# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:10:03 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (9Z,11E,13R)-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
 13R  13R  '(9Z,11E,13R)-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_13R
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
 13R  C1    C  C     0   0.549   0.9507  -0.2709   -9.1289
 13R  C2    C  CH2   0  -0.579   1.0792   0.3744   -7.7776
 13R  C3    C  CH2   0  -0.417   0.0593  -0.1118   -6.7611
 13R  C4    C  CH2   0  -0.413   0.2240   0.5871   -5.4171
 13R  C5    C  CH2   0  -0.412  -0.7885   0.1217   -4.3783
 13R  C6    C  CH2   0  -0.412  -0.6453   0.8391   -3.0417
 13R  C7    C  CH2   0  -0.416  -1.6697   0.3847   -2.0100
 13R  C8    C  CH2   0  -0.488  -1.5538   1.1394   -0.6836
 13R  C9    C  C1    0  -0.205  -2.6377   0.7530    0.2683
 13R  C10   C  C1    0  -0.257  -2.5163   0.2858    1.5169
 13R  C11   C  C1    0  -0.248  -1.2785   0.0766    2.2479
 13R  C12   C  C1    0  -0.255  -1.2406  -0.3852    3.5016
 13R  C13   C  CH1   0   0.008   0.0194  -0.5824    4.2844
 13R  C14   C  CH2   0  -0.466  -0.0765   0.0559    5.6646
 13R  C15   C  CH2   0  -0.417   1.1962  -0.0269    6.5003
 13R  C16   C  CH2   0  -0.407   1.0432   0.6816    7.8410
 13R  C17   C  CH2   0  -0.419   2.2998   0.6286    8.7007
 13R  C18   C  CH3   0  -0.662   2.1253   1.3268   10.0423
 13R  O19   O  O     0  -0.447   0.1312  -1.1026   -9.4314
 13R  O20   O  OH1   0  -0.599   1.8631   0.1860   -9.9833
 13R  O21   O  O2    0  -0.304   0.2547  -1.9727    4.5114
 13R  O22   O  OH1   0  -0.455   0.5712  -2.5953    3.2924
 13R  H21   H  HCH2  0   0.274   1.0010   1.4583   -7.9122
 13R  H22   H  HCH2  0   0.275   2.0976   0.1999   -7.4155
 13R  H31   H  HCH2  0   0.224   0.1578  -1.1919   -6.6239
 13R  H32   H  HCH2  0   0.224  -0.9516   0.0637   -7.1385
 13R  H41   H  HCH2  0   0.212   0.1284   1.6694   -5.5568
 13R  H42   H  HCH2  0   0.212   1.2379   0.4169   -5.0391
 13R  H51   H  HCH2  0   0.210  -0.6831  -0.9579   -4.2253
 13R  H52   H  HCH2  0   0.209  -1.8018   0.2780   -4.7637
 13R  H61   H  HCH2  0   0.210  -0.7459   1.9186   -3.1990
 13R  H62   H  HCH2  0   0.211   0.3649   0.6803   -2.6493
 13R  H71   H  HCH2  0   0.220  -1.5589  -0.6885   -1.8266
 13R  H72   H  HCH2  0   0.216  -2.6781   0.5248   -2.4131
 13R  H81   H  HCH2  0   0.236  -1.6336   2.2132   -0.8889
 13R  H82   H  HCH2  0   0.234  -0.5621   0.9802   -0.2554
 13R  H91   H  H     0   0.241  -3.6466   0.8610   -0.1203
 13R  H101  H  H     0   0.242  -3.4274   0.0435    2.0561
 13R  H111  H  H     0   0.249  -0.3417   0.3214    1.7559
 13R  H121  H  H     0   0.250  -2.1703  -0.6394    4.0077
 13R  H131  H  HCH1  0   0.228   0.8711  -0.1528    3.7403
 13R  H141  H  HCH2  0   0.230  -0.9152  -0.3890    6.2108
 13R  H142  H  HCH2  0   0.242  -0.3400   1.1064    5.5119
 13R  H151  H  HCH2  0   0.213   2.0259   0.4215    5.9436
 13R  H152  H  HCH2  0   0.221   1.4693  -1.0711    6.6734
 13R  H161  H  HCH2  0   0.209   0.2095   0.2334    8.3928
 13R  H162  H  HCH2  0   0.208   0.7658   1.7280    7.6719
 13R  H171  H  HCH2  0   0.211   3.1310   1.0865    8.1556
 13R  H172  H  HCH2  0   0.211   2.5828  -0.4157    8.8647
 13R  H181  H  HCH3  0   0.226   3.0376   1.2856   10.6384
 13R  H182  H  HCH3  0   0.216   1.8661   2.3791    9.9101
 13R  H183  H  HCH3  0   0.216   1.3279   0.8645   10.6277
 13R  H201  H  HOH1  0   0.478   1.7563  -0.2468  -10.8433
 13R  H221  H  HOH1  0   0.466  -0.2961  -2.7802    2.9024

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
 13R  C1   C2    single  1.503  0.020  1.503
 13R  C1   O19   double  1.206  0.020  1.206
