# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:33:59 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E,12Z,15Z)-octadeca-9,12,15-trienoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC/C=C\C\C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO[P](O)(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
 NKQ  NKQ  '(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E,12Z,15Z)-octadeca-9,12,15-trienoate'  ligand  66  29  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NKQ
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
 NKQ  OAA   O  OH1   0  -0.740   11.0878   1.0849  -1.3905
 NKQ  OAB   O  OH1   0  -0.730   11.6633  -1.3920  -0.9549
 NKQ  PAC   P  P     0   1.454   10.9877  -0.0969  -0.3191
 NKQ  OAD   O  O     0  -0.710   11.4845   0.3751   0.9865
 NKQ  OAE   O  O     0  -0.450    3.6360   1.2566   1.2995
 NKQ  OAF   O  O2    0  -0.585    9.4832  -0.6286  -0.3602
 NKQ  CAG   C  CH2   0  -0.185    8.4502   0.1627   0.2285
 NKQ  CAH   C  CH1   0  -0.058    7.1153  -0.3340  -0.3008
 NKQ  CAI   C  CH2   0  -0.189    6.0023   0.4068   0.4214
 NKQ  OAJ   O  O2    0  -0.460    4.7647  -0.1490  -0.0140
 NKQ  CAK   C  C     0   0.608    3.6452   0.3567   0.4977
 NKQ  CAL   C  CH2   0  -0.585    2.4280  -0.3365  -0.0494
 NKQ  CAM   C  CH2   0  -0.418    1.1194   0.1734   0.5322
 NKQ  CAN   C  CH2   0  -0.416   -0.0805  -0.5871  -0.0180
 NKQ  CAO   C  CH2   0  -0.413   -1.4033  -0.1048   0.5636
 NKQ  CAP   C  CH2   0  -0.414   -2.5987  -0.9212   0.0895
 NKQ  CAQ   C  CH2   0  -0.417   -3.9207  -0.4524   0.6849
 NKQ  CAR   C  CH2   0  -0.479   -5.0923  -1.3588   0.3093
 NKQ  CAS   C  C1    0  -0.206   -6.3743  -0.9601   0.9688
 NKQ  CAT   C  C1    0  -0.207   -7.5313  -0.7556   0.3463
 NKQ  CAU   C  CH2   0  -0.564   -8.8169  -0.3878   1.0291
 NKQ  CAV   C  C1    0  -0.205   -9.3778   0.9029   0.5079
 NKQ  CAW   C  C1    0  -0.209  -10.5339   1.0796  -0.1299
 NKQ  CAX   C  CH2   0  -0.578  -11.5646   0.0355  -0.4535
 NKQ  CAY   C  C1    0  -0.203  -12.7512   0.1660   0.4589
 NKQ  CAZ   C  C1    0  -0.212  -14.0000   0.4898   0.1276
 NKQ  CBA   C  CH2   0  -0.490  -14.5474   0.7728  -1.2363
 NKQ  CBB   C  CH3   0  -0.658  -15.5914  -0.2629  -1.6512
 NKQ  OBC   O  OH1   0  -0.649    7.0213  -0.2322  -1.6964
 NKQ  HAG   H  HCH2  0   0.252    8.4853   0.0652   1.3158
 NKQ  HAGA  H  HCH2  0   0.240    8.5778   1.2225  -0.0173
 NKQ  HAH   H  HCH1  0   0.256    7.0293  -1.4004  -0.0691
 NKQ  HAI   H  HCH2  0   0.246    6.1129   0.2887   1.5022
 NKQ  HAIA  H  HCH2  0   0.241    6.0398   1.4777   0.1977
 NKQ  HAL   H  HCH2  0   0.275    2.4343  -0.2256  -1.1387
 NKQ  HALA  H  HCH2  0   0.273    2.5349  -1.4105   0.1332
