# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:02:30 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  54  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   0.549   1.1779  -0.7594   -8.7686
 13S  C2    C  CH2   0  -0.579   1.0310   0.1481   -7.5794
 13S  C3    C  CH2   0  -0.418   0.1050  -0.3904   -6.5019
 13S  C4    C  CH2   0  -0.414  -0.0039   0.5655   -5.3204
 13S  C5    C  CH2   0  -0.413  -0.9153   0.0423   -4.2179
 13S  C6    C  CH2   0  -0.414  -1.0231   0.9920   -3.0315
 13S  C7    C  CH2   0  -0.414  -1.9477   0.4757   -1.9368
 13S  C8    C  CH2   0  -0.492  -2.0300   1.4219   -0.7358
 13S  C9    C  C1    0  -0.220  -3.0218   0.9505    0.2783
 13S  C10   C  C1    0  -0.246  -2.7726   0.4517    1.4954
 13S  C11   C  C1    0  -0.252  -1.4641   0.2783    2.1051
 13S  C12   C  C1    0  -0.282  -1.3078  -0.2587    3.3186
 13S  C13   C  CH1   0   0.042  -0.0177  -0.4957    4.0427
 13S  C14   C  CH2   0  -0.445  -0.1002   0.0481    5.4707
 13S  C15   C  CH2   0  -0.441   1.1110  -0.2312    6.3549
 13S  C16   C  CH2   0  -0.405   0.8522   0.1263    7.8134
 13S  C17   C  CH2   0  -0.419   2.0472  -0.1470    8.7183
 13S  C18   C  CH3   0  -0.663   1.7775   0.2072   10.1738
 13S  O19   O  O     0  -0.447   0.5873  -1.7987   -8.9307
 13S  O20   O  OH1   0  -0.598   2.0504  -0.2807   -9.6518
 13S  O21   O  O2    0  -0.311   1.0297   0.0986    3.2866
 13S  O22   O  OH1   0  -0.452   2.2111  -0.6508    3.4271
 13S  H21   H  HCH2  0   0.276   0.6756   1.1193   -7.9403
 13S  H22   H  HCH2  0   0.273   2.0276   0.3392   -7.1690
 13S  H31   H  HCH2  0   0.224   0.4694  -1.3599   -6.1513
 13S  H32   H  HCH2  0   0.225  -0.8899  -0.5662   -6.9194
 13S  H41   H  HCH2  0   0.213  -0.3745   1.5361   -5.6681
 13S  H42   H  HCH2  0   0.212   0.9940   0.7521   -4.9085
 13S  H51   H  HCH2  0   0.210  -0.5463  -0.9298   -3.8727
 13S  H52   H  HCH2  0   0.210  -1.9143  -0.1409   -4.6288
 13S  H61   H  HCH2  0   0.211  -1.3818   1.9677   -3.3776
 13S  H62   H  HCH2  0   0.211  -0.0253   1.1660   -2.6136
 13S  H71   H  HCH2  0   0.218  -1.6042  -0.5059   -1.5952
 13S  H72   H  HCH2  0   0.217  -2.9503   0.3222   -2.3498
 13S  H81   H  HCH2  0   0.234  -2.3319   2.4130   -1.0909
 13S  H82   H  HCH2  0   0.234  -1.0349   1.5412   -0.3017
 13S  H91   H  H     0   0.238  -4.0607   0.9998   -0.0350
 13S  H101  H  H     0   0.237  -3.6213   0.1359    2.0955
 13S  H111  H  H     0   0.249  -0.5958   0.5942    1.5390
 13S  H121  H  H     0   0.259  -2.1884  -0.5740    3.8729
 13S  H131  H  HCH1  0   0.240   0.1499  -1.5805    4.0915
 13S  H141  H  HCH2  0   0.228  -0.9812  -0.4074    5.9346
 13S  H142  H  HCH2  0   0.233  -0.2983   1.1239    5.4343
 13S  H151  H  HCH2  0   0.210   1.9800   0.3415    6.0136
 13S  H152  H  HCH2  0   0.220   1.3843  -1.2894    6.2853
 13S  H161  H  HCH2  0   0.211  -0.0141  -0.4378    8.1765
 13S  H162  H  HCH2  0   0.211   0.5763   1.1841    7.8866
 13S  H171  H  HCH2  0   0.212   2.9128   0.4167    8.3561
