# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:06:23 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C/C=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
 LNL  LNL  '(9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid'  ligand  49  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LNL
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
 LNL  O1    O  OC    -1  -0.635   0.6307   1.4058  -9.5064
 LNL  C1    C  C      0   0.409   0.2178   0.5744  -8.6691
 LNL  O2    O  O      0  -0.610  -0.0668  -0.6181  -8.8966
 LNL  C2    C  CH2    0  -0.580   0.0476   1.0968  -7.2321
 LNL  C3    C  CH2    0  -0.402  -0.4123   0.0854  -6.1948
 LNL  C4    C  CH2    0  -0.408  -0.5564   0.6981  -4.8066
 LNL  C5    C  CH2    0  -0.411  -1.0040  -0.2958  -3.7421
 LNL  C6    C  CH2    0  -0.411  -1.1554   0.3378  -2.3648
 LNL  C7    C  CH2    0  -0.414  -1.5794  -0.6483  -1.2842
 LNL  C8    C  CH2    0  -0.488  -1.7552   0.0170   0.0814
 LNL  C9    C  C1     0  -0.204  -2.2066  -0.9453   1.1342
 LNL  C10   C  C1     0  -0.216  -1.6054  -1.2251   2.2897
 LNL  C11   C  CH2    0  -0.577  -0.3449  -0.6068   2.8257
 LNL  C12   C  C1     0  -0.199  -0.6655   0.3896   3.9024
 LNL  C13   C  C1     0  -0.206  -0.2713   0.3752   5.1744
 LNL  C14   C  CH2    0  -0.581   0.6348  -0.6172   5.8448
 LNL  C15   C  C1     0  -0.208   1.9631   0.0199   6.1444
 LNL  C16   C  C1     0  -0.208   2.4096   0.4331   7.3294
 LNL  C17   C  CH2    0  -0.490   1.7218   0.3276   8.6544
 LNL  C18   C  CH3    0  -0.657   2.5071  -0.5420   9.6347
 LNL  H21   H  HCH2   0   0.216  -0.6562   1.9376  -7.2614
 LNL  H22   H  HCH2   0   0.214   0.9993   1.5397  -6.9153
 LNL  H31   H  HCH2   0   0.199   0.2950  -0.7484  -6.1502
 LNL  H32   H  HCH2   0   0.200  -1.3692  -0.3488  -6.4993
 LNL  H41   H  HCH2   0   0.202  -1.2715   1.5279  -4.8487
 LNL  H42   H  HCH2   0   0.201   0.3991   1.1414  -4.5033
 LNL  H51   H  HCH2   0   0.205  -0.2834  -1.1194  -3.6866
 LNL  H52   H  HCH2   0   0.205  -1.9568  -0.7458  -4.0421
 LNL  H61   H  HCH2   0   0.208  -1.8874   1.1515  -2.4200
 LNL  H62   H  HCH2   0   0.208  -0.2071   0.8033  -2.0745
 LNL  H71   H  HCH2   0   0.216  -0.8365  -1.4484  -1.2037
 LNL  H72   H  HCH2   0   0.212  -2.5182  -1.1302  -1.5769
 LNL  H81   H  HCH2   0   0.230  -2.5019   0.8138  -0.0128
 LNL  H82   H  HCH2   0   0.229  -0.8230   0.5073   0.3712
 LNL  H9    H  H      0   0.230  -3.1317  -1.4717   0.9110
 LNL  H10   H  H      0   0.235  -2.0801  -1.9458   2.9492
 LNL  H111  H  HCH2   0   0.252   0.2048  -0.1017   2.0276
 LNL  H112  H  HCH2   0   0.251   0.3124  -1.3929   3.2036
 LNL  H12   H  H      0   0.237  -1.3089   1.2058   3.5852
 LNL  H13   H  H      0   0.237  -0.6055   1.1888   5.8121
 LNL  H141  H  HCH2   0   0.252   0.7893  -1.4928   5.2109
 LNL  H142  H  HCH2   0   0.252   0.1618  -0.9757   6.7617
 LNL  H15   H  H      0   0.236   2.5975   0.1808   5.2775
 LNL  H16   H  H      0   0.230   3.3960   0.8903   7.3602
 LNL  H171  H  HCH2   0   0.232   0.7083  -0.0616   8.5443
 LNL  H172  H  HCH2   0   0.233   1.6167   1.3312   9.0786
 LNL  H181  H  HCH3   0   0.229   2.0140  -0.5832  10.6064
 LNL  H182  H  HCH3   0   0.223   2.6023  -1.5630   9.2631
 LNL  H183  H  HCH3   0   0.221   3.5138  -0.1506   9.7903

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
 LNL  O1   C1    deloc   1.250  0.020  1.250
 LNL  C1   O2    deloc   1.247  0.020  1.247