 NKQ  HAM   H  HCH2  0   0.224    1.1365   0.0774   1.6213
 NKQ  HAMA  H  HCH2  0   0.225    1.0067   1.2396   0.3178
 NKQ  HAN   H  HCH2  0   0.213   -0.1057  -0.4963  -1.1094
 NKQ  HANA  H  HCH2  0   0.212    0.0383  -1.6553   0.1942
 NKQ  HAO   H  HCH2  0   0.209   -1.3519  -0.1483   1.6572
 NKQ  HAOA  H  HCH2  0   0.211   -1.5509   0.9502   0.3090
 NKQ  HAP   H  HCH2  0   0.211   -2.6574  -0.8879  -1.0037
 NKQ  HAPA  H  HCH2  0   0.209   -2.4416  -1.9733   0.3523
 NKQ  HAQ   H  HCH2  0   0.212   -3.8310  -0.4186   1.7761
 NKQ  HAQA  H  HCH2  0   0.217   -4.1292   0.5727   0.3637
 NKQ  HAR   H  HCH2  0   0.227   -5.2202  -1.3791  -0.7771
 NKQ  HARA  H  HCH2  0   0.226   -4.8427  -2.3835   0.6098
 NKQ  HAS   H  H     0   0.227   -6.3372  -0.8479   2.0515
 NKQ  HAT   H  H     0   0.233   -7.5807  -0.8640  -0.7352
 NKQ  HAU   H  HCH2  0   0.246   -9.5403  -1.1975   0.9048
 NKQ  HAV   H  H     0   0.237   -8.7521   1.7758   0.6726
 NKQ  HAW   H  H     0   0.238  -10.7980   2.0894  -0.4304
 NKQ  HAX   H  HCH2  0   0.253  -11.8652   0.1402  -1.4981
 NKQ  HAXA  H  HCH2  0   0.251  -11.1463  -0.9687  -0.3512
 NKQ  HAY   H  H     0   0.235  -12.5363  -0.0158   1.5083
 NKQ  HAZ   H  H     0   0.231  -14.7322   0.5349   0.9302
 NKQ  HBA   H  HCH2  0   0.233  -15.0136   1.7629  -1.2315
 NKQ  HBAA  H  HCH2  0   0.233  -13.7527   0.8126  -1.9826
 NKQ  HBB   H  HCH3  0   0.223  -15.1471  -1.2559  -1.7289
 NKQ  HBBA  H  HCH3  0   0.221  -16.4029  -0.3198  -0.9238
 NKQ  HBBB  H  HCH3  0   0.229  -16.0296  -0.0147  -2.6184
 NKQ  HOBC  H  HOH1  0   0.448    7.0737   0.6960  -1.9512
 NKQ  HOAA  H  HOH1  0   0.495   10.8374   0.8545  -2.2953
 NKQ  HOAB  H  HOH1  0   0.505   12.6291  -1.3921  -0.9150
 NKQ  HAUA  H  HCH2  0   0.249   -8.6398  -0.2970   2.1055

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
 NKQ  OAA  PAC   single  1.598  0.020  1.598
 NKQ  OAB  PAC   single  1.593  0.020  1.593
 NKQ  PAC  OAD   double  1.475  0.020  1.475
 NKQ  PAC  OAF   single  1.596  0.020  1.596
 NKQ  OAE  CAK   double  1.205  0.020  1.205
 NKQ  OAF  CAG   single  1.428  0.020  1.428
 NKQ  CAG  CAH   single  1.519  0.020  1.519
 NKQ  CAH  CAI   single  1.520  0.020  1.520
 NKQ  CAH  OBC   single  1.402  0.020  1.402
 NKQ  CAI  OAJ   single  1.425  0.020  1.425
 NKQ  OAJ  CAK   single  1.331  0.020  1.331
 NKQ  CAK  CAL   single  1.504  0.020  1.504
 NKQ  CAL  CAM   single  1.520  0.020  1.520
 NKQ  CAM  CAN   single  1.523  0.020  1.523
 NKQ  CAN  CAO   single  1.523  0.020  1.523
 NKQ  CAO  CAP   single  1.523  0.020  1.523
 NKQ  CAP  CAQ   single  1.524  0.020  1.524
 NKQ  CAQ  CAR   single  1.528  0.020  1.528
 NKQ  CAR  CAS   single  1.496  0.020  1.496
 NKQ  CAS  CAT   double  1.330  0.020  1.330