 13S  H172  H  HCH2  0   0.212   2.3224  -1.2035    8.6429
 13S  H181  H  HCH3  0   0.227   2.6421  -0.0012   10.8048
 13S  H182  H  HCH3  0   0.216   1.5341   1.2657   10.2845
 13S  H183  H  HCH3  0   0.216   0.9358  -0.3656   10.5677
 13S  H201  H  HOH1  0   0.478   2.1158  -0.8802  -10.4098
 13S  H221  H  HOH1  0   0.472   2.6970  -0.1682    4.1101

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  1.503  0.020  1.503
 13S  C1   O19   double  1.206  0.020  1.206
 13S  C1   O20   single  1.331  0.020  1.331
 13S  C2   C3    single  1.519  0.020  1.519
 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  1.523  0.020  1.523
 13S  C4   H41   single  0.970  0.020  1.090
 13S  C4   H42   single  0.970  0.020  1.090
 13S  C5   C6    single  1.523  0.020  1.523
 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  1.531  0.020  1.531
 13S  C7   H71   single  0.970  0.020  1.090
 13S  C7   H72   single  0.970  0.020  1.090
 13S  C8   C9    single  1.495  0.020  1.495
 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  1.524  0.020  1.524
 13S  C15  H151  single  0.970  0.020  1.090
 13S  C15  H152  single  0.970  0.020  1.090
 13S  C16  C17   single  1.524  0.020  1.524
 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  O20  H201  single  0.850  0.020  0.980
 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   122.81  3.000
 13S  O20   C1   C2    111.84  3.000
 13S  O19   C1   C2    125.36  3.000
 13S  H22   C2   H21   105.31  3.000
 13S  H22   C2   C3    110.54  3.000
 13S  H21   C2   C3    110.49  3.000
 13S  H22   C2   C1    108.25  3.000
 13S  H21   C2   C1    107.84  3.000
 13S  C3    C2   C1    113.99  3.000
 13S  H32   C3   H31   106.45  3.000
 13S  H32   C3   C4    109.39  3.000
 13S  H31   C3   C4    109.36  3.000
 13S  H32   C3   C2    109.93  3.000
 13S  H31   C3   C2    109.78  3.000
 13S  C4    C3   C2    111.79  3.000
 13S  H42   C4   H41   106.05  3.000
 13S  H42   C4   C5    109.35  3.000
 13S  H41   C4   C5    109.37  3.000
 13S  H42   C4   C3    109.47  3.000
 13S  H41   C4   C3    109.50  3.000
 13S  C5    C4   C3    112.87  3.000
 13S  H52   C5   H51   106.08  3.000
 13S  H52   C5   C6    109.38  3.000
 13S  H51   C5   C6    109.36  3.000
 13S  H52   C5   C4    109.36  3.000
 13S  H51   C5   C4    109.35  3.000
 13S  C6    C5   C4    113.08  3.000
 13S  H62   C6   H61   106.09  3.000
 13S  H62   C6   C7    109.43  3.000
 13S  H61   C6   C7    109.28  3.000
 13S  H62   C6   C5    109.37  3.000
 13S  H61   C6   C5    109.40  3.000
 13S  C7    C6   C5    113.04  3.000
 13S  H72   C7   H71   106.22  3.000
 13S  H72   C7   C8    109.46  3.000
 13S  H71   C7   C8    109.04  3.000
 13S  H72   C7   C6    109.41  3.000
 13S  H71   C7   C6    109.74  3.000
 13S  C8    C7   C6    112.76  3.000
 13S  H82   C8   H81   106.33  3.000
 13S  H82   C8   C9    111.67  3.000
 13S  H81   C8   C9    108.81  3.000
 13S  H82   C8   C7    109.29  3.000
