# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 19:30:44 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (9Z)-11-{(2S,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
 10X  10X  '(9Z)-11-{(2S,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_10X
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
 10X  CAA  C  CH3    0  -0.658   8.3064  -1.3626  -1.4611
 10X  CAH  C  CH2    0  -0.487   6.7997  -1.2166  -1.2547
 10X  CAD  C  C1     0  -0.199   6.2808  -2.1735  -0.2271
 10X  CAF  C  C1     0  -0.220   5.7976  -1.8816   0.9788
 10X  CAO  C  CH2    0  -0.551   5.6380  -0.5099   1.5668
 10X  CAT  C  CH1    0   0.010   4.2266  -0.0057   1.4129
 10X  OAR  O  O2     0  -0.479   3.8460   0.4262   0.1140
 10X  CAU  C  CH1    0   0.009   3.9180   1.3958   1.1501
 10X  CAP  C  CH2    0  -0.550   2.6167   2.0290   1.5693
 10X  CAG  C  C1     0  -0.221   2.1456   3.0357   0.5614
 10X  CAE  C  C1     0  -0.199   1.2175   2.8381  -0.3729
 10X  CAI  C  CH2    0  -0.488   0.4236   1.5924  -0.6084
 10X  CAJ  C  CH2    0  -0.413  -1.0561   1.7710  -0.2663
 10X  CAK  C  CH2    0  -0.412  -1.8848   0.5312  -0.5750
 10X  CAL  C  CH2    0  -0.411  -3.3615   0.6902  -0.2371
 10X  CAM  C  CH2    0  -0.409  -4.1826  -0.5552  -0.5456
 10X  CAN  C  CH2    0  -0.402  -5.6617  -0.4087  -0.2091
 10X  CAQ  C  CH2    0  -0.582  -6.4579  -1.6648  -0.5219
 10X  CAS  C  C      0   0.410  -7.9608  -1.6206  -0.1972
 10X  OAC  O  O      0  -0.610  -8.4333  -0.5533   0.2415
 10X  OAB  O  OC    -1  -0.635  -8.5961  -2.6767  -0.4066
 10X  H1   H  HCH3   0   0.221   8.5710  -2.3858  -1.7329
 10X  H2   H  HCH3   0   0.229   8.6596  -0.7063  -2.2572
 10X  H3   H  HCH3   0   0.222   8.8523  -1.1106  -0.5512
 10X  H4   H  HCH2   0   0.231   6.5548  -0.1870  -0.9920
 10X  H5   H  HCH2   0   0.232   6.2927  -1.4171  -2.2034
 10X  H6   H  H      0   0.231   6.3319  -3.2227  -0.5073
 10X  H7   H  H      0   0.235   5.4579  -2.7031   1.6029
 10X  H8   H  HCH2   0   0.251   5.8679  -0.5436   2.6353
 10X  H9   H  HCH2   0   0.249   6.3329   0.2037   1.1195
 10X  H10  H  HCH1   0   0.245   3.4684  -0.6001   1.9249
 10X  H11  H  HCH1   0   0.245   4.7569   2.0869   1.0562
 10X  H12  H  HCH2   0   0.248   1.8686   1.2508   1.7336
 10X  H13  H  HCH2   0   0.251   2.7758   2.5219   2.5324
 10X  H14  H  H      0   0.234   2.6352   4.0045   0.5975
 10X  H15  H  H      0   0.231   0.9844   3.6687  -1.0346
 10X  H16  H  HCH2   0   0.229   0.5089   1.3166  -1.6651
 10X  H17  H  HCH2   0   0.227   0.8331   0.7524  -0.0439
 10X  H18  H  HCH2   0   0.215  -1.1504   2.0219   0.7952
