# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 22:54:08 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  50  20  .  2021-08-13  2021-08-13  
;
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  OH1   0  -0.599   0.5269   1.4387   -9.5874
 LNL  C1    C  C     0   0.549   0.1455   0.5089   -8.7149
 LNL  O2    O  O     0  -0.446  -0.1174  -0.6224   -9.0397
 LNL  C2    C  CH2   0  -0.579   0.0520   1.0576   -7.3187
 LNL  C3    C  CH2   0  -0.418  -0.3817   0.0346   -6.2816
 LNL  C4    C  CH2   0  -0.414  -0.4795   0.6482   -4.8913
 LNL  C5    C  CH2   0  -0.413  -0.8955  -0.3533   -3.8219
 LNL  C6    C  CH2   0  -0.413  -1.0145   0.2733   -2.4381
 LNL  C7    C  CH2   0  -0.415  -1.3942  -0.7254   -1.3530
 LNL  C8    C  CH2   0  -0.488  -1.5342  -0.0749    0.0233
 LNL  C9    C  C1    0  -0.203  -1.9285  -1.0558    1.0817
 LNL  C10   C  C1    0  -0.218  -1.3175  -1.2879    2.2425
 LNL  C11   C  CH2   0  -0.578  -0.1067  -0.5809    2.7854
 LNL  C12   C  C1    0  -0.201  -0.5231   0.4393    3.8059
 LNL  C13   C  C1    0  -0.205  -0.2379   0.4587    5.1065
 LNL  C14   C  CH2   0  -0.577   0.6327  -0.4951    5.8735
 LNL  C15   C  C1    0  -0.207   1.8678   0.2137    6.3520
 LNL  C16   C  C1    0  -0.208   2.1924   0.5316    7.6043
 LNL  C17   C  CH2   0  -0.490   1.4281   0.2312    8.8560
 LNL  C18   C  CH3   0  -0.660   2.2474  -0.6106    9.8331
 LNL  HO1   H  HOH1  0   0.478   0.5568   1.0612  -10.4791
 LNL  H21   H  HCH2  0   0.275  -0.6439   1.9030   -7.3385
 LNL  H22   H  HCH2  0   0.274   1.0246   1.4840   -7.0532
 LNL  H31   H  HCH2  0   0.224   0.3243  -0.8000   -6.2665
 LNL  H32   H  HCH2  0   0.224  -1.3517  -0.3857   -6.5631
 LNL  H41   H  HCH2  0   0.212  -1.1956   1.4775   -4.9090
 LNL  H42   H  HCH2  0   0.212   0.4859   1.0871   -4.6162
 LNL  H51   H  HCH2  0   0.210  -0.1730  -1.1760   -3.7883
 LNL  H52   H  HCH2  0   0.209  -1.8552  -0.8022   -4.1007
 LNL  H61   H  HCH2  0   0.210  -1.7571   1.0787   -2.4674
 LNL  H62   H  HCH2  0   0.209  -0.0644   0.7493   -2.1730
 LNL  H71   H  HCH2  0   0.217  -0.6404  -1.5174   -1.3014
 LNL  H72   H  HCH2  0   0.213  -2.3364  -1.2148   -1.6214
 LNL  H81   H  HCH2  0   0.231  -2.2957   0.7098   -0.0359
 LNL  H82   H  HCH2  0   0.230  -0.6018   0.4311    0.2860
 LNL  H9    H  H     0   0.230  -2.8164  -1.6433    0.8599
 LNL  H10   H  H     0   0.236  -1.7438  -2.0390    2.9010
 LNL  H111  H  HCH2  0   0.252   0.4446  -0.0845    1.9829
 LNL  H112  H  HCH2  0   0.252   0.5739  -1.3119    3.2260
 LNL  H12   H  H     0   0.237  -1.1546   1.2349    3.4195
 LNL  H13   H  H     0   0.238  -0.6494   1.2707    5.6999
 LNL  H141  H  HCH2  0   0.251   0.9221  -1.3462    5.2518
 LNL  H142  H  HCH2  0   0.252   0.0667  -0.9024    6.7150
 LNL  H15   H  H     0   0.235   2.5556   0.5036    5.5624
 LNL  H16   H  H     0   0.230   3.1306   1.0614    7.7542
 LNL  H171  H  HCH2  0   0.233   0.4924  -0.2795    8.6271
 LNL  H172  H  HCH2  0   0.233   1.1515   1.1726    9.3423
 LNL  H181  H  HCH3  0   0.230   1.6830  -0.8178   10.7430
 LNL  H182  H  HCH3  0   0.223   2.5271  -1.5661    9.3880
 LNL  H183  H  HCH3  0   0.222   3.1650  -0.0964   10.1228

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    single  1.331  0.020  1.331
 LNL  O1   HO1   single  0.850  0.020  0.980
 LNL  C1   O2    double  1.206  0.020  1.206
 LNL  C1   C2    single  1.503  0.020  1.503
 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  1.523  0.020  1.523
 LNL  C3   H31   single  0.970  0.020  1.090
 LNL  C3   H32   single  0.970  0.020  1.090
 LNL  C4   C5    single  1.523  0.020  1.523
 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  1.502  0.020  1.502
 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  HO1   O1   C1    109.88  3.000
 LNL  C2    C1   O2    125.38  3.000
 LNL  C2    C1   O1    111.83  3.000
 LNL  O2    C1   O1    122.77  3.000
 LNL  H22   C2   H21   105.56  3.000
 LNL  H22   C2   C3    110.50  3.000
 LNL  H21   C2   C3    110.52  3.000
 LNL  H22   C2   C1    108.20  3.000
 LNL  H21   C2   C1    107.73  3.000
