# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:16:37 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 8-[4,5,6,7-tetrakis(iodanyl)benzimidazol-1-yl]octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCn1cnc2c(I)c(I)c(I)c(I)c12
#
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
 A0Z  A0Z  '8-[4,5,6,7-tetrakis(iodanyl)benzimidazol-1-yl]octanoic acid'  ligand  39  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0Z
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
 A0Z  CBA  C  CR15  0   0.136   -0.3922  -3.2561   1.2528
 A0Z  CBD  C  CH2   0  -0.413   -5.6391  -1.2948  -0.2029
 A0Z  CBE  C  CH2   0  -0.416   -7.0370  -0.8687   0.2254
 A0Z  CBF  C  CH2   0  -0.425   -4.6448  -1.2999   0.9502
 A0Z  CBG  C  CH2   0  -0.418   -8.0465  -0.9130  -0.9143
 A0Z  CBI  C  CH2   0  -0.429   -3.2324  -1.6703   0.5196
 A0Z  CBJ  C  CH2   0  -0.580   -9.4281  -0.4684  -0.4642
 A0Z  CBL  C  CH2   0  -0.332   -2.3134  -1.8085   1.7248
 A0Z  CCH  C  C     0   0.550  -10.4656  -0.5147  -1.5507
 A0Z  CCO  C  CR6   0  -0.220    2.4964  -0.0891   0.0503
 A0Z  CCP  C  CR6   0  -0.228    1.4074   0.7591   0.3699
 A0Z  CCQ  C  CR6   0  -0.314    2.3693  -1.4617   0.1865
 A0Z  CCR  C  CR6   0  -0.255    0.1912   0.2447   0.8243
 A0Z  CCS  C  CR56  0   0.224    1.1594  -1.9828   0.6328
 A0Z  CCT  C  CR56  0   0.440    0.0716  -1.1424   0.9482
 A0Z  IAW  I  I     0   0.139    4.3240   0.6941  -0.6316
 A0Z  IAX  I  I     0   0.144    1.6308   2.8412   0.1564
 A0Z  IAY  I  I     0   0.132    3.8669  -2.8605  -0.2269
 A0Z  IAZ  I  I     0   0.154   -1.4098   1.5066   1.3251
 A0Z  NBS  N  N     0  -0.438    0.8362  -3.2895   0.8339
 A0Z  NDB  N  NR5   0  -0.516   -0.9182  -2.0117   1.3549
 A0Z  OAI  O  O     0  -0.446  -10.2660  -0.8552  -2.6904
 A0Z  H1   H  HCR5  0   0.306   -0.9800  -4.1243   1.5143
 A0Z  H2   H  HCH2  0   0.214   -5.6820  -2.2950  -0.6470
 A0Z  H3   H  HCH2  0   0.214   -5.2817  -0.6266  -0.9938
 A0Z  H4   H  HCH2  0   0.214   -7.3796  -1.5146   1.0413
 A0Z  H5   H  HCH2  0   0.214   -6.9951   0.1444   0.6397
 A0Z  H6   H  HCH2  0   0.220   -4.6262  -0.3123   1.4238
 A0Z  H7   H  HCH2  0   0.221   -4.9893  -1.9977   1.7210
 A0Z  H8   H  HCH2  0   0.225   -7.7006  -0.2766  -1.7335
 A0Z  H9   H  HCH2  0   0.225   -8.0975  -1.9291  -1.3142
 A0Z  H10  H  HCH2  0   0.239   -3.2383  -2.6152  -0.0321
 A0Z  H11  H  HCH2  0   0.234   -2.8442  -0.9121  -0.1652
 A0Z  H12  H  HCH2  0   0.275   -9.7789  -1.0875   0.3681