 LNL  C1   C2    single  1.538  0.020  1.538
 LNL  C2   C3    single  1.520  0.020  1.520
 LNL  C2   H21   single  0.970  0.020  1.090
 LNL  C2   H22   single  0.970  0.020  1.090
 LNL  C3   C4    single  1.524  0.020  1.524
 LNL  C3   H31   single  0.970  0.020  1.090
 LNL  C3   H32   single  0.970  0.020  1.090
 LNL  C4   C5    single  1.524  0.020  1.524
 LNL  C4   H41   single  0.970  0.020  1.090
 LNL  C4   H42   single  0.970  0.020  1.090
 LNL  C5   C6    single  1.524  0.020  1.524
 LNL  C5   H51   single  0.970  0.020  1.090
 LNL  C5   H52   single  0.970  0.020  1.090
 LNL  C6   C7    single  1.523  0.020  1.523
 LNL  C6   H61   single  0.970  0.020  1.090
 LNL  C6   H62   single  0.970  0.020  1.090
 LNL  C7   C8    single  1.529  0.020  1.529
 LNL  C7   H71   single  0.970  0.020  1.090
 LNL  C7   H72   single  0.970  0.020  1.090
 LNL  C8   C9    single  1.496  0.020  1.496
 LNL  C8   H81   single  0.970  0.020  1.090
 LNL  C8   H82   single  0.970  0.020  1.090
 LNL  C9   C10   double  1.332  0.020  1.332
 LNL  C9   H9    single  0.930  0.020  1.080
 LNL  C10  C11   single  1.503  0.020  1.503
 LNL  C10  H10   single  0.930  0.020  1.080
 LNL  C11  C12   single  1.502  0.020  1.502
 LNL  C11  H111  single  0.970  0.020  1.090
 LNL  C11  H112  single  0.970  0.020  1.090
 LNL  C12  C13   double  1.332  0.020  1.332
 LNL  C12  H12   single  0.930  0.020  1.080
 LNL  C13  C14   single  1.502  0.020  1.502
 LNL  C13  H13   single  0.930  0.020  1.080
 LNL  C14  C15   single  1.503  0.020  1.503
 LNL  C14  H141  single  0.970  0.020  1.090
 LNL  C14  H142  single  0.970  0.020  1.090
 LNL  C15  C16   double  1.332  0.020  1.332
 LNL  C15  H15   single  0.930  0.020  1.080
 LNL  C16  C17   single  1.497  0.020  1.497
 LNL  C16  H16   single  0.930  0.020  1.080
 LNL  C17  C18   single  1.528  0.020  1.528
 LNL  C17  H171  single  0.970  0.020  1.090
 LNL  C17  H172  single  0.970  0.020  1.090
 LNL  C18  H181  single  0.970  0.020  1.090
 LNL  C18  H182  single  0.970  0.020  1.090
 LNL  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
 LNL  C2    C1   O2    118.03  3.000
 LNL  C2    C1   O1    115.87  3.000
 LNL  O2    C1   O1    126.10  3.000
 LNL  H22   C2   H21   104.77  3.000
 LNL  H22   C2   C3    109.53  3.000
 LNL  H21   C2   C3    109.52  3.000
 LNL  H22   C2   C1    108.12  3.000
 LNL  H21   C2   C1    107.83  3.000
 LNL  C3    C2   C1    116.42  3.000
 LNL  H32   C3   H31   105.92  3.000
 LNL  H32   C3   C4    109.29  3.000
 LNL  H31   C3   C4    109.29  3.000
 LNL  H32   C3   C2    109.80  3.000
 LNL  H31   C3   C2    109.83  3.000
 LNL  C4    C3   C2    112.50  3.000
 LNL  H42   C4   H41   105.85  3.000
 LNL  H42   C4   C5    109.06  3.000
 LNL  H41   C4   C5    109.21  3.000
 LNL  H42   C4   C3    109.40  3.000
 LNL  H41   C4   C3    109.33  3.000
 LNL  C5    C4   C3    113.69  3.000
 LNL  H52   C5   H51   106.08  3.000
 LNL  H52   C5   C6    109.38  3.000
 LNL  H51   C5   C6    109.41  3.000
 LNL  H52   C5   C4    109.39  3.000
 LNL  H51   C5   C4    109.42  3.000
 LNL  C6    C5   C4    112.92  3.000
 LNL  H62   C6   H61   106.02  3.000
 LNL  H62   C6   C7    109.14  3.000
 LNL  H61   C6   C7    109.31  3.000
 LNL  H62   C6   C5    109.28  3.000
 LNL  H61   C6   C5    109.25  3.000
 LNL  C7    C6   C5    113.56  3.000
 LNL  H72   C7   H71   106.25  3.000
 LNL  H72   C7   C8    109.36  3.000
 LNL  H71   C7   C8    109.29  3.000
