   C9   C8    127.94  3.000
 13S  H101  C10  C11   115.79  3.000
 13S  H101  C10  C9    117.61  3.000
 13S  C11   C10  C9    126.60  3.000
 13S  H111  C11  C12   119.84  3.000
 13S  H111  C11  C10   118.00  3.000
 13S  C12   C11  C10   122.16  3.000
 13S  H121  C12  C13   113.99  3.000
 13S  H121  C12  C11   118.90  3.000
 13S  C13   C12  C11   127.11  3.000
 13S  H131  C13  O21   108.89  3.000
 13S  H131  C13  C14   108.67  3.000
 13S  O21   C13  C14   112.69  3.000
 13S  H131  C13  C12   108.38  3.000
 13S  O21   C13  C12   108.12  3.000
 13S  C14   C13  C12   110.01  3.000
 13S  H142  C14  H141  106.12  3.000
 13S  H142  C14  C15   109.83  3.000
 13S  H141  C14  C15   108.59  3.000
 13S  H142  C14  C13   109.08  3.000
 13S  H141  C14  C13   106.87  3.000
 13S  C15   C14  C13   115.88  3.000
 13S  H152  C15  H151  106.84  3.000
 13S  H152  C15  C16   109.33  3.000
 13S  H151  C15  C16   108.15  3.000
 13S  H152  C15  C14   110.01  3.000
 13S  H151  C15  C14   110.50  3.000
 13S  C16   C15  C14   111.85  3.000
 13S  H162  C16  H161  106.00  3.000
 13S  H162  C16  C17   109.32  3.000
 13S  H161  C16  C17   109.37  3.000
 13S  H162  C16  C15   109.35  3.000
 13S  H161  C16  C15   109.18  3.000
 13S  C17   C16  C15   113.36  3.000
 13S  H172  C17  H171  106.02  3.000
 13S  H172  C17  C18   109.56  3.000
 13S  H171  C17  C18   109.65  3.000
 13S  H172  C17  C16   109.27  3.000
 13S  H171  C17  C16   109.37  3.000
 13S  C18   C17  C16   112.74  3.000
 13S  H183  C18  H182  107.49  3.000
 13S  H183  C18  H181  107.61  3.000
 13S  H182  C18  H181  107.63  3.000
 13S  H183  C18  C17   111.08  3.000
 13S  H182  C18  C17   111.23  3.000
 13S  H181  C18  C17   111.60  3.000
 13S  O22   O21  C13   110.11  3.000
 13S  H221  O22  O21   103.20  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
 13S  Var_01  C11   C10  C9   C8      1.32   0.0  2
 13S  Var_02  C13   C12  C11  C10  -178.73   0.0  2
 13S  Var_03  C4    C3   C2   C1   -178.31  30.0  3
 13S  Var_04  C5    C4   C3   C2    179.89  30.0  3
 13S  Var_05  O19   C1   C2   C3      0.91  30.0  2
 13S  Var_06  C6    C5   C4   C3   -178.46  30.0  3
 13S  Var_07  C7    C6   C5   C4   -179.59  30.0  3
 13S  Var_08  C8    C7   C6   C5   -177.92  30.0  3
 13S  Var_09  C9    C8   C7   C6    177.72  30.0  3
 13S  Var_10  C10   C9   C8   C7    125.44  30.0  3
 13S  Var_11  C12   C11  C10  C9    179.59  30.0  2
 13S  Var_12  C16   C15  C14  C13  -170.11  30.0  3
 13S  Var_13  C17   C16  C15  C14  -179.02  30.0  3
 13S  Var_14  C18   C17  C16  C15  -179.43  30.0  3
 13S  Var_15  H181  C18  C17  C16   179.86  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
 13S  chir_01  C13  C12  C14  O21  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
 13S  plan-1  C1    0.020
 13S  plan-1  C2    0.020
 13S  plan-1  O19   0.020
 13S  plan-1  O20   0.020
 13S  plan-2  C8    0.020
 13S  plan-2  C9    0.020
 13S  plan-2  C10   0.020
 13S  plan-2  C11   0.020
 13S  plan-2  H91   0.020
 13S  plan-2  H101  0.020
 13S  plan-3  C10   0.020
 13S  plan-3  C11   0.020
 13S  plan-3  C12   0.020
 13S  plan-3  C13   0.020
 13S  plan-3  H111  0.020
 13S  plan-3  H121  0.020

