# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 23:37:29 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCn1cc[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
 B73  B73  3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium  ligand  58  27  .  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_B73
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
 B73  CAA   C  CH3    0  -0.663  13.7254  -1.8937  -0.2528
 B73  OAB   O  OP    -1  -0.903  -6.8828   0.4538   1.2413
 B73  OAC   O  OP    -1  -0.919  -6.5161  -2.3469  -1.0352
 B73  OAD   O  OP    -1  -0.910  -5.8562   1.0569  -1.0397
 B73  OAE   O  O      0  -0.922  -4.6373   1.6636   1.1306
 B73  OAF   O  O      0  -0.913  -6.3602  -2.7578   1.5056
 B73  OAG   O  OP    -1  -0.932  -4.5133  -3.5865  -0.0467
 B73  CAH   C  CR15   0  -0.124  -1.7401   2.2065  -0.8496
 B73  CAI   C  CR15   0  -0.061  -2.8106   1.4628  -1.2212
 B73  CAJ   C  CR15   0   0.246  -1.5754   0.2428   0.1016
 B73  CAK   C  CH2    0  -0.419  12.6251  -1.1609   0.5019
 B73  CAL   C  CH2    0  -0.406  11.3391  -1.0344  -0.3055
 B73  CAM   C  CH2    0  -0.412  10.2243  -0.3085   0.4368
 B73  CAN   C  CH2    0  -0.411   8.9215  -0.2503  -0.3504
 B73  CAO   C  CH2    0  -0.412   7.7918   0.4561   0.3887
 B73  CAP   C  CH2    0  -0.412   6.4634   0.3878  -0.3542
 B73  CAQ   C  CH2    0  -0.413   5.3156   1.0720   0.3777
 B73  CAR   C  CH2    0  -0.413   3.9697   0.8535  -0.3025
 B73  CAS   C  CH2    0  -0.424   2.8065   1.5139   0.4267
 B73  CAT   C  CH2    0  -0.433   1.4609   1.1576  -0.1911
 B73  CAU   C  CH2    0  -0.306   0.3021   1.7796   0.5729
 B73  CAV   C  CH2    0  -0.304  -3.6143  -0.8867  -0.7184
 B73  CAW   C  CH1    0  -0.754  -4.6518  -0.9267   0.3863
 B73  NAX   N  NR5    0  -0.417  -0.9858   1.4267  -0.0098
 B73  NAY   N  NR5    1  -0.385  -2.6723   0.2390  -0.6326
 B73  PAZ   P  P      0   1.195  -5.6006   0.6815   0.4343
 B73  PBA   P  P      0   1.178  -5.6100  -2.5215   0.1902
 B73  HAA   H  HCH3   0   0.225  14.6335  -1.9841   0.3445
 B73  HAAA  H  HCH3   0   0.216  13.4089  -2.9016  -0.5284
 B73  HAAB  H  HCH3   0   0.216  13.9870  -1.3699  -1.1742
 B73  HAH   H  HCR5   0   0.312  -1.4632   3.2178  -1.0917
 B73  HAI   H  HCR5   0   0.303  -3.6894   1.7004  -1.7946
 B73  HAJ   H  HCR5   0   0.344  -1.2012  -0.5876   0.6766
 B73  HAK   H  HCH2   0   0.210  12.4104  -1.6844   1.4389
 B73  HAKA  H  HCH2   0   0.210  12.9761  -0.1641   0.7866
 B73  HAL   H  HCH2   0   0.206  11.5516  -0.5132  -1.2458
 B73  HALA  H  HCH2   0   0.205  10.9921  -2.0347  -0.5888
 B73  HAM   H  HCH2   0   0.205  10.0416  -0.8087   1.3948
 B73  HAMA  H  HCH2   0   0.207  10.5520   0.7071   0.6853
 B73  HAN   H  HCH2   0   0.207   9.0975   0.2473  -1.3107
 B73  HANA  H  HCH2   0   0.205   8.6059  -1.2709  -0.5953
 B73  HAO   H  HCH2   0   0.205   7.6693   0.0039   1.3795
 B73  HAOA  H  HCH2   0   0.207   8.0654   1.5019   0.5658
 B73  HAP   H  HCH2   0   0.208   6.5779   0.8303  -1.3499
 B73  HAPA  H  HCH2   0   0.206   6.2051  -0.6641  -0.5209
 B73  HAQ   H  HCH2   0   0.207   5.2613   0.6917   1.4037
 B73  HAQA  H  HCH2   0   0.209   5.5185   2.1450   0.4625