 NKQ  CAT  CAU   single  1.501  0.020  1.501
 NKQ  CAU  CAV   single  1.501  0.020  1.501
 NKQ  CAV  CAW   double  1.332  0.020  1.332
 NKQ  CAW  CAX   single  1.502  0.020  1.502
 NKQ  CAX  CAY   single  1.503  0.020  1.503
 NKQ  CAY  CAZ   double  1.332  0.020  1.332
 NKQ  CAZ  CBA   single  1.497  0.020  1.497
 NKQ  CBA  CBB   single  1.528  0.020  1.528
 NKQ  CAG  HAG   single  0.970  0.020  1.090
 NKQ  CAG  HAGA  single  0.970  0.020  1.090
 NKQ  CAH  HAH   single  0.970  0.020  1.090
 NKQ  CAI  HAI   single  0.970  0.020  1.090
 NKQ  CAI  HAIA  single  0.970  0.020  1.090
 NKQ  CAL  HAL   single  0.970  0.020  1.090
 NKQ  CAL  HALA  single  0.970  0.020  1.090
 NKQ  CAM  HAM   single  0.970  0.020  1.090
 NKQ  CAM  HAMA  single  0.970  0.020  1.090
 NKQ  CAN  HAN   single  0.970  0.020  1.090
 NKQ  CAN  HANA  single  0.970  0.020  1.090
 NKQ  CAO  HAO   single  0.970  0.020  1.090
 NKQ  CAO  HAOA  single  0.970  0.020  1.090
 NKQ  CAP  HAP   single  0.970  0.020  1.090
 NKQ  CAP  HAPA  single  0.970  0.020  1.090
 NKQ  CAQ  HAQ   single  0.970  0.020  1.090
 NKQ  CAQ  HAQA  single  0.970  0.020  1.090
 NKQ  CAR  HAR   single  0.970  0.020  1.090
 NKQ  CAR  HARA  single  0.970  0.020  1.090
 NKQ  CAS  HAS   single  0.930  0.020  1.080
 NKQ  CAT  HAT   single  0.930  0.020  1.080
 NKQ  CAU  HAU   single  0.970  0.020  1.090
 NKQ  CAV  HAV   single  0.930  0.020  1.080
 NKQ  CAW  HAW   single  0.930  0.020  1.080
 NKQ  CAX  HAX   single  0.970  0.020  1.090
 NKQ  CAX  HAXA  single  0.970  0.020  1.090
 NKQ  CAY  HAY   single  0.930  0.020  1.080
 NKQ  CAZ  HAZ   single  0.930  0.020  1.080
 NKQ  CBA  HBA   single  0.970  0.020  1.090
 NKQ  CBA  HBAA  single  0.970  0.020  1.090
 NKQ  CBB  HBB   single  0.970  0.020  1.090
 NKQ  CBB  HBBA  single  0.970  0.020  1.090
 NKQ  CBB  HBBB  single  0.970  0.020  1.090
 NKQ  OBC  HOBC  single  0.850  0.020  0.980
 NKQ  CAU  HAUA  single  0.970  0.020  1.090
 NKQ  OAA  HOAA  single  0.850  0.020  0.980
 NKQ  OAB  HOAB  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
 NKQ  HOAA  OAA  PAC   115.78  3.000
 NKQ  HOAB  OAB  PAC   114.04  3.000
 NKQ  OAF   PAC  OAD   116.55  3.000
 NKQ  OAF   PAC  OAB    96.81  3.000
 NKQ  OAD   PAC  OAB   118.08  3.000
 NKQ  OAF   PAC  OAA   106.74  3.000
 NKQ  OAD   PAC  OAA   109.62  3.000
 NKQ  OAB   PAC  OAA   107.88  3.000
 NKQ  CAG   OAF  PAC   119.12  3.000
 NKQ  HAGA  CAG  HAG   107.82  3.000
 NKQ  HAGA  CAG  CAH   109.90  3.000
 NKQ  HAG   CAG  CAH   110.24  3.000
 NKQ  HAGA  CAG  OAF   111.05  3.000
 NKQ  HAG   CAG  OAF   109.74  3.000
 NKQ  CAH   CAG  OAF   108.10  3.000
 NKQ  HAH   CAH  OBC   106.03  3.000
 NKQ  HAH   CAH  CAI   108.47  3.000