 13R  C1   O20   single  1.331  0.020  1.331
 13R  C2   C3    single  1.520  0.020  1.520
 13R  C2   H21   single  0.970  0.020  1.090
 13R  C2   H22   single  0.970  0.020  1.090
 13R  C3   C4    single  1.524  0.020  1.524
 13R  C3   H31   single  0.970  0.020  1.090
 13R  C3   H32   single  0.970  0.020  1.090
 13R  C4   C5    single  1.523  0.020  1.523
 13R  C4   H41   single  0.970  0.020  1.090
 13R  C4   H42   single  0.970  0.020  1.090
 13R  C5   C6    single  1.524  0.020  1.524
 13R  C5   H51   single  0.970  0.020  1.090
 13R  C5   H52   single  0.970  0.020  1.090
 13R  C6   C7    single  1.523  0.020  1.523
 13R  C6   H61   single  0.970  0.020  1.090
 13R  C6   H62   single  0.970  0.020  1.090
 13R  C7   C8    single  1.530  0.020  1.530
 13R  C7   H71   single  0.970  0.020  1.090
 13R  C7   H72   single  0.970  0.020  1.090
 13R  C8   C9    single  1.493  0.020  1.493
 13R  C8   H81   single  0.970  0.020  1.090
 13R  C8   H82   single  0.970  0.020  1.090
 13R  C9   C10   double  1.339  0.020  1.339
 13R  C9   H91   single  0.930  0.020  1.080
 13R  C10  C11   single  1.453  0.020  1.453
 13R  C10  H101  single  0.930  0.020  1.080
 13R  C11  C12   double  1.337  0.020  1.337
 13R  C11  H111  single  0.930  0.020  1.080
 13R  C12  C13   single  1.496  0.020  1.496
 13R  C12  H121  single  0.930  0.020  1.080
 13R  C13  C14   single  1.524  0.020  1.524
 13R  C13  O21   single  1.428  0.020  1.428
 13R  C13  H131  single  0.970  0.020  1.090
 13R  C14  C15   single  1.525  0.020  1.525
 13R  C14  H141  single  0.970  0.020  1.090
 13R  C14  H142  single  0.970  0.020  1.090
 13R  C15  C16   single  1.524  0.020  1.524
 13R  C15  H151  single  0.970  0.020  1.090
 13R  C15  H152  single  0.970  0.020  1.090
 13R  C16  C17   single  1.523  0.020  1.523
 13R  C16  H161  single  0.970  0.020  1.090
 13R  C16  H162  single  0.970  0.020  1.090
 13R  C17  C18   single  1.522  0.020  1.522
 13R  C17  H171  single  0.970  0.020  1.090
 13R  C17  H172  single  0.970  0.020  1.090
 13R  C18  H181  single  0.970  0.020  1.090
 13R  C18  H182  single  0.970  0.020  1.090
 13R  C18  H183  single  0.970  0.020  1.090
 13R  O20  H201  single  0.850  0.020  0.980
 13R  O21  O22   single  1.405  0.020  1.405
 13R  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
 13R  O20   C1   O19   122.79  3.000
 13R  O20   C1   C2    111.79  3.000
 13R  O19   C1   C2    125.42  3.000
 13R  H22   C2   H21   105.36  3.000
 13R  H22   C2   C3    110.61  3.000
 13R  H21   C2   C3    110.54  3.000
 13R  H22   C2   C1    107.97  3.000
 13R  H21   C2   C1    107.96  3.000
 13R  C3    C2   C1    113.99  3.000
 13R  H32   C3   H31   106.57  3.000
 13R  H32   C3   C4    109.32  3.000
 13R  H31   C3   C4    109.43  3.000
 13R  H32   C3   C2    109.78  3.000
 13R  H31   C3   C2    109.85  3.000
 13R  C4    C3   C2    111.76  3.000
 13R  H42   C4   H41   106.17  3.000
 13R  H42   C4   C5    109.41  3.000
 13R  H41   C4   C5    109.32  3.000
 13R  H42   C4   C3    109.46  3.000
 13R  H41   C4   C3    109.34  3.000
 13R  C5    C4   C3    112.92  3.000
 13R  H52   C5   H51   106.19  3.000
 13R  H52   C5   C6    109.17  3.000
 13R  H51   C5   C6    109.42  3.000
 13R  H52   C5   C4    109.35  3.000
 13R  H51   C5   C4    109.42  3.000
 13R  C6    C5   C4    113.07  3.000
 13R  H62   C6   H61   106.20  3.000
 13R  H62   C6   C7    109.54  3.000
 13R  H61   C6   C7    109.23  3.000
 13R  H62   C6   C5    109.43  3.000
 13R  H61   C6   C5    109.23  3.000
 13R  C7    C6   C5    112.98  3.000
 13R  H72   C7   H71   106.29  3.000
 13R  H72   C7   C8    109.01  3.000
 13R  H71   C7   C8    109.31  3.000
 13R  H72   C7   C6    109.38  3.000
