# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:53:50 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: [(2~{S})-2,3-bis(oxidanyl)propyl] heptadec-9-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](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
 LH9  LH9  '[(2~{S})-2,3-bis(oxidanyl)propyl] heptadec-9-enoate'  ligand  62  24  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LH9
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
 LH9  C1   C  CH3   0  -0.661   -7.7660   9.3809  40.5719
 LH9  C10  C  CH2   0  -0.493   -8.1858   4.8022  33.3642
 LH9  C11  C  CH2   0  -0.414   -8.7232   3.7721  32.3665
 LH9  C12  C  CH2   0  -0.421   -9.4022   4.3838  31.1465
 LH9  C13  C  CH2   0  -0.410   -9.7306   3.3577  30.0690
 LH9  C14  C  CH2   0  -0.415  -10.4224   3.9709  28.8579
 LH9  C15  C  CH2   0  -0.418  -10.6584   2.9681  27.7363
 LH9  C16  C  CH2   0  -0.581  -11.3153   3.6166  26.5267
 LH9  C17  C  C     0   0.609  -11.5434   2.6655  25.3839
 LH9  C18  C  CH2   0  -0.219  -11.9648   2.5383  23.0597
 LH9  C19  C  CH1   0  -0.024  -11.9501   3.4643  21.8569
 LH9  C2   C  CH2   0  -0.429   -8.6088   9.6339  39.3299
 LH9  C20  C  CH2   0  -0.153  -10.6155   4.1709  21.7095
 LH9  C3   C  CH2   0  -0.424   -7.7686   9.7057  38.0570
 LH9  C4   C  CH2   0  -0.428   -8.5698   9.9682  36.7756
 LH9  C5   C  CH2   0  -0.415   -9.0046   8.7205  36.0104
 LH9  C6   C  CH2   0  -0.428   -9.9173   7.7685  36.7746
 LH9  C7   C  CH2   0  -0.485  -10.5180   6.6756  35.8840
 LH9  C8   C  C1    0  -0.211   -9.4861   5.7812  35.2731
 LH9  C9   C  C1    0  -0.205   -9.2375   5.6776  33.9703
 LH9  O1   O  O     0  -0.455  -11.5796   1.4637  25.4790
 LH9  O2   O  O2    0  -0.458  -11.7215   3.3107  24.2367
 LH9  O3   O  OH1   0  -0.665  -12.9641   4.4390  21.9113
 LH9  O4   O  OH1   0  -0.672  -10.5726   4.7953  20.4479
 LH9  H1   H  HCH3  0   0.225   -8.3765   9.3583  41.4756
 LH9  H3   H  HCH3  0   0.215   -7.2421   8.4254  40.5049
 LH9  H2   H  HCH3  0   0.214   -7.0112  10.1593  40.7028
 LH9  H19  H  HCH2  0   0.233   -7.6409   4.2843  34.1580
 LH9  H18  H  HCH2  0   0.223   -7.4511   5.4301  32.8459
 LH9  H20  H  HCH2  0   0.213   -9.4184   3.0986  32.8776
 LH9  H21  H  HCH2  0   0.218   -7.8850   3.1521  32.0327
 LH9  H23  H  HCH2  0   0.208   -8.7501   5.1537  30.7187
 LH9  H22  H  HCH2  0   0.213  -10.3217   4.8966  31.4459
 LH9  H24  H  HCH2  0   0.210  -10.3623   2.5685  30.4908
 LH9  H25  H  HCH2  0   0.208   -8.8055   2.8669  29.7466
 LH9  H27  H  HCH2  0   0.211   -9.8163   4.8016  28.4802
 LH9  H26  H  HCH2  0   0.213  -11.3777   4.4087  29.1670
 LH9  H29  H  HCH2  0   0.226  -11.2786   2.1460  28.1025
 LH9  H28  H  HCH2  0   0.224   -9.7021   2.5271  27.4404
 LH9  H30  H  HCH2  0   0.264  -10.7238   4.4656  26.1754
 LH9  H31  H  HCH2  0   0.278  -12.2907   4.0318  26.8054
 LH9  H32  H  HCH2  0   0.253  -12.9319   2.0324  23.1371
 LH9  H33  H  HCH2  0   0.241  -11.1977   1.7700  22.9375
 LH9  H34  H  HCH1  0   0.224  -12.0768   2.8042  20.9851
