# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:27:44 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: [(2~{R},3~{S},4~{S},5~{S},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hexadecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 9R2  9R2  '[(2~{R},3~{S},4~{S},5~{S},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hexadecanoate'  ligand  71  29  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9R2
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
 9R2  CAQ  C  CH3   0  -0.662   15.7981   0.6273   0.2949
 9R2  CAP  C  CH2   0  -0.418   14.5513  -0.2264   0.1099
 9R2  CAO  C  CH2   0  -0.406   13.2615   0.5777   0.2182
 9R2  CAN  C  CH2   0  -0.411   12.0069  -0.2671   0.0376
 9R2  CAM  C  CH2   0  -0.411   10.7163   0.5342   0.1531
 9R2  CAL  C  CH2   0  -0.411    9.4651  -0.3131  -0.0403
 9R2  CAK  C  CH2   0  -0.412    8.1701   0.4805   0.0775
 9R2  CAJ  C  CH2   0  -0.411    6.9249  -0.3742  -0.1212
 9R2  CAI  C  CH2   0  -0.412    5.6237   0.4096  -0.0061
 9R2  CAH  C  CH2   0  -0.411    4.3867  -0.4554  -0.2120
 9R2  CAG  C  CH2   0  -0.412    3.0774   0.3156  -0.1023
 9R2  CAF  C  CH2   0  -0.412    1.8525  -0.5625  -0.3233
 9R2  CAE  C  CH2   0  -0.416    0.5327   0.1888  -0.2046
 9R2  CAD  C  CH2   0  -0.417   -0.6709  -0.7094  -0.4585
 9R2  CAC  C  CH2   0  -0.582   -1.9908   0.0333  -0.3151
 9R2  CAB  C  C     0   0.608   -3.1902  -0.8283  -0.6039
 9R2  OAA  O  O     0  -0.455   -3.1634  -1.8739  -1.2042
 9R2  O6   O  O2    0  -0.463   -4.3103  -0.2915  -0.1322
 9R2  C6   C  CH2   0  -0.181   -5.5325  -0.9917  -0.3737
 9R2  C5   C  CH1   0  -0.017   -6.6403  -0.2282   0.3159
 9R2  O5   O  O2    0  -0.499   -6.7162   1.0435  -0.2977
 9R2  C1   C  CH1   0   0.216   -7.7062   1.9017   0.2030
 9R2  O1   O  OH1   0  -0.667   -7.5109   2.2265   1.5420
 9R2  C2   C  CH1   0  -0.029   -9.0939   1.2670   0.0725
 9R2  O2   O  OH1   0  -0.668   -9.4230   1.0831  -1.2811
 9R2  C3   C  CH1   0   0.004   -9.0911  -0.0993   0.7538
 9R2  O3   O  OH1   0  -0.673  -10.3009  -0.7959   0.5729
 9R2  C4   C  CH1   0   0.024   -7.9721  -0.9724   0.1964
 9R2  O4   O  OH1   0  -0.675   -7.8483  -2.1732   0.9198
 9R2  HA6  H  HCH3  0   0.215   15.8578   1.4100  -0.4639
 9R2  HA4  H  HCH3  0   0.215   15.7975   1.1169   1.2708
 9R2  HA5  H  HCH3  0   0.225   16.7087   0.0309   0.2265
 9R2  HA2  H  HCH2  0   0.210   14.5865  -0.7241  -0.8644
 9R2  HA3  H  HCH2  0   0.209   14.5418  -1.0262   0.8570
 9R2  HA1  H  HCH2  0   0.205   13.2277   1.0754   1.1941
 9R2  HA0  H  HCH2  0   0.205   13.2713   1.3798  -0.5286
 9R2  HAZ  H  HCH2  0   0.205   12.0393  -0.7623  -0.9395
 9R2  HAY  H  HCH2  0   0.206   12.0013  -1.0707   0.7827
 9R2  HAX  H  HCH2  0   0.206   10.6785   1.0200   1.1347
