# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:56:23 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  51  21  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.447   9.0896  -0.4312   0.8182
 10Y  C1   C  C     0   0.550   8.8589  -0.5676  -0.3578
 10Y  O2   O  OH1   0  -0.599   9.8152  -0.5847  -1.2832
 10Y  C2   C  CH2   0  -0.580   7.4929  -0.7358  -0.9617
 10Y  C3   C  CH2   0  -0.418   6.3626  -0.7240   0.0542
 10Y  C4   C  CH2   0  -0.414   5.0046  -0.9088  -0.6113
 10Y  C5   C  CH2   0  -0.413   3.8494  -0.9051   0.3823
 10Y  C6   C  CH2   0  -0.413   2.4942  -1.1071  -0.2830
 10Y  C7   C  CH2   0  -0.416   1.3326  -1.1091   0.7028
 10Y  C8   C  CH2   0  -0.488  -0.0143  -1.3464   0.0197
 10Y  C9   C  C1    0  -0.197  -1.1507  -1.4045   0.9911
 10Y  C10  C  C1    0  -0.219  -2.2907  -0.7164   0.9537
 10Y  C11  C  CH2   0  -0.566  -2.7150   0.2724  -0.0933
 10Y  C12  C  CH1   0   0.014  -3.6793  -0.3637  -1.0628
 10Y  O3   O  O2    0  -0.486  -4.9844  -0.6704  -0.5894
 10Y  C13  C  CH1   0   0.014  -4.8614   0.2856  -1.6313
 10Y  C14  C  CH2   0  -0.557  -5.2995   1.6959  -1.3300
 10Y  C15  C  C1    0  -0.215  -6.7958   1.7827  -1.2619
 10Y  C16  C  C1    0  -0.198  -7.5325   1.8013  -0.1534
 10Y  C17  C  CH2   0  -0.486  -7.0445   1.7798   1.2607
 10Y  C18  C  CH3   0  -0.658  -7.3319   3.0958   1.9818
 10Y  H1   H  HOH1  0   0.478  10.6823  -0.4796  -0.8643
 10Y  H2   H  HCH2  0   0.275   7.3502   0.0565  -1.7034
 10Y  H3   H  HCH2  0   0.275   7.4867  -1.6707  -1.5320
 10Y  H4   H  HCH2  0   0.225   6.5159  -1.5177   0.7903
 10Y  H5   H  HCH2  0   0.225   6.3716   0.2189   0.6083
 10Y  H6   H  HCH2  0   0.213   4.8495  -0.1159  -1.3508
 10Y  H7   H  HCH2  0   0.212   4.9975  -1.8510  -1.1708
 10Y  H8   H  HCH2  0   0.209   4.0086  -1.6930   1.1265
 10Y  H9   H  HCH2  0   0.210   3.8487   0.0406   0.9357
 10Y  H10  H  HCH2  0   0.210   2.3350  -0.3210  -1.0290
 10Y  H11  H  HCH2  0   0.209   2.4998  -2.0534  -0.8356
 10Y  H12  H  HCH2  0   0.214   1.4966  -1.8840   1.4590
 10Y  H13  H  HCH2  0   0.217   1.3058  -0.1563   1.2413
 10Y  H14  H  HCH2  0   0.230  -0.1796  -0.5771  -0.7373
 10Y  H15  H  HCH2  0   0.232   0.0328  -2.2989  -0.5214
 10Y  H16  H  H     0   0.231  -1.0157  -2.1030   1.8133
 10Y  H17  H  H     0   0.236  -3.0188  -0.8979   1.7384
 10Y  H18  H  HCH2  0   0.252  -3.1659   1.1392   0.3952
 10Y  H19  H  HCH2  0   0.253  -1.8612   0.6405  -0.6655
 10Y  H20  H  HCH1  0   0.244  -3.2255  -1.1606  -1.6539
 10Y  H21  H  HCH1  0   0.243  -5.1953  -0.0774  -2.6045
 10Y  H22  H  HCH2  0   0.247  -4.8419   2.0568  -0.4092
 10Y  H23  H  HCH2  0   0.252  -4.9321   2.3373  -2.1359
 10Y  H24  H  H     0   0.236  -7.3118   1.8030  -2.2173
