# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:11:07 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 3-(decyloxy)-1-(2,2-diphosphonoethyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCOc1ccc[n+](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
 B71  B71  3-(decyloxy)-1-(2,2-diphosphonoethyl)pyridinium  ligand  55  27  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B71
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
 B71  CAA   C  CH3    0  -0.663    3.0737  -4.8909   -1.2179
 B71  CAL   C  CH2    0  -0.418    2.4488  -5.1695   -2.5779
 B71  CAM   C  CH2    0  -0.406    0.9614  -4.8427   -2.6254
 B71  CAN   C  CH2    0  -0.411    0.3286  -5.1091   -3.9853
 B71  CAO   C  CH2    0  -0.412   -1.1556  -4.7706   -4.0387
 B71  CAP   C  CH2    0  -0.412   -1.7806  -5.0319   -5.4033
 B71  CAQ   C  CH2    0  -0.413   -3.2600  -4.6762   -5.4691
 B71  CAR   C  CH2    0  -0.425   -3.8739  -4.9425   -6.8377
 B71  CAS   C  CH2    0  -0.455   -5.3467  -4.5582   -6.9127
 B71  CAT   C  CH2    0  -0.202   -5.9168  -4.8506   -8.2826
 B71  OAV   O  O2     0  -0.470   -7.2911  -4.4478   -8.2893
 B71  CAW   C  CR6    0   0.323   -7.9181  -4.3730   -9.4654
 B71  CAK   C  CR16   0  -0.040   -7.3633  -4.8628  -10.6447
 B71  CAI   C  CR16   0  -0.234   -9.1687  -3.7746   -9.5125
 B71  CAH   C  CR16   0  -0.342   -9.8150  -3.6505  -10.7339
 B71  CAJ   C  CR16   0   0.021   -9.2143  -4.1293  -11.8724
 B71  NAY   N  NR6    1  -0.379   -8.0216  -4.7346  -11.7959
 B71  CAU   C  CH2    0  -0.327   -7.3456  -5.1598  -13.0470
 B71  CAX   C  CH1    0  -0.751   -6.3387  -4.1452  -13.5607
 B71  PBA   P  P      0   1.213   -4.9339  -3.9114  -12.3432
 B71  OAF   O  O      0  -0.892   -4.6258  -5.3230  -11.7988
 B71  OAG   O  OP    -1  -0.885   -3.7607  -3.2606  -13.0744
 B71  OAC   O  OP    -1  -0.885   -5.5322  -2.9937  -11.2507
 B71  PAZ   P  P      0   1.181   -5.8845  -4.6559  -15.3071
 B71  OAD   O  OP    -1  -0.924   -7.2436  -4.9738  -15.9686
 B71  OAE   O  O      0  -0.918   -4.9974  -5.9000  -15.1742
 B71  OAB   O  OP    -1  -0.908   -5.1994  -3.4476  -15.9516
 B71  HAA1  H  HCH3   0   0.215    2.5932  -5.4800   -0.4343
 B71  HAA2  H  HCH3   0   0.215    2.9716  -3.8384   -0.9455
 B71  HAA3  H  HCH3   0   0.225    4.1373  -5.1320   -1.2064
 B71  HAL1  H  HCH2   0   0.210    2.9693  -4.5902   -3.3469
 B71  HAL2  H  HCH2   0   0.210    2.5960  -6.2214   -2.8418
 B71  HAM1  H  HCH2   0   0.205    0.4381  -5.4257   -1.8587
 B71  HAM2  H  HCH2   0   0.205    0.8147  -3.7906   -2.3557
 B71  HAN1  H  HCH2   0   0.206    0.4696  -6.1626   -4.2521
 B71  HAN2  H  HCH2   0   0.206    0.8579  -4.5310   -4.7510
 B71  HAO1  H  HCH2   0   0.206   -1.6879  -5.3504   -3.2764
 B71  HAO2  H  HCH2   0   0.206   -1.2962  -3.7176   -3.7698
 B71  HAP1  H  HCH2   0   0.208   -1.6495  -6.0871   -5.6671
 B71  HAP2  H  HCH2   0   0.208   -1.2390  -4.4609   -6.1656
 B71  HAQ1  H  HCH2   0   0.210   -3.3907  -3.6196   -5.2108
 B71  HAQ2  H  HCH2   0   0.210   -3.8056  -5.2444   -4.7080
 B71  HAR1  H  HCH2   0   0.216   -3.7579  -6.0030   -7.0863
