# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 03:46:30 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: hydrogen [(1S)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC[n+]1ccn(C[C@H]([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
 BH8  BH8  'hydrogen [(1S)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate'  ligand  52  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BH8
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
 BH8  OAD  O  OP    -1  -0.887  -2.5891  -2.6336   0.5412
 BH8  PAX  P  P      0   1.198  -2.3635  -1.1246   0.6228
 BH8  OAE  O  OP    -1  -0.905  -2.5224  -0.5453   2.0471
 BH8  OAB  O  O      0  -0.884  -1.0198  -0.6945  -0.0122
 BH8  CAU  C  CH1    0  -0.753  -3.6608  -0.2693  -0.4184
 BH8  PAY  P  P      0   1.179  -5.3889  -0.9899  -0.4303
 BH8  OAF  O  OP    -1  -0.910  -5.3085  -2.3408  -1.1492
 BH8  OAG  O  O      0  -0.921  -5.8336  -1.0721   1.0362
 BH8  OAC  O  OP    -1  -0.929  -6.2131   0.0430  -1.2323
 BH8  CAT  C  CH2    0  -0.302  -3.7846   1.1951  -0.0298
 BH8  NAW  N  NR5    0  -0.406  -2.5342   1.9545  -0.1493
 BH8  CAJ  C  CR15   0   0.277  -1.5084   1.8671   0.6798
 BH8  CAI  C  CR15   0  -0.106  -2.1635   2.7154  -1.2282
 BH8  CAH  C  CR15   0  -0.113  -0.8878   3.1146  -1.0165
 BH8  NAV  N  NR5    1  -0.419  -0.5068   2.5878   0.1949
 BH8  CAS  C  CH2    0  -0.307   0.8376   2.6234   0.7470
 BH8  CAR  C  CH2    0  -0.435   1.7195   1.5494   0.1266
 BH8  CAQ  C  CH2    0  -0.421   3.1408   1.5993   0.6706
 BH8  CAP  C  CH2    0  -0.412   4.0452   0.5528   0.0307
 BH8  CAO  C  CH2    0  -0.411   5.4961   0.6477   0.4852
 BH8  CAN  C  CH2    0  -0.411   6.3987  -0.3812  -0.1846
 BH8  CAM  C  CH2    0  -0.411   7.8611  -0.2643   0.2264
 BH8  CAL  C  CH2    0  -0.406   8.7624  -1.2748  -0.4725
 BH8  CAK  C  CH2    0  -0.418  10.2308  -1.1477  -0.0857
 BH8  CAA  C  CH3    0  -0.663  11.1204  -2.1518  -0.8060
 BH8  H3   H  HCH1   0   0.168  -3.3127  -0.3065  -1.4603
 BH8  H6   H  HCH2   0   0.237  -4.5125   1.7045  -0.6589
 BH8  H7   H  HCH2   0   0.238  -4.1171   1.2778   1.0032
 BH8  H8   H  HCR5   0   0.331  -1.5263   1.2949   1.5972
 BH8  H9   H  HCR5   0   0.309  -2.8379   2.9235  -2.0407
 BH8  H10  H  HCR5   0   0.312  -0.2360   3.7370  -1.6045
 BH8  H11  H  HCH2   0   0.267   1.2422   3.6203   0.5709
 BH8  H12  H  HCH2   0   0.270   0.7572   2.4896   1.8256
 BH8  H13  H  HCH2   0   0.248   1.2600   0.5739   0.3037
 BH8  H14  H  HCH2   0   0.224   1.7429   1.6926  -0.9582
 BH8  H15  H  HCH2   0   0.213   3.5594   2.5959   0.4942
 BH8  H16  H  HCH2   0   0.217   3.1304   1.4590   1.7567
 BH8  H17  H  HCH2   0   0.212   3.6576  -0.4474   0.2517
 BH8  H18  H  HCH2   0   0.209   4.0022   0.6605  -1.0587
 BH8  H19  H  HCH2   0   0.206   5.8742   1.6535   0.2711