 B73  HAR   H  HCH2   0   0.213   4.0137   1.2227  -1.3325
 B73  HARA  H  HCH2   0   0.210   3.7824  -0.2235  -0.3749
 B73  HAS   H  HCH2   0   0.219   2.8155   1.2045   1.4772
 B73  HASA  H  HCH2   0   0.222   2.9385   2.6007   0.4274
 B73  HAT   H  HCH2   0   0.238   1.4248   1.4859  -1.2336
 B73  HATA  H  HCH2   0   0.236   1.3440   0.0698  -0.1988
 B73  HAU   H  HCH2   0   0.278   0.3026   1.4571   1.6140
 B73  HAUA  H  HCH2   0   0.277   0.3687   2.8666   0.5697
 B73  HAV   H  HCH2   0   0.237  -3.0124  -1.7940  -0.7204
 B73  HAVA  H  HCH2   0   0.240  -4.1033  -0.8046  -1.6866
 B73  HAW   H  HCH1   0   0.164  -4.1137  -1.0122   1.3414

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
 B73  CAA  CAK   single    1.522  0.020  1.522
 B73  CAA  HAA   single    0.970  0.020  1.090
 B73  CAA  HAAA  single    0.970  0.020  1.090
 B73  CAA  HAAB  single    0.970  0.020  1.090
 B73  PAZ  OAB   deloc     1.532  0.020  1.532
 B73  PBA  OAC   deloc     1.534  0.020  1.534
 B73  PAZ  OAD   deloc     1.542  0.020  1.542
 B73  OAE  PAZ   deloc     1.542  0.020  1.542
 B73  OAF  PBA   deloc     1.533  0.020  1.533
 B73  PBA  OAG   deloc     1.547  0.020  1.547
 B73  NAX  CAH   aromatic  1.372  0.020  1.372
 B73  CAH  CAI   aromatic  1.355  0.020  1.355
 B73  CAH  HAH   single    0.930  0.020  1.080
 B73  NAY  CAI   aromatic  1.365  0.020  1.365
 B73  CAI  HAI   single    0.930  0.020  1.080
 B73  CAJ  NAX   aromatic  1.327  0.020  1.327
 B73  CAJ  NAY   aromatic  1.320  0.020  1.320
 B73  CAJ  HAJ   single    0.930  0.020  1.080
 B73  CAK  CAL   single    1.524  0.020  1.524
 B73  CAK  HAK   single    0.970  0.020  1.090
 B73  CAK  HAKA  single    0.970  0.020  1.090
 B73  CAL  CAM   single    1.523  0.020  1.523
 B73  CAL  HAL   single    0.970  0.020  1.090
 B73  CAL  HALA  single    0.970  0.020  1.090
 B73  CAM  CAN   single    1.523  0.020  1.523
 B73  CAM  HAM   single    0.970  0.020  1.090
 B73  CAM  HAMA  single    0.970  0.020  1.090
 B73  CAN  CAO   single    1.524  0.020  1.524
 B73  CAN  HAN   single    0.970  0.020  1.090
 B73  CAN  HANA  single    0.970  0.020  1.090
 B73  CAO  CAP   single    1.524  0.020  1.524
 B73  CAO  HAO   single    0.970  0.020  1.090
 B73  CAO  HAOA  single    0.970  0.020  1.090
 B73  CAP  CAQ   single    1.524  0.020  1.524
 B73  CAP  HAP   single    0.970  0.020  1.090
 B73  CAP  HAPA  single    0.970  0.020  1.090
 B73  CAQ  CAR   single    1.524  0.020  1.524
 B73  CAQ  HAQ   single    0.970  0.020  1.090
 B73  CAQ  HAQA  single    0.970  0.020  1.090
 B73  CAR  CAS   single    1.523  0.020  1.523
 B73  CAR  HAR   single    0.970  0.020  1.090
 B73  CAR  HARA  single    0.970  0.020  1.090
 B73  CAS  CAT   single    1.523  0.020  1.523
 B73  CAS  HAS   single    0.970  0.020  1.090
 B73  CAS  HASA  single    0.970  0.020  1.090
 B73  CAT  CAU   single    1.521  0.020  1.521
 B73  CAT  HAT   single    0.970  0.020  1.090
 B73  CAT  HATA  single    0.970  0.020  1.090
 B73  CAU  NAX   single    1.457  0.020  1.457
 B73  CAU  HAU   single    0.970  0.020  1.090
 B73  CAU  HAUA  single    0.970  0.020  1.090
