# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:42:49 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2,3-dihydroxypropyl (9Z)-octadec-9-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC\C=C/CCCCCCCC(=O)OCC(O)CO
#
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
 A6L  A6L  '2,3-dihydroxypropyl (9Z)-octadec-9-enoate'  ligand  65  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A6L
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
 A6L  CA   C  CH2   0  -0.584   -4.5299   0.0468  -0.0454
 A6L  C    C  C     0   0.607   -5.9489   0.3876   0.3189
 A6L  OXT  O  O2    0  -0.459   -6.7746  -0.6181   0.0480
 A6L  C3   C  CH2   0  -0.418   -3.5421   1.1725   0.2162
 A6L  C4   C  CH2   0  -0.415   -2.1280   0.7923  -0.2040
 A6L  C5   C  CH2   0  -0.413   -1.1141   1.9018   0.0454
 A6L  C6   C  CH2   0  -0.413    0.2932   1.5322  -0.4057
 A6L  C7   C  CH2   0  -0.415    1.3206   2.6255  -0.1412
 A6L  C8   C  CH2   0  -0.487    2.7150   2.2559  -0.6488
 A6L  C9   C  C1    0  -0.206    3.7211   3.3362  -0.4041
 A6L  C10  C  C1    0  -0.222    4.8754   3.2333   0.2543
 A6L  C11  C  CH2   0  -0.490    5.4576   2.0007   0.8748
 A6L  C12  C  CH2   0  -0.410    6.6338   1.4488   0.0649
 A6L  C13  C  CH2   0  -0.413    7.2445   0.1972   0.6818
 A6L  C14  C  CH2   0  -0.411    8.4123  -0.3597  -0.1242
 A6L  C15  C  CH2   0  -0.411    8.9923  -1.6409   0.4616
 A6L  C16  C  CH2   0  -0.406   10.1580  -2.1996  -0.3458
 A6L  C17  C  CH2   0  -0.418   10.7250  -3.4920   0.2286
 A6L  C18  C  CH3   0  -0.662   11.8847  -4.0483  -0.5867
 A6L  O    O  O     0  -0.453   -6.3154   1.4334   0.7942
 A6L  H1   H  HCH2  0   0.274   -4.2389  -0.8533   0.5061
 A6L  H2   H  HCH2  0   0.272   -4.5101  -0.2413  -1.1013
 A6L  H4   H  HCH2  0   0.224   -3.8516   2.0706  -0.3253
 A6L  H5   H  HCH2  0   0.224   -3.5494   1.4335   1.2777
 A6L  H6   H  HCH2  0   0.213   -1.8152  -0.1108   0.3315
 A6L  H7   H  HCH2  0   0.212   -2.1232   0.5301  -1.2675
 A6L  H8   H  HCH2  0   0.209   -1.4354   2.8111  -0.4745
 A6L  H9   H  HCH2  0   0.209   -1.1030   2.1502   1.1121
 A6L  H10  H  HCH2  0   0.210    0.6082   0.6121   0.0991
 A6L  H11  H  HCH2  0   0.209    0.2801   1.2996  -1.4762
 A6L  H12  H  HCH2  0   0.213    0.9955   3.5569  -0.6173
 A6L  H13  H  HCH2  0   0.216    1.3684   2.8321   0.9326
 A6L  H14  H  HCH2  0   0.229    3.0315   1.3148  -0.1939
 A6L  H15  H  HCH2  0   0.228    2.6521   2.0662  -1.7266
 A6L  H16  H  H     0   0.226    3.4592   4.3094  -0.8131
 A6L  H17  H  H     0   0.227    5.4929   4.1249   0.3300
 A6L  H18  H  HCH2  0   0.227    5.8058   2.2378   1.8856
 A6L  H19  H  HCH2  0   0.227    4.7010   1.2201   0.9863
 A6L  H20  H  HCH2  0   0.214    6.2908   1.2254  -0.9502
 A6L  H21  H  HCH2  0   0.213    7.4021   2.2230  -0.0351
 A6L  H22  H  HCH2  0   0.209    7.5780   0.4178   1.7017
 A6L  H23  H  HCH2  0   0.208    6.4700  -0.5721   0.7748
 A6L  H24  H  HCH2  0   0.206    8.0837  -0.5496  -1.1520
 A6L  H25  H  HCH2  0   0.207    9.2000   0.3986  -0.1931
 A6L  H26  H  HCH2  0   0.206    9.3197  -1.4554   1.4906
 A6L  H27  H  HCH2  0   0.206    8.2027  -2.3978   0.5267
 A6L  H28  H  HCH2  0   0.205    9.8332  -2.3749  -1.3777