 9R2  HAW  H  HCH2  0   0.206   10.7244   1.3444  -0.5849
 9R2  HAV  H  HCH2  0   0.206    9.5032  -0.7977  -1.0226
 9R2  HAU  H  HCH2  0   0.206    9.4602  -1.1250   0.6958
 9R2  HAT  H  HCH2  0   0.206    8.1283   0.9633   1.0605
 9R2  HAS  H  HCH2  0   0.206    8.1745   1.2929  -0.6580
 9R2  HAR  H  HCH2  0   0.206    6.9694  -0.8564  -1.1044
 9R2  HAQ  H  HCH2  0   0.206    6.9232  -1.1878   0.6131
 9R2  HAP  H  HCH2  0   0.206    5.5743   0.8894   0.9779
 9R2  HAO  H  HCH2  0   0.206    5.6245   1.2240  -0.7395
 9R2  HAN  H  HCH2  0   0.206    4.4404  -0.9358  -1.1955
 9R2  HAM  H  HCH2  0   0.206    4.3888  -1.2700   0.5211
 9R2  HAL  H  HCH2  0   0.207    3.0156   0.7891   0.8840
 9R2  HAK  H  HCH2  0   0.207    3.0751   1.1335  -0.8315
 9R2  HAJ  H  HCH2  0   0.208    1.9145  -1.0266  -1.3140
 9R2  HAI  H  HCH2  0   0.208    1.8632  -1.3877   0.3974
 9R2  HAH  H  HCH2  0   0.212    0.4575   0.6379   0.7917
 9R2  HAG  H  HCH2  0   0.212    0.5225   1.0224  -0.9156
 9R2  HAF  H  HCH2  0   0.225   -0.5956  -1.1378  -1.4609
 9R2  HAE  H  HCH2  0   0.224   -0.6496  -1.5512   0.2399
 9R2  HAD  H  HCH2  0   0.266   -2.0884   0.4647   0.6843
 9R2  HAC  H  HCH2  0   0.277   -2.0244   0.8817  -1.0085
 9R2  H61  H  HCH2  0   0.238   -5.7246  -1.0583  -1.4486
 9R2  H62  H  HCH2  0   0.251   -5.4735  -2.0043   0.0269
 9R2  H5   H  HCH1  0   0.232   -6.3948  -0.1316   1.3829
 9R2  H11  H  HCH1  0   0.237   -7.6446   2.7920  -0.4358
 9R2  H12  H  HOH1  0   0.463   -6.7159   2.7644   1.6241
 9R2  H21  H  HCH1  0   0.233   -9.8210   1.9215   0.5736
 9R2  H22  H  HOH1  0   0.455   -9.5615   1.9464  -1.6826
 9R2  H31  H  HCH1  0   0.228   -8.8907   0.0589   1.8223
 9R2  H32  H  HOH1  0   0.457  -10.9598  -0.4314   1.1714
 9R2  H41  H  HCH1  0   0.217   -8.1718  -1.1729  -0.8665
 9R2  H42  H  HOH1  0   0.454   -8.6801  -2.6523   0.8477

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
 9R2  CAQ  CAP  single  1.522  0.020  1.522
 9R2  CAP  CAO  single  1.524  0.020  1.524
 9R2  CAO  CAN  single  1.523  0.020  1.523
 9R2  CAN  CAM  single  1.524  0.020  1.524
 9R2  CAM  CAL  single  1.523  0.020  1.523
 9R2  CAL  CAK  single  1.523  0.020  1.523
 9R2  CAK  CAJ  single  1.523  0.020  1.523
 9R2  CAJ  CAI  single  1.523  0.020  1.523
 9R2  CAI  CAH  single  1.523  0.020  1.523
 9R2  CAH  CAG  single  1.523  0.020  1.523
 9R2  CAG  CAF  single  1.523  0.020  1.523
 9R2  CAF  CAE  single  1.523  0.020  1.523
 9R2  CAE  CAD  single  1.523  0.020  1.523
 9R2  CAD  CAC  single  1.521  0.020  1.521
 9R2  CAC  CAB  single  1.505  0.020  1.505
 9R2  CAB  OAA  double  1.206  0.020  1.206
 9R2  CAB  O6   single  1.329  0.020  1.329
 9R2  O2   C2   single  1.405  0.020  1.405
 9R2  O5   C1   single  1.403  0.020  1.403