 B71  HAR2  H  HCH2   0   0.217   -3.3155  -4.3887   -7.5997
 B71  HAS1  H  HCH2   0   0.227   -5.9096  -5.1063   -6.1512
 B71  HAS2  H  HCH2   0   0.227   -5.4587  -3.4930   -6.6901
 B71  HAT1  H  HCH2   0   0.218   -5.8457  -5.9223   -8.5021
 B71  HAT2  H  HCH2   0   0.256   -5.3772  -4.3093   -9.0660
 B71  HAK   H  HCR6   0   0.346   -6.3996  -5.3615  -10.7133
 B71  HAI   H  HCR6   0   0.294   -9.6236  -3.3965   -8.6061
 B71  HAH   H  HCR6   0   0.296  -10.7826  -3.1767  -10.8034
 B71  HAJ   H  HCR6   0   0.320   -9.6596  -4.0487  -12.8522
 B71  HAU1  H  HCH2   0   0.243   -8.1330  -5.3299  -13.7784
 B71  HAU2  H  HCH2   0   0.250   -6.8556  -6.1083  -12.8371
 B71  HAX   H  HCH1   0   0.175   -6.8609  -3.1826  -13.6565

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
 B71  CAA  CAL   single    1.522  0.020  1.522
 B71  CAA  HAA1  single    0.970  0.020  1.090
 B71  CAA  HAA2  single    0.970  0.020  1.090
 B71  CAA  HAA3  single    0.970  0.020  1.090
 B71  CAL  CAM   single    1.524  0.020  1.524
 B71  CAL  HAL1  single    0.970  0.020  1.090
 B71  CAL  HAL2  single    0.970  0.020  1.090
 B71  CAM  CAN   single    1.523  0.020  1.523
 B71  CAM  HAM1  single    0.970  0.020  1.090
 B71  CAM  HAM2  single    0.970  0.020  1.090
 B71  CAN  CAO   single    1.523  0.020  1.523
 B71  CAN  HAN1  single    0.970  0.020  1.090
 B71  CAN  HAN2  single    0.970  0.020  1.090
 B71  CAO  CAP   single    1.524  0.020  1.524
 B71  CAO  HAO1  single    0.970  0.020  1.090
 B71  CAO  HAO2  single    0.970  0.020  1.090
 B71  CAP  CAQ   single    1.523  0.020  1.523
 B71  CAP  HAP1  single    0.970  0.020  1.090
 B71  CAP  HAP2  single    0.970  0.020  1.090
 B71  CAQ  CAR   single    1.523  0.020  1.523
 B71  CAQ  HAQ1  single    0.970  0.020  1.090
 B71  CAQ  HAQ2  single    0.970  0.020  1.090
 B71  CAR  CAS   single    1.524  0.020  1.524
 B71  CAR  HAR1  single    0.970  0.020  1.090
 B71  CAR  HAR2  single    0.970  0.020  1.090
 B71  CAS  CAT   single    1.512  0.020  1.512
 B71  CAS  HAS1  single    0.970  0.020  1.090
 B71  CAS  HAS2  single    0.970  0.020  1.090
 B71  CAT  OAV   single    1.432  0.020  1.432
 B71  CAT  HAT1  single    0.970  0.020  1.090
 B71  CAT  HAT2  single    0.970  0.020  1.090
 B71  OAV  CAW   single    1.335  0.020  1.335
 B71  CAW  CAI   aromatic  1.387  0.020  1.387
 B71  CAW  CAK   aromatic  1.392  0.020  1.392
 B71  CAK  NAY   aromatic  1.332  0.020  1.332
 B71  CAK  HAK   single    0.930  0.020  1.080
 B71  CAI  CAH   aromatic  1.387  0.020  1.387
 B71  CAI  HAI   single    0.930  0.020  1.080
 B71  CAH  CAJ   aromatic  1.373  0.020  1.373
 B71  CAH  HAH   single    0.930  0.020  1.080
 B71  CAJ  NAY   aromatic  1.340  0.020  1.340
 B71  CAJ  HAJ   single    0.930  0.020  1.080
 B71  NAY  CAU   single    1.484  0.020  1.484
 B71  CAU  CAX   single    1.519  0.020  1.519
 B71  CAU  HAU1  single    0.970  0.020  1.090
 B71  CAU  HAU2  single    0.970  0.020  1.090
 B71  CAX  PBA   single    1.874  0.020  1.874
 B71  CAX  PAZ   single    1.875  0.020  1.875
