# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 14:30:15 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: hydrogen [(1S)-1-hydroxy-2-(3-octyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC[n+]1ccn(C[C@@](O)([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
 N1Z  N1Z  'hydrogen [(1S)-1-hydroxy-2-(3-octyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate'  ligand  50  24  .  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_N1Z
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
 N1Z  CAA   C  CH3    0  -0.662  10.7068  -1.4875  -0.2018
 N1Z  OAB   O  O      0  -0.707  -4.9605  -1.3816  -1.3115
 N1Z  OAG   O  OP    -1  -0.737  -2.0087   1.6597   1.4881
 N1Z  OAD   O  OH1    0  -0.657  -2.0424  -1.3023   1.3593
 N1Z  OAE   O  OH1    0  -0.777  -5.1377  -1.5593   1.3094
 N1Z  OAF   O  OH1    0  -0.750  -3.8166  -3.2476   0.1021
 N1Z  OAH   O  O      0  -0.790  -4.4249   0.7330   1.8457
 N1Z  OAC   O  OH1    0  -0.771  -3.7509   1.6847  -0.4158
 N1Z  CAI   C  CR15   0  -0.103  -0.6560   1.3865  -1.5967
 N1Z  CAJ   C  CR15   0  -0.082   0.4883   1.9664  -1.1669
 N1Z  CAK   C  CR15   0   0.291   0.2073   0.1078  -0.0411
 N1Z  CAL   C  CH2    0  -0.420   9.6029  -0.7568   0.5498
 N1Z  CAM   C  CH2    0  -0.406   8.3061  -0.6699  -0.2451
 N1Z  CAN   C  CH2    0  -0.413   7.1875   0.0523   0.4951
 N1Z  CAO   C  CH2    0  -0.413   5.8749   0.0632  -0.2772
 N1Z  CAP   C  CH2    0  -0.424   4.7432   0.7649   0.4632
 N1Z  CAQ   C  CH2    0  -0.431   3.4177   0.6570  -0.2790
 N1Z  CAR   C  CH2    0  -0.316   2.2863   1.3291   0.4826
 N1Z  NAT   N  NR5    0  -0.422  -0.8066   0.2228  -0.8870
 N1Z  NAU   N  NR5    1  -0.414   1.0062   1.1502  -0.1957
 N1Z  CAV   C  CT     0  -0.352  -2.7681  -0.7302   0.2927
 N1Z  PAW   P  P      0   1.351  -4.3096  -1.7164  -0.0202
 N1Z  PAX   P  P      0   1.344  -3.2154   0.9699   0.9467
 N1Z  HAA   H  HCH3   0   0.226  11.6211  -1.5544   0.3890
 N1Z  HAAA  H  HCH3   0   0.216  10.4023  -2.5045  -0.4563
 N1Z  HAAB  H  HCH3   0   0.216  10.9531  -0.9767  -1.1347
 N1Z  HOAD  H  HOH1   0   0.460  -1.8981  -2.2428   1.1917
 N1Z  HOAE  H  HOH1   0   0.491  -4.9641  -0.5956   1.6699
 N1Z  HOAF  H  HOH1   0   0.495  -3.6805  -3.6799  -0.7509
 N1Z  HOAC  H  HOH1   0   0.477  -3.2827   2.5046  -0.6133
 N1Z  HAI   H  HCR5   0   0.335  -1.3575   1.6958  -2.3518
 N1Z  HAJ   H  HCR5   0   0.332   0.9709   2.8789  -1.4705
 N1Z  HAK   H  HCR5   0   0.357   0.3691  -0.7010   0.6499
 N1Z  HAL   H  HCH2   0   0.210   9.4078  -1.2635   1.5002
 N1Z  HALA  H  HCH2   0   0.211   9.9402   0.2516   0.8089
 N1Z  HAM   H  HCH2   0   0.207   8.4986  -0.1653  -1.1987
 N1Z  HAMA  H  HCH2   0   0.206   7.9733  -1.6818  -0.5029