 B73  NAY  CAV   single    1.470  0.020  1.470
 B73  CAW  CAV   single    1.516  0.020  1.516
 B73  CAV  HAV   single    0.970  0.020  1.090
 B73  CAV  HAVA  single    0.970  0.020  1.090
 B73  CAW  PBA   single    1.871  0.020  1.871
 B73  CAW  PAZ   single    1.868  0.020  1.868
 B73  CAW  HAW   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
 B73  HAAB  CAA  HAAA  107.42  3.000
 B73  HAAB  CAA  HAA   107.61  3.000
 B73  HAAA  CAA  HAA   107.64  3.000
 B73  HAAB  CAA  CAK   111.14  3.000
 B73  HAAA  CAA  CAK   111.10  3.000
 B73  HAA   CAA  CAK   111.72  3.000
 B73  HAH   CAH  NAX   122.04  3.000
 B73  HAH   CAH  CAI   131.08  3.000
 B73  NAX   CAH  CAI   106.87  3.000
 B73  HAI   CAI  NAY   120.70  3.000
 B73  HAI   CAI  CAH   132.07  3.000
 B73  NAY   CAI  CAH   107.08  3.000
 B73  HAJ   CAJ  NAY   125.69  3.000
 B73  HAJ   CAJ  NAX   125.32  3.000
 B73  NAY   CAJ  NAX   108.97  3.000
 B73  HAKA  CAK  HAK   106.01  3.000
 B73  HAKA  CAK  CAL   109.44  3.000
 B73  HAK   CAK  CAL   109.13  3.000
 B73  HAKA  CAK  CAA   109.61  3.000
 B73  HAK   CAK  CAA   109.63  3.000
 B73  CAL   CAK  CAA   112.79  3.000
 B73  HALA  CAL  HAL   105.88  3.000
 B73  HALA  CAL  CAM   109.22  3.000
 B73  HAL   CAL  CAM   109.47  3.000
 B73  HALA  CAL  CAK   109.17  3.000
 B73  HAL   CAL  CAK   109.30  3.000
 B73  CAM   CAL  CAK   113.52  3.000
 B73  HAMA  CAM  HAM   105.94  3.000
 B73  HAMA  CAM  CAN   109.73  3.000
 B73  HAM   CAM  CAN   109.06  3.000
 B73  HAMA  CAM  CAL   109.47  3.000
 B73  HAM   CAM  CAL   109.29  3.000
 B73  CAN   CAM  CAL   113.09  3.000
 B73  HANA  CAN  HAN   105.86  3.000
 B73  HANA  CAN  CAO   109.06  3.000
 B73  HAN   CAN  CAO   109.49  3.000
 B73  HANA  CAN  CAM   109.04  3.000
 B73  HAN   CAN  CAM   109.44  3.000
 B73  CAO   CAN  CAM   113.65  3.000
 B73  HAOA  CAO  HAO   106.00  3.000
 B73  HAOA  CAO  CAP   109.84  3.000
 B73  HAO   CAO  CAP   108.96  3.000
 B73  HAOA  CAO  CAN   109.63  3.000
 B73  HAO   CAO  CAN   109.28  3.000
 B73  CAP   CAO  CAN   112.90  3.000
 B73  HAPA  CAP  HAP   105.90  3.000
 B73  HAPA  CAP  CAQ   109.06  3.000
 B73  HAP   CAP  CAQ   109.51  3.000
 B73  HAPA  CAP  CAO   108.82  3.000
 B73  HAP   CAP  CAO   109.52  3.000
 B73  CAQ   CAP  CAO   113.73  3.000
 B73  HAQA  CAQ  HAQ   106.07  3.000
 B73  HAQA  CAQ  CAR   109.80  3.000
 B73  HAQ   CAQ  CAR   108.94  3.000
 B73  HAQA  CAQ  CAP   109.72  3.000
 B73  HAQ   CAQ  CAP   109.35  3.000
 B73  CAR   CAQ  CAP   112.74  3.000
 B73  HARA  CAR  HAR   106.03  3.000
 B73  HARA  CAR  CAS   109.10  3.000
 B73  HAR   CAR  CAS   109.56  3.000
 B73  HARA  CAR  CAQ   108.75  3.000
 B73  HAR   CAR  CAQ   109.64  3.000
 B73  CAS   CAR  CAQ   113.48  3.000
 B73  HASA  CAS  HAS   106.19  3.000
 B73  HASA  CAS  CAT   109.82  3.000
 B73  HAS   CAS  CAT   109.29  3.000
 B73  HASA  CAS  CAR   109.79  3.000
 B73  HAS   CAS  CAR   109.29  3.000
 B73  CAT   CAS  CAR   112.27  3.000
 B73  HATA  CAT  HAT   106.75  3.000
 B73  HATA  CAT  CAU   109.19  3.000
 B73  HAT   CAT  CAU   109.32  3.000
 B73  HATA  CAT  CAS   109.26  3.000
 B73  HAT   CAT  CAS   110.23  3.000
 B73  CAU   CAT  CAS   111.95  3.000