 LH9  H5   H  HCH2  0   0.211   -9.1566  10.5747  39.4433
 LH9  H4   H  HCH2  0   0.220   -9.3683   8.8539  39.2402
 LH9  H36  H  HCH2  0   0.198   -9.8192   3.4227  21.8169
 LH9  H35  H  HCH2  0   0.205  -10.4877   4.8962  22.5224
 LH9  H7   H  HCH2  0   0.209   -7.1884   8.7812  37.9487
 LH9  H6   H  HCH2  0   0.217   -7.0296  10.5018  38.1897
 LH9  H8   H  HCH2  0   0.223   -7.9677  10.5774  36.0963
 LH9  H9   H  HCH2  0   0.209   -9.4481  10.5768  37.0184
 LH9  H11  H  HCH2  0   0.212   -8.1125   8.1793  35.6804
 LH9  H10  H  HCH2  0   0.210   -9.5163   9.0326  35.0932
 LH9  H13  H  HCH2  0   0.218  -10.7365   8.3337  37.2297
 LH9  H12  H  HCH2  0   0.216   -9.3705   7.3025  37.6005
 LH9  H15  H  HCH2  0   0.223  -11.1158   7.1441  35.0961
 LH9  H14  H  HCH2  0   0.233  -11.2082   6.0751  36.4857
 LH9  H39  H  H     0   0.223   -8.8914   5.1923  35.9704
 LH9  H17  H  H     0   0.226   -9.8286   6.2794  33.2825
 LH9  H37  H  HOH1  0   0.453  -13.8171   3.9966  21.8600
 LH9  H38  H  HOH1  0   0.455   -9.7533   5.2948  20.3921

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
 LH9  O4   C20  single  1.408  0.020  1.408
 LH9  C20  C19  single  1.517  0.020  1.517
 LH9  C19  O3   single  1.408  0.020  1.408
 LH9  C19  C18  single  1.518  0.020  1.518
 LH9  C18  O2   single  1.429  0.020  1.429
 LH9  O2   C17  single  1.328  0.020  1.328
 LH9  C17  O1   double  1.206  0.020  1.206
 LH9  C17  C16  single  1.504  0.020  1.504
 LH9  C16  C15  single  1.522  0.020  1.522
 LH9  C15  C14  single  1.523  0.020  1.523
 LH9  C14  C13  single  1.524  0.020  1.524
 LH9  C13  C12  single  1.524  0.020  1.524
 LH9  C12  C11  single  1.524  0.020  1.524
 LH9  C11  C10  single  1.531  0.020  1.531
 LH9  C10  C9   single  1.497  0.020  1.497
 LH9  C9   C8   double  1.330  0.020  1.330
 LH9  C8   C7   single  1.496  0.020  1.496
 LH9  C7   C6   single  1.532  0.020  1.532
 LH9  C5   C6   single  1.524  0.020  1.524
 LH9  C5   C4   single  1.527  0.020  1.527
 LH9  C4   C3   single  1.534  0.020  1.534
 LH9  C3   C2   single  1.527  0.020  1.527
 LH9  C2   C1   single  1.522  0.020  1.522
 LH9  C1   H1   single  0.970  0.020  1.090
 LH9  C1   H3   single  0.970  0.020  1.090
 LH9  C1   H2   single  0.970  0.020  1.090
 LH9  C10  H19  single  0.970  0.020  1.090
 LH9  C10  H18  single  0.970  0.020  1.090
 LH9  C11  H20  single  0.970  0.020  1.090
 LH9  C11  H21  single  0.970  0.020  1.090
 LH9  C12  H23  single  0.970  0.020  1.090
 LH9  C12  H22  single  0.970  0.020  1.090
 LH9  C13  H24  single  0.970  0.020  1.090
 LH9  C13  H25  single  0.970  0.020  1.090
 LH9  C14  H27  single  0.970  0.020  1.090
 LH9  C14  H26  single  0.970  0.020  1.090
 LH9  C15  H29  single  0.970  0.020  1.090
 LH9  C15  H28  single  0.970  0.020  1.090
 LH9  C16  H30  single  0.970  0.020  1.090
 LH9  C16  H31  single  0.970  0.020  1.090
 LH9  C18  H32  single  0.970  0.020  1.090
 LH9  C18  H33  single  0.970  0.020  1.090
 LH9  C19  H34  single  0.970  0.020  1.090
 LH9  C2   H5   single  0.970  0.020  1.090
