# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:47:28 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (11E,13E,15Z)-octadeca-11,13,15-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C=C/C=C/CCCCCCCCCC(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
 ODT  ODT  '(11E,13E,15Z)-octadeca-11,13,15-trienoic acid'  ligand  49  20  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ODT
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
 ODT  O1    O  O      0  -0.610   -8.9842   1.5273  -0.9566
 ODT  C1    C  C      0   0.409   -9.0914   0.8627   0.0929
 ODT  O2    O  OC    -1  -0.636  -10.1448   0.6653   0.7364
 ODT  C2    C  CH2    0  -0.580   -7.8206   0.2156   0.6703
 ODT  C3    C  CH2    0  -0.401   -6.5347   0.4416  -0.1080
 ODT  C4    C  CH2    0  -0.408   -5.3337  -0.2425   0.5340
 ODT  C5    C  CH2    0  -0.409   -4.0282  -0.0202  -0.2194
 ODT  C6    C  CH2    0  -0.409   -2.8386  -0.7152   0.4308
 ODT  C7    C  CH2    0  -0.412   -1.5232  -0.4941  -0.3058
 ODT  C8    C  CH2    0  -0.413   -0.3438  -1.1877   0.3640
 ODT  C9    C  CH2    0  -0.414    0.9790  -0.9691  -0.3594
 ODT  C10   C  CH2    0  -0.485    2.1533  -1.6481   0.3499
 ODT  C11   C  C1     0  -0.213    3.4419  -1.4858  -0.3849
 ODT  C12   C  C1     0  -0.248    4.4873  -0.7750   0.0557
 ODT  C13   C  C1     0  -0.246    5.7260  -0.6202  -0.6759
 ODT  C14   C  C1     0  -0.275    6.7734   0.1026  -0.2397
 ODT  C15   C  C1     0  -0.249    8.0082   0.2344  -0.9855
 ODT  C16   C  C1     0  -0.218    9.0911   0.9376  -0.6241
 ODT  C17   C  CH2    0  -0.491    9.2845   1.7374   0.6237
 ODT  C18   C  CH3    0  -0.658   10.4034   1.1687   1.4962
 ODT  H21   H  HCH2   0   0.214   -8.0040  -0.8608   0.7715
 ODT  H22   H  HCH2   0   0.215   -7.6927   0.5739   1.6989
 ODT  H31   H  HCH2   0   0.199   -6.3378   1.5146  -0.1928
 ODT  H32   H  HCH2   0   0.199   -6.6533   0.0775  -1.1328
 ODT  H41   H  HCH2   0   0.201   -5.5252  -1.3191   0.6095
 ODT  H42   H  HCH2   0   0.201   -5.2182   0.1129   1.5644
 ODT  H51   H  HCH2   0   0.204   -3.8286   1.0550  -0.2883
 ODT  H52   H  HCH2   0   0.204   -4.1392  -0.3735  -1.2507
 ODT  H61   H  HCH2   0   0.205   -3.0382  -1.7907   0.4957
 ODT  H62   H  HCH2   0   0.205   -2.7353  -0.3656   1.4642
 ODT  H71   H  HCH2   0   0.206   -1.3227   0.5808  -0.3740
 ODT  H72   H  HCH2   0   0.207   -1.6204  -0.8501  -1.3373
 ODT  H81   H  HCH2   0   0.209   -0.5432  -2.2629   0.4313
 ODT  H82   H  HCH2   0   0.209   -0.2530  -0.8323   1.3963
 ODT  H91   H  HCH2   0   0.217    1.1817   0.1033  -0.4407
 ODT  H92   H  HCH2   0   0.215    0.9014  -1.3454  -1.3846
 ODT  H101  H  HCH2   0   0.230    1.9288  -2.7156   0.4539
 ODT  H102  H  HCH2   0   0.230    2.2507  -1.2480   1.3630
 ODT  H11   H  H      0   0.239    3.5119  -1.9744  -1.3548
 ODT  H12   H  H      0   0.238    4.4204  -0.2793   1.0218
 ODT  H13   H  H      0   0.243    5.7982  -1.1301  -1.6340
 ODT  H14   H  H      0   0.246    6.6907   0.6090   0.7176
 ODT  H15   H  H      0   0.238    8.0456  -0.3011  -1.9300
 ODT  H16   H  H      0   0.238    9.9423   0.9222  -1.2987
 ODT  H171  H  HCH2   0   0.236    8.3630   1.7988   1.2034
 ODT  H172  H  HCH2   0   0.237    9.5425   2.7642   0.3462
 ODT  H181  H  HCH3   0   0.231   10.5733   1.7969   2.3711
 ODT  H182  H  HCH3   0   0.225   10.1564   0.1659   1.8459
 ODT  H183  H  HCH3   0   0.223   11.3426   1.1065   0.9445

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