 9R2  O5   C5   single  1.414  0.020  1.414
 9R2  C1   O1   single  1.392  0.020  1.392
 9R2  C1   C2   single  1.532  0.020  1.532
 9R2  O6   C6   single  1.429  0.020  1.429
 9R2  C2   C3   single  1.527  0.020  1.527
 9R2  C6   C5   single  1.512  0.020  1.512
 9R2  C5   C4   single  1.530  0.020  1.530
 9R2  C4   C3   single  1.525  0.020  1.525
 9R2  C4   O4   single  1.407  0.020  1.407
 9R2  C3   O3   single  1.408  0.020  1.408
 9R2  CAQ  HA6  single  0.970  0.020  1.090
 9R2  CAQ  HA4  single  0.970  0.020  1.090
 9R2  CAQ  HA5  single  0.970  0.020  1.090
 9R2  CAP  HA2  single  0.970  0.020  1.090
 9R2  CAP  HA3  single  0.970  0.020  1.090
 9R2  CAO  HA1  single  0.970  0.020  1.090
 9R2  CAO  HA0  single  0.970  0.020  1.090
 9R2  CAN  HAZ  single  0.970  0.020  1.090
 9R2  CAN  HAY  single  0.970  0.020  1.090
 9R2  CAM  HAX  single  0.970  0.020  1.090
 9R2  CAM  HAW  single  0.970  0.020  1.090
 9R2  CAL  HAV  single  0.970  0.020  1.090
 9R2  CAL  HAU  single  0.970  0.020  1.090
 9R2  CAK  HAT  single  0.970  0.020  1.090
 9R2  CAK  HAS  single  0.970  0.020  1.090
 9R2  CAJ  HAR  single  0.970  0.020  1.090
 9R2  CAJ  HAQ  single  0.970  0.020  1.090
 9R2  CAI  HAP  single  0.970  0.020  1.090
 9R2  CAI  HAO  single  0.970  0.020  1.090
 9R2  CAH  HAN  single  0.970  0.020  1.090
 9R2  CAH  HAM  single  0.970  0.020  1.090
 9R2  CAG  HAL  single  0.970  0.020  1.090
 9R2  CAG  HAK  single  0.970  0.020  1.090
 9R2  CAF  HAJ  single  0.970  0.020  1.090
 9R2  CAF  HAI  single  0.970  0.020  1.090
 9R2  CAE  HAH  single  0.970  0.020  1.090
 9R2  CAE  HAG  single  0.970  0.020  1.090
 9R2  CAD  HAF  single  0.970  0.020  1.090
 9R2  CAD  HAE  single  0.970  0.020  1.090
 9R2  CAC  HAD  single  0.970  0.020  1.090
 9R2  CAC  HAC  single  0.970  0.020  1.090
 9R2  C6   H61  single  0.970  0.020  1.090
 9R2  C6   H62  single  0.970  0.020  1.090
 9R2  C5   H5   single  0.970  0.020  1.090
 9R2  C1   H11  single  0.970  0.020  1.090
 9R2  O1   H12  single  0.850  0.020  0.980
 9R2  C2   H21  single  0.970  0.020  1.090
 9R2  O2   H22  single  0.850  0.020  0.980
 9R2  C3   H31  single  0.970  0.020  1.090
 9R2  O3   H32  single  0.850  0.020  0.980
 9R2  C4   H41  single  0.970  0.020  1.090
 9R2  O4   H42  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
 9R2  HA5  CAQ  HA4  107.56  3.000
 9R2  HA5  CAQ  HA6  107.63  3.000
 9R2  HA4  CAQ  HA6  107.44  3.000
 9R2  HA5  CAQ  CAP  111.69  3.000
 9R2  HA4  CAQ  CAP  111.08  3.000
 9R2  HA6  CAQ  CAP  111.24  3.000
 9R2  HA3  CAP  HA2  105.99  3.000
 9R2  HA3  CAP  CAO  109.26  3.000
 9R2  HA2  CAP  CAO  109.30  3.000
 9R2  HA3  CAP  CAQ  109.51  3.000
 9R2  HA2  CAP  CAQ  109.68  3.000
 9R2  CAO  CAP  CAQ  112.87  3.000
 9R2  HA0  CAO  HA1  105.94  3.000
