# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 10:11:04 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  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_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   0.409   1.5196  -0.2345  -8.6905
 13R  C2    C  CH2    0  -0.580   1.2507   0.5882  -7.4183
 13R  C3    C  CH2    0  -0.403   0.4168  -0.0911  -6.3439
 13R  C4    C  CH2    0  -0.409   0.2144   0.7869  -5.1147
 13R  C5    C  CH2    0  -0.411  -0.6636   0.1434  -4.0483
 13R  C6    C  CH2    0  -0.413  -0.8433   1.0208  -2.8158
 13R  C7    C  CH2    0  -0.414  -1.8205   0.4447  -1.7993
 13R  C8    C  CH2    0  -0.493  -1.9528   1.3229  -0.5520
 13R  C9    C  C1     0  -0.215  -3.0608   0.8758   0.3453
 13R  C10   C  C1     0  -0.251  -2.9567   0.2940   1.5465
 13R  C11   C  C1     0  -0.259  -1.7234  -0.0426   2.2375
 13R  C12   C  C1     0  -0.222  -1.6889  -0.5848   3.4572
 13R  C13   C  CH1    0   0.008  -0.4240  -0.8967   4.1908
 13R  C14   C  CH2    0  -0.464  -0.2379   0.0089   5.4060
 13R  C15   C  CH2    0  -0.418   1.0705  -0.2105   6.1587
 13R  C16   C  CH2    0  -0.409   1.2628   0.7941   7.2884
 13R  C17   C  CH2    0  -0.419   2.5689   0.5965   8.0480
 13R  C18   C  CH3    0  -0.663   2.7509   1.6016   9.1770
 13R  O19   O  O      0  -0.611   1.1976  -1.4392  -8.6847
 13R  O20   O  OC    -1  -0.634   2.0621   0.3781  -9.6352
 13R  O21   O  O2     0  -0.308  -0.4378  -2.2249   4.7021
 13R  O22   O  OH1    0  -0.454  -0.4788  -3.1350   3.6302
 13R  H21   H  HCH2   0   0.212   0.7791   1.5343  -7.7065
 13R  H22   H  HCH2   0   0.218   2.2210   0.8772  -6.9949
 13R  H31   H  HCH2   0   0.201   0.8923  -1.0294  -6.0449
 13R  H32   H  HCH2   0   0.199  -0.5608  -0.3668  -6.7524
 13R  H41   H  HCH2   0   0.202  -0.2338   1.7409  -5.4154
 13R  H42   H  HCH2   0   0.202   1.1894   1.0382  -4.6809
 13R  H51   H  HCH2   0   0.207  -0.2342  -0.8202  -3.7532
 13R  H52   H  HCH2   0   0.205  -1.6454  -0.0826  -4.4799
 13R  H61   H  HCH2   0   0.209  -1.1968   2.0108  -3.1256
 13R  H62   H  HCH2   0   0.210   0.1298   1.1831  -2.3391
 13R  H71   H  HCH2   0   0.218  -1.5030  -0.5589  -1.5000
 13R  H72   H  HCH2   0   0.217  -2.8017   0.3269  -2.2711
 13R  H81   H  HCH2   0   0.234  -2.1602   2.3501  -0.8707
 13R  H82   H  HCH2   0   0.234  -0.9961   1.3521  -0.0257
 13R  H91   H  H      0   0.239  -4.0624   1.0376  -0.0423
 13R  H101  H  H      0   0.239  -3.8747   0.0345   2.0658
 13R  H111  H  H      0   0.246  -0.7828   0.1502   1.7291
 13R  H121  H  H      0   0.247  -2.6185  -0.7872   3.9860
 13R  H131  H  HCH1   0   0.225   0.4372  -0.7668   3.5196
 13R  H141  H  HCH2   0   0.230  -1.0904  -0.1052   6.0839
 13R  H142  H  HCH2   0   0.240  -0.2764   1.0386   5.0404
 13R  H151  H  HCH2   0   0.213   1.9092  -0.1313   5.4586
 13R  H152  H  HCH2   0   0.221   1.1076  -1.2227   6.5697
 13R  H161  H  HCH2   0   0.209   0.4219   0.7202   7.9867
 13R  H162  H  HCH2   0   0.208   1.2305   1.8113   6.8819