 ODT  O1   C1    deloc   1.247  0.020  1.247
 ODT  C1   O2    deloc   1.250  0.020  1.250
 ODT  C1   C2    single  1.539  0.020  1.539
 ODT  C2   C3    single  1.520  0.020  1.520
 ODT  C2   H21   single  0.970  0.020  1.090
 ODT  C2   H22   single  0.970  0.020  1.090
 ODT  C3   C4    single  1.524  0.020  1.524
 ODT  C3   H31   single  0.970  0.020  1.090
 ODT  C3   H32   single  0.970  0.020  1.090
 ODT  C4   C5    single  1.524  0.020  1.524
 ODT  C4   H41   single  0.970  0.020  1.090
 ODT  C4   H42   single  0.970  0.020  1.090
 ODT  C5   C6    single  1.523  0.020  1.523
 ODT  C5   H51   single  0.970  0.020  1.090
 ODT  C5   H52   single  0.970  0.020  1.090
 ODT  C6   C7    single  1.524  0.020  1.524
 ODT  C6   H61   single  0.970  0.020  1.090
 ODT  C6   H62   single  0.970  0.020  1.090
 ODT  C7   C8    single  1.523  0.020  1.523
 ODT  C7   H71   single  0.970  0.020  1.090
 ODT  C7   H72   single  0.970  0.020  1.090
 ODT  C8   C9    single  1.523  0.020  1.523
 ODT  C8   H81   single  0.970  0.020  1.090
 ODT  C8   H82   single  0.970  0.020  1.090
 ODT  C9   C10   single  1.531  0.020  1.531
 ODT  C9   H91   single  0.970  0.020  1.090
 ODT  C9   H92   single  0.970  0.020  1.090
 ODT  C10  C11   single  1.492  0.020  1.492
 ODT  C10  H101  single  0.970  0.020  1.090
 ODT  C10  H102  single  0.970  0.020  1.090
 ODT  C11  C12   double  1.339  0.020  1.339
 ODT  C11  H11   single  0.930  0.020  1.080
 ODT  C12  C13   single  1.447  0.020  1.447
 ODT  C12  H12   single  0.930  0.020  1.080
 ODT  C13  C14   double  1.345  0.020  1.345
 ODT  C13  H13   single  0.930  0.020  1.080
 ODT  C14  C15   single  1.449  0.020  1.449
 ODT  C14  H14   single  0.930  0.020  1.080
 ODT  C15  C16   double  1.341  0.020  1.341
 ODT  C15  H15   single  0.930  0.020  1.080
 ODT  C16  C17   single  1.495  0.020  1.495
 ODT  C16  H16   single  0.930  0.020  1.080
 ODT  C17  C18   single  1.529  0.020  1.529
 ODT  C17  H171  single  0.970  0.020  1.090
 ODT  C17  H172  single  0.970  0.020  1.090
 ODT  C18  H181  single  0.970  0.020  1.090
 ODT  C18  H182  single  0.970  0.020  1.090
 ODT  C18  H183  single  0.970  0.020  1.090

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
 ODT  C2    C1   O2    115.87  3.000
 ODT  C2    C1   O1    117.97  3.000
 ODT  O2    C1   O1    126.15  3.000
 ODT  H22   C2   H21   104.69  3.000
 ODT  H22   C2   C3    109.45  3.000
 ODT  H21   C2   C3    109.55  3.000
 ODT  H22   C2   C1    108.12  3.000
 ODT  H21   C2   C1    108.02  3.000
 ODT  C3    C2   C1    116.36  3.000
 ODT  H32   C3   H31   105.85  3.000
 ODT  H32   C3   C4    109.31  3.000
 ODT  H31   C3   C4    109.33  3.000
 ODT  H32   C3   C2    109.79  3.000
 ODT  H31   C3   C2    109.74  3.000
 ODT  C4    C3   C2    112.60  3.000
 ODT  H42   C4   H41   105.80  3.000
 ODT  H42   C4   C5    109.10  3.000
 ODT  H41   C4   C5    109.09  3.000
 ODT  H42   C4   C3    109.48  3.000
 ODT  H41   C4   C3    109.40  3.000
 ODT  C5    C4   C3    113.67  3.000
 ODT  H52   C5   H51   106.00  3.000
 ODT  H52   C5   C6    109.50  3.000
 ODT  H51   C5   C6    109.41  3.000
 ODT  H52   C5   C4    109.36  3.000
 ODT  H51   C5   C4    109.29  3.000
 ODT  C6    C5   C4    113.04  3.000
 ODT  H62   C6   H61   105.93  3.000
 ODT  H62   C6   C7    109.16  3.000
 ODT  H61   C6   C7    109.17  3.000
 ODT  H62   C6   C5    109.31  3.000
 ODT  H61   C6   C5    109.32  3.000
 ODT  C7    C6   C5    113.67  3.000
 ODT  H72   C7   H71   106.05  3.000
 ODT  H72   C7   C8    109.55  3.000
