# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 20:16:44 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  50  20  .  2021-08-19  2021-08-19  
;
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  -0.447   -9.2922   0.4573  -1.3080
 ODT  C1    C  C     0   0.550   -9.2075   0.1339  -0.1491
 ODT  O2    O  OH1   0  -0.599  -10.2730  -0.0710   0.6216
 ODT  C2    C  CH2   0  -0.580   -7.9232  -0.0790   0.6018
 ODT  C3    C  CH2   0  -0.417   -6.6769   0.0569  -0.2574
 ODT  C4    C  CH2   0  -0.414   -5.4056  -0.1729   0.5495
 ODT  C5    C  CH2   0  -0.412   -4.1389  -0.0499  -0.2874
 ODT  C6    C  CH2   0  -0.412   -2.8698  -0.3175   0.5116
 ODT  C7    C  CH2   0  -0.412   -1.5954  -0.1989  -0.3152
 ODT  C8    C  CH2   0  -0.413   -0.3446  -0.5913   0.4619
 ODT  C9    C  CH2   0  -0.416    0.9391  -0.4533  -0.3476
 ODT  C10   C  CH2   0  -0.485    2.1519  -1.0479   0.3699
 ODT  C11   C  C1    0  -0.208    3.4125  -0.9326  -0.4198
 ODT  C12   C  C1    0  -0.252    4.5386  -0.3536   0.0145
 ODT  C13   C  C1    0  -0.246    5.7575  -0.2706  -0.7611
 ODT  C14   C  C1    0  -0.273    6.9074   0.2524  -0.2990
 ODT  C15   C  C1    0  -0.246    8.1262   0.3078  -1.0791
 ODT  C16   C  C1    0  -0.222    9.3179   0.7564  -0.6598
 ODT  C17   C  CH2   0  -0.493    9.6617   1.2773   0.6992
 ODT  C18   C  CH3   0  -0.657   10.5008   0.2751   1.4932
 ODT  HO2   H  HOH1  0   0.477  -11.0823   0.0804   0.1112
 ODT  H21   H  HCH2  0   0.273   -7.9597  -1.0653   1.0752
 ODT  H22   H  HCH2  0   0.276   -7.8983   0.6383   1.4294
 ODT  H31   H  HCH2  0   0.224   -6.6464   1.0512  -0.7109
 ODT  H32   H  HCH2  0   0.224   -6.7167  -0.6588  -1.0832
 ODT  H41   H  HCH2  0   0.211   -5.4395  -1.1670   1.0090
 ODT  H42   H  HCH2  0   0.212   -5.3651   0.5424   1.3783
 ODT  H51   H  HCH2  0   0.209   -4.0910   0.9508  -0.7308
 ODT  H52   H  HCH2  0   0.208   -4.1896  -0.7519  -1.1271
 ODT  H61   H  HCH2  0   0.206   -2.9247  -1.3222   0.9455
 ODT  H62   H  HCH2  0   0.208   -2.8205   0.3754   1.3586
 ODT  H71   H  HCH2  0   0.209   -1.4951   0.8261  -0.6882
 ODT  H72   H  HCH2  0   0.207   -1.6765  -0.8385  -1.2009
 ODT  H81   H  HCH2  0   0.208   -0.4484  -1.6286   0.7988
 ODT  H82   H  HCH2  0   0.211   -0.2700   0.0170   1.3696
 ODT  H91   H  HCH2  0   0.219    1.1250   0.6018  -0.5701
 ODT  H92   H  HCH2  0   0.214    0.8154  -0.9524  -1.3149
 ODT  H101  H  HCH2  0   0.232    1.9481  -2.1080   0.5629
 ODT  H102  H  HCH2  0   0.231    2.2811  -0.5751   1.3479
 ODT  H11   H  H     0   0.238    3.3964  -1.3616  -1.4201
 ODT  H12   H  H     0   0.238    4.5623   0.0748   1.0141
 ODT  H13   H  H     0   0.242    5.7267  -0.6723  -1.7715
 ODT  H14   H  H     0   0.245    6.9294   0.6409   0.7149
 ODT  H15   H  H     0   0.238    8.0538  -0.0655  -2.0967
