# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 15:28:40 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-[(2~{S},3~{S})-3-[(1~{E},3~{E},5~{Z},8~{Z})-tetradeca-1,3,5,8-tetraenyl]oxiran-2-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC/C=C\C\C=C/C=C/C=C/[C@@H]1O[C@H]1CCCC(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
 DJ3  DJ3  '4-[(2~{S},3~{S})-3-[(1~{E},3~{E},5~{Z},8~{Z})-tetradeca-1,3,5,8-tetraenyl]oxiran-2-yl]butanoic acid'  ligand  52  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DJ3
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
 DJ3  OAB  O  O      0  -0.610  -10.0877  -0.5171  -0.1251
 DJ3  CAU  C  C      0   0.409   -9.7167   0.6230   0.2176
 DJ3  OAC  O  OC    -1  -0.632  -10.4487   1.6264   0.3564
 DJ3  CAR  C  CH2    0  -0.578   -8.2250   0.8254   0.5347
 DJ3  CAQ  C  CH2    0  -0.414   -7.2870  -0.2507   0.0126
 DJ3  CAS  C  CH2    0  -0.460   -5.8295   0.0360   0.3637
 DJ3  CAW  C  CH1    0   0.001   -4.8898  -1.0117  -0.1586
 DJ3  OAT  O  O2     0  -0.497   -4.7693  -2.2157   0.5806
 DJ3  CAV  C  CH1    0  -0.061   -3.6372  -1.3461   0.5256
 DJ3  CAK  C  C1     0  -0.238   -2.4626  -1.8340  -0.2100
 DJ3  CAG  C  C1     0  -0.247   -1.2054  -1.5667   0.1670
 DJ3  CAE  C  C1     0  -0.245   -0.0360  -1.9822  -0.5722
 DJ3  CAD  C  C1     0  -0.265    1.2222  -1.6651  -0.2159
 DJ3  CAF  C  C1     0  -0.252    2.3839  -2.0557  -0.9847
 DJ3  CAH  C  C1     0  -0.206    3.6552  -1.7113  -0.7352
 DJ3  CAM  C  CH2    0  -0.570    4.1628  -0.8608   0.3944
 DJ3  CAI  C  C1     0  -0.227    5.4582  -1.3937   0.9376
 DJ3  CAJ  C  C1     0  -0.198    6.6811  -0.9439   0.6607
 DJ3  CAN  C  CH2    0  -0.489    7.0487   0.2220  -0.2013
 DJ3  CAP  C  CH2    0  -0.414    7.8514   1.2766   0.5626
 DJ3  CAO  C  CH2    0  -0.408    8.2066   2.4817  -0.2980
 DJ3  CAL  C  CH2    0  -0.419    9.0238   3.5319   0.4444
 DJ3  CAA  C  CH3    0  -0.662    9.3388   4.7482  -0.4151
 DJ3  HAY  H  HCH2   0   0.212   -7.9126   1.8066   0.1622
 DJ3  HAX  H  HCH2   0   0.223   -8.1234   0.8902   1.6258
 DJ3  HAV  H  HCH2   0   0.214   -7.5763  -1.2217   0.4201
 DJ3  HAW  H  HCH2   0   0.210   -7.3843  -0.3342  -1.0744
 DJ3  HAZ  H  HCH2   0   0.228   -5.5278   0.9978  -0.0629
 DJ3  HA0  H  HCH2   0   0.228   -5.7145   0.1291   1.4485
 DJ3  HA2  H  HCH1   0   0.244   -4.9215  -1.1575  -1.2399
 DJ3  HA1  H  HCH1   0   0.252   -3.4197  -0.8265   1.4591
 DJ3  HAK  H  H      0   0.256   -2.6485  -2.4055  -1.1158
 DJ3  HAG  H  H      0   0.251   -1.0345  -0.9933   1.0750
 DJ3  HAE  H  H      0   0.249   -0.2020  -2.5720  -1.4702
 DJ3  HAD  H  H      0   0.251    1.3735  -1.0705   0.6801
 DJ3  HAF  H  H      0   0.244    2.1901  -2.6718  -1.8579
 DJ3  HAH  H  H      0   0.247    4.4147  -2.0637  -1.4257
 DJ3  HAN  H  HCH2   0   0.259    4.2889   0.1661   0.0387