 10Y  H25  H  H     0   0.231  -8.6120   1.8599  -0.2681
 10Y  H26  H  HCH2  0   0.233  -7.5472   0.9663   1.7920
 10Y  H27  H  HCH2  0   0.227  -5.9776   1.5568   1.3059
 10Y  H28  H  HCH3  0   0.223  -6.7953   3.9219   1.5138
 10Y  H29  H  HCH3  0   0.221  -8.3961   3.3360   1.9578
 10Y  H30  H  HCH3  0   0.229  -7.0268   3.0459   3.0274

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  1.500  0.020  1.500
 10Y  C18  C17  single  1.528  0.020  1.528
 10Y  C14  C13  single  1.507  0.020  1.507
 10Y  C13  O3   single  1.419  0.020  1.419
 10Y  C13  C12  single  1.464  0.020  1.464
 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  1.524  0.020  1.524
 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   double  1.206  0.020  1.206
 10Y  C2   C1   single  1.503  0.020  1.503
 10Y  C1   O2   single  1.331  0.020  1.331
 10Y  O2   H1   single  0.850  0.020  0.980
 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   111.85  3.000
 10Y  O2   C1   O1   122.82  3.000
 10Y  C2   C1   O1   125.33  3.000
 10Y  H1   O2   C1   109.94  3.000
 10Y  H3   C2   H2   105.33  3.000
 10Y  H3   C2   C3   110.52  3.000
 10Y  H2   C2   C3   110.51  3.000
 10Y  H3   C2   C1   108.06  3.000
 10Y  H2   C2   C1   108.05  3.000
 10Y  C3   C2   C1   113.98  3.000
 10Y  H5   C3   H4   106.48  3.000
 10Y  H5   C3   C4   109.47  3.000
 10Y  H4   C3   C4   109.33  3.000
 10Y  H5   C3   C2   109.83  3.000
 10Y  H4   C3   C2   109.88  3.000
 10Y  C4   C3   C2   111.71  3.000
 10Y  H7   C4   H6   106.07  3.000
 10Y  H7   C4   C5   109.28  3.000
 10Y  H6   C4   C5   109.34  3.000
 10Y  H7   C4   C3   109.45  3.000
 10Y  H6   C4   C3   109.47  3.000
 10Y  C5   C4   C3   112.99  3.000
 10Y  H9   C5   H8   106.13  3.000
 10Y  H9   C5   C6   109.54  3.000
 10Y  H8   C5   C6   109.31  3.000
 10Y  H9   C5   C4   109.39  3.000
 10Y  H8   C5   C4   109.34  3.000
 10Y  C6   C5   C4   112.92  3.000
 10Y  H11  C6   H10  106.08  3.000
 10Y  H11  C6   C7   109.21  3.000
 10Y  H10  C6   C7   109.32  3.000
 10Y  H11  C6   C5   109.28  3.000
 10Y  H10  C6   C5   109.37  3.000
 10Y  C7   C6   C5   113.33  3.000
 10Y  H13  C7   H12  106.25  3.000
 10Y  H13  C7   C8   109.48  3.000
 10Y  H12  C7   C8   109.31  3.000
 10Y  H13  C7   C6   109.62  3.000
 10Y  H12  C7   C6   109.48  3.000
 10Y  C8   C7   C6   112.51  3.000
 10Y  H15  C8   H14  106.05  3.000
 10Y  H15  C8   C9   108.62  3.000
 10Y  H14  C8   C9   111.25  3.000
 10Y  H15  C8   C7   108.52  3.000
 10Y  H14  C8   C7   109.50  3.000
 10Y  C9   C8   C7   112.65  3.000
 10Y  H16  C9   C10  117.34  3.000
 10Y  H16  C9   C8   114.94  3.000
 10Y  C10  C9   C8   127.72  3.000
 10Y  H17  C10  C11  115.12  3.000
 10Y  H17  C10  C9   117.86  3.000