 13S  H81   C8   C7    108.65  3.000
 13S  C9    C8   C7    111.90  3.000
 13S  H91   C9   C10   117.20  3.000
 13S  H91   C9   C8    115.13  3.000
 13S  C10   C9   C8    127.65  3.000
 13S  H101  C10  C11   115.89  3.000
 13S  H101  C10  C9    117.72  3.000
 13S  C11   C10  C9    126.39  3.000
 13S  H111  C11  C12   119.86  3.000
 13S  H111  C11  C10   117.86  3.000
 13S  C12   C11  C10   122.28  3.000
 13S  H121  C12  C13   113.90  3.000
 13S  H121  C12  C11   119.00  3.000
 13S  C13   C12  C11   127.10  3.000
 13S  H131  C13  O21   108.90  3.000
 13S  H131  C13  C14   108.52  3.000
 13S  O21   C13  C14   112.79  3.000
 13S  H131  C13  C12   108.00  3.000
 13S  O21   C13  C12   108.13  3.000
 13S  C14   C13  C12   110.39  3.000
 13S  H142  C14  H141  106.10  3.000
 13S  H142  C14  C15   110.05  3.000
 13S  H141  C14  C15   108.49  3.000
 13S  H142  C14  C13   109.15  3.000
 13S  H141  C14  C13   106.91  3.000
 13S  C15   C14  C13   115.66  3.000
 13S  H152  C15  H151  106.71  3.000
 13S  H152  C15  C16   109.26  3.000
 13S  H151  C15  C16   108.08  3.000
 13S  H152  C15  C14   109.77  3.000
 13S  H151  C15  C14   110.71  3.000
 13S  C16   C15  C14   112.15  3.000
 13S  H162  C16  H161  106.01  3.000
 13S  H162  C16  C17   109.33  3.000
 13S  H161  C16  C17   109.33  3.000
 13S  H162  C16  C15   109.47  3.000
 13S  H161  C16  C15   109.31  3.000
 13S  C17   C16  C15   113.15  3.000
 13S  H172  C17  H171  105.99  3.000
 13S  H172  C17  C18   109.57  3.000
 13S  H171  C17  C18   109.68  3.000
 13S  H172  C17  C16   109.24  3.000
 13S  H171  C17  C16   109.35  3.000
 13S  C18   C17  C16   112.78  3.000
 13S  H183  C18  H182  107.47  3.000
 13S  H183  C18  H181  107.59  3.000
 13S  H182  C18  H181  107.66  3.000
 13S  H183  C18  C17   111.08  3.000
 13S  H182  C18  C17   111.23  3.000
 13S  H181  C18  C17   111.62  3.000
 13S  H201  O20  C1    109.94  3.000
 13S  O22   O21  C13   110.06  3.000
 13S  H221  O22  O21   103.11  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  CONST_01  H201  O20  C1   C2    180.00   0.0  0
 13S  Var_01    C11   C10  C9   C8      0.97   0.0  2
 13S  Var_02    C13   C12  C11  C10   179.55   0.0  2
 13S  Var_03    C4    C3   C2   C1    179.83  30.0  3
 13S  Var_04    C5    C4   C3   C2   -179.37  30.0  3
 13S  Var_05    O19   C1   C2   C3      3.48  30.0  2
 13S  Var_06    C6    C5   C4   C3    179.76  30.0  3
 13S  Var_07    C7    C6   C5   C4    179.31  30.0  3
 13S  Var_08    C8    C7   C6   C5    178.88  30.0  3
 13S  Var_09    C9    C8   C7   C6    175.56  30.0  3
 13S  Var_10    C10   C9   C8   C7    109.48  30.0  3
 13S  Var_11    C12   C11  C10  C9   -178.42  30.0  2
 13S  Var_12    C16   C15  C14  C13  -170.10  30.0  3
 13S  Var_13    C17   C16  C15  C14   179.86  30.0  3
 13S  Var_14    C18   C17  C16  C15  -179.75  30.0  3
 13S  Var_15    H181  C18  C17  C16   179.66  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-1  H201  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

