# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:14:52 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (10E,12Z)-octadeca-10,12-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C=C/CCCCCCCCC(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
 ODD  ODD  '(10E,12Z)-octadeca-10,12-dienoic acid'  ligand  51  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 GRAND
;

data_comp_ODD
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
 ODD  O2    O  O      0  -0.610   -9.0610   1.1895   0.8398
 ODD  C1    C  C      0   0.410   -9.0751   0.3106  -0.0444
 ODD  O1    O  OC    -1  -0.635  -10.0866  -0.1214  -0.6386
 ODD  C2    C  CH2    0  -0.581   -7.7345  -0.3205  -0.4577
 ODD  C3    C  CH2    0  -0.402   -6.4906   0.2130   0.2342
 ODD  C4    C  CH2    0  -0.409   -5.2211  -0.4918  -0.2293
 ODD  C5    C  CH2    0  -0.410   -3.9555   0.0071   0.4568
 ODD  C6    C  CH2    0  -0.411   -2.7040  -0.7346   0.0039
 ODD  C7    C  CH2    0  -0.414   -1.4284  -0.2625   0.6908
 ODD  C8    C  CH2    0  -0.417   -0.2019  -1.0593   0.2649
 ODD  C9    C  CH2    0  -0.482    1.0828  -0.6181   0.9692
 ODD  C10   C  C1     0  -0.206    2.2379  -1.5017   0.6330
 ODD  C11   C  C1     0  -0.267    3.3939  -1.1039   0.0914
 ODD  C12   C  C1     0  -0.252    4.4765  -2.0227  -0.2225
 ODD  C13   C  C1     0  -0.221    5.6779  -1.7099  -0.7231
 ODD  C14   C  CH2    0  -0.488    6.2062  -0.3498  -1.0468
 ODD  C15   C  CH2    0  -0.413    7.3638   0.0417  -0.1247
 ODD  C16   C  CH2    0  -0.408    7.9729   1.3926  -0.4763
 ODD  C17   C  CH2    0  -0.419    9.1161   1.7919   0.4486
 ODD  C18   C  CH3    0  -0.662    9.7192   3.1430   0.0904
 ODD  H21   H  HCH2   0   0.215   -7.6268  -0.2085  -1.5431
 ODD  H22   H  HCH2   0   0.216   -7.8047  -1.4031  -0.2955
 ODD  H31   H  HCH2   0   0.200   -6.5909   0.0992   1.3177
 ODD  H32   H  HCH2   0   0.200   -6.3949   1.2882   0.0535
 ODD  H41   H  HCH2   0   0.202   -5.1147  -0.3738  -1.3138
 ODD  H42   H  HCH2   0   0.201   -5.3213  -1.5695  -0.0552
 ODD  H51   H  HCH2   0   0.204   -4.0653  -0.0979   1.5420
 ODD  H52   H  HCH2   0   0.205   -3.8357   1.0796   0.2674
 ODD  H61   H  HCH2   0   0.207   -2.5929  -0.6286  -1.0810
 ODD  H62   H  HCH2   0   0.206   -2.8345  -1.8066   0.1899
 ODD  H71   H  HCH2   0   0.208   -1.5499  -0.3424   1.7768
 ODD  H72   H  HCH2   0   0.210   -1.2709   0.8008   0.4799
 ODD  H81   H  HCH2   0   0.218   -0.0663  -0.9777  -0.8182
 ODD  H82   H  HCH2   0   0.214   -0.3734  -2.1213   0.4712
 ODD  H91   H  HCH2   0   0.230    0.9116  -0.6470   2.0519
 ODD  H92   H  HCH2   0   0.230    1.3125   0.4210   0.7168
 ODD  H10   H  H      0   0.236    2.1013  -2.5611   0.8447
 ODD  H11   H  H      0   0.237    3.5368  -0.0480  -0.1206
 ODD  H12   H  H      0   0.235    4.2712  -3.0706  -0.0208
 ODD  H13   H  H      0   0.235    6.3758  -2.5259  -0.8896
 ODD  H141  H  HCH2   0   0.231    5.4233   0.4095  -0.9909
 ODD  H142  H  HCH2   0   0.232    6.5661  -0.3439  -2.0817
 ODD  H151  H  HCH2   0   0.215    8.1389  -0.7309  -0.1683
 ODD  H152  H  HCH2   0   0.217    7.0070   0.0580   0.9099
 ODD  H161  H  HCH2   0   0.209    7.1940   2.1625  -0.4436
 ODD  H162  H  HCH2   0   0.209    8.3334   1.3703  -1.5108
 ODD  H171  H  HCH2   0   0.211    9.8937   1.0226   0.4161
 ODD  H172  H  HCH2   0   0.211    8.7543   1.8132   1.4814
 ODD  H181  H  HCH3   0   0.226   10.5369   3.4097   0.7610
 ODD  H182  H  HCH3   0   0.216   10.1147   3.1399  -0.9272
 ODD  H183  H  HCH3   0   0.216    8.9716   3.9363   0.1496

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