 LNL  H72   C7   C6    109.51  3.000
 LNL  H71   C7   C6    109.66  3.000
 LNL  C8    C7   C6    112.58  3.000
 LNL  H82   C8   H81   106.13  3.000
 LNL  H82   C8   C9    111.07  3.000
 LNL  H81   C8   C9    108.82  3.000
 LNL  H82   C8   C7    109.51  3.000
 LNL  H81   C8   C7    108.53  3.000
 LNL  C9    C8   C7    112.54  3.000
 LNL  H9    C9   C10   117.40  3.000
 LNL  H9    C9   C8    115.06  3.000
 LNL  C10   C9   C8    127.54  3.000
 LNL  H10   C10  C11   115.02  3.000
 LNL  H10   C10  C9    117.96  3.000
 LNL  C11   C10  C9    126.97  3.000
 LNL  H112  C11  H111  106.42  3.000
 LNL  H112  C11  C12   110.98  3.000
 LNL  H111  C11  C12   108.93  3.000
 LNL  H112  C11  C10   109.39  3.000
 LNL  H111  C11  C10   110.58  3.000
 LNL  C12   C11  C10   110.47  3.000
 LNL  H12   C12  C13   117.53  3.000
 LNL  H12   C12  C11   114.55  3.000
 LNL  C13   C12  C11   127.91  3.000
 LNL  H13   C13  C14   114.74  3.000
 LNL  H13   C13  C12   117.48  3.000
 LNL  C14   C13  C12   127.74  3.000
 LNL  H142  C14  H141  106.59  3.000
 LNL  H142  C14  C15   110.76  3.000
 LNL  H141  C14  C15   109.30  3.000
 LNL  H142  C14  C13   109.29  3.000
 LNL  H141  C14  C13   110.86  3.000
 LNL  C15   C14  C13   110.00  3.000
 LNL  H15   C15  C16   117.92  3.000
 LNL  H15   C15  C14   114.82  3.000
 LNL  C16   C15  C14   127.22  3.000
 LNL  H16   C16  C17   114.92  3.000
 LNL  H16   C16  C15   117.36  3.000
 LNL  C17   C16  C15   127.71  3.000
 LNL  H172  C17  H171  106.08  3.000
 LNL  H172  C17  C18   108.82  3.000
 LNL  H171  C17  C18   109.83  3.000
 LNL  H172  C17  C16   108.82  3.000
 LNL  H171  C17  C16   111.26  3.000
 LNL  C18   C17  C16   111.84  3.000
 LNL  H183  C18  H182  107.69  3.000
 LNL  H183  C18  H181  107.68  3.000
 LNL  H182  C18  H181  107.92  3.000
 LNL  H183  C18  C17   111.20  3.000
 LNL  H182  C18  C17   111.05  3.000
 LNL  H181  C18  C17   111.15  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
 LNL  Var_01  C11   C10  C9   C8      1.86   0.0  2
 LNL  Var_02  C14   C13  C12  C11     2.33   0.0  2
 LNL  Var_03  C17   C16  C15  C14     2.06   0.0  2
 LNL  Var_04  C3    C2   C1   O1   -178.15  30.0  3
 LNL  Var_05  C4    C3   C2   C1   -179.77  30.0  3
 LNL  Var_06  C5    C4   C3   C2   -179.46  30.0  3
 LNL  Var_07  C6    C5   C4   C3   -179.44  30.0  3
 LNL  Var_08  C7    C6   C5   C4   -179.00  30.0  3
 LNL  Var_09  C8    C7   C6   C5   -178.70  30.0  3
 LNL  Var_10  C9    C8   C7   C6    178.48  30.0  3
 LNL  Var_11  C10   C9   C8   C7    122.89  30.0  3
 LNL  Var_12  C12   C11  C10  C9    103.59  30.0  3
 LNL  Var_13  C13   C12  C11  C10   120.01  30.0  3
 LNL  Var_14  C15   C14  C13  C12   108.68  30.0  3
 LNL  Var_15  C16   C15  C14  C13   104.52  30.0  3
 LNL  Var_16  C18   C17  C16  C15   117.50  30.0  3
 LNL  Var_17  H181  C18  C17  C16   178.04  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
 LNL  plan-1  O1   0.020
 LNL  plan-1  C1   0.020
 LNL  plan-1  O2   0.020
 LNL  plan-1  C2   0.020
 LNL  plan-2  C8   0.020
 LNL  plan-2  C9   0.020
 LNL  plan-2  C10  0.020
 LNL  plan-2  C11  0.020
 LNL  plan-2  H9   0.020
 LNL  plan-2  H10  0.020
 LNL  plan-3  C11  0.020
 LNL  plan-3  C12  0.020
 LNL  plan-3  C13  0.020
 LNL  plan-3  C14  0.020
 LNL  plan-3  H12  0.020
 LNL  plan-3  H13  0.020
 LNL  plan-4  C14  0.020
 LNL  plan-4  C15  0.020
 LNL  plan-4  C16  0.020
 LNL  plan-4  C17  0.020
 LNL  plan-4  H15  0.020
 LNL  plan-4  H16  0.020