 A0Z  H13  H  HCH2  0   0.276   -9.3946   0.5525  -0.0700
 A0Z  H14  H  HCH2  0   0.274   -2.3931  -0.9576   2.3957
 A0Z  H15  H  HCH2  0   0.282   -2.6003  -2.6818   2.3109
 A0Z  O1   O  OH1   0  -0.598  -11.6613  -0.1295  -1.1119
 A0Z  H16  H  HOH1  0   0.478  -12.3070  -0.1731  -1.8327

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
 A0Z  IAW  CCO  single    2.102  0.020  2.102
 A0Z  IAX  CCP  single    2.105  0.020  2.105
 A0Z  CCO  CCP  aromatic  1.417  0.020  1.417
 A0Z  CCO  CCQ  aromatic  1.385  0.020  1.385
 A0Z  IAY  CCQ  single    2.091  0.020  2.091
 A0Z  CCP  CCR  aromatic  1.396  0.020  1.396
 A0Z  CCQ  CCS  aromatic  1.391  0.020  1.391
 A0Z  CCR  IAZ  single    2.099  0.020  2.099
 A0Z  CCR  CCT  aromatic  1.398  0.020  1.398
 A0Z  CCS  CCT  aromatic  1.410  0.020  1.410
 A0Z  CCS  NBS  aromatic  1.361  0.020  1.361
 A0Z  CCT  NDB  aromatic  1.379  0.020  1.379
 A0Z  NBS  CBA  aromatic  1.298  0.020  1.298
 A0Z  NDB  CBA  aromatic  1.355  0.020  1.355
 A0Z  NDB  CBL  single    1.458  0.020  1.458
 A0Z  CBL  CBI  single    1.522  0.020  1.522
 A0Z  CBF  CBI  single    1.522  0.020  1.522
 A0Z  CBF  CBD  single    1.523  0.020  1.523
 A0Z  OAI  CCH  double    1.206  0.020  1.206
 A0Z  CBE  CBD  single    1.523  0.020  1.523
 A0Z  CBE  CBG  single    1.523  0.020  1.523
 A0Z  CCH  CBJ  single    1.503  0.020  1.503
 A0Z  CBJ  CBG  single    1.520  0.020  1.520
 A0Z  CBA  H1   single    0.930  0.020  1.080
 A0Z  CBD  H2   single    0.970  0.020  1.090
 A0Z  CBD  H3   single    0.970  0.020  1.090
 A0Z  CBE  H4   single    0.970  0.020  1.090
 A0Z  CBE  H5   single    0.970  0.020  1.090
 A0Z  CBF  H6   single    0.970  0.020  1.090
 A0Z  CBF  H7   single    0.970  0.020  1.090
 A0Z  CBG  H8   single    0.970  0.020  1.090
 A0Z  CBG  H9   single    0.970  0.020  1.090
 A0Z  CBI  H10  single    0.970  0.020  1.090
 A0Z  CBI  H11  single    0.970  0.020  1.090
 A0Z  CBJ  H12  single    0.970  0.020  1.090
 A0Z  CBJ  H13  single    0.970  0.020  1.090
 A0Z  CBL  H14  single    0.970  0.020  1.090
 A0Z  CBL  H15  single    0.970  0.020  1.090
 A0Z  CCH  O1   single    1.331  0.020  1.331
 A0Z  O1   H16  single    0.850  0.020  0.980

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
 A0Z  H1   CBA  NDB  120.57  3.000
 A0Z  H1   CBA  NBS  124.89  3.000
 A0Z  NDB  CBA  NBS  114.53  3.000
 A0Z  H3   CBD  H2   106.09  3.000
 A0Z  H3   CBD  CBF  109.62  3.000
 A0Z  H2   CBD  CBF  109.25  3.000
 A0Z  H3   CBD  CBE  109.38  3.000