 N1Z  HAN   H  HCH2   0   0.207   7.0274  -0.4276   1.4673
 N1Z  HANA  H  HCH2   0   0.210   7.4971   1.0802   0.7130
 N1Z  HAO   H  HCH2   0   0.213   6.0271   0.5424  -1.2504
 N1Z  HAOA  H  HCH2   0   0.212   5.5768  -0.9688  -0.4923
 N1Z  HAP   H  HCH2   0   0.221   4.6340   0.3263   1.4607
 N1Z  HAPA  H  HCH2   0   0.224   4.9993   1.8179   0.6172
 N1Z  HAQ   H  HCH2   0   0.242   3.5070   1.1059  -1.2722
 N1Z  HAQA  H  HCH2   0   0.238   3.1702  -0.3980  -0.4291
 N1Z  HAR   H  HCH2   0   0.285   2.1868   0.9174   1.4861
 N1Z  HARA  H  HCH2   0   0.287   2.4534   2.4006   0.5822
 N1Z  HAS   H  HCH2   0   0.303  -2.5381  -0.3494  -1.8327
 N1Z  HASA  H  HCH2   0   0.308  -1.5580  -1.6771  -1.2368
 N1Z  CAS   C  CH2    0  -0.324  -1.9401  -0.6845  -0.9901

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
 N1Z  CAA  CAL   single    1.522  0.020  1.522
 N1Z  CAA  HAA   single    0.970  0.020  1.090
 N1Z  CAA  HAAA  single    0.970  0.020  1.090
 N1Z  CAA  HAAB  single    0.970  0.020  1.090
 N1Z  OAB  PAW   double    1.484  0.020  1.484
 N1Z  OAD  CAV   single    1.411  0.020  1.411
 N1Z  OAD  HOAD  single    0.850  0.020  0.980
 N1Z  OAE  HOAE  single    0.850  0.020  0.980
 N1Z  OAF  HOAF  single    0.850  0.020  0.980
 N1Z  OAH  PAX   double    1.526  0.020  1.526
 N1Z  OAC  PAX   single    1.629  0.020  1.629
 N1Z  OAC  HOAC  single    0.850  0.020  0.980
 N1Z  CAI  CAJ   aromatic  1.353  0.020  1.353
 N1Z  CAI  HAI   single    0.930  0.020  1.080
 N1Z  CAJ  HAJ   single    0.930  0.020  1.080
 N1Z  CAK  NAT   aromatic  1.325  0.020  1.325
 N1Z  CAK  NAU   aromatic  1.322  0.020  1.322
 N1Z  CAK  HAK   single    0.930  0.020  1.080
 N1Z  CAL  CAM   single    1.524  0.020  1.524
 N1Z  CAL  HAL   single    0.970  0.020  1.090
 N1Z  CAL  HALA  single    0.970  0.020  1.090
 N1Z  CAM  CAN   single    1.523  0.020  1.523
 N1Z  CAM  HAM   single    0.970  0.020  1.090
 N1Z  CAM  HAMA  single    0.970  0.020  1.090
 N1Z  CAN  CAO   single    1.523  0.020  1.523
 N1Z  CAN  HAN   single    0.970  0.020  1.090
 N1Z  CAN  HANA  single    0.970  0.020  1.090
 N1Z  CAO  CAP   single    1.524  0.020  1.524
 N1Z  CAO  HAO   single    0.970  0.020  1.090
 N1Z  CAO  HAOA  single    0.970  0.020  1.090
 N1Z  CAP  HAP   single    0.970  0.020  1.090
 N1Z  CAP  HAPA  single    0.970  0.020  1.090
 N1Z  CAQ  CAP   single    1.523  0.020  1.523
 N1Z  CAQ  CAR   single    1.521  0.020  1.521
 N1Z  CAQ  HAQ   single    0.970  0.020  1.090
 N1Z  CAQ  HAQA  single    0.970  0.020  1.090
 N1Z  CAR  HAR   single    0.970  0.020  1.090
 N1Z  CAR  HARA  single    0.970  0.020  1.090
 N1Z  CAS  NAT   single    1.455  0.020  1.455
 N1Z  CAS  CAV   single    1.527  0.020  1.527