 ODT  H16   H  H     0   0.239   10.1435   0.7122  -1.3640
 ODT  H171  H  HCH2  0   0.236    8.7651   1.5335   1.2657
 ODT  H172  H  HCH2  0   0.237   10.2302   2.2052   0.5897
 ODT  H181  H  HCH3  0   0.231   10.7871   0.6871   2.4613
 ODT  H182  H  HCH3  0   0.224    9.9453  -0.6465   1.6696
 ODT  H183  H  HCH3  0   0.224   11.4157   0.0136   0.9597

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    double  1.206  0.020  1.206
 ODT  C1   O2    single  1.331  0.020  1.331
 ODT  C1   C2    single  1.503  0.020  1.503
 ODT  O2   HO2   single  0.850  0.020  0.980
 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  1.523  0.020  1.523
 ODT  C3   H31   single  0.970  0.020  1.090
 ODT  C3   H32   single  0.970  0.020  1.090
 ODT  C4   C5    single  1.523  0.020  1.523
 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  1.524  0.020  1.524
 ODT  C7   H71   single  0.970  0.020  1.090
 ODT  C7   H72   single  0.970  0.020  1.090
 ODT  C8   C9    single  1.524  0.020  1.524
 ODT  C8   H81   single  0.970  0.020  1.090
 ODT  C8   H82   single  0.970  0.020  1.090
 ODT  C9   C10   single  1.529  0.020  1.529
 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  1.448  0.020  1.448
 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    111.90  3.000
 ODT  C2    C1   O1    125.31  3.000
 ODT  O2    C1   O1    122.79  3.000
 ODT  HO2   O2   C1    109.85  3.000
 ODT  H22   C2   H21   105.31  3.000
 ODT  H22   C2   C3    110.48  3.000
 ODT  H21   C2   C3    110.63  3.000
 ODT  H22   C2   C1    107.70  3.000
 ODT  H21   C2   C1    108.38  3.000
 ODT  C3    C2   C1    113.93  3.000
 ODT  H32   C3   H31   106.44  3.000
 ODT  H32   C3   C4    109.37  3.000
 ODT  H31   C3   C4    109.49  3.000
 ODT  H32   C3   C2    109.79  3.000
 ODT  H31   C3   C2    109.80  3.000
 ODT  C4    C3   C2    111.80  3.000
 ODT  H42   C4   H41   106.04  3.000
 ODT  H42   C4   C5    109.40  3.000
 ODT  H41   C4   C5    109.23  3.000
 ODT  H42   C4   C3    109.45  3.000
 ODT  H41   C4   C3    109.47  3.000
 ODT  C5    C4   C3    113.01  3.000
 ODT  H52   C5   H51   106.09  3.000
 ODT  H52   C5   C6    109.15  3.000
 ODT  H51   C5   C6    109.65  3.000
 ODT  H52   C5   C4    109.32  3.000
 ODT  H51   C5   C4    109.42  3.000
 ODT  C6    C5   C4    112.98  3.000
 ODT  H62   C6   H61   106.02  3.000
 ODT  H62   C6   C7    109.43  3.000
 ODT  H61   C6   C7    109.15  3.000
 ODT  H62   C6   C5    109.39  3.000
 ODT  H61   C6   C5    109.09  3.000
 ODT  C7    C6   C5    113.49  3.000
 ODT  H72   C7   H71   106.13  3.000
 ODT  H72   C7   C8    108.83  3.000
 ODT  H71   C7   C8    109.84  3.000
 ODT  H72   C7   C6    109.35  3.000
 ODT  H71   C7   C6    109.52  3.000
 ODT  C8    C7   C6    112.94  3.000
 ODT  H82   C8   H81   106.11  3.000
 ODT  H82   C8   C9    109.43  3.000
 ODT  H81   C8   C9    109.20  3.000