 BH8  H20  H  HCH2   0   0.208   5.5504   0.5278   1.5729
 BH8  H21  H  HCH2   0   0.207   6.0357  -1.3889   0.0462
 BH8  H22  H  HCH2   0   0.206   6.3200  -0.2734  -1.2723
 BH8  H23  H  HCH2   0   0.205   8.2173   0.7487   0.0080
 BH8  H24  H  HCH2   0   0.206   7.9476  -0.3889   1.3115
 BH8  H25  H  HCH2   0   0.206   8.4154  -2.2895  -0.2469
 BH8  H26  H  HCH2   0   0.205   8.6636  -1.1560  -1.5574
 BH8  H27  H  HCH2   0   0.209  10.5752  -0.1318  -0.3032
 BH8  H28  H  HCH2   0   0.210  10.3339  -1.2772   0.9963
 BH8  H29  H  HCH3   0   0.216  10.8337  -3.1770  -0.5651
 BH8  H30  H  HCH3   0   0.215  11.0469  -2.0367  -1.8892
 BH8  H31  H  HCH3   0   0.225  12.1690  -2.0303  -0.5318

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
 BH8  CAA  CAK  single    1.523  0.020  1.523
 BH8  CAK  CAL  single    1.524  0.020  1.524
 BH8  CAM  CAL  single    1.524  0.020  1.524
 BH8  CAM  CAN  single    1.524  0.020  1.524
 BH8  CAN  CAO  single    1.524  0.020  1.524
 BH8  CAO  CAP  single    1.523  0.020  1.523
 BH8  CAP  CAQ  single    1.524  0.020  1.524
 BH8  CAQ  CAR  single    1.523  0.020  1.523
 BH8  CAR  CAS  single    1.522  0.020  1.522
 BH8  CAS  NAV  single    1.454  0.020  1.454
 BH8  NAV  CAJ  aromatic  1.326  0.020  1.326
 BH8  NAV  CAH  aromatic  1.375  0.020  1.375
 BH8  OAG  PAY  deloc     1.535  0.020  1.535
 BH8  CAJ  NAW  aromatic  1.322  0.020  1.322
 BH8  CAH  CAI  aromatic  1.353  0.020  1.353
 BH8  NAW  CAI  aromatic  1.371  0.020  1.371
 BH8  NAW  CAT  single    1.468  0.020  1.468
 BH8  CAT  CAU  single    1.520  0.020  1.520
 BH8  OAF  PAY  deloc     1.532  0.020  1.532
 BH8  PAY  CAU  single    1.872  0.020  1.872
 BH8  PAY  OAC  deloc     1.546  0.020  1.546
 BH8  CAU  PAX  single    1.870  0.020  1.870
 BH8  PAX  OAB  deloc     1.547  0.020  1.547
 BH8  PAX  OAE  deloc     1.546  0.020  1.546
 BH8  PAX  OAD  deloc     1.528  0.020  1.528
 BH8  CAU  H3   single    0.970  0.020  1.090
 BH8  CAT  H6   single    0.970  0.020  1.090
 BH8  CAT  H7   single    0.970  0.020  1.090
 BH8  CAJ  H8   single    0.930  0.020  1.080
 BH8  CAI  H9   single    0.930  0.020  1.080
 BH8  CAH  H10  single    0.930  0.020  1.080
 BH8  CAS  H11  single    0.970  0.020  1.090
 BH8  CAS  H12  single    0.970  0.020  1.090
 BH8  CAR  H13  single    0.970  0.020  1.090
 BH8  CAR  H14  single    0.970  0.020  1.090
 BH8  CAQ  H15  single    0.970  0.020  1.090
 BH8  CAQ  H16  single    0.970  0.020  1.090
 BH8  CAP  H17  single    0.970  0.020  1.090
 BH8  CAP  H18  single    0.970  0.020  1.090
 BH8  CAO  H19  single    0.970  0.020  1.090
 BH8  CAO  H20  single    0.970  0.020  1.090
 BH8  CAN  H21  single    0.970  0.020  1.090
 BH8  CAN  H22  single    0.970  0.020  1.090