 ODD  O2   C1    deloc   1.247  0.020  1.247
 ODD  C1   O1    deloc   1.250  0.020  1.250
 ODD  C1   C2    single  1.538  0.020  1.538
 ODD  C2   C3    single  1.520  0.020  1.520
 ODD  C2   H21   single  0.970  0.020  1.090
 ODD  C2   H22   single  0.970  0.020  1.090
 ODD  C3   C4    single  1.524  0.020  1.524
 ODD  C3   H31   single  0.970  0.020  1.090
 ODD  C3   H32   single  0.970  0.020  1.090
 ODD  C4   C5    single  1.524  0.020  1.524
 ODD  C4   H41   single  0.970  0.020  1.090
 ODD  C4   H42   single  0.970  0.020  1.090
 ODD  C5   C6    single  1.524  0.020  1.524
 ODD  C5   H51   single  0.970  0.020  1.090
 ODD  C5   H52   single  0.970  0.020  1.090
 ODD  C6   C7    single  1.524  0.020  1.524
 ODD  C6   H61   single  0.970  0.020  1.090
 ODD  C6   H62   single  0.970  0.020  1.090
 ODD  C7   C8    single  1.523  0.020  1.523
 ODD  C7   H71   single  0.970  0.020  1.090
 ODD  C7   H72   single  0.970  0.020  1.090
 ODD  C8   C9    single  1.530  0.020  1.530
 ODD  C8   H81   single  0.970  0.020  1.090
 ODD  C8   H82   single  0.970  0.020  1.090
 ODD  C9   C10   single  1.493  0.020  1.493
 ODD  C9   H91   single  0.970  0.020  1.090
 ODD  C9   H92   single  0.970  0.020  1.090
 ODD  C10  C11   double  1.337  0.020  1.337
 ODD  C10  H10   single  0.930  0.020  1.080
 ODD  C11  C12   single  1.454  0.020  1.454
 ODD  C11  H11   single  0.930  0.020  1.080
 ODD  C12  C13   double  1.339  0.020  1.339
 ODD  C12  H12   single  0.930  0.020  1.080
 ODD  C13  C14   single  1.495  0.020  1.495
 ODD  C13  H13   single  0.930  0.020  1.080
 ODD  C14  C15   single  1.531  0.020  1.531
 ODD  C14  H141  single  0.970  0.020  1.090
 ODD  C14  H142  single  0.970  0.020  1.090
 ODD  C15  C16   single  1.523  0.020  1.523
 ODD  C15  H151  single  0.970  0.020  1.090
 ODD  C15  H152  single  0.970  0.020  1.090
 ODD  C16  C17   single  1.524  0.020  1.524
 ODD  C16  H161  single  0.970  0.020  1.090
 ODD  C16  H162  single  0.970  0.020  1.090
 ODD  C17  C18   single  1.522  0.020  1.522
 ODD  C17  H171  single  0.970  0.020  1.090
 ODD  C17  H172  single  0.970  0.020  1.090
 ODD  C18  H181  single  0.970  0.020  1.090
 ODD  C18  H182  single  0.970  0.020  1.090
 ODD  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
 ODD  C2    C1   O1    115.83  3.000
 ODD  C2    C1   O2    118.03  3.000
 ODD  O1    C1   O2    126.14  3.000
 ODD  H22   C2   H21   104.68  3.000
 ODD  H22   C2   C3    109.36  3.000
 ODD  H21   C2   C3    109.53  3.000
 ODD  H22   C2   C1    108.02  3.000
 ODD  H21   C2   C1    108.04  3.000
 ODD  C3    C2   C1    116.54  3.000
 ODD  H32   C3   H31   105.88  3.000
 ODD  H32   C3   C4    109.35  3.000
 ODD  H31   C3   C4    109.23  3.000
 ODD  H32   C3   C2    109.95  3.000
 ODD  H31   C3   C2    109.83  3.000
 ODD  C4    C3   C2    112.39  3.000
 ODD  H42   C4   H41   105.77  3.000
 ODD  H42   C4   C5    109.05  3.000
 ODD  H41   C4   C5    109.24  3.000
 ODD  H42   C4   C3    109.28  3.000
 ODD  H41   C4   C3    109.39  3.000
 ODD  C5    C4   C3    113.80  3.000
 ODD  H52   C5   H51   106.02  3.000
 ODD  H52   C5   C6    109.59  3.000
 ODD  H51   C5   C6    109.27  3.000
 ODD  H52   C5   C4    109.48  3.000
 ODD  H51   C5   C4    109.35  3.000
 ODD  C6    C5   C4    112.90  3.000
 ODD  H62   C6   H61   105.95  3.000
 ODD  H62   C6   C7    109.04  3.000
 ODD  H61   C6   C7    109.36  3.000
 ODD  H62   C6   C5    109.14  3.000
 ODD  H61   C6   C5    109.30  3.000
 ODD  C7    C6   C5    113.76  3.000
 ODD  H72   C7   H71   106.11  3.000