 DJ3  HAO  H  HCH2   0   0.256    3.4277  -0.8124   1.2005
 DJ3  HAI  H  H      0   0.238    5.3689  -2.2551   1.5927
 DJ3  HAJ  H  H      0   0.232    7.5207  -1.4594   1.1207
 DJ3  HAP  H  HCH2   0   0.232    7.6520  -0.1320  -1.0450
 DJ3  HAQ  H  HCH2   0   0.229    6.1614   0.6859  -0.6382
 DJ3  HAT  H  HCH2   0   0.216    7.2768   1.6059   1.4345
 DJ3  HAU  H  HCH2   0   0.214    8.7673   0.8222   0.9553
 DJ3  HAS  H  HCH2   0   0.209    8.7626   2.1498  -1.1820
 DJ3  HAR  H  HCH2   0   0.208    7.2855   2.9396  -0.6758
 DJ3  HAM  H  HCH2   0   0.211    8.4797   3.8451   1.3408
 DJ3  HAL  H  HCH2   0   0.211    9.9556   3.0805   0.7989
 DJ3  HAC  H  HCH3   0   0.216    8.4239   5.2407  -0.7504
 DJ3  HAB  H  HCH3   0   0.226    9.9302   5.4843   0.1298
 DJ3  HAA  H  HCH3   0   0.216    9.9033   4.4654  -1.3059

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
 DJ3  OAB  CAU  deloc   1.247  0.020  1.247
 DJ3  CAU  OAC  deloc   1.250  0.020  1.250
 DJ3  CAU  CAR  single  1.538  0.020  1.538
 DJ3  CAR  CAQ  single  1.520  0.020  1.520
 DJ3  CAQ  CAS  single  1.526  0.020  1.526
 DJ3  CAS  CAW  single  1.501  0.020  1.501
 DJ3  CAF  CAH  double  1.341  0.020  1.341
 DJ3  CAF  CAD  single  1.447  0.020  1.447
 DJ3  CAE  CAD  double  1.346  0.020  1.346
 DJ3  CAE  CAG  single  1.444  0.020  1.444
 DJ3  CAK  CAG  double  1.339  0.020  1.339
 DJ3  CAK  CAV  single  1.469  0.020  1.469
 DJ3  CAW  CAV  single  1.466  0.020  1.466
 DJ3  CAW  OAT  single  1.418  0.020  1.418
 DJ3  CAH  CAM  single  1.502  0.020  1.502
 DJ3  CAV  OAT  single  1.429  0.020  1.429
 DJ3  CAM  CAI  single  1.502  0.020  1.502
 DJ3  CAI  CAJ  double  1.332  0.020  1.332
 DJ3  CAN  CAJ  single  1.496  0.020  1.496
 DJ3  CAN  CAP  single  1.530  0.020  1.530
 DJ3  CAO  CAP  single  1.523  0.020  1.523
 DJ3  CAO  CAL  single  1.524  0.020  1.524
 DJ3  CAL  CAA  single  1.522  0.020  1.522
 DJ3  CAR  HAY  single  0.970  0.020  1.090
 DJ3  CAR  HAX  single  0.970  0.020  1.090
 DJ3  CAQ  HAV  single  0.970  0.020  1.090
 DJ3  CAQ  HAW  single  0.970  0.020  1.090
 DJ3  CAS  HAZ  single  0.970  0.020  1.090
 DJ3  CAS  HA0  single  0.970  0.020  1.090
 DJ3  CAW  HA2  single  0.970  0.020  1.090
 DJ3  CAV  HA1  single  0.970  0.020  1.090
 DJ3  CAK  HAK  single  0.930  0.020  1.080
 DJ3  CAG  HAG  single  0.930  0.020  1.080
 DJ3  CAE  HAE  single  0.930  0.020  1.080
 DJ3  CAD  HAD  single  0.930  0.020  1.080
 DJ3  CAF  HAF  single  0.930  0.020  1.080
 DJ3  CAH  HAH  single  0.930  0.020  1.080
 DJ3  CAM  HAN  single  0.970  0.020  1.090
 DJ3  CAM  HAO  single  0.970  0.020  1.090
 DJ3  CAI  HAI  single  0.930  0.020  1.080
 DJ3  CAJ  HAJ  single  0.930  0.020  1.080
 DJ3  CAN  HAP  single  0.970  0.020  1.090
 DJ3  CAN  HAQ  single  0.970  0.020  1.090
 DJ3  CAP  HAT  single  0.970  0.020  1.090