 B71  CAX  HAX   single    0.970  0.020  1.090
 B71  PBA  OAF   deloc     1.544  0.020  1.544
 B71  PBA  OAG   deloc     1.528  0.020  1.528
 B71  PBA  OAC   deloc     1.547  0.020  1.547
 B71  PAZ  OAE   deloc     1.534  0.020  1.534
 B71  PAZ  OAB   deloc     1.531  0.020  1.531
 B71  PAZ  OAD   deloc     1.545  0.020  1.545

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
 B71  HAA3  CAA  HAA2  107.56  3.000
 B71  HAA3  CAA  HAA1  107.60  3.000
 B71  HAA2  CAA  HAA1  107.45  3.000
 B71  HAA3  CAA  CAL   111.67  3.000
 B71  HAA2  CAA  CAL   111.15  3.000
 B71  HAA1  CAA  CAL   111.21  3.000
 B71  HAL2  CAL  HAL1  105.99  3.000
 B71  HAL2  CAL  CAM   109.27  3.000
 B71  HAL1  CAL  CAM   109.20  3.000
 B71  HAL2  CAL  CAA   109.64  3.000
 B71  HAL1  CAL  CAA   109.61  3.000
 B71  CAM   CAL  CAA   112.91  3.000
 B71  HAM2  CAM  HAM1  105.94  3.000
 B71  HAM2  CAM  CAN   109.39  3.000
 B71  HAM1  CAM  CAN   109.46  3.000
 B71  HAM2  CAM  CAL   109.20  3.000
 B71  HAM1  CAM  CAL   109.28  3.000
 B71  CAN   CAM  CAL   113.31  3.000
 B71  HAN2  CAN  HAN1  105.96  3.000
 B71  HAN2  CAN  CAO   109.20  3.000
 B71  HAN1  CAN  CAO   109.29  3.000
 B71  HAN2  CAN  CAM   109.32  3.000
 B71  HAN1  CAN  CAM   109.40  3.000
 B71  CAO   CAN  CAM   113.40  3.000
 B71  HAO2  CAO  HAO1  105.99  3.000
 B71  HAO2  CAO  CAP   109.39  3.000
 B71  HAO1  CAO  CAP   109.46  3.000
 B71  HAO2  CAO  CAN   109.27  3.000
 B71  HAO1  CAO  CAN   109.35  3.000
 B71  CAP   CAO  CAN   113.14  3.000
 B71  HAP2  CAP  HAP1  105.98  3.000
 B71  HAP2  CAP  CAQ   109.18  3.000
 B71  HAP1  CAP  CAQ   109.32  3.000
 B71  HAP2  CAP  CAO   109.33  3.000
 B71  HAP1  CAP  CAO   109.37  3.000
 B71  CAQ   CAP  CAO   113.40  3.000
 B71  HAQ2  CAQ  HAQ1  106.09  3.000
 B71  HAQ2  CAQ  CAR   109.44  3.000
 B71  HAQ1  CAQ  CAR   109.41  3.000
 B71  HAQ2  CAQ  CAP   109.43  3.000
 B71  HAQ1  CAQ  CAP   109.32  3.000
 B71  CAR   CAQ  CAP   112.92  3.000
 B71  HAR2  CAR  HAR1  106.12  3.000
 B71  HAR2  CAR  CAS   109.33  3.000
 B71  HAR1  CAR  CAS   109.59  3.000
 B71  HAR2  CAR  CAQ   109.35  3.000
 B71  HAR1  CAR  CAQ   109.30  3.000
 B71  CAS   CAR  CAQ   112.93  3.000
 B71  HAS2  CAS  HAS1  107.07  3.000
 B71  HAS2  CAS  CAT   109.51  3.000
 B71  HAS1  CAS  CAT   109.85  3.000
 B71  HAS2  CAS  CAR   109.54  3.000
 B71  HAS1  CAS  CAR   109.67  3.000
 B71  CAT   CAS  CAR   111.11  3.000
 B71  HAT2  CAT  HAT1  107.95  3.000
 B71  HAT2  CAT  OAV   109.31  3.000
 B71  HAT1  CAT  OAV   109.65  3.000
 B71  HAT2  CAT  CAS   111.53  3.000
 B71  HAT1  CAT  CAS   110.24  3.000
 B71  OAV   CAT  CAS   108.16  3.000
 B71  CAW   OAV  CAT   118.07  3.000
 B71  CAI   CAW  CAK   118.84  3.000
 B71  CAK   CAW  OAV   122.64  3.000
 B71  CAI   CAW  OAV   118.52  3.000
 B71  HAK   CAK  NAY   115.32  3.000
 B71  HAK   CAK  CAW   124.61  3.000
 B71  NAY   CAK  CAW   120.07  3.000
 B71  HAI   CAI  CAH   120.68  3.000
 B71  HAI   CAI  CAW   120.08  3.000
 B71  CAH   CAI  CAW   119.23  3.000
 B71  HAH   CAH  CAJ   119.45  3.000
 B71  HAH   CAH  CAI   120.89  3.000
 B71  CAJ   CAH  CAI   119.66  3.000