 BH8  CAM  H23  single    0.970  0.020  1.090
 BH8  CAM  H24  single    0.970  0.020  1.090
 BH8  CAL  H25  single    0.970  0.020  1.090
 BH8  CAL  H26  single    0.970  0.020  1.090
 BH8  CAK  H27  single    0.970  0.020  1.090
 BH8  CAK  H28  single    0.970  0.020  1.090
 BH8  CAA  H29  single    0.970  0.020  1.090
 BH8  CAA  H30  single    0.970  0.020  1.090
 BH8  CAA  H31  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
 BH8  CAU  PAX  OAB  104.29  3.000
 BH8  OAB  PAX  OAE  111.30  3.000
 BH8  CAU  PAX  OAE  105.68  3.000
 BH8  OAE  PAX  OAD  113.84  3.000
 BH8  OAB  PAX  OAD  112.39  3.000
 BH8  CAU  PAX  OAD  108.63  3.000
 BH8  H3   CAU  CAT  107.50  3.000
 BH8  H3   CAU  PAY  105.86  3.000
 BH8  CAT  CAU  PAY  107.29  3.000
 BH8  H3   CAU  PAX  107.01  3.000
 BH8  PAY  CAU  PAX  117.88  3.000
 BH8  CAT  CAU  PAX  110.78  3.000
 BH8  OAC  PAY  OAG  112.15  3.000
 BH8  OAC  PAY  OAF  111.94  3.000
 BH8  OAG  PAY  OAF  114.60  3.000
 BH8  OAC  PAY  CAU  103.78  3.000
 BH8  OAF  PAY  CAU  107.09  3.000
 BH8  OAG  PAY  CAU  106.38  3.000
 BH8  H7   CAT  H6   107.98  3.000
 BH8  H7   CAT  NAW  107.35  3.000
 BH8  H6   CAT  NAW  106.29  3.000
 BH8  H7   CAT  CAU  109.92  3.000
 BH8  H6   CAT  CAU  110.95  3.000
 BH8  NAW  CAT  CAU  114.09  3.000
 BH8  CAI  NAW  CAJ  108.69  3.000
 BH8  CAI  NAW  CAT  125.55  3.000
 BH8  CAJ  NAW  CAT  125.15  3.000
 BH8  H8   CAJ  NAV  127.62  3.000
 BH8  H8   CAJ  NAW  123.67  3.000
 BH8  NAV  CAJ  NAW  108.71  3.000
 BH8  H9   CAI  CAH  130.67  3.000
 BH8  H9   CAI  NAW  122.13  3.000
 BH8  CAH  CAI  NAW  107.19  3.000
 BH8  H10  CAH  NAV  122.36  3.000
 BH8  H10  CAH  CAI  131.00  3.000
 BH8  NAV  CAH  CAI  106.62  3.000
 BH8  CAS  NAV  CAH  125.55  3.000
 BH8  CAH  NAV  CAJ  108.74  3.000
 BH8  CAS  NAV  CAJ  124.96  3.000
 BH8  H12  CAS  H11  107.43  3.000
 BH8  H12  CAS  CAR  111.07  3.000
 BH8  H11  CAS  CAR  111.37  3.000
 BH8  H12  CAS  NAV  107.73  3.000
 BH8  H11  CAS  NAV  107.71  3.000
 BH8  CAR  CAS  NAV  111.33  3.000
 BH8  H14  CAR  H13  106.64  3.000
 BH8  H14  CAR  CAQ  109.26  3.000
 BH8  H13  CAR  CAQ  111.34  3.000
 BH8  H14  CAR  CAS  108.91  3.000
 BH8  H13  CAR  CAS  108.68  3.000
 BH8  CAQ  CAR  CAS  111.85  3.000
 BH8  H16  CAQ  H15  106.26  3.000
 BH8  H16  CAQ  CAP  109.52  3.000
 BH8  H15  CAQ  CAP  109.29  3.000
 BH8  H16  CAQ  CAR  109.95  3.000
 BH8  H15  CAQ  CAR  109.21  3.000
 BH8  CAP  CAQ  CAR  112.42  3.000
 BH8  H18  CAP  H17  106.05  3.000
 BH8  H18  CAP  CAO  109.15  3.000
 BH8  H17  CAP  CAO  109.50  3.000
 BH8  H18  CAP  CAQ  109.07  3.000
 BH8  H17  CAP  CAQ  109.41  3.000
 BH8  CAO  CAP  CAQ  113.40  3.000
 BH8  H20  CAO  H19  106.10  3.000
 BH8  H20  CAO  CAN  109.45  3.000
 BH8  H19  CAO  CAN  109.24  3.000
 BH8  H20  CAO  CAP  109.67  3.000