 N1Z  CAS  HAS   single    0.970  0.020  1.090
 N1Z  CAS  HASA  single    0.970  0.020  1.090
 N1Z  NAT  CAI   aromatic  1.371  0.020  1.371
 N1Z  NAU  CAJ   aromatic  1.370  0.020  1.370
 N1Z  NAU  CAR   single    1.460  0.020  1.460
 N1Z  CAV  PAW   single    1.857  0.020  1.857
 N1Z  PAW  OAE   single    1.574  0.020  1.574
 N1Z  PAW  OAF   single    1.613  0.020  1.613
 N1Z  PAX  OAG   single    1.492  0.020  1.492
 N1Z  PAX  CAV   single    1.876  0.020  1.876

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
 N1Z  HAAB  CAA  HAAA  107.44  3.000
 N1Z  HAAB  CAA  HAA   107.61  3.000
 N1Z  HAAA  CAA  HAA   107.63  3.000
 N1Z  HAAB  CAA  CAL   111.16  3.000
 N1Z  HAAA  CAA  CAL   111.10  3.000
 N1Z  HAA   CAA  CAL   111.71  3.000
 N1Z  HOAD  OAD  CAV   109.90  3.000
 N1Z  HOAE  OAE  PAW   107.25  3.000
 N1Z  HOAF  OAF  PAW   113.64  3.000
 N1Z  HOAC  OAC  PAX   112.62  3.000
 N1Z  HAI   CAI  NAT   122.38  3.000
 N1Z  NAT   CAI  CAJ   106.99  3.000
 N1Z  HAI   CAI  CAJ   130.63  3.000
 N1Z  HAJ   CAJ  NAU   122.39  3.000
 N1Z  NAU   CAJ  CAI   106.83  3.000
 N1Z  HAJ   CAJ  CAI   130.78  3.000
 N1Z  HAK   CAK  NAU   125.22  3.000
 N1Z  HAK   CAK  NAT   126.16  3.000
 N1Z  NAU   CAK  NAT   108.61  3.000
 N1Z  HALA  CAL  HAL   106.01  3.000
 N1Z  HALA  CAL  CAM   109.47  3.000
 N1Z  HAL   CAL  CAM   109.13  3.000
 N1Z  HALA  CAL  CAA   109.61  3.000
 N1Z  HAL   CAL  CAA   109.62  3.000
 N1Z  CAM   CAL  CAA   112.77  3.000
 N1Z  HAMA  CAM  HAM   105.90  3.000
 N1Z  HAMA  CAM  CAN   109.21  3.000
 N1Z  HAM   CAM  CAN   109.48  3.000
 N1Z  HAMA  CAM  CAL   109.18  3.000
 N1Z  HAM   CAM  CAL   109.31  3.000
 N1Z  CAN   CAM  CAL   113.48  3.000
 N1Z  HANA  CAN  HAN   106.01  3.000
 N1Z  HANA  CAN  CAO   109.74  3.000
 N1Z  HAN   CAN  CAO   109.09  3.000
 N1Z  HANA  CAN  CAM   109.51  3.000
 N1Z  HAN   CAN  CAM   109.31  3.000
 N1Z  CAO   CAN  CAM   112.94  3.000
 N1Z  HAOA  CAO  HAO   105.99  3.000
 N1Z  HAOA  CAO  CAP   109.10  3.000
 N1Z  HAO   CAO  CAP   109.48  3.000
 N1Z  HAOA  CAO  CAN   109.11  3.000
 N1Z  HAO   CAO  CAN   109.50  3.000
 N1Z  CAP   CAO  CAN   113.39  3.000
 N1Z  HAPA  CAP  HAP   106.29  3.000
 N1Z  HAPA  CAP  CAQ   109.90  3.000
 N1Z  HAP   CAP  CAQ   109.19  3.000
 N1Z  CAQ   CAP  CAO   112.15  3.000
 N1Z  HAPA  CAP  CAO   109.73  3.000
 N1Z  HAP   CAP  CAO   109.40  3.000
 N1Z  HAQA  CAQ  HAQ   106.84  3.000
 N1Z  HAQA  CAQ  CAR   109.07  3.000
 N1Z  HAQ   CAQ  CAR   109.52  3.000
 N1Z  HAQA  CAQ  CAP   109.39  3.000
 N1Z  HAQ   CAQ  CAP   110.03  3.000
 N1Z  CAR   CAQ  CAP   111.85  3.000
 N1Z  HARA  CAR  HAR   107.56  3.000
 N1Z  HARA  CAR  NAU   107.32  3.000
 N1Z  HAR   CAR  NAU   107.56  3.000
 N1Z  NAU   CAR  CAQ   111.45  3.000
 N1Z  HARA  CAR  CAQ   111.50  3.000