 10X  H19  H  HCH2   0   0.213  -1.4590   2.6272  -0.8180
 10X  H20  H  HCH2   0   0.208  -1.7808   0.2818  -1.6369
 10X  H21  H  HCH2   0   0.208  -1.4764  -0.3238  -0.0243
 10X  H22  H  HCH2   0   0.205  -3.4662   0.9409   0.8246
 10X  H23  H  HCH2   0   0.205  -3.7718   1.5431  -0.7894
 10X  H24  H  HCH2   0   0.202  -4.0737  -0.8053  -1.6074
 10X  H25  H  HCH2   0   0.202  -3.7661  -1.4070   0.0047
 10X  H26  H  HCH2   0   0.199  -5.7661  -0.1569   0.8507
 10X  H27  H  HCH2   0   0.200  -6.0751   0.4415  -0.7600
 10X  H28  H  HCH2   0   0.217  -6.3485  -1.9105  -1.5854
 10X  H29  H  HCH2   0   0.214  -6.0183  -2.5187   0.0070

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
 10X  CAD  CAH  single  1.497  0.020  1.497
 10X  CAD  CAF  double  1.331  0.020  1.331
 10X  CAH  CAA  single  1.528  0.020  1.528
 10X  CAF  CAO  single  1.501  0.020  1.501
 10X  CAO  CAT  single  1.507  0.020  1.507
 10X  CAT  OAR  single  1.421  0.020  1.421
 10X  CAT  CAU  single  1.459  0.020  1.459
 10X  OAR  CAU  single  1.421  0.020  1.421
 10X  CAU  CAP  single  1.507  0.020  1.507
 10X  CAG  CAP  single  1.500  0.020  1.500
 10X  CAG  CAE  double  1.332  0.020  1.332
 10X  CAE  CAI  single  1.496  0.020  1.496
 10X  CAJ  CAI  single  1.529  0.020  1.529
 10X  CAJ  CAK  single  1.523  0.020  1.523
 10X  CAK  CAL  single  1.523  0.020  1.523
 10X  CAL  CAM  single  1.523  0.020  1.523
 10X  CAM  CAN  single  1.524  0.020  1.524
 10X  CAN  CAQ  single  1.520  0.020  1.520
 10X  OAC  CAS  deloc   1.247  0.020  1.247
 10X  CAQ  CAS  single  1.538  0.020  1.538
 10X  CAS  OAB  deloc   1.250  0.020  1.250
 10X  CAA  H1   single  0.970  0.020  1.090
 10X  CAA  H2   single  0.970  0.020  1.090
 10X  CAA  H3   single  0.970  0.020  1.090
 10X  CAH  H4   single  0.970  0.020  1.090
 10X  CAH  H5   single  0.970  0.020  1.090
 10X  CAD  H6   single  0.930  0.020  1.080
 10X  CAF  H7   single  0.930  0.020  1.080
 10X  CAO  H8   single  0.970  0.020  1.090
 10X  CAO  H9   single  0.970  0.020  1.090
 10X  CAT  H10  single  0.970  0.020  1.090
 10X  CAU  H11  single  0.970  0.020  1.090
 10X  CAP  H12  single  0.970  0.020  1.090
 10X  CAP  H13  single  0.970  0.020  1.090
 10X  CAG  H14  single  0.930  0.020  1.080
 10X  CAE  H15  single  0.930  0.020  1.080
 10X  CAI  H16  single  0.970  0.020  1.090
 10X  CAI  H17  single  0.970  0.020  1.090
 10X  CAJ  H18  single  0.970  0.020  1.090
 10X  CAJ  H19  single  0.970  0.020  1.090
 10X  CAK  H20  single  0.970  0.020  1.090
 10X  CAK  H21  single  0.970  0.020  1.090