 B73  HAUA  CAU  HAU   107.35  3.000
 B73  HAUA  CAU  NAX   107.14  3.000
 B73  HAU   CAU  NAX   108.11  3.000
 B73  HAUA  CAU  CAT   111.10  3.000
 B73  HAU   CAU  CAT   111.00  3.000
 B73  NAX   CAU  CAT   111.93  3.000
 B73  HAVA  CAV  HAV   108.04  3.000
 B73  HAVA  CAV  NAY   106.39  3.000
 B73  HAV   CAV  NAY   106.49  3.000
 B73  HAVA  CAV  CAW   110.06  3.000
 B73  HAV   CAV  CAW   110.95  3.000
 B73  NAY   CAV  CAW   114.60  3.000
 B73  HAW   CAW  PBA   105.99  3.000
 B73  HAW   CAW  PAZ   107.05  3.000
 B73  PBA   CAW  PAZ   118.46  3.000
 B73  HAW   CAW  CAV   107.46  3.000
 B73  PAZ   CAW  CAV   110.10  3.000
 B73  PBA   CAW  CAV   107.26  3.000
 B73  CAU   NAX  CAJ   125.11  3.000
 B73  CAU   NAX  CAH   126.38  3.000
 B73  CAJ   NAX  CAH   108.31  3.000
 B73  CAV   NAY  CAJ   124.55  3.000
 B73  CAV   NAY  CAI   126.61  3.000
 B73  CAJ   NAY  CAI   108.75  3.000
 B73  CAW   PAZ  OAE   104.05  3.000
 B73  CAW   PAZ  OAD   105.62  3.000
 B73  OAE   PAZ  OAD   112.34  3.000
 B73  CAW   PAZ  OAB   108.10  3.000
 B73  OAE   PAZ  OAB   112.31  3.000
 B73  OAD   PAZ  OAB   113.63  3.000
 B73  CAW   PBA  OAG   103.88  3.000
 B73  CAW   PBA  OAF   106.99  3.000
 B73  OAG   PBA  OAF   111.86  3.000
 B73  CAW   PBA  OAC   106.81  3.000
 B73  OAG   PBA  OAC   112.01  3.000
 B73  OAF   PBA  OAC   114.46  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
 B73  CONST_01  NAY  CAJ  NAX  CAH     0.00   0.0  0
 B73  CONST_02  CAJ  NAY  CAI  CAH     0.00   0.0  0
 B73  CONST_03  CAJ  NAX  CAH  CAI     0.00   0.0  0
 B73  CONST_04  NAX  CAJ  NAY  CAI     0.00   0.0  0
 B73  CONST_05  NAY  CAI  CAH  NAX     0.00   0.0  0
 B73  CONST_06  CAV  NAY  CAI  CAH   180.00   0.0  0
 B73  CONST_07  CAU  NAX  CAH  CAI   180.00   0.0  0
 B73  CONST_08  NAY  CAJ  NAX  CAU   180.00   0.0  0
 B73  CONST_09  NAX  CAJ  NAY  CAV   180.00   0.0  0
 B73  CONST_10  HAJ  CAJ  NAX  CAH   180.00   0.0  0
 B73  CONST_11  HAH  CAH  NAX  CAJ   180.00   0.0  0
 B73  CONST_12  HAI  CAI  NAY  CAJ   180.00   0.0  0
 B73  Var_01    CAT  CAU  NAX  CAH   -99.43  30.0  1
 B73  Var_02    CAW  CAV  NAY  CAI   -91.60  30.0  2
 B73  Var_03    NAX  CAU  CAT  CAS  -179.38  30.0  3
 B73  Var_04    PBA  CAW  CAV  NAY  -173.90  30.0  2
 B73  Var_05    CAM  CAL  CAK  CAA   179.76  30.0  3
 B73  Var_06    CAV  CAW  PAZ  OAB   163.03  30.0  3
 B73  Var_07    CAN  CAM  CAL  CAK  -177.04  30.0  3
 B73  Var_08    CAO  CAN  CAM  CAL   179.18  30.0  3
 B73  Var_09    CAP  CAO  CAN  CAM  -174.48  30.0  3
 B73  Var_10    CAQ  CAP  CAO  CAN   179.20  30.0  3
 B73  Var_11    CAR  CAQ  CAP  CAO  -173.38  30.0  3
 B73  Var_12    CAS  CAR  CAQ  CAP   179.17  30.0  3
 B73  Var_13    CAT  CAS  CAR  CAQ  -173.97  30.0  3
 B73  Var_14    CAU  CAT  CAS  CAR   177.92  30.0  3
 B73  Var_15    HAA  CAA  CAK  CAL  -179.37  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
 B73  plan-1  CAH  0.020
 B73  plan-1  CAI  0.020
 B73  plan-1  CAJ  0.020
 B73  plan-1  CAU  0.020
 B73  plan-1  CAV  0.020
 B73  plan-1  NAX  0.020
 B73  plan-1  NAY  0.020
 B73  plan-1  HAH  0.020
 B73  plan-1  HAI  0.020
 B73  plan-1  HAJ  0.020