 ODT  H82   C8   C7    109.61  3.000
 ODT  H81   C8   C7    108.83  3.000
 ODT  C9    C8   C7    113.40  3.000
 ODT  H92   C9   H91   106.19  3.000
 ODT  H92   C9   C10   109.07  3.000
 ODT  H91   C9   C10   109.61  3.000
 ODT  H92   C9   C8    109.43  3.000
 ODT  H91   C9   C8    109.78  3.000
 ODT  C10   C9   C8    112.56  3.000
 ODT  H102  C10  H101  106.41  3.000
 ODT  H102  C10  C11   109.88  3.000
 ODT  H101  C10  C11   108.96  3.000
 ODT  H102  C10  C9    110.18  3.000
 ODT  H101  C10  C9    108.12  3.000
 ODT  C11   C10  C9    113.06  3.000
 ODT  H11   C11  C12   118.76  3.000
 ODT  H11   C11  C10   116.32  3.000
 ODT  C12   C11  C10   124.92  3.000
 ODT  H12   C12  C13   116.85  3.000
 ODT  H12   C12  C11   119.13  3.000
 ODT  C13   C12  C11   124.02  3.000
 ODT  H13   C13  C14   119.13  3.000
 ODT  H13   C13  C12   116.93  3.000
 ODT  C14   C13  C12   123.93  3.000
 ODT  H14   C14  C15   118.18  3.000
 ODT  H14   C14  C13   118.50  3.000
 ODT  C15   C14  C13   123.32  3.000
 ODT  H15   C15  C16   117.86  3.000
 ODT  H15   C15  C14   115.80  3.000
 ODT  C16   C15  C14   126.33  3.000
 ODT  H16   C16  C17   115.39  3.000
 ODT  H16   C16  C15   117.34  3.000
 ODT  C17   C16  C15   127.24  3.000
 ODT  H172  C17  H171  106.26  3.000
 ODT  H172  C17  C18   108.83  3.000
 ODT  H171  C17  C18   109.58  3.000
 ODT  H172  C17  C16   108.91  3.000
 ODT  H171  C17  C16   111.39  3.000
 ODT  C18   C17  C16   111.69  3.000
 ODT  H183  C18  H182  107.69  3.000
 ODT  H183  C18  H181  107.73  3.000
 ODT  H182  C18  H181  108.02  3.000
 ODT  H183  C18  C17   111.30  3.000
 ODT  H182  C18  C17   111.00  3.000
 ODT  H181  C18  C17   110.94  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  CONST_01  HO2   O2   C1   O1      0.00   0.0  0
 ODT  Var_01    C13   C12  C11  C10   179.01   0.0  2
 ODT  Var_02    C15   C14  C13  C12   178.90   0.0  2
 ODT  Var_03    C17   C16  C15  C14     0.95   0.0  2
 ODT  Var_04    C3    C2   C1   O1     -3.98  30.0  3
 ODT  Var_05    C4    C3   C2   C1   -179.79  30.0  3
 ODT  Var_06    C5    C4   C3   C2    179.71  30.0  3
 ODT  Var_07    C6    C5   C4   C3   -178.42  30.0  3
 ODT  Var_08    C7    C6   C5   C4    179.94  30.0  3
 ODT  Var_09    C8    C7   C6   C5   -174.79  30.0  3
 ODT  Var_10    C9    C8   C7   C6   -178.99  30.0  3
 ODT  Var_11    C10   C9   C8   C7   -171.31  30.0  3
 ODT  Var_12    C11   C10  C9   C8    179.35  30.0  3
 ODT  Var_13    C12   C11  C10  C9    124.46  30.0  3
 ODT  Var_14    C14   C13  C12  C11  -176.57  30.0  2
 ODT  Var_15    C16   C15  C14  C13  -176.66  30.0  2
 ODT  Var_16    C18   C17  C16  C15   106.26  30.0  3
 ODT  Var_17    H181  C18  C17  C16   177.11  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-1  HO2  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