 10X  CAL  H22  single  0.970  0.020  1.090
 10X  CAL  H23  single  0.970  0.020  1.090
 10X  CAM  H24  single  0.970  0.020  1.090
 10X  CAM  H25  single  0.970  0.020  1.090
 10X  CAN  H26  single  0.970  0.020  1.090
 10X  CAN  H27  single  0.970  0.020  1.090
 10X  CAQ  H28  single  0.970  0.020  1.090
 10X  CAQ  H29  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
 10X  H3   CAA  H2   107.93  3.000
 10X  H3   CAA  H1   107.64  3.000
 10X  H2   CAA  H1   107.70  3.000
 10X  H3   CAA  CAH  111.03  3.000
 10X  H2   CAA  CAH  111.13  3.000
 10X  H1   CAA  CAH  111.25  3.000
 10X  H5   CAH  H4   106.13  3.000
 10X  H5   CAH  CAD  108.51  3.000
 10X  H4   CAH  CAD  111.12  3.000
 10X  H5   CAH  CAA  108.80  3.000
 10X  H4   CAH  CAA  110.14  3.000
 10X  CAD  CAH  CAA  111.94  3.000
 10X  H6   CAD  CAF  117.52  3.000
 10X  H6   CAD  CAH  115.06  3.000
 10X  CAF  CAD  CAH  127.40  3.000
 10X  H7   CAF  CAO  115.65  3.000
 10X  H7   CAF  CAD  117.91  3.000
 10X  CAO  CAF  CAD  126.43  3.000
 10X  H9   CAO  H8   106.66  3.000
 10X  H9   CAO  CAT  109.60  3.000
 10X  H8   CAO  CAT  107.88  3.000
 10X  H9   CAO  CAF  111.66  3.000
 10X  H8   CAO  CAF  109.41  3.000
 10X  CAT  CAO  CAF  111.44  3.000
 10X  H10  CAT  CAU  117.44  3.000
 10X  H10  CAT  OAR  114.10  3.000
 10X  CAU  CAT  OAR   59.11  3.000
 10X  H10  CAT  CAO  114.88  3.000
 10X  CAU  CAT  CAO  122.55  3.000
 10X  OAR  CAT  CAO  116.50  3.000
 10X  CAU  OAR  CAT   61.79  3.000
 10X  H11  CAU  CAP  114.95  3.000
 10X  H11  CAU  OAR  114.11  3.000
 10X  CAP  CAU  OAR  116.48  3.000
 10X  H11  CAU  CAT  117.47  3.000
 10X  CAP  CAU  CAT  122.43  3.000
 10X  OAR  CAU  CAT   59.10  3.000
 10X  H13  CAP  H12  106.76  3.000
 10X  H13  CAP  CAG  109.56  3.000
 10X  H12  CAP  CAG  111.35  3.000
 10X  H13  CAP  CAU  107.99  3.000
 10X  H12  CAP  CAU  109.52  3.000
 10X  CAG  CAP  CAU  111.48  3.000
 10X  H14  CAG  CAE  118.02  3.000
 10X  H14  CAG  CAP  115.76  3.000
 10X  CAE  CAG  CAP  126.20  3.000
 10X  H15  CAE  CAI  115.25  3.000
 10X  H15  CAE  CAG  117.59  3.000
 10X  CAI  CAE  CAG  127.15  3.000
 10X  H17  CAI  H16  106.01  3.000
 10X  H17  CAI  CAJ  109.71  3.000
 10X  H16  CAI  CAJ  108.69  3.000
 10X  H17  CAI  CAE  111.12  3.000
 10X  H16  CAI  CAE  108.67  3.000
 10X  CAJ  CAI  CAE  112.40  3.000
 10X  H19  CAJ  H18  106.11  3.000
 10X  H19  CAJ  CAK  109.52  3.000
 10X  H18  CAJ  CAK  109.65  3.000
 10X  H19  CAJ  CAI  109.55  3.000
 10X  H18  CAJ  CAI  109.08  3.000
 10X  CAK  CAJ  CAI  112.71  3.000
 10X  H21  CAK  H20  105.91  3.000
 10X  H21  CAK  CAL  109.34  3.000
