# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 11:09:35 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: {2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCOc1cncc(CC([P](O)(O)=O)[P](O)(O)=O)c1
#
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
 K9H  K9H  '{2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)'  ligand  54  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K9H
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
 K9H  CAA   C  CH3    0  -0.659  -13.4568   1.0381  -0.3142
 K9H  OAB   O  OP    -1  -0.984    5.1585   3.0674   0.6427
 K9H  OAC   O  OP    -1  -0.896    4.2385  -1.9499  -1.1877
 K9H  OAD   O  OP    -1  -0.884    6.5418   2.1670  -1.2952
 K9H  OAE   O  O      0  -0.931    7.0102   1.3766   1.1166
 K9H  OAF   O  O      0  -0.938    5.7612  -1.8422   0.8721
 K9H  OAG   O  OP    -1  -0.923    6.6038  -1.0314  -1.4087
 K9H  CAH   C  CR16   0  -0.042    2.5343  -1.7235   1.2671
 K9H  CAI   C  CR16   0  -0.254    0.2875  -1.8990   0.8582
 K9H  CAJ   C  CR16   0  -0.322    1.3428   0.2357   0.6694
 K9H  CAK   C  CH2    0  -0.407  -12.2590   0.0983  -0.2887
 K9H  CAL   C  CH2    0  -0.389  -10.9279   0.8401  -0.2691
 K9H  CAM   C  CH2    0  -0.400   -9.7192  -0.0871  -0.2379
 K9H  CAN   C  CH2    0  -0.410   -8.3904   0.6581  -0.2145
 K9H  CAO   C  CH2    0  -0.421   -7.1818  -0.2682  -0.1586
 K9H  CAP   C  CH2    0  -0.409   -5.8535   0.4778  -0.1350
 K9H  CAQ   C  CH2    0  -0.423   -4.6517  -0.4505  -0.0150
 K9H  CAR   C  CH2    0  -0.446   -3.3218   0.2954   0.0002
 K9H  CAS   C  CH2    0  -0.209   -2.1663  -0.6490   0.2538
 K9H  NAU   N  N      0  -0.367    1.4467  -2.4670   1.1995
 K9H  OAV   O  O2     0  -0.477   -0.9590   0.0953   0.2562
 K9H  CAW   C  CR6    0   0.209    2.5489  -0.3463   1.0125
 K9H  CAX   C  CR6    0   0.277    0.1854  -0.5420   0.5838
 K9H  CAY   C  CH1    0  -0.679    4.7145   0.4954  -0.1029
 K9H  PAZ   P  P      0   1.119    5.9675   1.8649   0.0978
 K9H  PBA   P  P      0   1.174    5.3906  -1.2040  -0.4829
 K9H  HAA   H  HCH3   0   0.208  -14.3997   0.4901  -0.3269
 K9H  HAAA  H  HCH3   0   0.241  -13.4642   1.6883   0.5626
 K9H  HAAB  H  HCH3   0   0.204  -13.4347   1.6780  -1.1983
 K9H  HAH   H  HCR6   0   0.186    3.4644  -2.2117   1.5312
 K9H  HAI   H  HCR6   0   0.232   -0.5728  -2.5570   0.8184
 K9H  HAJ   H  HCR6   0   0.234    1.2815   1.3019   0.4757
 K9H  HAK   H  HCH2   0   0.171  -12.3220  -0.5540   0.5882
 K9H  HAKA  H  HCH2   0   0.233  -12.2921  -0.5633  -1.1602
 K9H  HAL   H  HCH2   0   0.188  -10.8633   1.4920  -1.1479
 K9H  HALA  H  HCH2   0   0.238  -10.8972   1.5047   0.6019
 K9H  HAM   H  HCH2   0   0.133   -9.7855  -0.7384   0.6410
 K9H  HAMA  H  HCH2   0   0.217   -9.7485  -0.7516  -1.1088
 K9H  HAN   H  HCH2   0   0.192   -8.3173   1.2995  -1.1001
 K9H  HANA  H  HCH2   0   0.231   -8.3682   1.3323   0.6492
 K9H  HAO   H  HCH2   0   0.196   -7.2560  -0.9044   0.7307
 K9H  HAOA  H  HCH2   0   0.246   -7.2028  -0.9472  -1.0182