 DJ3  CAP  HAU  single  0.970  0.020  1.090
 DJ3  CAO  HAS  single  0.970  0.020  1.090
 DJ3  CAO  HAR  single  0.970  0.020  1.090
 DJ3  CAL  HAM  single  0.970  0.020  1.090
 DJ3  CAL  HAL  single  0.970  0.020  1.090
 DJ3  CAA  HAC  single  0.970  0.020  1.090
 DJ3  CAA  HAB  single  0.970  0.020  1.090
 DJ3  CAA  HAA  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
 DJ3  CAR  CAU  OAC  116.07  3.000
 DJ3  CAR  CAU  OAB  117.74  3.000
 DJ3  OAC  CAU  OAB  126.18  3.000
 DJ3  HAX  CAR  HAY  105.00  3.000
 DJ3  HAX  CAR  CAQ  109.03  3.000
 DJ3  HAY  CAR  CAQ  109.97  3.000
 DJ3  HAX  CAR  CAU  107.60  3.000
 DJ3  HAY  CAR  CAU  108.93  3.000
 DJ3  CAQ  CAR  CAU  115.75  3.000
 DJ3  HAW  CAQ  HAV  106.21  3.000
 DJ3  HAW  CAQ  CAS  109.13  3.000
 DJ3  HAV  CAQ  CAS  109.52  3.000
 DJ3  HAW  CAQ  CAR  109.90  3.000
 DJ3  HAV  CAQ  CAR  109.74  3.000
 DJ3  CAS  CAQ  CAR  112.16  3.000
 DJ3  HA0  CAS  HAZ  106.41  3.000
 DJ3  HA0  CAS  CAW  109.78  3.000
 DJ3  HAZ  CAS  CAW  107.76  3.000
 DJ3  HA0  CAS  CAQ  110.13  3.000
 DJ3  HAZ  CAS  CAQ  109.79  3.000
 DJ3  CAW  CAS  CAQ  112.74  3.000
 DJ3  HA2  CAW  CAV  117.17  3.000
 DJ3  HA2  CAW  OAT  113.92  3.000
 DJ3  CAV  CAW  OAT   59.36  3.000
 DJ3  HA2  CAW  CAS  114.82  3.000
 DJ3  OAT  CAW  CAS  117.67  3.000
 DJ3  CAV  CAW  CAS  122.12  3.000
 DJ3  CAV  OAT  CAW   61.99  3.000
 DJ3  HA1  CAV  CAK  115.31  3.000
 DJ3  HA1  CAV  OAT  114.53  3.000
 DJ3  CAK  CAV  OAT  116.79  3.000
 DJ3  HA1  CAV  CAW  117.47  3.000
 DJ3  OAT  CAV  CAW   58.65  3.000
 DJ3  CAK  CAV  CAW  121.68  3.000
 DJ3  HAK  CAK  CAG  120.00  3.000
 DJ3  HAK  CAK  CAV  117.07  3.000
 DJ3  CAG  CAK  CAV  122.90  3.000
 DJ3  HAG  CAG  CAE  116.86  3.000
 DJ3  HAG  CAG  CAK  119.19  3.000
 DJ3  CAE  CAG  CAK  123.95  3.000
 DJ3  HAE  CAE  CAD  119.30  3.000
 DJ3  HAE  CAE  CAG  117.07  3.000
 DJ3  CAD  CAE  CAG  123.62  3.000
 DJ3  HAD  CAD  CAF  118.32  3.000
 DJ3  HAD  CAD  CAE  118.54  3.000
 DJ3  CAF  CAD  CAE  123.13  3.000
 DJ3  HAF  CAF  CAH  117.69  3.000
 DJ3  HAF  CAF  CAD  115.92  3.000
 DJ3  CAH  CAF  CAD  126.38  3.000
 DJ3  HAH  CAH  CAM  115.20  3.000
 DJ3  HAH  CAH  CAF  117.50  3.000
 DJ3  CAM  CAH  CAF  127.29  3.000
 DJ3  HAO  CAM  HAN  106.02  3.000
 DJ3  HAO  CAM  CAI  109.23  3.000
 DJ3  HAN  CAM  CAI  110.56  3.000
 DJ3  HAO  CAM  CAH  110.64  3.000
 DJ3  HAN  CAM  CAH  109.01  3.000
 DJ3  CAI  CAM  CAH  111.25  3.000
 DJ3  HAI  CAI  CAJ  117.96  3.000
 DJ3  HAI  CAI  CAM  115.38  3.000
 DJ3  CAJ  CAI  CAM  126.63  3.000
 DJ3  HAJ  CAJ  CAN  115.06  3.000
 DJ3  HAJ  CAJ  CAI  117.44  3.000
 DJ3  CAN  CAJ  CAI  127.49  3.000
 DJ3  HAQ  CAN  HAP  106.04  3.000
 DJ3  HAQ  CAN  CAP  109.46  3.000
 DJ3  HAP  CAN  CAP  108.56  3.000
 DJ3  HAQ  CAN  CAJ  111.21  3.000
 DJ3  HAP  CAN  CAJ  109.09  3.000