 NKQ  OBC   CAH  CAI   112.86  3.000
 NKQ  HAH   CAH  CAG   108.28  3.000
 NKQ  OBC   CAH  CAG   112.45  3.000
 NKQ  CAI   CAH  CAG   108.57  3.000
 NKQ  HAIA  CAI  HAI   107.72  3.000
 NKQ  HAIA  CAI  OAJ   110.42  3.000
 NKQ  HAI   CAI  OAJ   110.36  3.000
 NKQ  HAIA  CAI  CAH   110.78  3.000
 NKQ  HAI   CAI  CAH   110.07  3.000
 NKQ  OAJ   CAI  CAH   107.50  3.000
 NKQ  CAK   OAJ  CAI   117.70  3.000
 NKQ  CAL   CAK  OAJ   111.46  3.000
 NKQ  CAL   CAK  OAE   125.45  3.000
 NKQ  OAJ   CAK  OAE   123.09  3.000
 NKQ  HALA  CAL  HAL   105.36  3.000
 NKQ  HALA  CAL  CAM   110.45  3.000
 NKQ  HAL   CAL  CAM   110.59  3.000
 NKQ  HALA  CAL  CAK   108.21  3.000
 NKQ  HAL   CAL  CAK   108.09  3.000
 NKQ  CAM   CAL  CAK   113.76  3.000
 NKQ  HAMA  CAM  HAM   106.41  3.000
 NKQ  HAMA  CAM  CAN   109.56  3.000
 NKQ  HAM   CAM  CAN   109.15  3.000
 NKQ  HAMA  CAM  CAL   109.93  3.000
 NKQ  HAM   CAM  CAL   109.77  3.000
 NKQ  CAN   CAM  CAL   111.86  3.000
 NKQ  HANA  CAN  HAN   106.04  3.000
 NKQ  HANA  CAN  CAO   109.20  3.000
 NKQ  HAN   CAN  CAO   109.53  3.000
 NKQ  HANA  CAN  CAM   109.35  3.000
 NKQ  HAN   CAN  CAM   109.66  3.000
 NKQ  CAO   CAN  CAM   112.83  3.000
 NKQ  HAOA  CAO  HAO   106.05  3.000
 NKQ  HAOA  CAO  CAP   109.77  3.000
 NKQ  HAO   CAO  CAP   109.04  3.000
 NKQ  HAOA  CAO  CAN   109.46  3.000
 NKQ  HAO   CAO  CAN   109.13  3.000
 NKQ  CAP   CAO  CAN   113.14  3.000
 NKQ  HAPA  CAP  HAP   106.04  3.000
 NKQ  HAPA  CAP  CAQ   109.04  3.000
 NKQ  HAP   CAP  CAQ   109.52  3.000
 NKQ  HAPA  CAP  CAO   109.11  3.000
 NKQ  HAP   CAP  CAO   109.65  3.000
 NKQ  CAQ   CAP  CAO   113.22  3.000
 NKQ  HAQA  CAQ  HAQ   106.21  3.000
 NKQ  HAQA  CAQ  CAR   109.72  3.000
 NKQ  HAQ   CAQ  CAR   109.02  3.000
 NKQ  HAQA  CAQ  CAP   109.81  3.000
 NKQ  HAQ   CAQ  CAP   109.13  3.000
 NKQ  CAR   CAQ  CAP   112.74  3.000
 NKQ  HARA  CAR  HAR   106.35  3.000
 NKQ  HARA  CAR  CAS   108.86  3.000
 NKQ  HAR   CAR  CAS   110.03  3.000
 NKQ  HARA  CAR  CAQ   108.20  3.000
 NKQ  HAR   CAR  CAQ   110.17  3.000
 NKQ  CAS   CAR  CAQ   112.99  3.000
 NKQ  HAS   CAS  CAT   118.63  3.000
 NKQ  HAS   CAS  CAR   115.89  3.000
 NKQ  CAT   CAS  CAR   125.48  3.000
 NKQ  HAT   CAT  CAU   115.95  3.000
 NKQ  HAT   CAT  CAS   119.31  3.000
 NKQ  CAU   CAT  CAS   124.74  3.000
 NKQ  HAUA  CAU  HAU   106.28  3.000
 NKQ  HAUA  CAU  CAV   109.30  3.000
 NKQ  HAU   CAU  CAV   110.50  3.000
 NKQ  HAUA  CAU  CAT   109.21  3.000
 NKQ  HAU   CAU  CAT   109.49  3.000
 NKQ  CAV   CAU  CAT   111.89  3.000
 NKQ  HAV   CAV  CAW   117.76  3.000
 NKQ  HAV   CAV  CAU   115.02  3.000
 NKQ  CAW   CAV  CAU   127.21  3.000
 NKQ  HAW   CAW  CAX   114.81  3.000
 NKQ  HAW   CAW  CAV   117.83  3.000