 BH8  H19  CAO  CAP  109.12  3.000
 BH8  CAN  CAO  CAP  113.01  3.000
 BH8  H22  CAN  H21  106.01  3.000
 BH8  H22  CAN  CAM  109.22  3.000
 BH8  H21  CAN  CAM  109.38  3.000
 BH8  H22  CAN  CAO  109.10  3.000
 BH8  H21  CAN  CAO  109.40  3.000
 BH8  CAM  CAN  CAO  113.47  3.000
 BH8  H24  CAM  H23  106.07  3.000
 BH8  H24  CAM  CAL  109.40  3.000
 BH8  H23  CAM  CAL  109.24  3.000
 BH8  H24  CAM  CAN  109.52  3.000
 BH8  H23  CAM  CAN  109.22  3.000
 BH8  CAL  CAM  CAN  113.15  3.000
 BH8  H26  CAL  H25  106.00  3.000
 BH8  H26  CAL  CAK  109.22  3.000
 BH8  H25  CAL  CAK  109.28  3.000
 BH8  H26  CAL  CAM  109.20  3.000
 BH8  H25  CAL  CAM  109.41  3.000
 BH8  CAK  CAL  CAM  113.47  3.000
 BH8  H28  CAK  H27  106.06  3.000
 BH8  H28  CAK  CAA  109.55  3.000
 BH8  H27  CAK  CAA  109.52  3.000
 BH8  H28  CAK  CAL  109.37  3.000
 BH8  H27  CAK  CAL  109.28  3.000
 BH8  CAA  CAK  CAL  112.83  3.000
 BH8  H31  CAA  H30  107.60  3.000
 BH8  H31  CAA  H29  107.56  3.000
 BH8  H30  CAA  H29  107.47  3.000
 BH8  H31  CAA  CAK  111.68  3.000
 BH8  H30  CAA  CAK  111.13  3.000
 BH8  H29  CAA  CAK  111.20  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
 BH8  CONST_01  CAH  NAV  CAJ  NAW     0.00   0.0  0
 BH8  CONST_02  NAV  CAH  CAI  NAW     0.00   0.0  0
 BH8  CONST_03  CAI  CAH  NAV  CAJ     0.00   0.0  0
 BH8  CONST_04  CAH  CAI  NAW  CAJ     0.00   0.0  0
 BH8  CONST_05  NAV  CAJ  NAW  CAI     0.00   0.0  0
 BH8  CONST_06  NAV  CAJ  NAW  CAT   180.00   0.0  0
 BH8  CONST_07  CAH  CAI  NAW  CAT   180.00   0.0  0
 BH8  CONST_08  CAS  NAV  CAJ  NAW   180.00   0.0  0
 BH8  CONST_09  CAS  NAV  CAH  CAI   180.00   0.0  0
 BH8  CONST_10  H10  CAH  CAI  NAW   180.00   0.0  0
 BH8  CONST_11  H9   CAI  NAW  CAJ   180.00   0.0  0
 BH8  CONST_12  H8   CAJ  NAW  CAI   180.00   0.0  0
 BH8  Var_01    CAJ  NAW  CAT  CAU   -74.33  30.0  2
 BH8  Var_02    CAR  CAS  NAV  CAJ    89.61  30.0  2
 BH8  Var_03    CAQ  CAR  CAS  NAV   178.53  30.0  1
 BH8  Var_04    CAP  CAQ  CAR  CAS  -178.47  30.0  2
 BH8  Var_05    CAO  CAP  CAQ  CAR   175.87  30.0  1
 BH8  Var_06    CAN  CAO  CAP  CAQ  -178.64  30.0  2
 BH8  Var_07    CAM  CAN  CAO  CAP   178.01  30.0  1
 BH8  Var_08    CAL  CAM  CAN  CAO  -178.63  30.0  1
 BH8  Var_09    CAK  CAL  CAM  CAN   178.96  30.0  3
 BH8  Var_10    CAA  CAK  CAL  CAM  -179.24  30.0  1
 BH8  Var_11    H29  CAA  CAK  CAL   -61.07  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
 BH8  chir_01  CAU  CAT  PAY  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
 BH8  plan-1  CAT  0.020
 BH8  plan-1  NAW  0.020
 BH8  plan-1  CAJ  0.020
 BH8  plan-1  CAI  0.020
 BH8  plan-1  CAH  0.020
 BH8  plan-1  NAV  0.020
 BH8  plan-1  CAS  0.020
 BH8  plan-1  H8   0.020
 BH8  plan-1  H9   0.020
 BH8  plan-1  H10  0.020