 LH9  C2   H4   single  0.970  0.020  1.090
 LH9  C20  H36  single  0.970  0.020  1.090
 LH9  C20  H35  single  0.970  0.020  1.090
 LH9  C3   H7   single  0.970  0.020  1.090
 LH9  C3   H6   single  0.970  0.020  1.090
 LH9  C4   H8   single  0.970  0.020  1.090
 LH9  C4   H9   single  0.970  0.020  1.090
 LH9  C5   H11  single  0.970  0.020  1.090
 LH9  C5   H10  single  0.970  0.020  1.090
 LH9  C6   H13  single  0.970  0.020  1.090
 LH9  C6   H12  single  0.970  0.020  1.090
 LH9  C7   H15  single  0.970  0.020  1.090
 LH9  C7   H14  single  0.970  0.020  1.090
 LH9  C8   H39  single  0.930  0.020  1.080
 LH9  C9   H17  single  0.930  0.020  1.080
 LH9  O3   H37  single  0.850  0.020  0.980
 LH9  O4   H38  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
 LH9  H2   C1   H3   107.42  3.000
 LH9  H2   C1   H1   107.60  3.000
 LH9  H3   C1   H1   107.54  3.000
 LH9  H2   C1   C2   111.22  3.000
 LH9  H3   C1   C2   111.16  3.000
 LH9  H1   C1   C2   111.69  3.000
 LH9  H18  C10  H19  106.29  3.000
 LH9  H18  C10  C9   109.10  3.000
 LH9  H19  C10  C9   109.47  3.000
 LH9  H18  C10  C11  108.20  3.000
 LH9  H19  C10  C11  109.22  3.000
 LH9  C9   C10  C11  114.25  3.000
 LH9  H21  C11  H20  106.27  3.000
 LH9  H21  C11  C12  108.92  3.000
 LH9  H20  C11  C12  109.74  3.000
 LH9  H21  C11  C10  108.11  3.000
 LH9  H20  C11  C10  109.43  3.000
 LH9  C12  C11  C10  114.06  3.000
 LH9  H22  C12  H23  106.12  3.000
 LH9  H22  C12  C13  109.14  3.000
 LH9  H23  C12  C13  108.98  3.000
 LH9  H22  C12  C11  110.07  3.000
 LH9  H23  C12  C11  109.22  3.000
 LH9  C13  C12  C11  113.06  3.000
 LH9  H25  C13  H24  106.11  3.000
 LH9  H25  C13  C14  109.25  3.000
 LH9  H24  C13  C14  109.52  3.000
 LH9  H25  C13  C12  109.14  3.000
 LH9  H24  C13  C12  109.71  3.000
 LH9  C14  C13  C12  112.89  3.000
 LH9  H26  C14  H27  106.06  3.000
 LH9  H26  C14  C15  109.63  3.000
 LH9  H27  C14  C15  109.34  3.000
 LH9  H26  C14  C13  109.43  3.000
 LH9  H27  C14  C13  109.15  3.000
 LH9  C15  C14  C13  113.01  3.000
 LH9  H28  C15  H29  106.47  3.000
 LH9  H28  C15  C16  109.53  3.000
 LH9  H29  C15  C16  109.99  3.000
 LH9  H28  C15  C14  109.22  3.000
 LH9  H29  C15  C14  109.66  3.000
 LH9  C16  C15  C14  111.82  3.000
 LH9  H31  C16  H30  105.62  3.000
 LH9  H31  C16  C17  107.33  3.000
 LH9  H30  C16  C17  109.22  3.000
 LH9  H31  C16  C15  110.09  3.000
 LH9  H30  C16  C15  110.67  3.000
 LH9  C17  C16  C15  113.57  3.000
 LH9  O2   C17  O1   123.24  3.000
 LH9  O1   C17  C16  125.08  3.000
 LH9  O2   C17  C16  111.68  3.000
 LH9  H33  C18  H32  107.66  3.000
 LH9  H33  C18  O2   110.66  3.000
 LH9  H32  C18  O2   110.01  3.000
 LH9  H33  C18  C19  109.49  3.000
 LH9  H32  C18  C19  110.28  3.000
 LH9  O2   C18  C19  108.74  3.000
 LH9  H34  C19  O3   111.28  3.000
 LH9  H34  C19  C20  107.67  3.000
 LH9  O3   C19  C20  108.35  3.000
 LH9  H34  C19  C18  105.11  3.000
 LH9  O3   C19  C18  112.63  3.000
 LH9  C20  C19  C18  111.69  3.000
 LH9  H4   C2   H5   105.92  3.000
 LH9  H4   C2   C3   110.34  3.000