 K9H  HAP   H  HCH2   0   0.142   -5.7602   1.0850  -1.0422
 K9H  HAPA  H  HCH2   0   0.236   -5.8485   1.1829   0.7036
 K9H  HAQ   H  HCH2   0   0.238   -4.7486  -1.0428   0.9015
 K9H  HAQA  H  HCH2   0   0.224   -4.6596  -1.1683  -0.8420
 K9H  HAR   H  HCH2   0   0.241   -3.1783   0.8134  -0.9526
 K9H  HARA  H  HCH2   0   0.273   -3.3401   1.0618   0.7811
 K9H  HAS   H  HCH2   0   0.236   -2.3046  -1.1503   1.2195
 K9H  HASA  H  HCH2   0   0.207   -2.1312  -1.4297  -0.5162
 K9H  HAT   H  HCH2   0   0.193    3.5265   1.4923   1.3840
 K9H  HATA  H  HCH2   0   0.206    4.3924   0.0830   1.9701
 K9H  HAY   H  HCH1   0   0.164    4.0904   0.7821  -0.9626
 K9H  CAT   C  CH2    0  -0.616    3.8036   0.4656   1.1344

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
 K9H  CAK  CAA   single    1.523  0.020  1.523
 K9H  CAA  HAA   single    0.970  0.020  1.090
 K9H  CAA  HAAA  single    0.970  0.020  1.090
 K9H  CAA  HAAB  single    0.970  0.020  1.090
 K9H  OAB  PAZ   deloc     1.548  0.020  1.548
 K9H  PBA  OAC   deloc     1.543  0.020  1.543
 K9H  PAZ  OAD   deloc     1.537  0.020  1.537
 K9H  OAE  PAZ   deloc     1.537  0.020  1.537
 K9H  OAF  PBA   deloc     1.543  0.020  1.543
 K9H  PBA  OAG   deloc     1.536  0.020  1.536
 K9H  CAH  NAU   aromatic  1.319  0.020  1.319
 K9H  CAH  CAW   aromatic  1.401  0.020  1.401
 K9H  CAH  HAH   single    0.930  0.020  1.080
 K9H  NAU  CAI   aromatic  1.335  0.020  1.335
 K9H  CAI  CAX   aromatic  1.388  0.020  1.388
 K9H  CAI  HAI   single    0.930  0.020  1.080
 K9H  CAW  CAJ   aromatic  1.382  0.020  1.382
 K9H  CAJ  CAX   aromatic  1.397  0.020  1.397
 K9H  CAJ  HAJ   single    0.930  0.020  1.080
 K9H  CAL  CAK   single    1.524  0.020  1.524
 K9H  CAK  HAK   single    0.970  0.020  1.090
 K9H  CAK  HAKA  single    0.970  0.020  1.090
 K9H  CAM  CAL   single    1.524  0.020  1.524
 K9H  CAL  HAL   single    0.970  0.020  1.090
 K9H  CAL  HALA  single    0.970  0.020  1.090
 K9H  CAN  CAM   single    1.524  0.020  1.524
 K9H  CAM  HAM   single    0.970  0.020  1.090
 K9H  CAM  HAMA  single    0.970  0.020  1.090
 K9H  CAO  CAN   single    1.524  0.020  1.524
 K9H  CAN  HAN   single    0.970  0.020  1.090
 K9H  CAN  HANA  single    0.970  0.020  1.090
 K9H  CAP  CAO   single    1.524  0.020  1.524
 K9H  CAO  HAO   single    0.970  0.020  1.090
 K9H  CAO  HAOA  single    0.970  0.020  1.090
 K9H  CAQ  CAP   single    1.523  0.020  1.523
 K9H  CAP  HAP   single    0.970  0.020  1.090
 K9H  CAP  HAPA  single    0.970  0.020  1.090
 K9H  CAR  CAQ   single    1.525  0.020  1.525
 K9H  CAQ  HAQ   single    0.970  0.020  1.090
 K9H  CAQ  HAQA  single    0.970  0.020  1.090
 K9H  CAS  CAR   single    1.514  0.020  1.514
 K9H  CAR  HAR   single    0.970  0.020  1.090
 K9H  CAR  HARA  single    0.970  0.020  1.090
 K9H  OAV  CAS   single    1.418  0.020  1.418
 K9H  CAS  HAS   single    0.970  0.020  1.090
 K9H  CAS  HASA  single    0.970  0.020  1.090