 B71  HAJ   CAJ  NAY   116.93  3.000
 B71  HAJ   CAJ  CAH   123.10  3.000
 B71  NAY   CAJ  CAH   119.97  3.000
 B71  CAU   NAY  CAJ   119.13  3.000
 B71  CAU   NAY  CAK   118.40  3.000
 B71  CAJ   NAY  CAK   122.19  3.000
 B71  HAU2  CAU  HAU1  108.62  3.000
 B71  HAU2  CAU  CAX   110.42  3.000
 B71  HAU1  CAU  CAX   110.91  3.000
 B71  HAU2  CAU  NAY   106.99  3.000
 B71  HAU1  CAU  NAY   106.36  3.000
 B71  CAX   CAU  NAY   113.31  3.000
 B71  HAX   CAX  PAZ   105.80  3.000
 B71  HAX   CAX  PBA   107.67  3.000
 B71  PAZ   CAX  PBA   117.23  3.000
 B71  HAX   CAX  CAU   107.42  3.000
 B71  PAZ   CAX  CAU   107.07  3.000
 B71  PBA   CAX  CAU   111.14  3.000
 B71  OAC   PBA  OAG   112.47  3.000
 B71  OAC   PBA  OAF   111.75  3.000
 B71  OAG   PBA  OAF   113.89  3.000
 B71  OAC   PBA  CAX   104.06  3.000
 B71  OAG   PBA  CAX   108.53  3.000
 B71  OAF   PBA  CAX   105.34  3.000
 B71  OAB   PAZ  OAE   114.69  3.000
 B71  OAB   PAZ  OAD   112.08  3.000
 B71  OAE   PAZ  OAD   112.27  3.000
 B71  OAD   PAZ  CAX   103.99  3.000
 B71  OAB   PAZ  CAX   106.58  3.000
 B71  OAE   PAZ  CAX   106.28  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
 B71  CONST_01  CAJ   CAH  CAI  CAW     0.00   0.0  0
 B71  CONST_02  CAJ   NAY  CAK  CAW     0.00   0.0  0
 B71  CONST_03  CAH   CAI  CAW  CAK     0.00   0.0  0
 B71  CONST_04  CAH   CAJ  NAY  CAK     0.00   0.0  0
 B71  CONST_05  NAY   CAK  CAW  CAI     0.00   0.0  0
 B71  CONST_06  NAY   CAJ  CAH  CAI     0.00   0.0  0
 B71  CONST_07  CAH   CAI  CAW  OAV   180.00   0.0  0
 B71  CONST_08  NAY   CAK  CAW  OAV   180.00   0.0  0
 B71  CONST_09  CAU   NAY  CAK  CAW   180.00   0.0  0
 B71  CONST_10  CAU   NAY  CAJ  CAH   180.00   0.0  0
 B71  CONST_11  HAH   CAH  CAI  CAW   180.00   0.0  0
 B71  CONST_12  HAI   CAI  CAW  CAK   180.00   0.0  0
 B71  CONST_13  HAJ   CAJ  NAY  CAK   180.00   0.0  0
 B71  CONST_14  HAK   CAK  CAW  CAI   180.00   0.0  0
 B71  Var_01    CAI   CAW  OAV  CAT  -169.35  30.0  2
 B71  Var_02    CAX   CAU  NAY  CAK   -78.63  30.0  2
 B71  Var_03    PBA   CAX  CAU  NAY    63.31  30.0  3
 B71  Var_04    HAT1  CAT  OAV  CAW   -72.53  30.0  1
 B71  Var_05    CAN   CAM  CAL  CAA   179.60  30.0  3
 B71  Var_06    CAO   CAN  CAM  CAL  -179.46  30.0  3
 B71  Var_07    CAP   CAO  CAN  CAM   179.68  30.0  3
 B71  Var_08    CAQ   CAP  CAO  CAN  -179.16  30.0  3
 B71  Var_09    CAR   CAQ  CAP  CAO  -179.96  30.0  3
 B71  Var_10    CAS   CAR  CAQ  CAP  -178.74  30.0  3
 B71  Var_11    CAT   CAS  CAR  CAQ  -179.50  30.0  3
 B71  Var_12    OAV   CAT  CAS  CAR  -179.10  30.0  3
 B71  Var_13    OAF   PBA  CAX  CAU    39.60  30.0  3
 B71  Var_14    OAE   PAZ  CAX  CAU   -72.89  30.0  3
 B71  Var_15    HAA1  CAA  CAL  CAM    59.77  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
 B71  plan-1  OAV  0.020
 B71  plan-1  CAW  0.020
 B71  plan-1  CAK  0.020
 B71  plan-1  CAI  0.020
 B71  plan-1  CAH  0.020
 B71  plan-1  CAJ  0.020
 B71  plan-1  NAY  0.020
 B71  plan-1  CAU  0.020
 B71  plan-1  HAK  0.020
 B71  plan-1  HAI  0.020
 B71  plan-1  HAH  0.020
 B71  plan-1  HAJ  0.020