 A0Z  H2   CBD  CBE  109.48  3.000
 A0Z  CBF  CBD  CBE  112.80  3.000
 A0Z  H5   CBE  H4   105.99  3.000
 A0Z  H5   CBE  CBG  109.59  3.000
 A0Z  H4   CBE  CBG  109.44  3.000
 A0Z  H5   CBE  CBD  109.27  3.000
 A0Z  H4   CBE  CBD  109.36  3.000
 A0Z  CBG  CBE  CBD  112.95  3.000
 A0Z  H7   CBF  H6   105.99  3.000
 A0Z  H7   CBF  CBI  109.63  3.000
 A0Z  H6   CBF  CBI  109.02  3.000
 A0Z  H7   CBF  CBD  109.25  3.000
 A0Z  H6   CBF  CBD  109.60  3.000
 A0Z  CBI  CBF  CBD  113.11  3.000
 A0Z  H9   CBG  H8   106.36  3.000
 A0Z  H9   CBG  CBJ  109.75  3.000
 A0Z  H8   CBG  CBJ  109.84  3.000
 A0Z  H9   CBG  CBE  109.37  3.000
 A0Z  H8   CBG  CBE  109.51  3.000
 A0Z  CBJ  CBG  CBE  111.87  3.000
 A0Z  H11  CBI  H10  106.57  3.000
 A0Z  H11  CBI  CBL  110.17  3.000
 A0Z  H10  CBI  CBL  108.91  3.000
 A0Z  H11  CBI  CBF  109.75  3.000
 A0Z  H10  CBI  CBF  110.35  3.000
 A0Z  CBL  CBI  CBF  111.00  3.000
 A0Z  H13  CBJ  H12  105.27  3.000
 A0Z  H13  CBJ  CCH  108.07  3.000
 A0Z  H12  CBJ  CCH  108.12  3.000
 A0Z  H13  CBJ  CBG  110.58  3.000
 A0Z  H12  CBJ  CBG  110.55  3.000
 A0Z  CCH  CBJ  CBG  113.86  3.000
 A0Z  H15  CBL  H14  106.03  3.000
 A0Z  H15  CBL  NDB  106.06  3.000
 A0Z  H14  CBL  NDB  109.64  3.000
 A0Z  H15  CBL  CBI  109.85  3.000
 A0Z  H14  CBL  CBI  111.93  3.000
 A0Z  NDB  CBL  CBI  112.93  3.000
 A0Z  O1   CCH  OAI  122.83  3.000
 A0Z  O1   CCH  CBJ  111.89  3.000
 A0Z  OAI  CCH  CBJ  125.28  3.000
 A0Z  IAW  CCO  CCQ  118.74  3.000
 A0Z  CCQ  CCO  CCP  120.04  3.000
 A0Z  IAW  CCO  CCP  121.22  3.000
 A0Z  IAX  CCP  CCR  119.33  3.000
 A0Z  CCR  CCP  CCO  121.48  3.000
 A0Z  IAX  CCP  CCO  119.19  3.000
 A0Z  IAY  CCQ  CCS  115.84  3.000
 A0Z  CCS  CCQ  CCO  118.85  3.000
 A0Z  IAY  CCQ  CCO  125.30  3.000
 A0Z  IAZ  CCR  CCT  120.68  3.000
 A0Z  CCT  CCR  CCP  117.96  3.000
 A0Z  IAZ  CCR  CCP  121.36  3.000
 A0Z  NBS  CCS  CCT  110.85  3.000
 A0Z  NBS  CCS  CCQ  127.86  3.000
 A0Z  CCT  CCS  CCQ  121.29  3.000
 A0Z  NDB  CCT  CCS  104.12  3.000
 A0Z  NDB  CCT  CCR  135.50  3.000
 A0Z  CCS  CCT  CCR  120.37  3.000
 A0Z  CCS  NBS  CBA  104.34  3.000
 A0Z  CCT  NDB  CBL  132.39  3.000
 A0Z  CBL  NDB  CBA  121.24  3.000
 A0Z  CCT  NDB  CBA  106.15  3.000
 A0Z  H16  O1   CCH  109.91  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
 A0Z  CONST_01  CCQ  CCS  NBS  CBA   180.00   0.0  0
 A0Z  CONST_02  CCT  CCS  NBS  CBA     0.00   0.0  0
 A0Z  CONST_03  CCR  CCT  NDB  CBA   180.00   0.0  0
 A0Z  CONST_04  CCS  CCT  NDB  CBA     0.00   0.0  0