 ODT  H71   C7   C8    109.41  3.000
 ODT  H72   C7   C6    109.36  3.000
 ODT  H71   C7   C6    109.30  3.000
 ODT  C8    C7   C6    112.94  3.000
 ODT  H82   C8   H81   105.99  3.000
 ODT  H82   C8   C9    109.20  3.000
 ODT  H81   C8   C9    109.15  3.000
 ODT  H82   C8   C7    109.32  3.000
 ODT  H81   C8   C7    109.45  3.000
 ODT  C9    C8   C7    113.46  3.000
 ODT  H92   C9   H91   106.28  3.000
 ODT  H92   C9   C10   109.62  3.000
 ODT  H91   C9   C10   109.09  3.000
 ODT  H92   C9   C8    109.50  3.000
 ODT  H91   C9   C8    109.68  3.000
 ODT  C10   C9   C8    112.49  3.000
 ODT  H102  C10  H101  106.66  3.000
 ODT  H102  C10  C11   109.85  3.000
 ODT  H101  C10  C11   109.25  3.000
 ODT  H102  C10  C9    109.59  3.000
 ODT  H101  C10  C9    108.60  3.000
 ODT  C11   C10  C9    112.71  3.000
 ODT  H11   C11  C12   118.78  3.000
 ODT  H11   C11  C10   116.46  3.000
 ODT  C12   C11  C10   124.75  3.000
 ODT  H12   C12  C13   116.93  3.000
 ODT  H12   C12  C11   119.09  3.000
 ODT  C13   C12  C11   123.98  3.000
 ODT  H13   C13  C14   119.06  3.000
 ODT  H13   C13  C12   116.87  3.000
 ODT  C14   C13  C12   124.07  3.000
 ODT  H14   C14  C15   118.44  3.000
 ODT  H14   C14  C13   118.48  3.000
 ODT  C15   C14  C13   123.07  3.000
 ODT  H15   C15  C16   117.71  3.000
 ODT  H15   C15  C14   115.60  3.000
 ODT  C16   C15  C14   126.69  3.000
 ODT  H16   C16  C17   115.13  3.000
 ODT  H16   C16  C15   117.27  3.000
 ODT  C17   C16  C15   127.59  3.000
 ODT  H172  C17  H171  106.33  3.000
 ODT  H172  C17  C18   108.73  3.000
 ODT  H171  C17  C18   109.64  3.000
 ODT  H172  C17  C16   108.71  3.000
 ODT  H171  C17  C16   111.39  3.000
 ODT  C18   C17  C16   111.85  3.000
 ODT  H183  C18  H182  107.74  3.000
 ODT  H183  C18  H181  107.73  3.000
 ODT  H182  C18  H181  107.93  3.000
 ODT  H183  C18  C17   111.27  3.000
 ODT  H182  C18  C17   111.06  3.000
 ODT  H181  C18  C17   110.96  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
 ODT  Var_01  C13   C12  C11  C10  -179.50   0.0  2
 ODT  Var_02  C15   C14  C13  C12   179.49   0.0  2
 ODT  Var_03  C17   C16  C15  C14     0.41   0.0  2
 ODT  Var_04  C3    C2   C1   O1     -0.40  30.0  3
 ODT  Var_05  C4    C3   C2   C1   -179.65  30.0  3
 ODT  Var_06  C5    C4   C3   C2   -179.43  30.0  3
 ODT  Var_07  C6    C5   C4   C3   -179.74  30.0  3
 ODT  Var_08  C7    C6   C5   C4   -179.59  30.0  3
 ODT  Var_09  C8    C7   C6   C5    179.58  30.0  3
 ODT  Var_10  C9    C8   C7   C6   -179.73  30.0  3
 ODT  Var_11  C10   C9   C8   C7    178.67  30.0  3
 ODT  Var_12  C11   C10  C9   C8    177.58  30.0  3
 ODT  Var_13  C12   C11  C10  C9    112.99  30.0  3
 ODT  Var_14  C14   C13  C12  C11   179.43  30.0  2
 ODT  Var_15  C16   C15  C14  C13   179.69  30.0  2
 ODT  Var_16  C18   C17  C16  C15   116.04  30.0  3
 ODT  Var_17  H181  C18  C17  C16   176.52  30.0  3

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
 ODT  plan-1  O1   0.020
 ODT  plan-1  C1   0.020
 ODT  plan-1  O2   0.020
 ODT  plan-1  C2   0.020
 ODT  plan-2  C10  0.020
 ODT  plan-2  C11  0.020
 ODT  plan-2  C12  0.020
 ODT  plan-2  C13  0.020
 ODT  plan-2  H11  0.020
 ODT  plan-2  H12  0.020
 ODT  plan-3  C12  0.020
 ODT  plan-3  C13  0.020
 ODT  plan-3  C14  0.020
 ODT  plan-3  C15  0.020
 ODT  plan-3  H13  0.020
 ODT  plan-3  H14  0.020
 ODT  plan-4  C14  0.020
 ODT  plan-4  C15  0.020
 ODT  plan-4  C16  0.020
 ODT  plan-4  C17  0.020
 ODT  plan-4  H15  0.020
 ODT  plan-4  H16  0.020