 10X  H20  CAK  CAL  109.32  3.000
 10X  H21  CAK  CAJ  109.30  3.000
 10X  H20  CAK  CAJ  109.27  3.000
 10X  CAL  CAK  CAJ  113.43  3.000
 10X  H23  CAL  H22  105.93  3.000
 10X  H23  CAL  CAM  109.41  3.000
 10X  H22  CAL  CAM  109.38  3.000
 10X  H23  CAL  CAK  109.42  3.000
 10X  H22  CAL  CAK  109.36  3.000
 10X  CAM  CAL  CAK  113.10  3.000
 10X  H25  CAM  H24  105.74  3.000
 10X  H25  CAM  CAN  109.42  3.000
 10X  H24  CAM  CAN  109.40  3.000
 10X  H25  CAM  CAL  109.19  3.000
 10X  H24  CAM  CAL  109.22  3.000
 10X  CAN  CAM  CAL  113.57  3.000
 10X  H27  CAN  H26  105.83  3.000
 10X  H27  CAN  CAQ  109.92  3.000
 10X  H26  CAN  CAQ  109.85  3.000
 10X  H27  CAN  CAM  109.28  3.000
 10X  H26  CAN  CAM  109.18  3.000
 10X  CAQ  CAN  CAM  112.56  3.000
 10X  H29  CAQ  H28  104.68  3.000
 10X  H29  CAQ  CAS  108.19  3.000
 10X  H28  CAQ  CAS  107.97  3.000
 10X  H29  CAQ  CAN  109.53  3.000
 10X  H28  CAQ  CAN  109.42  3.000
 10X  CAS  CAQ  CAN  116.40  3.000
 10X  OAB  CAS  OAC  126.12  3.000
 10X  OAB  CAS  CAQ  115.91  3.000
 10X  OAC  CAS  CAQ  117.97  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
 10X  Var_01  CAP  CAU  OAR  CAT  -113.58  30.0  1
 10X  Var_02  OAR  CAT  CAO  CAF   -75.05  30.0  3
 10X  Var_03  CAG  CAP  CAU  CAT  -144.02  30.0  3
 10X  Var_04  CAT  CAO  CAF  CAD    97.96  30.0  3
 10X  Var_05  CAE  CAG  CAP  CAU    99.82  30.0  1
 10X  Var_06  CAO  CAF  CAD  CAH     1.45   0.0  2
 10X  Var_07  CAI  CAE  CAG  CAP     1.37   0.0  2
 10X  Var_08  CAF  CAD  CAH  CAA   111.85  30.0  1
 10X  Var_09  CAJ  CAI  CAE  CAG   111.49  30.0  3
 10X  Var_10  CAK  CAJ  CAI  CAE   176.87  30.0  1
 10X  Var_11  CAL  CAK  CAJ  CAI   179.86  30.0  3
 10X  Var_12  CAM  CAL  CAK  CAJ  -179.86  30.0  3
 10X  Var_13  CAN  CAM  CAL  CAK   179.89  30.0  3
 10X  Var_14  CAQ  CAN  CAM  CAL  -179.83  30.0  3
 10X  Var_15  CAS  CAQ  CAN  CAM   179.17  30.0  3
 10X  Var_16  OAC  CAS  CAQ  CAN     2.99  30.0  3
 10X  Var_17  H1   CAA  CAH  CAD    56.30  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
 10X  chir_01  CAT  CAO  OAR  CAU  both
 10X  chir_02  CAU  OAR  CAP  CAT  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
 10X  plan-1  CAQ  0.020
 10X  plan-1  CAS  0.020
 10X  plan-1  OAC  0.020
 10X  plan-1  OAB  0.020
 10X  plan-2  CAH  0.020
 10X  plan-2  CAD  0.020
 10X  plan-2  CAF  0.020
 10X  plan-2  CAO  0.020
 10X  plan-2  H6   0.020
 10X  plan-2  H7   0.020
 10X  plan-3  CAP  0.020
 10X  plan-3  CAG  0.020
 10X  plan-3  CAE  0.020
 10X  plan-3  CAI  0.020
 10X  plan-3  H14  0.020
 10X  plan-3  H15  0.020