 13R  H171  H  HCH2   0   0.211   3.4085   0.6726   7.3500
 13R  H172  H  HCH2   0   0.211   2.6026  -0.4203   8.4517
 13R  H181  H  HCH3   0   0.226   3.6917   1.4467   9.7066
 13R  H182  H  HCH3   0   0.216   2.7518   2.6246   8.7957
 13R  H183  H  HCH3   0   0.216   1.9429   1.5237   9.9065
 13R  H221  H  HOH1   0   0.469   0.4534  -3.3719   3.5220

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  1.539  0.020  1.539
 13R  C1   O19   deloc   1.247  0.020  1.247
 13R  C1   O20   deloc   1.250  0.020  1.250
 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  1.524  0.020  1.524
 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  1.531  0.020  1.531
 13R  C7   H71   single  0.970  0.020  1.090
 13R  C7   H72   single  0.970  0.020  1.090
 13R  C8   C9    single  1.494  0.020  1.494
 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  1.335  0.020  1.335
 13R  C11  H111  single  0.930  0.020  1.080
 13R  C12  C13   single  1.495  0.020  1.495
 13R  C12  H121  single  0.930  0.020  1.080
 13R  C13  C14   single  1.527  0.020  1.527
 13R  C13  O21   single  1.423  0.020  1.423
 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  1.524  0.020  1.524
 13R  C16  H161  single  0.970  0.020  1.090
 13R  C16  H162  single  0.970  0.020  1.090
 13R  C17  C18   single  1.523  0.020  1.523
 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  O21  O22   single  1.407  0.020  1.407
 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   126.09  3.000
 13R  O20   C1   C2    116.03  3.000
 13R  O19   C1   C2    117.88  3.000
 13R  H22   C2   H21   104.75  3.000
 13R  H22   C2   C3    109.27  3.000
 13R  H21   C2   C3    109.61  3.000
 13R  H22   C2   C1    107.77  3.000
 13R  H21   C2   C1    108.63  3.000
 13R  C3    C2   C1    116.19  3.000
 13R  H32   C3   H31   105.92  3.000
 13R  H32   C3   C4    109.11  3.000
 13R  H31   C3   C4    109.36  3.000
 13R  H32   C3   C2    109.79  3.000
 13R  H31   C3   C2    109.77  3.000
 13R  C4    C3   C2    112.67  3.000
 13R  H42   C4   H41   105.82  3.000
 13R  H42   C4   C5    109.41  3.000
 13R  H41   C4   C5    108.90  3.000
 13R  H42   C4   C3    109.45  3.000
 13R  H41   C4   C3    109.54  3.000
 13R  C5    C4   C3    113.43  3.000
 13R  H52   C5   H51   106.02  3.000
 13R  H52   C5   C6    109.37  3.000
 13R  H51   C5   C6    109.56  3.000
 13R  H52   C5   C4    109.13  3.000
 13R  H51   C5   C4    109.52  3.000
 13R  C6    C5   C4    113.01  3.000
 13R  H62   C6   H61   106.00  3.000
 13R  H62   C6   C7    109.60  3.000
 13R  H61   C6   C7    108.87  3.000
 13R  H62   C6   C5    109.42  3.000
 13R  H61   C6   C5    109.25  3.000
 13R  C7    C6   C5    113.43  3.000
 13R  H72   C7   H71   106.20  3.000
 13R  H72   C7   C8    109.59  3.000
 13R  H71   C7   C8    109.16  3.000
 13R  H72   C7   C6    109.15  3.000
 13R  H71   C7   C6    110.08  3.000
 13R  C8    C7   C6    112.47  3.000
 13R  H82   C8   H81   106.32  3.000