 LNL  C3    C2   C1    113.95  3.000
 LNL  H32   C3   H31   106.43  3.000
 LNL  H32   C3   C4    109.44  3.000
 LNL  H31   C3   C4    109.66  3.000
 LNL  H32   C3   C2    109.64  3.000
 LNL  H31   C3   C2    109.81  3.000
 LNL  C4    C3   C2    111.72  3.000
 LNL  H42   C4   H41   106.07  3.000
 LNL  H42   C4   C5    109.14  3.000
 LNL  H41   C4   C5    109.30  3.000
 LNL  H42   C4   C3    109.52  3.000
 LNL  H41   C4   C3    109.40  3.000
 LNL  C5    C4   C3    113.18  3.000
 LNL  H52   C5   H51   106.13  3.000
 LNL  H52   C5   C6    109.35  3.000
 LNL  H51   C5   C6    109.42  3.000
 LNL  H52   C5   C4    109.27  3.000
 LNL  H51   C5   C4    109.58  3.000
 LNL  C6    C5   C4    112.87  3.000
 LNL  H62   C6   H61   105.95  3.000
 LNL  H62   C6   C7    109.20  3.000
 LNL  H61   C6   C7    109.39  3.000
 LNL  H62   C6   C5    109.32  3.000
 LNL  H61   C6   C5    109.33  3.000
 LNL  C7    C6   C5    113.38  3.000
 LNL  H72   C7   H71   106.30  3.000
 LNL  H72   C7   C8    109.39  3.000
 LNL  H71   C7   C8    109.17  3.000
 LNL  H72   C7   C6    109.45  3.000
 LNL  H71   C7   C6    109.66  3.000
 LNL  C8    C7   C6    112.66  3.000
 LNL  H82   C8   H81   105.93  3.000
 LNL  H82   C8   C9    111.00  3.000
 LNL  H81   C8   C9    108.95  3.000
 LNL  H82   C8   C7    109.59  3.000
 LNL  H81   C8   C7    108.66  3.000
 LNL  C9    C8   C7    112.47  3.000
 LNL  H9    C9   C10   117.26  3.000
 LNL  H9    C9   C8    115.16  3.000
 LNL  C10   C9   C8    127.58  3.000
 LNL  H10   C10  C11   114.99  3.000
 LNL  H10   C10  C9    117.96  3.000
 LNL  C11   C10  C9    127.01  3.000
 LNL  H112  C11  H111  106.62  3.000
 LNL  H112  C11  C12   110.70  3.000
 LNL  H111  C11  C12   109.28  3.000
 LNL  H112  C11  C10   109.45  3.000
 LNL  H111  C11  C10   110.77  3.000
 LNL  C12   C11  C10   109.97  3.000
 LNL  H12   C12  C13   117.46  3.000
 LNL  H12   C12  C11   114.63  3.000
 LNL  C13   C12  C11   127.89  3.000
 LNL  H13   C13  C14   114.53  3.000
 LNL  H13   C13  C12   117.59  3.000
 LNL  C14   C13  C12   127.85  3.000
 LNL  H142  C14  H141  106.55  3.000
 LNL  H142  C14  C15   110.88  3.000
 LNL  H141  C14  C15   109.32  3.000
 LNL  H142  C14  C13   109.25  3.000
 LNL  H141  C14  C13   110.95  3.000
 LNL  C15   C14  C13   109.85  3.000
 LNL  H15   C15  C16   117.73  3.000
 LNL  H15   C15  C14   114.51  3.000
 LNL  C16   C15  C14   127.76  3.000
 LNL  H16   C16  C17   115.01  3.000
 LNL  H16   C16  C15   117.12  3.000
 LNL  C17   C16  C15   127.86  3.000
 LNL  H172  C17  H171  106.21  3.000
 LNL  H172  C17  C18   108.97  3.000
 LNL  H171  C17  C18   109.65  3.000
 LNL  H172  C17  C16   109.13  3.000
 LNL  H171  C17  C16   110.89  3.000
 LNL  C18   C17  C16   111.81  3.000
 LNL  H183  C18  H182  107.80  3.000
 LNL  H183  C18  H181  107.66  3.000
 LNL  H182  C18  H181  107.87  3.000
 LNL  H183  C18  C17   111.17  3.000
 LNL  H182  C18  C17   111.05  3.000
 LNL  H181  C18  C17   111.14  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  CONST_01  HO1   O1   C1   O2      0.00   0.0  0
 LNL  Var_01    C11   C10  C9   C8      2.26   0.0  2
 LNL  Var_02    C14   C13  C12  C11     3.50   0.0  2
 LNL  Var_03    C17   C16  C15  C14     1.81   0.0  2
 LNL  Var_04    C3    C2   C1   O1    179.95  30.0  3
 LNL  Var_05    C4    C3   C2   C1   -179.16  30.0  3
 LNL  Var_06    C5    C4   C3   C2   -179.29  30.0  3
 LNL  Var_07    C6    C5   C4   C3   -179.01  30.0  3
 LNL  Var_08    C7    C6   C5   C4   -178.48  30.0  3
 LNL  Var_09    C8    C7   C6   C5   -178.94  30.0  3
 LNL  Var_10    C9    C8   C7   C6    179.09  30.0  3
 LNL  Var_11    C10   C9   C8   C7    126.47  30.0  3
 LNL  Var_12    C12   C11  C10  C9    100.82  30.0  3
 LNL  Var_13    C13   C12  C11  C10   115.75  30.0  3
 LNL  Var_14    C15   C14  C13  C12   112.63  30.0  3
 LNL  Var_15    C16   C15  C14  C13   110.61  30.0  3
 LNL  Var_16    C18   C17  C16  C15   120.53  30.0  3
 LNL  Var_17    H181  C18  C17  C16   179.66  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-1  HO1  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