 A0Z  CONST_05  CCT  CCR  CCP  CCO     0.00   0.0  0
 A0Z  CONST_06  CCT  CCS  CCQ  CCO     0.00   0.0  0
 A0Z  CONST_07  NBS  CCS  CCQ  CCO   180.00   0.0  0
 A0Z  CONST_08  CCS  CCQ  CCO  CCP     0.00   0.0  0
 A0Z  CONST_09  CCS  CCT  CCR  CCP     0.00   0.0  0
 A0Z  CONST_10  NDB  CCT  CCR  CCP   180.00   0.0  0
 A0Z  CONST_11  CCR  CCP  CCO  CCQ     0.00   0.0  0
 A0Z  CONST_12  CCR  CCT  CCS  CCQ     0.00   0.0  0
 A0Z  CONST_13  NDB  CCT  CCS  CCQ   180.00   0.0  0
 A0Z  CONST_14  NBS  CCS  CCT  CCR   180.00   0.0  0
 A0Z  CONST_15  NDB  CBA  NBS  CCS     0.00   0.0  0
 A0Z  CONST_16  NBS  CBA  NDB  CCT     0.00   0.0  0
 A0Z  CONST_17  NDB  CCT  CCS  NBS     0.00   0.0  0
 A0Z  CONST_18  CCR  CCT  NDB  CBL     0.00   0.0  0
 A0Z  CONST_19  CCS  CCT  NDB  CBL   180.00   0.0  0
 A0Z  CONST_20  NBS  CBA  NDB  CBL   180.00   0.0  0
 A0Z  CONST_21  IAZ  CCR  CCP  CCO   180.00   0.0  0
 A0Z  CONST_22  IAY  CCQ  CCO  CCP   180.00   0.0  0
 A0Z  CONST_23  IAX  CCP  CCO  CCQ   180.00   0.0  0
 A0Z  CONST_24  IAW  CCO  CCP  CCR   180.00   0.0  0
 A0Z  CONST_25  IAW  CCO  CCQ  CCS   180.00   0.0  0
 A0Z  CONST_26  IAZ  CCR  CCT  CCS   180.00   0.0  0
 A0Z  CONST_27  IAX  CCP  CCR  CCT   180.00   0.0  0
 A0Z  CONST_28  IAY  CCQ  CCS  CCT   180.00   0.0  0
 A0Z  CONST_29  NBS  CCS  CCQ  IAY     0.00   0.0  0
 A0Z  CONST_30  NDB  CCT  CCR  IAZ     0.00   0.0  0
 A0Z  CONST_31  H1   CBA  NBS  CCS   180.00   0.0  0
 A0Z  CONST_32  H16  O1   CCH  CBJ   180.00   0.0  0
 A0Z  Var_01    CBI  CBL  NDB  CBA   -94.08  30.0  2
 A0Z  Var_02    NDB  CBL  CBI  CBF  -173.41  30.0  1
 A0Z  Var_03    CBL  CBI  CBF  CBD  -173.84  30.0  3
 A0Z  Var_04    CBJ  CBG  CBE  CBD  -179.35  30.0  3
 A0Z  Var_05    CBI  CBF  CBD  CBE  -177.67  30.0  1
 A0Z  Var_06    CCH  CBJ  CBG  CBE  -179.13  30.0  1
 A0Z  Var_07    CBG  CBE  CBD  CBF  -177.82  30.0  1
 A0Z  Var_08    OAI  CCH  CBJ  CBG    -0.58  30.0  2

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
 A0Z  plan-1  CBA  0.020
 A0Z  plan-1  CBL  0.020
 A0Z  plan-1  CCO  0.020
 A0Z  plan-1  CCP  0.020
 A0Z  plan-1  CCQ  0.020
 A0Z  plan-1  CCR  0.020
 A0Z  plan-1  CCS  0.020
 A0Z  plan-1  CCT  0.020
 A0Z  plan-1  IAW  0.020
 A0Z  plan-1  IAX  0.020
 A0Z  plan-1  IAY  0.020
 A0Z  plan-1  IAZ  0.020
 A0Z  plan-1  NBS  0.020
 A0Z  plan-1  NDB  0.020
 A0Z  plan-1  H1   0.020
 A0Z  plan-2  CBJ  0.020
 A0Z  plan-2  CCH  0.020
 A0Z  plan-2  OAI  0.020
 A0Z  plan-2  O1   0.020
 A0Z  plan-2  H16  0.020

