# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 23:38:48 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C[C@@H]1O[C@@H]1C\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
 10Y  10Y  '(9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid'  ligand  50  21  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_10Y
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
 10Y  O1   O  O      0  -0.610   9.0664  -0.7026   0.8112
 10Y  C1   C  C      0   0.410   8.9362  -0.7442  -0.4281
 10Y  O2   O  OC    -1  -0.636   9.8613  -0.7067  -1.2679
 10Y  C2   C  CH2    0  -0.581   7.5129  -0.8614  -1.0011
 10Y  C3   C  CH2    0  -0.402   6.3772  -0.8520   0.0091
 10Y  C4   C  CH2    0  -0.409   5.0099  -1.0117  -0.6456
 10Y  C5   C  CH2    0  -0.410   3.8555  -1.0092   0.3491
 10Y  C6   C  CH2    0  -0.412   2.4975  -1.2039  -0.3134
 10Y  C7   C  CH2    0  -0.415   1.3357  -1.1998   0.6722
 10Y  C8   C  CH2    0  -0.488  -0.0118  -1.4386  -0.0092
 10Y  C9   C  C1     0  -0.198  -1.1486  -1.4849   0.9623
 10Y  C10  C  C1     0  -0.219  -2.2840  -0.7896   0.9224
 10Y  C11  C  CH2    0  -0.565  -2.7049   0.1954  -0.1293
 10Y  C12  C  CH1    0   0.014  -3.7118  -0.4260  -1.0644
 10Y  O3   O  O2     0  -0.487  -5.0171  -0.6715  -0.5574
 10Y  C13  C  CH1    0   0.014  -4.8799   0.2547  -1.6244
 10Y  C14  C  CH2    0  -0.559  -5.2574   1.6877  -1.3479
 10Y  C15  C  C1     0  -0.217  -6.7460   1.8321  -1.2256
 10Y  C16  C  C1     0  -0.198  -7.4391   1.8898  -0.0903
 10Y  C17  C  CH2    0  -0.485  -6.9000   1.8609   1.3052
 10Y  C18  C  CH3    0  -0.658  -7.1333   3.1835   2.0334
 10Y  H2   H  HCH2   0   0.215   7.3677  -0.0517  -1.7257
 10Y  H3   H  HCH2   0   0.216   7.4639  -1.7811  -1.5972
 10Y  H4   H  HCH2   0   0.200   6.5226  -1.6549   0.7378
 10Y  H5   H  HCH2   0   0.199   6.3970   0.0803   0.5826
 10Y  H6   H  HCH2   0   0.202   4.8585  -0.2088  -1.3762
 10Y  H7   H  HCH2   0   0.201   4.9888  -1.9459  -1.2192
 10Y  H8   H  HCH2   0   0.205   4.0130  -1.8010   1.0899
 10Y  H9   H  HCH2   0   0.205   3.8585  -0.0665   0.9080
 10Y  H10  H  HCH2   0   0.208   2.3419  -0.4173  -1.0598
 10Y  H11  H  HCH2   0   0.207   2.4978  -2.1501  -0.8665
 10Y  H12  H  HCH2   0   0.213   1.4985  -1.9715   1.4319
 10Y  H13  H  HCH2   0   0.216   1.3103  -0.2444   1.2063
 10Y  H14  H  HCH2   0   0.230  -0.1752  -0.6749  -0.7722
 10Y  H15  H  HCH2   0   0.232   0.0327  -2.3958  -0.5423
 10Y  H16  H  H      0   0.231  -1.0165  -2.1783   1.7893
 10Y  H17  H  H      0   0.236  -3.0116  -0.9603   1.7100
 10Y  H18  H  HCH2   0   0.252  -3.1184   1.0822   0.3565
 10Y  H19  H  HCH2   0   0.253  -1.8551   0.5304  -0.7273
 10Y  H20  H  HCH1   0   0.245  -3.2998  -1.2532  -1.6442
 10Y  H21  H  HCH1   0   0.243  -5.2487  -0.1176  -2.5812
 10Y  H22  H  HCH2   0   0.249  -4.7517   2.0588  -0.4569
 10Y  H23  H  HCH2   0   0.253  -4.8993   2.2923  -2.1856
 10Y  H24  H  H      0   0.236  -7.2971   1.8638  -2.1608
 10Y  H25  H  H      0   0.231  -8.5192   1.9888  -0.1657
 10Y  H26  H  HCH2   0   0.233  -7.4003   1.0593   1.8568
 10Y  H27  H  HCH2   0   0.227  -5.8373   1.6148   1.3117
 10Y  H28  H  HCH3   0   0.222  -6.5974   3.9986   1.5456
 10Y  H29  H  HCH3   0   0.221  -8.1926   3.4456   2.0476
 10Y  H30  H  HCH3   0   0.229  -6.7917   3.1282   3.0675

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
 10Y  C16  C15  double  1.331  0.020  1.331
 10Y  C16  C17  single  1.496  0.020  1.496
 10Y  C15  C14  single  1.501  0.020  1.501