 K9H  CAT  CAY   single    1.537  0.020  1.537
 K9H  CAT  CAW   single    1.499  0.020  1.499
 K9H  CAT  HAT   single    0.970  0.020  1.090
 K9H  CAT  HATA  single    0.970  0.020  1.090
 K9H  CAX  OAV   single    1.350  0.020  1.350
 K9H  PAZ  CAY   single    1.867  0.020  1.867
 K9H  PBA  CAY   single    1.868  0.020  1.868
 K9H  CAY  HAY   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
 K9H  HAAB  CAA  HAAA  107.54  3.000
 K9H  HAAB  CAA  HAA   107.62  3.000
 K9H  HAAA  CAA  HAA   107.62  3.000
 K9H  HAAB  CAA  CAK   111.07  3.000
 K9H  HAAA  CAA  CAK   111.07  3.000
 K9H  HAA   CAA  CAK   111.73  3.000
 K9H  HAH   CAH  CAW   118.60  3.000
 K9H  HAH   CAH  NAU   117.80  3.000
 K9H  CAW   CAH  NAU   123.61  3.000
 K9H  HAI   CAI  CAX   121.86  3.000
 K9H  HAI   CAI  NAU   116.12  3.000
 K9H  CAX   CAI  NAU   122.02  3.000
 K9H  HAJ   CAJ  CAX   119.28  3.000
 K9H  HAJ   CAJ  CAW   120.47  3.000
 K9H  CAX   CAJ  CAW   120.24  3.000
 K9H  HAKA  CAK  HAK   106.02  3.000
 K9H  HAKA  CAK  CAL   109.32  3.000
 K9H  HAK   CAK  CAL   109.27  3.000
 K9H  HAKA  CAK  CAA   109.63  3.000
 K9H  HAK   CAK  CAA   109.63  3.000
 K9H  CAL   CAK  CAA   112.76  3.000
 K9H  HALA  CAL  HAL   105.96  3.000
 K9H  HALA  CAL  CAM   109.30  3.000
 K9H  HAL   CAL  CAM   109.37  3.000
 K9H  HALA  CAL  CAK   109.26  3.000
 K9H  HAL   CAL  CAK   109.31  3.000
 K9H  CAM   CAL  CAK   113.38  3.000
 K9H  HAMA  CAM  HAM   105.99  3.000
 K9H  HAMA  CAM  CAN   109.40  3.000
 K9H  HAM   CAM  CAN   109.33  3.000
 K9H  HAMA  CAM  CAL   109.36  3.000
 K9H  HAM   CAM  CAL   109.28  3.000
 K9H  CAN   CAM  CAL   113.23  3.000
 K9H  HANA  CAN  HAN   105.99  3.000
 K9H  HANA  CAN  CAO   109.21  3.000
 K9H  HAN   CAN  CAO   109.42  3.000
 K9H  HANA  CAN  CAM   109.31  3.000
 K9H  HAN   CAN  CAM   109.39  3.000
 K9H  CAO   CAN  CAM   113.26  3.000
 K9H  HAOA  CAO  HAO   106.00  3.000
 K9H  HAOA  CAO  CAP   109.41  3.000
 K9H  HAO   CAO  CAP   109.31  3.000
 K9H  HAOA  CAO  CAN   109.43  3.000
 K9H  HAO   CAO  CAN   109.21  3.000
 K9H  CAP   CAO  CAN   113.23  3.000
 K9H  HAPA  CAP  HAP   106.07  3.000
 K9H  HAPA  CAP  CAQ   109.17  3.000
 K9H  HAP   CAP  CAQ   109.62  3.000
 K9H  HAPA  CAP  CAO   109.33  3.000
 K9H  HAP   CAP  CAO   109.44  3.000
 K9H  CAQ   CAP  CAO   113.00  3.000
 K9H  HAQA  CAQ  HAQ   106.06  3.000
 K9H  HAQA  CAQ  CAR   109.55  3.000
 K9H  HAQ   CAQ  CAR   109.47  3.000
 K9H  HAQA  CAQ  CAP   109.53  3.000
 K9H  HAQ   CAQ  CAP   109.00  3.000
 K9H  CAR   CAQ  CAP   113.00  3.000
 K9H  HARA  CAR  HAR   106.99  3.000
 K9H  HARA  CAR  CAS   109.28  3.000
 K9H  HAR   CAR  CAS   109.95  3.000
 K9H  HARA  CAR  CAQ   109.58  3.000
 K9H  HAR   CAR  CAQ   109.71  3.000
 K9H  CAS   CAR  CAQ   111.24  3.000
 K9H  HASA  CAS  HAS   107.26  3.000
 K9H  HASA  CAS  OAV   110.32  3.000
 K9H  HAS   CAS  OAV   110.23  3.000
 K9H  HASA  CAS  CAR   110.53  3.000
 K9H  HAS   CAS  CAR   109.66  3.000
 K9H  OAV   CAS  CAR   108.82  3.000