 LH9  H5   C2   C3   108.75  3.000
 LH9  H4   C2   C1   109.47  3.000
 LH9  H5   C2   C1   109.60  3.000
 LH9  C3   C2   C1   112.54  3.000
 LH9  H35  C20  H36  107.07  3.000
 LH9  H35  C20  O4   111.54  3.000
 LH9  H36  C20  O4   111.58  3.000
 LH9  H35  C20  C19  109.78  3.000
 LH9  H36  C20  C19  108.12  3.000
 LH9  O4   C20  C19  108.68  3.000
 LH9  H6   C3   H7   105.54  3.000
 LH9  H6   C3   C4   109.24  3.000
 LH9  H7   C3   C4   109.76  3.000
 LH9  H6   C3   C2   107.74  3.000
 LH9  H7   C3   C2   109.50  3.000
 LH9  C4   C3   C2   114.65  3.000
 LH9  H9   C4   H8   105.64  3.000
 LH9  H9   C4   C5   109.67  3.000
 LH9  H8   C4   C5   107.50  3.000
 LH9  H9   C4   C3   109.19  3.000
 LH9  H8   C4   C3   109.08  3.000
 LH9  C5   C4   C3   115.31  3.000
 LH9  H10  C5   H11  105.62  3.000
 LH9  H10  C5   C6   108.54  3.000
 LH9  H11  C5   C6   109.29  3.000
 LH9  H10  C5   C4   108.65  3.000
 LH9  H11  C5   C4   108.85  3.000
 LH9  C6   C5   C4   115.44  3.000
 LH9  H12  C6   H13  106.27  3.000
 LH9  H12  C6   C7   109.31  3.000
 LH9  H13  C6   C7   108.45  3.000
 LH9  H12  C6   C5   110.19  3.000
 LH9  H13  C6   C5   109.52  3.000
 LH9  C7   C6   C5   112.88  3.000
 LH9  H14  C7   H15  106.62  3.000
 LH9  H14  C7   C8   109.35  3.000
 LH9  H15  C7   C8   109.80  3.000
 LH9  H14  C7   C6   108.60  3.000
 LH9  H15  C7   C6   109.10  3.000
 LH9  C8   C7   C6   113.16  3.000
 LH9  H39  C8   C9   118.86  3.000
 LH9  H39  C8   C7   116.00  3.000
 LH9  C9   C8   C7   125.13  3.000
 LH9  H17  C9   C8   118.32  3.000
 LH9  H17  C9   C10  116.69  3.000
 LH9  C8   C9   C10  124.99  3.000
 LH9  C18  O2   C17  118.15  3.000
 LH9  H37  O3   C19  108.55  3.000
 LH9  H38  O4   C20  107.96  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
 LH9  Var_01  C7   C8   C9   C10   178.71   0.0  2
 LH9  Var_02  C4   C3   C2   C1   -179.63  30.0  2
 LH9  Var_03  C13  C12  C11  C10   170.90  30.0  1
 LH9  Var_04  C14  C13  C12  C11   179.39  30.0  1
 LH9  Var_05  C8   C9   C10  C11   121.41  30.0  3
 LH9  Var_06  C15  C14  C13  C12   175.71  30.0  1
 LH9  Var_07  C9   C10  C11  C12    61.98  30.0  3
 LH9  Var_08  C16  C15  C14  C13  -178.43  30.0  2
 LH9  Var_09  C17  C16  C15  C14   178.92  30.0  1
 LH9  Var_10  O2   C17  C16  C15  -160.70  30.0  1
 LH9  Var_11  C19  C18  O2   C17  -172.50  30.0  1
 LH9  Var_12  C5   C4   C3   C2    -93.10  30.0  2
 LH9  Var_13  C6   C5   C4   C3     60.93  30.0  1
 LH9  Var_14  C7   C6   C5   C4    169.72  30.0  3
 LH9  Var_15  C8   C7   C6   C5     62.04  30.0  1
 LH9  Var_16  C9   C8   C7   C6   -115.62  30.0  2
 LH9  Var_17  H1   C1   C2   C3    178.51  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
 LH9  chir_01  C19  C20  O3  C18  positiv

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
 LH9  plan-1  C16  0.020
 LH9  plan-1  C17  0.020
 LH9  plan-1  O1   0.020
 LH9  plan-1  O2   0.020
 LH9  plan-2  C10  0.020
 LH9  plan-2  C7   0.020
 LH9  plan-2  C8   0.020
 LH9  plan-2  C9   0.020
 LH9  plan-2  H39  0.020
 LH9  plan-2  H17  0.020