 A6L  H29  H  HCH2  0   0.206   10.9536  -1.4483  -0.4030
 A6L  H30  H  HCH2  0   0.210   11.0525  -3.3179   1.2583
 A6L  H31  H  HCH2  0   0.209    9.9288  -4.2407   0.2866
 A6L  H32  H  HCH3  0   0.225   12.2727  -4.9702  -0.1519
 A6L  H33  H  HCH3  0   0.215   11.5765  -4.2707  -1.6101
 A6L  H34  H  HCH3  0   0.215   12.7093  -3.3350  -0.6404
 A6L  C1   C  CH2   0  -0.187   -8.1631  -0.4335   0.3190
 A6L  C2   C  CH1   0  -0.050   -8.8920  -1.6905  -0.1246
 A6L  C19  C  CH2   0  -0.164  -10.3654  -1.5641   0.2305
 A6L  O2   O  OH1   0  -0.667  -11.0093  -2.7776  -0.0685
 A6L  O1   O  OH1   0  -0.655   -8.6860  -1.9694  -1.4876
 A6L  H3   H  HCH2  0   0.240   -8.3204  -0.2619   1.3868
 A6L  H35  H  HCH2  0   0.235   -8.5411   0.4415  -0.2198
 A6L  H36  H  HCH1  0   0.241   -8.4779  -2.5449   0.4213
 A6L  H37  H  HCH2  0   0.203  -10.4518  -1.3084   1.2946
 A6L  H38  H  HCH2  0   0.199  -10.7993  -0.7239  -0.3317
 A6L  H39  H  HOH1  0   0.457  -11.9457  -2.6719   0.1201
 A6L  H40  H  HOH1  0   0.445   -9.0884  -1.2675  -2.0114

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
 A6L  O    C    double  1.206  0.020  1.206
 A6L  CA   C    single  1.504  0.020  1.504
 A6L  CA   C3   single  1.520  0.020  1.520
 A6L  C    OXT  single  1.329  0.020  1.329
 A6L  C4   C3   single  1.523  0.020  1.523
 A6L  C4   C5   single  1.524  0.020  1.524
 A6L  C6   C5   single  1.523  0.020  1.523
 A6L  C6   C7   single  1.523  0.020  1.523
 A6L  C17  C18  single  1.523  0.020  1.523
 A6L  C17  C16  single  1.524  0.020  1.524
 A6L  C16  C15  single  1.524  0.020  1.524
 A6L  C8   C7   single  1.529  0.020  1.529
 A6L  C8   C9   single  1.496  0.020  1.496
 A6L  C14  C15  single  1.524  0.020  1.524
 A6L  C14  C13  single  1.524  0.020  1.524
 A6L  C9   C10  double  1.333  0.020  1.333
 A6L  C12  C13  single  1.523  0.020  1.523
 A6L  C12  C11  single  1.531  0.020  1.531
 A6L  C10  C11  single  1.498  0.020  1.498
 A6L  CA   H1   single  0.970  0.020  1.090
 A6L  CA   H2   single  0.970  0.020  1.090
 A6L  C3   H4   single  0.970  0.020  1.090
 A6L  C3   H5   single  0.970  0.020  1.090
 A6L  C4   H6   single  0.970  0.020  1.090
 A6L  C4   H7   single  0.970  0.020  1.090
 A6L  C5   H8   single  0.970  0.020  1.090
 A6L  C5   H9   single  0.970  0.020  1.090
 A6L  C6   H10  single  0.970  0.020  1.090
 A6L  C6   H11  single  0.970  0.020  1.090
 A6L  C7   H12  single  0.970  0.020  1.090
 A6L  C7   H13  single  0.970  0.020  1.090
 A6L  C8   H14  single  0.970  0.020  1.090
 A6L  C8   H15  single  0.970  0.020  1.090
 A6L  C9   H16  single  0.930  0.020  1.080
 A6L  C10  H17  single  0.930  0.020  1.080
 A6L  C11  H18  single  0.970  0.020  1.090
 A6L  C11  H19  single  0.970  0.020  1.090
 A6L  C12  H20  single  0.970  0.020  1.090
 A6L  C12  H21  single  0.970  0.020  1.090
 A6L  C13  H22  single  0.970  0.020  1.090
 A6L  C13  H23  single  0.970  0.020  1.090
 A6L  C14  H24  single  0.970  0.020  1.090
 A6L  C14  H25  single  0.970  0.020  1.090
 A6L  C15  H26  single  0.970  0.020  1.090
 A6L  C15  H27  single  0.970  0.020  1.090
 A6L  C16  H28  single  0.970  0.020  1.090
 A6L  C16  H29  single  0.970  0.020  1.090