 13R  H71   C7   C6    109.75  3.000
 13R  C8    C7   C6    112.89  3.000
 13R  H82   C8   H81   106.41  3.000
 13R  H82   C8   C9    111.81  3.000
 13R  H81   C8   C9    108.66  3.000
 13R  H82   C8   C7    109.68  3.000
 13R  H81   C8   C7    108.37  3.000
 13R  C9    C8   C7    111.70  3.000
 13R  H91   C9   C10   116.90  3.000
 13R  H91   C9   C8    114.85  3.000
 13R  C10   C9   C8    128.24  3.000
 13R  H101  C10  C11   115.65  3.000
 13R  H101  C10  C9    117.71  3.000
 13R  C11   C10  C9    126.64  3.000
 13R  H111  C11  C12   118.58  3.000
 13R  H111  C11  C10   118.33  3.000
 13R  C12   C11  C10   123.08  3.000
 13R  H121  C12  C13   116.43  3.000
 13R  H121  C12  C11   119.51  3.000
 13R  C13   C12  C11   124.06  3.000
 13R  H131  C13  O21   109.38  3.000
 13R  H131  C13  C14   109.49  3.000
 13R  O21   C13  C14   105.92  3.000
 13R  H131  C13  C12   110.02  3.000
 13R  O21   C13  C12   110.50  3.000
 13R  C14   C13  C12   111.45  3.000
 13R  H142  C14  H141  105.98  3.000
 13R  H142  C14  C15   109.26  3.000
 13R  H141  C14  C15   110.10  3.000
 13R  H142  C14  C13   106.92  3.000
 13R  H141  C14  C13   109.25  3.000
 13R  C15   C14  C13   114.91  3.000
 13R  H152  C15  H151  106.40  3.000
 13R  H152  C15  C16   109.26  3.000
 13R  H151  C15  C16   109.44  3.000
 13R  H152  C15  C14   110.32  3.000
 13R  H151  C15  C14   109.36  3.000
 13R  C16   C15  C14   111.91  3.000
 13R  H162  C16  H161  106.01  3.000
 13R  H162  C16  C17   109.21  3.000
 13R  H161  C16  C17   109.22  3.000
 13R  H162  C16  C15   109.49  3.000
 13R  H161  C16  C15   109.22  3.000
 13R  C17   C16  C15   113.42  3.000
 13R  H172  C17  H171  106.11  3.000
 13R  H172  C17  C18   109.58  3.000
 13R  H171  C17  C18   109.52  3.000
 13R  H172  C17  C16   109.33  3.000
 13R  H171  C17  C16   109.32  3.000
 13R  C18   C17  C16   112.75  3.000
 13R  H183  C18  H182  107.43  3.000
 13R  H183  C18  H181  107.56  3.000
 13R  H182  C18  H181  107.53  3.000
 13R  H183  C18  C17   111.23  3.000
 13R  H182  C18  C17   111.25  3.000
 13R  H181  C18  C17   111.62  3.000
 13R  H201  O20  C1    109.93  3.000
 13R  O22   O21  C13   109.30  3.000
 13R  H221  O22  O21   103.43  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
 13R  CONST_01  H201  O20  C1   C2    180.00   0.0  0
 13R  Var_01    C11   C10  C9   C8      1.57   0.0  2
 13R  Var_02    C13   C12  C11  C10  -178.70   0.0  2
 13R  Var_03    C4    C3   C2   C1   -179.27  30.0  3
 13R  Var_04    C5    C4   C3   C2    179.86  30.0  3
 13R  Var_05    O19   C1   C2   C3      0.03  30.0  2
 13R  Var_06    C6    C5   C4   C3   -178.81  30.0  3
 13R  Var_07    C7    C6   C5   C4    179.28  30.0  3
 13R  Var_08    C8    C7   C6   C5   -178.10  30.0  3
 13R  Var_09    C9    C8   C7   C6    175.38  30.0  3
 13R  Var_10    C10   C9   C8   C7    124.59  30.0  3
 13R  Var_11    C12   C11  C10  C9    179.43  30.0  2
 13R  Var_12    C16   C15  C14  C13   177.62  30.0  3
 13R  Var_13    C17   C16  C15  C14  -179.58  30.0  3
 13R  Var_14    C18   C17  C16  C15  -179.34  30.0  3
 13R  Var_15    H181  C18  C17  C16  -179.49  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
 13R  chir_01  C13  C12  C14  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
 13R  plan-1  C1    0.020
 13R  plan-1  C2    0.020
 13R  plan-1  O19   0.020
 13R  plan-1  O20   0.020
 13R  plan-1  H201  0.020
 13R  plan-2  C8    0.020
 13R  plan-2  C9    0.020
 13R  plan-2  C10   0.020
 13R  plan-2  C11   0.020
 13R  plan-2  H91   0.020
 13R  plan-2  H101  0.020
 13R  plan-3  C10   0.020
 13R  plan-3  C11   0.020
 13R  plan-3  C12   0.020
 13R  plan-3  C13   0.020
 13R  plan-3  H111  0.020
 13R  plan-3  H121  0.020