 10Y  C11  C10  C9   126.99  3.000
 10Y  H19  C11  H18  106.84  3.000
 10Y  H19  C11  C12  107.78  3.000
 10Y  H18  C11  C12  110.99  3.000
 10Y  H19  C11  C10  111.50  3.000
 10Y  H18  C11  C10  109.11  3.000
 10Y  C12  C11  C10  110.56  3.000
 10Y  H20  C12  C13  116.71  3.000
 10Y  H20  C12  O3   113.87  3.000
 10Y  C13  C12  O3    58.91  3.000
 10Y  H20  C12  C11  112.98  3.000
 10Y  O3   C12  C11  117.64  3.000
 10Y  C13  C12  C11  125.38  3.000
 10Y  C13  O3   C12   62.01  3.000
 10Y  H21  C13  C14  113.62  3.000
 10Y  H21  C13  O3   113.83  3.000
 10Y  C14  C13  O3   117.28  3.000
 10Y  H21  C13  C12  116.49  3.000
 10Y  O3   C13  C12   59.08  3.000
 10Y  C14  C13  C12  124.91  3.000
 10Y  H23  C14  H22  106.70  3.000
 10Y  H23  C14  C15  109.55  3.000
 10Y  H22  C14  C15  111.17  3.000
 10Y  H23  C14  C13  107.69  3.000
 10Y  H22  C14  C13  110.90  3.000
 10Y  C15  C14  C13  110.68  3.000
 10Y  H24  C15  C16  118.00  3.000
 10Y  H24  C15  C14  115.78  3.000
 10Y  C16  C15  C14  126.19  3.000
 10Y  H25  C16  C17  115.11  3.000
 10Y  H25  C16  C15  117.54  3.000
 10Y  C17  C16  C15  127.33  3.000
 10Y  H27  C17  H26  106.10  3.000
 10Y  H27  C17  C18  109.91  3.000
 10Y  H26  C17  C18  108.96  3.000
 10Y  H27  C17  C16  111.16  3.000
 10Y  H26  C17  C16  108.65  3.000
 10Y  C18  C17  C16  111.86  3.000
 10Y  H30  C18  H29  107.70  3.000
 10Y  H30  C18  H28  107.97  3.000
 10Y  H29  C18  H28  107.67  3.000
 10Y  H30  C18  C17  111.13  3.000
 10Y  H29  C18  C17  111.27  3.000
 10Y  H28  C18  C17  110.94  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  CONST_01  H1   O2   C1   O1      0.00   0.0  0
 10Y  Var_01    O3   C13  C12  C11  -103.66  30.0  1
 10Y  Var_02    C14  C13  O3   C12  -116.21  30.0  1
 10Y  Var_03    C13  C12  C11  C10   140.37  30.0  2
 10Y  Var_04    C15  C14  C13  C12  -142.84  30.0  1
 10Y  Var_05    C12  C11  C10  C9    100.48  30.0  2
 10Y  Var_06    C16  C15  C14  C13   100.06  30.0  1
 10Y  Var_07    C11  C10  C9   C8      1.03   0.0  2
 10Y  Var_08    C17  C16  C15  C14     1.89   0.0  2
 10Y  Var_09    C3   C2   C1   O1     -0.06  30.0  2
 10Y  Var_10    C4   C3   C2   C1   -179.55  30.0  1
 10Y  Var_11    C5   C4   C3   C2    179.85  30.0  2
 10Y  Var_12    C6   C5   C4   C3   -179.30  30.0  1
 10Y  Var_13    C7   C6   C5   C4    179.83  30.0  2
 10Y  Var_14    C8   C7   C6   C5   -178.63  30.0  1
 10Y  Var_15    C9   C8   C7   C6    177.66  30.0  3
 10Y  Var_16    C10  C9   C8   C7    128.13  30.0  1
 10Y  Var_17    C18  C17  C16  C15   112.58  30.0  3
 10Y  Var_18    H28  C18  C17  C16   -63.33  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-1  H1   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