 A6L  C17  H30  single  0.970  0.020  1.090
 A6L  C17  H31  single  0.970  0.020  1.090
 A6L  C18  H32  single  0.970  0.020  1.090
 A6L  C18  H33  single  0.970  0.020  1.090
 A6L  C18  H34  single  0.970  0.020  1.090
 A6L  OXT  C1   single  1.427  0.020  1.427
 A6L  C1   C2   single  1.519  0.020  1.519
 A6L  C2   C19  single  1.521  0.020  1.521
 A6L  C19  O2   single  1.406  0.020  1.406
 A6L  C2   O1   single  1.406  0.020  1.406
 A6L  C1   H3   single  0.970  0.020  1.090
 A6L  C1   H35  single  0.970  0.020  1.090
 A6L  C2   H36  single  0.970  0.020  1.090
 A6L  C19  H37  single  0.970  0.020  1.090
 A6L  C19  H38  single  0.970  0.020  1.090
 A6L  O2   H39  single  0.850  0.020  0.980
 A6L  O1   H40  single  0.850  0.020  0.980

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
 A6L  H2   CA   H1   105.34  3.000
 A6L  H2   CA   C3   110.44  3.000
 A6L  H1   CA   C3   110.45  3.000
 A6L  H2   CA   C    108.08  3.000
 A6L  H1   CA   C    108.36  3.000
 A6L  C3   CA   C    113.80  3.000
 A6L  O    C    OXT  123.22  3.000
 A6L  OXT  C    CA   111.43  3.000
 A6L  O    C    CA   125.36  3.000
 A6L  C1   OXT  C    117.90  3.000
 A6L  H5   C3   H4   106.43  3.000
 A6L  H5   C3   C4   109.49  3.000
 A6L  H4   C3   C4   109.34  3.000
 A6L  H5   C3   CA   109.85  3.000
 A6L  H4   C3   CA   109.82  3.000
 A6L  C4   C3   CA   111.77  3.000
 A6L  H7   C4   H6   106.02  3.000
 A6L  H7   C4   C5   109.29  3.000
 A6L  H6   C4   C5   109.28  3.000
 A6L  H7   C4   C3   109.37  3.000
 A6L  H6   C4   C3   109.63  3.000
 A6L  C5   C4   C3   113.01  3.000
 A6L  H9   C5   H8   106.07  3.000
 A6L  H9   C5   C6   109.52  3.000
 A6L  H8   C5   C6   109.37  3.000
 A6L  H9   C5   C4   109.35  3.000
 A6L  H8   C5   C4   109.36  3.000
 A6L  C6   C5   C4   112.93  3.000
 A6L  H11  C6   H10  105.98  3.000
 A6L  H11  C6   C7   109.27  3.000
 A6L  H10  C6   C7   109.19  3.000
 A6L  H11  C6   C5   109.26  3.000
 A6L  H10  C6   C5   109.44  3.000
 A6L  C7   C6   C5   113.42  3.000
 A6L  H13  C7   H12  106.19  3.000
 A6L  H13  C7   C8   109.36  3.000
 A6L  H12  C7   C8   109.37  3.000
 A6L  H13  C7   C6   109.59  3.000
 A6L  H12  C7   C6   109.55  3.000
 A6L  C8   C7   C6   112.57  3.000
 A6L  H15  C8   H14  106.08  3.000
 A6L  H15  C8   C9   108.92  3.000
 A6L  H14  C8   C9   111.04  3.000
 A6L  H15  C8   C7   108.41  3.000
 A6L  H14  C8   C7   109.53  3.000
 A6L  C9   C8   C7   112.61  3.000
 A6L  H16  C9   C10  117.61  3.000
 A6L  H16  C9   C8   114.99  3.000
 A6L  C10  C9   C8   127.40  3.000
 A6L  H17  C10  C11  115.17  3.000
 A6L  H17  C10  C9   117.58  3.000
 A6L  C11  C10  C9   127.22  3.000
 A6L  H19  C11  H18  106.30  3.000
 A6L  H19  C11  C12  109.17  3.000
 A6L  H18  C11  C12  108.79  3.000
 A6L  H19  C11  C10  111.16  3.000
 A6L  H18  C11  C10  109.14  3.000
 A6L  C12  C11  C10  112.09  3.000
 A6L  H21  C12  H20  106.22  3.000
 A6L  H21  C12  C13  109.66  3.000
 A6L  H20  C12  C13  109.49  3.000
 A6L  H21  C12  C11  109.41  3.000
 A6L  H20  C12  C11  108.87  3.000
 A6L  C13  C12  C11  112.96  3.000
 A6L  H23  C13  H22  106.11  3.000
 A6L  H23  C13  C14  109.26  3.000
 A6L  H22  C13  C14  109.43  3.000
 A6L  H23  C13  C12  109.14  3.000