 DJ3  CAP  CAN  CAJ  112.24  3.000
 DJ3  HAU  CAP  HAT  106.15  3.000
 DJ3  HAU  CAP  CAO  109.63  3.000
 DJ3  HAT  CAP  CAO  109.54  3.000
 DJ3  HAU  CAP  CAN  109.38  3.000
 DJ3  HAT  CAP  CAN  109.24  3.000
 DJ3  CAO  CAP  CAN  112.69  3.000
 DJ3  HAR  CAO  HAS  105.96  3.000
 DJ3  HAR  CAO  CAL  109.31  3.000
 DJ3  HAS  CAO  CAL  109.24  3.000
 DJ3  HAR  CAO  CAP  109.24  3.000
 DJ3  HAS  CAO  CAP  109.55  3.000
 DJ3  CAL  CAO  CAP  113.28  3.000
 DJ3  HAL  CAL  HAM  106.03  3.000
 DJ3  HAL  CAL  CAA  109.65  3.000
 DJ3  HAM  CAL  CAA  109.68  3.000
 DJ3  HAL  CAL  CAO  109.28  3.000
 DJ3  HAM  CAL  CAO  109.25  3.000
 DJ3  CAA  CAL  CAO  112.74  3.000
 DJ3  HAA  CAA  HAB  107.59  3.000
 DJ3  HAA  CAA  HAC  107.43  3.000
 DJ3  HAB  CAA  HAC  107.67  3.000
 DJ3  HAA  CAA  CAL  111.14  3.000
 DJ3  HAB  CAA  CAL  111.69  3.000
 DJ3  HAC  CAA  CAL  111.12  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
 DJ3  Var_01  OAT  CAV  CAW  CAS   105.39  30.0  1
 DJ3  Var_02  CAK  CAV  OAT  CAW  -112.41  30.0  1
 DJ3  Var_03  CAV  CAW  CAS  CAQ  -149.77  30.0  3
 DJ3  Var_04  CAG  CAK  CAV  CAW   147.50  30.0  1
 DJ3  Var_05  CAE  CAG  CAK  CAV  -177.03   0.0  2
 DJ3  Var_06  CAW  CAS  CAQ  CAR  -179.39  30.0  3
 DJ3  Var_07  CAF  CAD  CAE  CAG  -178.23   0.0  2
 DJ3  Var_08  CAM  CAH  CAF  CAD     0.61   0.0  2
 DJ3  Var_09  CAN  CAJ  CAI  CAM     2.81   0.0  2
 DJ3  Var_10  CAQ  CAR  CAU  OAB    17.51  30.0  3
 DJ3  Var_11  CAS  CAQ  CAR  CAU   179.59  30.0  3
 DJ3  Var_12  CAD  CAE  CAG  CAK   177.27  30.0  1
 DJ3  Var_13  CAH  CAF  CAD  CAE   175.83  30.0  1
 DJ3  Var_14  CAI  CAM  CAH  CAF   140.76  30.0  3
 DJ3  Var_15  CAJ  CAI  CAM  CAH    99.92  30.0  3
 DJ3  Var_16  CAP  CAN  CAJ  CAI   121.18  30.0  2
 DJ3  Var_17  CAO  CAP  CAN  CAJ  -178.82  30.0  3
 DJ3  Var_18  CAL  CAO  CAP  CAN  -179.17  30.0  1
 DJ3  Var_19  CAA  CAL  CAO  CAP  -178.40  30.0  3
 DJ3  Var_20  HAC  CAA  CAL  CAO    60.21  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
 DJ3  chir_01  CAW  CAS  CAV  OAT  both
 DJ3  chir_02  CAV  OAT  CAW  CAK  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
 DJ3  plan-1  OAB  0.020
 DJ3  plan-1  CAU  0.020
 DJ3  plan-1  OAC  0.020
 DJ3  plan-1  CAR  0.020
 DJ3  plan-2  CAD  0.020
 DJ3  plan-2  CAF  0.020
 DJ3  plan-2  CAH  0.020
 DJ3  plan-2  CAM  0.020
 DJ3  plan-2  HAF  0.020
 DJ3  plan-2  HAH  0.020
 DJ3  plan-3  CAG  0.020
 DJ3  plan-3  CAE  0.020
 DJ3  plan-3  CAD  0.020
 DJ3  plan-3  CAF  0.020
 DJ3  plan-3  HAE  0.020
 DJ3  plan-3  HAD  0.020
 DJ3  plan-4  CAV  0.020
 DJ3  plan-4  CAK  0.020
 DJ3  plan-4  CAG  0.020
 DJ3  plan-4  CAE  0.020
 DJ3  plan-4  HAK  0.020
 DJ3  plan-4  HAG  0.020
 DJ3  plan-5  CAM  0.020
 DJ3  plan-5  CAI  0.020
 DJ3  plan-5  CAJ  0.020
 DJ3  plan-5  CAN  0.020
 DJ3  plan-5  HAI  0.020
 DJ3  plan-5  HAJ  0.020