 10Y  C18  C17  single  1.528  0.020  1.528
 10Y  C14  C13  single  1.507  0.020  1.507
 10Y  C13  O3   single  1.420  0.020  1.420
 10Y  C13  C12  single  1.463  0.020  1.463
 10Y  O3   C12  single  1.422  0.020  1.422
 10Y  C12  C11  single  1.508  0.020  1.508
 10Y  C11  C10  single  1.501  0.020  1.501
 10Y  C10  C9   double  1.332  0.020  1.332
 10Y  C9   C8   single  1.496  0.020  1.496
 10Y  C7   C8   single  1.529  0.020  1.529
 10Y  C7   C6   single  1.523  0.020  1.523
 10Y  C6   C5   single  1.523  0.020  1.523
 10Y  C5   C4   single  1.524  0.020  1.524
 10Y  C4   C3   single  1.524  0.020  1.524
 10Y  C3   C2   single  1.520  0.020  1.520
 10Y  O1   C1   deloc   1.247  0.020  1.247
 10Y  C2   C1   single  1.539  0.020  1.539
 10Y  C1   O2   deloc   1.250  0.020  1.250
 10Y  C2   H2   single  0.970  0.020  1.090
 10Y  C2   H3   single  0.970  0.020  1.090
 10Y  C3   H4   single  0.970  0.020  1.090
 10Y  C3   H5   single  0.970  0.020  1.090
 10Y  C4   H6   single  0.970  0.020  1.090
 10Y  C4   H7   single  0.970  0.020  1.090
 10Y  C5   H8   single  0.970  0.020  1.090
 10Y  C5   H9   single  0.970  0.020  1.090
 10Y  C6   H10  single  0.970  0.020  1.090
 10Y  C6   H11  single  0.970  0.020  1.090
 10Y  C7   H12  single  0.970  0.020  1.090
 10Y  C7   H13  single  0.970  0.020  1.090
 10Y  C8   H14  single  0.970  0.020  1.090
 10Y  C8   H15  single  0.970  0.020  1.090
 10Y  C9   H16  single  0.930  0.020  1.080
 10Y  C10  H17  single  0.930  0.020  1.080
 10Y  C11  H18  single  0.970  0.020  1.090
 10Y  C11  H19  single  0.970  0.020  1.090
 10Y  C12  H20  single  0.970  0.020  1.090
 10Y  C13  H21  single  0.970  0.020  1.090
 10Y  C14  H22  single  0.970  0.020  1.090
 10Y  C14  H23  single  0.970  0.020  1.090
 10Y  C15  H24  single  0.930  0.020  1.080
 10Y  C16  H25  single  0.930  0.020  1.080
 10Y  C17  H26  single  0.970  0.020  1.090
 10Y  C17  H27  single  0.970  0.020  1.090
 10Y  C18  H28  single  0.970  0.020  1.090
 10Y  C18  H29  single  0.970  0.020  1.090
 10Y  C18  H30  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
 10Y  C2   C1   O2   115.89  3.000
 10Y  O2   C1   O1   126.13  3.000
 10Y  C2   C1   O1   117.98  3.000
 10Y  H3   C2   H2   104.72  3.000
 10Y  H3   C2   C3   109.45  3.000
 10Y  H2   C2   C3   109.62  3.000
 10Y  H3   C2   C1   107.91  3.000
 10Y  H2   C2   C1   108.21  3.000
 10Y  C3   C2   C1   116.31  3.000
 10Y  H5   C3   H4   105.88  3.000
 10Y  H5   C3   C4   109.29  3.000
 10Y  H4   C3   C4   109.18  3.000
 10Y  H5   C3   C2   109.87  3.000
 10Y  H4   C3   C2   109.81  3.000
 10Y  C4   C3   C2   112.59  3.000
 10Y  H7   C4   H6   105.83  3.000
 10Y  H7   C4   C5   109.16  3.000
 10Y  H6   C4   C5   109.22  3.000
 10Y  H7   C4   C3   109.34  3.000
 10Y  H6   C4   C3   109.48  3.000
 10Y  C5   C4   C3   113.51  3.000
 10Y  H9   C5   H8   106.05  3.000
 10Y  H9   C5   C6   109.52  3.000
 10Y  H8   C5   C6   109.25  3.000
 10Y  H9   C5   C4   109.40  3.000
 10Y  H8   C5   C4   109.35  3.000
 10Y  C6   C5   C4   113.03  3.000
 10Y  H11  C6   H10  106.02  3.000
 10Y  H11  C6   C7   109.21  3.000
 10Y  H10  C6   C7   109.30  3.000
 10Y  H11  C6   C5   109.24  3.000
 10Y  H10  C6   C5   109.34  3.000
 10Y  C7   C6   C5   113.46  3.000
 10Y  H13  C7   H12  106.26  3.000
 10Y  H13  C7   C8   109.47  3.000
 10Y  H12  C7   C8   109.28  3.000
 10Y  H13  C7   C6   109.62  3.000
 10Y  H12  C7   C6   109.48  3.000
 10Y  C8   C7   C6   112.54  3.000