 ODD  H72   C7   C8    109.76  3.000
 ODD  H71   C7   C8    109.16  3.000
 ODD  H72   C7   C6    109.53  3.000
 ODD  H71   C7   C6    109.35  3.000
 ODD  C8    C7   C6    112.70  3.000
 ODD  H82   C8   H81   106.14  3.000
 ODD  H82   C8   C9    108.93  3.000
 ODD  H81   C8   C9    109.27  3.000
 ODD  H82   C8   C7    109.17  3.000
 ODD  H81   C8   C7    109.72  3.000
 ODD  C9    C8   C7    113.36  3.000
 ODD  H92   C9   H91   106.60  3.000
 ODD  H92   C9   C10   110.36  3.000
 ODD  H91   C9   C10   109.12  3.000
 ODD  H92   C9   C8    110.13  3.000
 ODD  H91   C9   C8    108.41  3.000
 ODD  C10   C9   C8    112.05  3.000
 ODD  H10   C10  C11   118.47  3.000
 ODD  H10   C10  C9    115.79  3.000
 ODD  C11   C10  C9    125.74  3.000
 ODD  H11   C11  C12   118.30  3.000
 ODD  H11   C11  C10   118.81  3.000
 ODD  C12   C11  C10   122.89  3.000
 ODD  H12   C12  C13   117.66  3.000
 ODD  H12   C12  C11   115.38  3.000
 ODD  C13   C12  C11   126.96  3.000
 ODD  H13   C13  C14   115.04  3.000
 ODD  H13   C13  C12   117.28  3.000
 ODD  C14   C13  C12   127.65  3.000
 ODD  H142  C14  H141  106.27  3.000
 ODD  H142  C14  C15   108.61  3.000
 ODD  H141  C14  C15   109.48  3.000
 ODD  H142  C14  C13   109.00  3.000
 ODD  H141  C14  C13   111.61  3.000
 ODD  C15   C14  C13   111.69  3.000
 ODD  H152  C15  H151  106.19  3.000
 ODD  H152  C15  C16   109.59  3.000
 ODD  H151  C15  C16   109.48  3.000
 ODD  H152  C15  C14   109.07  3.000
 ODD  H151  C15  C14   109.32  3.000
 ODD  C16   C15  C14   112.97  3.000
 ODD  H162  C16  H161  106.04  3.000
 ODD  H162  C16  C17   109.36  3.000
 ODD  H161  C16  C17   109.34  3.000
 ODD  H162  C16  C15   109.36  3.000
 ODD  H161  C16  C15   109.39  3.000
 ODD  C17   C16  C15   113.10  3.000
 ODD  H172  C17  H171  106.06  3.000
 ODD  H172  C17  C18   109.62  3.000
 ODD  H171  C17  C18   109.60  3.000
 ODD  H172  C17  C16   109.26  3.000
 ODD  H171  C17  C16   109.32  3.000
 ODD  C18   C17  C16   112.77  3.000
 ODD  H183  C18  H182  107.50  3.000
 ODD  H183  C18  H181  107.61  3.000
 ODD  H182  C18  H181  107.59  3.000
 ODD  H183  C18  C17   111.15  3.000
 ODD  H182  C18  C17   111.12  3.000
 ODD  H181  C18  C17   111.67  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
 ODD  Var_01  C12   C11  C10  C9   -179.43   0.0  2
 ODD  Var_02  C14   C13  C12  C11     1.63   0.0  2
 ODD  Var_03  C3    C2   C1   O2     -1.41  30.0  3
 ODD  Var_04  C4    C3   C2   C1    179.10  30.0  3
 ODD  Var_05  C5    C4   C3   C2   -179.31  30.0  3
 ODD  Var_06  C6    C5   C4   C3    178.57  30.0  3
 ODD  Var_07  C7    C6   C5   C4   -179.29  30.0  3
 ODD  Var_08  C8    C7   C6   C5    177.54  30.0  3
 ODD  Var_09  C9    C8   C7   C6   -178.72  30.0  3
 ODD  Var_10  C10   C9   C8   C7    174.39  30.0  3
 ODD  Var_11  C11   C10  C9   C8    122.66  30.0  3
 ODD  Var_12  C13   C12  C11  C10  -177.69  30.0  2
 ODD  Var_13  C15   C14  C13  C12   113.00  30.0  3
 ODD  Var_14  C16   C15  C14  C13   176.97  30.0  3
 ODD  Var_15  C17   C16  C15  C14   179.40  30.0  3
 ODD  Var_16  C18   C17  C16  C15   180.00  30.0  3
 ODD  Var_17  H181  C18  C17  C16  -179.82  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
 ODD  plan-1  O2   0.020
 ODD  plan-1  C1   0.020
 ODD  plan-1  O1   0.020
 ODD  plan-1  C2   0.020
 ODD  plan-2  C9   0.020
 ODD  plan-2  C10  0.020
 ODD  plan-2  C11  0.020
 ODD  plan-2  C12  0.020
 ODD  plan-2  H10  0.020
 ODD  plan-2  H11  0.020
 ODD  plan-3  C11  0.020
 ODD  plan-3  C12  0.020
 ODD  plan-3  C13  0.020
 ODD  plan-3  C14  0.020
 ODD  plan-3  H12  0.020
 ODD  plan-3  H13  0.020