 9R2  HA0  CAO  CAN  109.42  3.000
 9R2  HA1  CAO  CAN  109.39  3.000
 9R2  HA0  CAO  CAP  109.28  3.000
 9R2  HA1  CAO  CAP  109.21  3.000
 9R2  CAN  CAO  CAP  113.33  3.000
 9R2  HAY  CAN  HAZ  105.96  3.000
 9R2  HAY  CAN  CAM  109.26  3.000
 9R2  HAZ  CAN  CAM  109.29  3.000
 9R2  HAY  CAN  CAO  109.28  3.000
 9R2  HAZ  CAN  CAO  109.39  3.000
 9R2  CAM  CAN  CAO  113.39  3.000
 9R2  HAW  CAM  HAX  106.00  3.000
 9R2  HAW  CAM  CAL  109.38  3.000
 9R2  HAX  CAM  CAL  109.39  3.000
 9R2  HAW  CAM  CAN  109.36  3.000
 9R2  HAX  CAM  CAN  109.28  3.000
 9R2  CAL  CAM  CAN  113.18  3.000
 9R2  HAU  CAL  HAV  105.94  3.000
 9R2  HAU  CAL  CAK  109.28  3.000
 9R2  HAV  CAL  CAK  109.22  3.000
 9R2  HAU  CAL  CAM  109.30  3.000
 9R2  HAV  CAL  CAM  109.34  3.000
 9R2  CAK  CAL  CAM  113.49  3.000
 9R2  HAS  CAK  HAT  106.00  3.000
 9R2  HAS  CAK  CAJ  109.37  3.000
 9R2  HAT  CAK  CAJ  109.45  3.000
 9R2  HAS  CAK  CAL  109.32  3.000
 9R2  HAT  CAK  CAL  109.35  3.000
 9R2  CAJ  CAK  CAL  113.10  3.000
 9R2  HAQ  CAJ  HAR  105.94  3.000
 9R2  HAQ  CAJ  CAI  109.27  3.000
 9R2  HAR  CAJ  CAI  109.19  3.000
 9R2  HAQ  CAJ  CAK  109.29  3.000
 9R2  HAR  CAJ  CAK  109.31  3.000
 9R2  CAI  CAJ  CAK  113.55  3.000
 9R2  HAO  CAI  HAP  106.00  3.000
 9R2  HAO  CAI  CAH  109.40  3.000
 9R2  HAP  CAI  CAH  109.47  3.000
 9R2  HAO  CAI  CAJ  109.34  3.000
 9R2  HAP  CAI  CAJ  109.36  3.000
 9R2  CAH  CAI  CAJ  113.03  3.000
 9R2  HAM  CAH  HAN  105.92  3.000
 9R2  HAM  CAH  CAG  109.25  3.000
 9R2  HAN  CAH  CAG  109.18  3.000
 9R2  HAM  CAH  CAI  109.28  3.000
 9R2  HAN  CAH  CAI  109.30  3.000
 9R2  CAG  CAH  CAI  113.63  3.000
 9R2  HAK  CAG  HAL  106.04  3.000
 9R2  HAK  CAG  CAF  109.39  3.000
 9R2  HAL  CAG  CAF  109.54  3.000
 9R2  HAK  CAG  CAH  109.36  3.000
 9R2  HAL  CAG  CAH  109.39  3.000
 9R2  CAF  CAG  CAH  112.89  3.000
 9R2  HAI  CAF  HAJ  105.97  3.000
 9R2  HAI  CAF  CAE  109.19  3.000
 9R2  HAJ  CAF  CAE  109.17  3.000
 9R2  HAI  CAF  CAG  109.32  3.000
 9R2  HAJ  CAF  CAG  109.26  3.000
 9R2  CAE  CAF  CAG  113.64  3.000
 9R2  HAG  CAE  HAH  106.12  3.000
 9R2  HAG  CAE  CAD  109.46  3.000
 9R2  HAH  CAE  CAD  109.83  3.000
 9R2  HAG  CAE  CAF  109.43  3.000
 9R2  HAH  CAE  CAF  109.42  3.000
 9R2  CAD  CAE  CAF  112.38  3.000
 9R2  HAE  CAD  HAF  106.42  3.000
 9R2  HAE  CAD  CAC  109.42  3.000
 9R2  HAF  CAD  CAC  109.74  3.000
 9R2  HAE  CAD  CAE  109.39  3.000
 9R2  HAF  CAD  CAE  109.25  3.000
 9R2  CAC  CAD  CAE  112.45  3.000
 9R2  HAC  CAC  HAD  105.68  3.000
 9R2  HAC  CAC  CAB  107.29  3.000
 9R2  HAD  CAC  CAB  109.29  3.000
 9R2  HAC  CAC  CAD  110.17  3.000
 9R2  HAD  CAC  CAD  110.88  3.000
 9R2  CAB  CAC  CAD  113.20  3.000
 9R2  O6   CAB  OAA  123.08  3.000
 9R2  O6   CAB  CAC  111.87  3.000