 10Y  H15  C8   H14  106.08  3.000
 10Y  H15  C8   C9   108.63  3.000
 10Y  H14  C8   C9   111.20  3.000
 10Y  H15  C8   C7   108.50  3.000
 10Y  H14  C8   C7   109.52  3.000
 10Y  C9   C8   C7   112.65  3.000
 10Y  H16  C9   C10  117.34  3.000
 10Y  H16  C9   C8   114.92  3.000
 10Y  C10  C9   C8   127.74  3.000
 10Y  H17  C10  C11  115.06  3.000
 10Y  H17  C10  C9   117.86  3.000
 10Y  C11  C10  C9   127.05  3.000
 10Y  H19  C11  H18  106.80  3.000
 10Y  H19  C11  C12  107.85  3.000
 10Y  H18  C11  C12  110.94  3.000
 10Y  H19  C11  C10  111.52  3.000
 10Y  H18  C11  C10  109.10  3.000
 10Y  C12  C11  C10  110.57  3.000
 10Y  H20  C12  C13  116.79  3.000
 10Y  H20  C12  O3   113.91  3.000
 10Y  C13  C12  O3    58.93  3.000
 10Y  H20  C12  C11  112.94  3.000
 10Y  O3   C12  C11  117.58  3.000
 10Y  C13  C12  C11  125.35  3.000
 10Y  C13  O3   C12   62.00  3.000
 10Y  H21  C13  C14  113.62  3.000
 10Y  H21  C13  O3   113.82  3.000
 10Y  C14  C13  O3   117.27  3.000
 10Y  H21  C13  C12  116.53  3.000
 10Y  O3   C13  C12   59.07  3.000
 10Y  C14  C13  C12  124.88  3.000
 10Y  H23  C14  H22  106.63  3.000
 10Y  H23  C14  C15  109.52  3.000
 10Y  H22  C14  C15  111.16  3.000
 10Y  H23  C14  C13  107.64  3.000
 10Y  H22  C14  C13  110.95  3.000
 10Y  C15  C14  C13  110.79  3.000
 10Y  H24  C15  C16  117.96  3.000
 10Y  H24  C15  C14  115.85  3.000
 10Y  C16  C15  C14  126.17  3.000
 10Y  H25  C16  C17  115.11  3.000
 10Y  H25  C16  C15  117.52  3.000
 10Y  C17  C16  C15  127.36  3.000
 10Y  H27  C17  H26  106.09  3.000
 10Y  H27  C17  C18  109.96  3.000
 10Y  H26  C17  C18  108.91  3.000
 10Y  H27  C17  C16  111.15  3.000
 10Y  H26  C17  C16  108.64  3.000
 10Y  C18  C17  C16  111.89  3.000
 10Y  H30  C18  H29  107.69  3.000
 10Y  H30  C18  H28  107.95  3.000
 10Y  H29  C18  H28  107.66  3.000
 10Y  H30  C18  C17  111.12  3.000
 10Y  H29  C18  C17  111.25  3.000
 10Y  H28  C18  C17  111.02  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
 10Y  Var_01  O3   C13  C12  C11  -103.61  30.0  1
 10Y  Var_02  C14  C13  O3   C12  -116.18  30.0  1
 10Y  Var_03  C13  C12  C11  C10   141.05  30.0  2
 10Y  Var_04  C15  C14  C13  C12  -141.77  30.0  2
 10Y  Var_05  C12  C11  C10  C9    102.44  30.0  1
 10Y  Var_06  C16  C15  C14  C13    99.03  30.0  1
 10Y  Var_07  C11  C10  C9   C8      1.19   0.0  2
 10Y  Var_08  C17  C16  C15  C14     1.74   0.0  2
 10Y  Var_09  C3   C2   C1   O1      2.71  30.0  2
 10Y  Var_10  C4   C3   C2   C1   -178.39  30.0  2
 10Y  Var_11  C5   C4   C3   C2    179.83  30.0  1
 10Y  Var_12  C6   C5   C4   C3   -178.58  30.0  1
 10Y  Var_13  C7   C6   C5   C4   -179.86  30.0  2
 10Y  Var_14  C8   C7   C6   C5   -178.27  30.0  1
 10Y  Var_15  C9   C8   C7   C6    177.90  30.0  3
 10Y  Var_16  C10  C9   C8   C7    127.81  30.0  2
 10Y  Var_17  C18  C17  C16  C15   113.77  30.0  3
 10Y  Var_18  H28  C18  C17  C16   -63.37  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
 10Y  chir_01  C12  C13  O3   C11  both
 10Y  chir_02  C13  O3   C12  C14  both

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
 10Y  plan-1  O1   0.020
 10Y  plan-1  C1   0.020
 10Y  plan-1  O2   0.020
 10Y  plan-1  C2   0.020
 10Y  plan-2  C14  0.020
 10Y  plan-2  C15  0.020
 10Y  plan-2  C16  0.020
 10Y  plan-2  C17  0.020
 10Y  plan-2  H24  0.020
 10Y  plan-2  H25  0.020
 10Y  plan-3  C8   0.020
 10Y  plan-3  C9   0.020
 10Y  plan-3  C10  0.020
 10Y  plan-3  C11  0.020
 10Y  plan-3  H16  0.020
 10Y  plan-3  H17  0.020