 A6L  H22  C13  C12  109.49  3.000
 A6L  C14  C13  C12  113.16  3.000
 A6L  H25  C14  H24  106.06  3.000
 A6L  H25  C14  C15  109.42  3.000
 A6L  H24  C14  C15  109.21  3.000
 A6L  H25  C14  C13  109.34  3.000
 A6L  H24  C14  C13  109.25  3.000
 A6L  C15  C14  C13  113.30  3.000
 A6L  H27  C15  H26  106.05  3.000
 A6L  H27  C15  C16  109.23  3.000
 A6L  H26  C15  C16  109.33  3.000
 A6L  H27  C15  C14  109.24  3.000
 A6L  H26  C15  C14  109.42  3.000
 A6L  C16  C15  C14  113.31  3.000
 A6L  H29  C16  H28  106.01  3.000
 A6L  H29  C16  C17  109.34  3.000
 A6L  H28  C16  C17  109.24  3.000
 A6L  H29  C16  C15  109.37  3.000
 A6L  H28  C16  C15  109.31  3.000
 A6L  C17  C16  C15  113.32  3.000
 A6L  H31  C17  H30  106.05  3.000
 A6L  H31  C17  C18  109.42  3.000
 A6L  H30  C17  C18  109.51  3.000
 A6L  H31  C17  C16  109.24  3.000
 A6L  H30  C17  C16  109.34  3.000
 A6L  C18  C17  C16  113.04  3.000
 A6L  H34  C18  H33  107.47  3.000
 A6L  H34  C18  H32  107.65  3.000
 A6L  H33  C18  H32  107.57  3.000
 A6L  H34  C18  C17  111.28  3.000
 A6L  H33  C18  C17  111.18  3.000
 A6L  H32  C18  C17  111.49  3.000
 A6L  H35  C1   H3   107.80  3.000
 A6L  H35  C1   C2   110.60  3.000
 A6L  H3   C1   C2   110.25  3.000
 A6L  H35  C1   OXT  110.24  3.000
 A6L  H3   C1   OXT  110.25  3.000
 A6L  C2   C1   OXT  107.72  3.000
 A6L  H36  C2   O1   105.85  3.000
 A6L  H36  C2   C19  108.35  3.000
 A6L  O1   C2   C19  112.62  3.000
 A6L  H36  C2   C1   108.57  3.000
 A6L  O1   C2   C1   112.14  3.000
 A6L  C19  C2   C1   109.14  3.000
 A6L  H38  C19  H37  106.64  3.000
 A6L  H38  C19  O2   111.71  3.000
 A6L  H37  C19  O2   111.78  3.000
 A6L  H38  C19  C2   109.04  3.000
 A6L  H37  C19  C2   108.78  3.000
 A6L  O2   C19  C2   108.80  3.000
 A6L  H39  O2   C19  108.03  3.000
 A6L  H40  O1   C2   108.73  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
 A6L  Var_01  C11  C10  C9   C8      1.80   0.0  2
 A6L  Var_02  C5   C4   C3   CA    179.97  30.0  1
 A6L  Var_03  C4   C3   CA   C    -178.44  30.0  3
 A6L  Var_04  C2   C1   OXT  C     177.75  30.0  3
 A6L  Var_05  C3   CA   C    OXT   178.81  30.0  1
 A6L  Var_06  C6   C5   C4   C3   -178.64  30.0  3
 A6L  Var_07  C7   C6   C5   C4   -179.08  30.0  1
 A6L  Var_08  C8   C7   C6   C5   -177.84  30.0  3
 A6L  Var_09  C9   C8   C7   C6    179.31  30.0  2
 A6L  Var_10  C10  C9   C8   C7    124.07  30.0  3
 A6L  Var_11  C12  C11  C10  C9    106.08  30.0  3
 A6L  Var_12  C13  C12  C11  C10   179.78  30.0  1
 A6L  Var_13  C14  C13  C12  C11   179.75  30.0  3
 A6L  Var_14  C15  C14  C13  C12  -177.84  30.0  1
 A6L  Var_15  C16  C15  C14  C13   179.87  30.0  3
 A6L  Var_16  C17  C16  C15  C14  -179.16  30.0  1
 A6L  Var_17  C18  C17  C16  C15   179.72  30.0  1
 A6L  Var_18  H32  C18  C17  C16   179.82  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A6L  chir_01  C2  C1  C19  O1  negativ

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
 A6L  plan-1  CA   0.020
 A6L  plan-1  C    0.020
 A6L  plan-1  OXT  0.020
 A6L  plan-1  O    0.020
 A6L  plan-2  C8   0.020
 A6L  plan-2  C9   0.020
 A6L  plan-2  C10  0.020
 A6L  plan-2  C11  0.020
 A6L  plan-2  H16  0.020
 A6L  plan-2  H17  0.020