 9R2  OAA  CAB  CAC  125.05  3.000
 9R2  C6   O6   CAB  117.58  3.000
 9R2  H62  C6   H61  108.30  3.000
 9R2  H62  C6   C5   109.93  3.000
 9R2  H61  C6   C5   110.50  3.000
 9R2  H62  C6   O6   110.28  3.000
 9R2  H61  C6   O6   110.25  3.000
 9R2  C5   C6   O6   107.58  3.000
 9R2  H5   C5   C4   108.24  3.000
 9R2  H5   C5   O5   110.75  3.000
 9R2  C4   C5   O5   110.90  3.000
 9R2  H5   C5   C6   108.88  3.000
 9R2  C4   C5   C6   110.88  3.000
 9R2  O5   C5   C6   107.19  3.000
 9R2  C1   O5   C5   115.67  3.000
 9R2  H11  C1   C2   109.72  3.000
 9R2  H11  C1   O1   111.27  3.000
 9R2  C2   C1   O1   107.81  3.000
 9R2  H11  C1   O5   104.42  3.000
 9R2  C2   C1   O5   110.83  3.000
 9R2  O1   C1   O5   112.78  3.000
 9R2  H12  O1   C1   109.16  3.000
 9R2  H21  C2   C3   109.31  3.000
 9R2  H21  C2   O2   111.24  3.000
 9R2  C3   C2   O2   108.25  3.000
 9R2  H21  C2   C1   108.29  3.000
 9R2  C3   C2   C1   109.34  3.000
 9R2  O2   C2   C1   110.40  3.000
 9R2  H22  O2   C2   108.56  3.000
 9R2  H31  C3   C4   107.71  3.000
 9R2  H31  C3   O3   110.67  3.000
 9R2  C4   C3   O3   107.48  3.000
 9R2  H31  C3   C2   107.79  3.000
 9R2  O3   C3   C2   112.58  3.000
 9R2  C4   C3   C2   110.52  3.000
 9R2  H32  O3   C3   108.73  3.000
 9R2  H41  C4   O4   110.92  3.000
 9R2  H41  C4   C3   108.93  3.000
 9R2  O4   C4   C3   111.42  3.000
 9R2  H41  C4   C5   108.80  3.000
 9R2  O4   C4   C5   107.35  3.000
 9R2  C3   C4   C5   109.37  3.000
 9R2  H42  O4   C4   108.07  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
 9R2  Var_01  C5   C6   O6   CAB   177.06  30.0  3
 9R2  Var_02  CAN  CAO  CAP  CAQ  -179.88  30.0  3
 9R2  Var_03  CAM  CAN  CAO  CAP   179.69  30.0  3
 9R2  Var_04  CAL  CAM  CAN  CAO   179.50  30.0  3
 9R2  Var_05  CAK  CAL  CAM  CAN   179.84  30.0  3
 9R2  Var_06  CAJ  CAK  CAL  CAM   179.84  30.0  3
 9R2  Var_07  CAI  CAJ  CAK  CAL  -179.97  30.0  3
 9R2  Var_08  CAH  CAI  CAJ  CAK   179.78  30.0  3
 9R2  Var_09  CAG  CAH  CAI  CAJ  -179.90  30.0  3
 9R2  Var_10  CAF  CAG  CAH  CAI   179.48  30.0  3
 9R2  Var_11  CAE  CAF  CAG  CAH   179.46  30.0  3
 9R2  Var_12  CAD  CAE  CAF  CAG   178.83  30.0  3
 9R2  Var_13  CAC  CAD  CAE  CAF   178.94  30.0  3
 9R2  Var_14  CAB  CAC  CAD  CAE   178.23  30.0  3
 9R2  Var_15  OAA  CAB  CAC  CAD   -17.98  30.0  3
 9R2  Var_16  HA6  CAQ  CAP  CAO   -60.45  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
 9R2  chir_01  C5  O5  C6  C4  positiv
 9R2  chir_02  C1  O5  O1  C2  positiv
 9R2  chir_03  C2  O2  C1  C3  positiv
 9R2  chir_04  C3  O3  C2  C4  positiv
 9R2  chir_05  C4  O4  C3  C5  negativ

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
 9R2  plan-1  CAC  0.020
 9R2  plan-1  CAB  0.020
 9R2  plan-1  OAA  0.020
 9R2  plan-1  O6   0.020