 13R  H82   C8   C9    111.60  3.000
 13R  H81   C8   C9    108.36  3.000
 13R  H82   C8   C7    109.40  3.000
 13R  H81   C8   C7    108.49  3.000
 13R  C9    C8   C7    112.44  3.000
 13R  H91   C9   C10   117.17  3.000
 13R  H91   C9   C8    115.15  3.000
 13R  C10   C9   C8    127.68  3.000
 13R  H101  C10  C11   115.76  3.000
 13R  H101  C10  C9    117.85  3.000
 13R  C11   C10  C9    126.39  3.000
 13R  H111  C11  C12   118.49  3.000
 13R  H111  C11  C10   118.11  3.000
 13R  C12   C11  C10   123.39  3.000
 13R  H121  C12  C13   116.45  3.000
 13R  H121  C12  C11   119.81  3.000
 13R  C13   C12  C11   123.70  3.000
 13R  H131  C13  O21   109.70  3.000
 13R  H131  C13  C14   108.68  3.000
 13R  O21   C13  C14   105.59  3.000
 13R  H131  C13  C12   109.78  3.000
 13R  O21   C13  C12   111.27  3.000
 13R  C14   C13  C12   111.71  3.000
 13R  H142  C14  H141  106.12  3.000
 13R  H142  C14  C15   109.31  3.000
 13R  H141  C14  C15   110.32  3.000
 13R  H142  C14  C13   106.75  3.000
 13R  H141  C14  C13   109.63  3.000
 13R  C15   C14  C13   114.33  3.000
 13R  H152  C15  H151  106.34  3.000
 13R  H152  C15  C16   109.11  3.000
 13R  H151  C15  C16   109.24  3.000
 13R  H152  C15  C14   110.35  3.000
 13R  H151  C15  C14   109.33  3.000
 13R  C16   C15  C14   112.28  3.000
 13R  H162  C16  H161  106.05  3.000
 13R  H162  C16  C17   109.30  3.000
 13R  H161  C16  C17   109.35  3.000
 13R  H162  C16  C15   109.46  3.000
 13R  H161  C16  C15   109.34  3.000
 13R  C17   C16  C15   113.09  3.000
 13R  H172  C17  H171  106.03  3.000
 13R  H172  C17  C18   109.64  3.000
 13R  H171  C17  C18   109.59  3.000
 13R  H172  C17  C16   109.31  3.000
 13R  H171  C17  C16   109.31  3.000
 13R  C18   C17  C16   112.74  3.000
 13R  H183  C18  H182  107.51  3.000
 13R  H183  C18  H181  107.70  3.000
 13R  H182  C18  H181  107.58  3.000
 13R  H183  C18  C17   111.10  3.000
 13R  H182  C18  C17   111.08  3.000
 13R  H181  C18  C17   111.68  3.000
 13R  O22   O21  C13   109.28  3.000
 13R  H221  O22  O21   102.44  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  Var_01  C11   C10  C9   C8     -0.63   0.0  2
 13R  Var_02  C13   C12  C11  C10  -178.13   0.0  2
 13R  Var_03  C4    C3   C2   C1    179.30  30.0  3
 13R  Var_04  C5    C4   C3   C2    177.81  30.0  3
 13R  Var_05  O19   C1   C2   C3     -9.25  30.0  2
 13R  Var_06  C6    C5   C4   C3    179.18  30.0  3
 13R  Var_07  C7    C6   C5   C4    174.70  30.0  3
 13R  Var_08  C8    C7   C6   C5    178.30  30.0  3
 13R  Var_09  C9    C8   C7   C6    171.07  30.0  3
 13R  Var_10  C10   C9   C8   C7    109.29  30.0  3
 13R  Var_11  C12   C11  C10  C9    177.76  30.0  2
 13R  Var_12  C16   C15  C14  C13   175.13  30.0  3
 13R  Var_13  C17   C16  C15  C14  -179.67  30.0  3
 13R  Var_14  C18   C17  C16  C15  -179.84  30.0  3
 13R  Var_15  H181  C18  C17  C16  -179.82  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-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