 NKQ  CAX   CAW  CAV   127.33  3.000
 NKQ  HAXA  CAX  HAX   106.44  3.000
 NKQ  HAXA  CAX  CAY   108.98  3.000
 NKQ  HAX   CAX  CAY   110.80  3.000
 NKQ  HAXA  CAX  CAW   110.85  3.000
 NKQ  HAX   CAX  CAW   109.16  3.000
 NKQ  CAY   CAX  CAW   110.53  3.000
 NKQ  HAY   CAY  CAZ   117.80  3.000
 NKQ  HAY   CAY  CAX   114.57  3.000
 NKQ  CAZ   CAY  CAX   127.63  3.000
 NKQ  HAZ   CAZ  CBA   114.74  3.000
 NKQ  HAZ   CAZ  CAY   117.25  3.000
 NKQ  CBA   CAZ  CAY   127.99  3.000
 NKQ  HBAA  CBA  HBA   106.27  3.000
 NKQ  HBAA  CBA  CBB   109.67  3.000
 NKQ  HBA   CBA  CBB   108.87  3.000
 NKQ  HBAA  CBA  CAZ   111.34  3.000
 NKQ  HBA   CBA  CAZ   108.84  3.000
 NKQ  CBB   CBA  CAZ   111.67  3.000
 NKQ  HBBB  CBB  HBBA  107.71  3.000
 NKQ  HBBB  CBB  HBB   107.93  3.000
 NKQ  HBBA  CBB  HBB   107.63  3.000
 NKQ  HBBB  CBB  CBA   111.17  3.000
 NKQ  HBBA  CBB  CBA   111.25  3.000
 NKQ  HBB   CBB  CBA   110.99  3.000
 NKQ  HOBC  OBC  CAH   109.22  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
 NKQ  Var_01  CAU  CAT  CAS  CAR   178.44   0.0  2
 NKQ  Var_02  CAX  CAW  CAV  CAU     1.43   0.0  2
 NKQ  Var_03  CBA  CAZ  CAY  CAX     1.65   0.0  2
 NKQ  Var_04  CAH  CAG  OAF  PAC   163.14  30.0  3
 NKQ  Var_05  CAM  CAL  CAK  OAE    -1.60  30.0  3
 NKQ  Var_06  CAL  CAK  OAJ  CAI  -179.61  30.0  3
 NKQ  Var_07  CAN  CAM  CAL  CAK  -178.19  30.0  3
 NKQ  Var_08  CAO  CAN  CAM  CAL   179.30  30.0  3
 NKQ  Var_09  CAP  CAO  CAN  CAM  -176.15  30.0  3
 NKQ  Var_10  CAQ  CAP  CAO  CAN   179.22  30.0  3
 NKQ  Var_11  CAR  CAQ  CAP  CAO  -174.50  30.0  3
 NKQ  Var_12  CAS  CAR  CAQ  CAP   175.92  30.0  3
 NKQ  Var_13  CAT  CAS  CAR  CAQ   128.26  30.0  3
 NKQ  Var_14  CAV  CAU  CAT  CAS   122.32  30.0  3
 NKQ  Var_15  CAW  CAV  CAU  CAT   116.73  30.0  3
 NKQ  Var_16  CAY  CAX  CAW  CAV   105.06  30.0  3
 NKQ  Var_17  CAZ  CAY  CAX  CAW   115.02  30.0  3
 NKQ  Var_18  CBB  CBA  CAZ  CAY   115.57  30.0  3
 NKQ  Var_19  HAI  CAI  OAJ  CAK    59.93  30.0  1
 NKQ  Var_20  HBB  CBB  CBA  CAZ   -63.40  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
 NKQ  chir_01  CAH  CAG  CAI  OBC  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
 NKQ  plan-1  OAE  0.020
 NKQ  plan-1  OAJ  0.020
 NKQ  plan-1  CAK  0.020
 NKQ  plan-1  CAL  0.020
 NKQ  plan-2  CAR  0.020
 NKQ  plan-2  CAS  0.020
 NKQ  plan-2  CAT  0.020
 NKQ  plan-2  CAU  0.020
 NKQ  plan-2  HAS  0.020
 NKQ  plan-2  HAT  0.020
 NKQ  plan-3  CAU  0.020
 NKQ  plan-3  CAV  0.020
 NKQ  plan-3  CAW  0.020
 NKQ  plan-3  CAX  0.020
 NKQ  plan-3  HAV  0.020
 NKQ  plan-3  HAW  0.020
 NKQ  plan-4  CAX  0.020
 NKQ  plan-4  CAY  0.020
 NKQ  plan-4  CAZ  0.020
 NKQ  plan-4  CBA  0.020
 NKQ  plan-4  HAY  0.020
 NKQ  plan-4  HAZ  0.020