 K9H  CAI   NAU  CAH   119.28  3.000
 K9H  CAX   OAV  CAS   118.31  3.000
 K9H  CAT   CAW  CAJ   121.48  3.000
 K9H  CAT   CAW  CAH   121.76  3.000
 K9H  CAJ   CAW  CAH   116.74  3.000
 K9H  OAV   CAX  CAJ   117.02  3.000
 K9H  OAV   CAX  CAI   124.87  3.000
 K9H  CAJ   CAX  CAI   118.11  3.000
 K9H  HAY   CAY  PBA   106.46  3.000
 K9H  HAY   CAY  PAZ   105.88  3.000
 K9H  PBA   CAY  PAZ   116.50  3.000
 K9H  HAY   CAY  CAT   107.34  3.000
 K9H  PBA   CAY  CAT   111.14  3.000
 K9H  PAZ   CAY  CAT   109.00  3.000
 K9H  CAY   PAZ  OAE   107.06  3.000
 K9H  CAY   PAZ  OAD   107.31  3.000
 K9H  OAE   PAZ  OAD   114.18  3.000
 K9H  CAY   PAZ  OAB   104.88  3.000
 K9H  OAE   PAZ  OAB   111.58  3.000
 K9H  OAD   PAZ  OAB   111.20  3.000
 K9H  CAY   PBA  OAG   107.84  3.000
 K9H  CAY   PBA  OAF   106.54  3.000
 K9H  OAG   PBA  OAF   112.71  3.000
 K9H  CAY   PBA  OAC   105.21  3.000
 K9H  OAG   PBA  OAC   111.65  3.000
 K9H  OAF   PBA  OAC   112.37  3.000
 K9H  HATA  CAT  HAT   106.93  3.000
 K9H  HATA  CAT  CAY   107.67  3.000
 K9H  HAT   CAT  CAY   108.42  3.000
 K9H  HATA  CAT  CAW   108.90  3.000
 K9H  HAT   CAT  CAW   108.37  3.000
 K9H  CAY   CAT  CAW   116.17  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
 K9H  CONST_01  CAX  CAI  NAU  CAH     0.00   0.0  0
 K9H  CONST_02  CAX  CAJ  CAW  CAH     0.00   0.0  0
 K9H  CONST_03  CAW  CAH  NAU  CAI     0.00   0.0  0
 K9H  CONST_04  CAW  CAJ  CAX  CAI     0.00   0.0  0
 K9H  CONST_05  NAU  CAH  CAW  CAJ     0.00   0.0  0
 K9H  CONST_06  NAU  CAI  CAX  CAJ     0.00   0.0  0
 K9H  CONST_07  NAU  CAH  CAW  CAT   180.00   0.0  0
 K9H  CONST_08  CAX  CAJ  CAW  CAT   180.00   0.0  0
 K9H  CONST_09  OAV  CAX  CAI  NAU   180.00   0.0  0
 K9H  CONST_10  CAW  CAJ  CAX  OAV   180.00   0.0  0
 K9H  CONST_11  HAI  CAI  NAU  CAH   180.00   0.0  0
 K9H  CONST_12  HAJ  CAJ  CAW  CAH   180.00   0.0  0
 K9H  CONST_13  HAH  CAH  NAU  CAI   180.00   0.0  0
 K9H  Var_01    CAY  CAT  CAW  CAH    85.45  30.0  2
 K9H  Var_02    PAZ  CAY  CAT  CAW   166.15  30.0  3
 K9H  Var_03    HAS  CAS  OAV  CAX    53.93  30.0  3
 K9H  Var_04    CAM  CAL  CAK  CAA   179.77  30.0  2
 K9H  Var_05    CAT  CAY  PAZ  OAB   -43.62  30.0  3
 K9H  Var_06    CAN  CAM  CAL  CAK  -179.84  30.0  1
 K9H  Var_07    CAO  CAN  CAM  CAL   178.99  30.0  2
 K9H  Var_08    CAP  CAO  CAN  CAM  -180.00  30.0  1
 K9H  Var_09    CAQ  CAP  CAO  CAN   177.38  30.0  2
 K9H  Var_10    CAR  CAQ  CAP  CAO   179.66  30.0  2
 K9H  Var_11    CAS  CAR  CAQ  CAP   174.53  30.0  1
 K9H  Var_12    OAV  CAS  CAR  CAQ   179.94  30.0  1
 K9H  Var_13    HAA  CAA  CAK  CAL  -179.94  30.0  3

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
 K9H  plan-1  CAH  0.020
 K9H  plan-1  CAI  0.020
 K9H  plan-1  CAJ  0.020
 K9H  plan-1  NAU  0.020
 K9H  plan-1  OAV  0.020
 K9H  plan-1  CAW  0.020
 K9H  plan-1  CAX  0.020
 K9H  plan-1  HAH  0.020
 K9H  plan-1  HAI  0.020
 K9H  plan-1  HAJ  0.020
 K9H  plan-1  CAT  0.020