 N1Z  HAR   CAR  CAQ   111.24  3.000
 N1Z  CAS   NAT  CAK   125.93  3.000
 N1Z  CAS   NAT  CAI   125.30  3.000
 N1Z  CAK   NAT  CAI   108.66  3.000
 N1Z  CAR   NAU  CAK   124.90  3.000
 N1Z  CAR   NAU  CAJ   126.00  3.000
 N1Z  CAK   NAU  CAJ   108.91  3.000
 N1Z  PAX   CAV  PAW   110.01  3.000
 N1Z  PAX   CAV  CAS   113.26  3.000
 N1Z  PAW   CAV  CAS   108.93  3.000
 N1Z  PAX   CAV  OAD   103.09  3.000
 N1Z  PAW   CAV  OAD   109.82  3.000
 N1Z  CAS   CAV  OAD   111.60  3.000
 N1Z  CAV   PAW  OAF   103.75  3.000
 N1Z  OAF   PAW  OAE   101.04  3.000
 N1Z  CAV   PAW  OAE   103.97  3.000
 N1Z  OAF   PAW  OAB   114.46  3.000
 N1Z  OAE   PAW  OAB   118.79  3.000
 N1Z  CAV   PAW  OAB   113.01  3.000
 N1Z  CAV   PAX  OAC   100.63  3.000
 N1Z  CAV   PAX  OAH   104.70  3.000
 N1Z  OAC   PAX  OAH   107.48  3.000
 N1Z  CAV   PAX  OAG   110.66  3.000
 N1Z  OAC   PAX  OAG   111.50  3.000
 N1Z  OAH   PAX  OAG   119.96  3.000
 N1Z  HASA  CAS  HAS   107.33  3.000
 N1Z  HASA  CAS  CAV   110.62  3.000
 N1Z  HAS   CAS  CAV   111.23  3.000
 N1Z  HASA  CAS  NAT   108.07  3.000
 N1Z  HAS   CAS  NAT   106.94  3.000
 N1Z  CAV   CAS  NAT   112.41  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
 N1Z  CONST_01  CAK  NAU  CAJ  CAI     0.00   0.0  0
 N1Z  CONST_02  NAU  CAK  NAT  CAI     0.00   0.0  0
 N1Z  CONST_03  CAK  NAT  CAI  CAJ     0.00   0.0  0
 N1Z  CONST_04  NAT  CAK  NAU  CAJ     0.00   0.0  0
 N1Z  CONST_05  NAU  CAJ  CAI  NAT     0.00   0.0  0
 N1Z  CONST_06  CAR  NAU  CAJ  CAI   180.00   0.0  0
 N1Z  CONST_07  CAS  NAT  CAI  CAJ   180.00   0.0  0
 N1Z  CONST_08  NAT  CAK  NAU  CAR   180.00   0.0  0
 N1Z  CONST_09  NAU  CAK  NAT  CAS   180.00   0.0  0
 N1Z  CONST_10  HAK  CAK  NAT  CAI   180.00   0.0  0
 N1Z  CONST_11  HAI  CAI  NAT  CAK   180.00   0.0  0
 N1Z  CONST_12  HAJ  CAJ  NAU  CAK   180.00   0.0  0
 N1Z  Var_01    CAV  CAS  NAT  CAI  -113.37  30.0  3
 N1Z  Var_02    CAQ  CAR  NAU  CAJ   -88.07  30.0  2
 N1Z  Var_03    NAU  CAR  CAQ  CAP  -176.52  30.0  3
 N1Z  Var_04    CAN  CAM  CAL  CAA   179.70  30.0  3
 N1Z  Var_05    CAO  CAN  CAM  CAL  -176.74  30.0  3
 N1Z  Var_06    CAP  CAO  CAN  CAM   179.13  30.0  3
 N1Z  Var_07    CAQ  CAP  CAO  CAN  -175.16  30.0  3
 N1Z  Var_08    CAR  CAQ  CAP  CAO   178.56  30.0  1
 N1Z  Var_09    HAA  CAA  CAL  CAM  -179.04  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
 N1Z  chir_01  CAV  CAS  PAW  PAX  positiv

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
 N1Z  plan-1  CAI  0.020
 N1Z  plan-1  CAJ  0.020
 N1Z  plan-1  CAK  0.020
 N1Z  plan-1  CAR  0.020
 N1Z  plan-1  NAT  0.020
 N1Z  plan-1  NAU  0.020
 N1Z  plan-1  HAI  0.020
 N1Z  plan-1  HAJ  0.020
 N1Z  plan-1  HAK  0.020
 N1Z  plan-1  CAS  0.020

