# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:20:39 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 4,5,6,7-tetraiodo-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1c(I)c(I)c2nc[nH]c2c1I
#
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
 K8X  K8X  4,5,6,7-tetraiodo-1H-benzimidazole  ligand  15  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K8X
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
 K8X  C1    C  CR6   0  -0.268  -1.4265   1.0112   0.0016
 K8X  C2    C  CR56  0   0.451  -0.7086   2.1985  -0.0157
 K8X  C3    C  CR56  0   0.229   0.6928   2.2283  -0.0355
 K8X  C4    C  CR6   0  -0.313   1.4105   1.0352  -0.0371
 K8X  C5    C  CR6   0  -0.218   0.7130  -0.1663  -0.0205
 K8X  C6    C  CR6   0  -0.231  -0.7056  -0.1781  -0.0014
 K8X  I13   I  I     0   0.152  -3.5113   1.1590   0.0300
 K8X  I15   I  I     0   0.145  -1.7616  -1.9927   0.0223
 K8X  I17   I  I     0   0.139   1.7951  -1.9676  -0.0243
 K8X  I19   I  I     0   0.132   3.4916   1.2215  -0.0640
 K8X  N21   N  NR15  0  -0.659  -1.0809   3.5097  -0.0196
 K8X  C23   C  CR15  0   0.135   0.0550   4.2431  -0.0411
 K8X  N25   N  N     0  -0.434   1.1382   3.5194  -0.0510
 K8X  H23   H  HCR5  0   0.305   0.0256   5.3218  -0.0488
 K8X  HN21  H  HNR5  0   0.435  -2.0190   3.8828  -0.0111

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
 K8X  I13  C1    single    2.090  0.020  2.090
 K8X  C2   C1    aromatic  1.388  0.020  1.388
 K8X  C1   C6    aromatic  1.391  0.020  1.391
 K8X  N21  C2    aromatic  1.363  0.020  1.363
 K8X  C2   C3    aromatic  1.402  0.020  1.402
 K8X  N25  C3    aromatic  1.366  0.020  1.366
 K8X  C3   C4    aromatic  1.392  0.020  1.392
 K8X  C4   C5    aromatic  1.389  0.020  1.389
 K8X  C4   I19   single    2.090  0.020  2.090
 K8X  C6   C5    aromatic  1.419  0.020  1.419
 K8X  C5   I17   single    2.101  0.020  2.101
 K8X  C6   I15   single    2.100  0.020  2.100
 K8X  C23  N21   aromatic  1.352  0.020  1.352
 K8X  C23  N25   aromatic  1.303  0.020  1.303
 K8X  C23  H23   single    0.930  0.020  1.080
 K8X  N21  HN21  single    0.860  0.020  1.020

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
 K8X  I13   C1   C6   125.27  3.000
 K8X  C6    C1   C2   117.62  3.000
 K8X  I13   C1   C2   117.11  3.000
 K8X  N21   C2   C3   104.63  3.000
 K8X  C3    C2   C1   122.38  3.000
 K8X  N21   C2   C1   132.99  3.000
 K8X  N25   C3   C4   129.94  3.000
 K8X  C4    C3   C2   119.81  3.000
 K8X  N25   C3   C2   110.26  3.000
 K8X  I19   C4   C5   125.26  3.000
 K8X  I19   C4   C3   115.91  3.000
 K8X  C5    C4   C3   118.84  3.000
 K8X  I17   C5   C6   120.52  3.000
 K8X  I17   C5   C4   118.87  3.000
 K8X  C6    C5   C4   120.62  3.000
 K8X  I15   C6   C5   120.68  3.000
 K8X  I15   C6   C1   118.58  3.000
 K8X  C5    C6   C1   120.74  3.000
 K8X  HN21  N21  C23  125.47  3.000
 K8X  HN21  N21  C2   127.53  3.000
 K8X  C23   N21  C2   106.99  3.000
 K8X  H23   C23  N25  125.30  3.000
 K8X  H23   C23  N21  121.28  3.000
 K8X  N25   C23  N21  113.41  3.000
 K8X  C23   N25  C3   104.71  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
 K8X  CONST_01  C23   N21  C2   C1   180.00  0.0  0
 K8X  CONST_02  N25   C3   C2   C1   180.00  0.0  0
 K8X  CONST_03  C4    C3   C2   C1     0.00  0.0  0
 K8X  CONST_04  C4    C5   C6   C1     0.00  0.0  0
 K8X  CONST_05  C5    C6   C1   C2     0.00  0.0  0
 K8X  CONST_06  N25   C23  N21  C2     0.00  0.0  0
 K8X  CONST_07  C23   N25  C3   C2     0.00  0.0  0
 K8X  CONST_08  C5    C4   C3   C2     0.00  0.0  0
 K8X  CONST_09  C6    C1   C2   C3     0.00  0.0  0
 K8X  CONST_10  C23   N21  C2   C3     0.00  0.0  0
 K8X  CONST_11  N21   C23  N25  C3     0.00  0.0  0
 K8X  CONST_12  C6    C5   C4   C3     0.00  0.0  0
 K8X  CONST_13  N21   C2   C3   C4   180.00  0.0  0
 K8X  CONST_14  C23   N25  C3   C4   180.00  0.0  0
 K8X  CONST_15  N25   C3   C4   C5   180.00  0.0  0
 K8X  CONST_16  N21   C2   C1   C6   180.00  0.0  0
 K8X  CONST_17  N25   C3   C2   N21    0.00  0.0  0
 K8X  CONST_18  I17   C5   C6   C1   180.00  0.0  0
 K8X  CONST_19  I15   C6   C1   C2   180.00  0.0  0
 K8X  CONST_20  I19   C4   C3   C2   180.00  0.0  0
 K8X  CONST_21  I13   C1   C2   C3   180.00  0.0  0
 K8X  CONST_22  I17   C5   C4   C3   180.00  0.0  0
 K8X  CONST_23  I15   C6   C5   C4   180.00  0.0  0
 K8X  CONST_24  I13   C1   C6   C5   180.00  0.0  0
 K8X  CONST_25  I19   C4   C5   C6   180.00  0.0  0
 K8X  CONST_26  N21   C2   C1   I13    0.00  0.0  0
 K8X  CONST_27  N25   C3   C4   I19    0.00  0.0  0
 K8X  CONST_28  HN21  N21  C2   C1     0.00  0.0  0
 K8X  CONST_29  H23   C23  N21  C2   180.00  0.0  0

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
 K8X  plan-1  C1    0.020
 K8X  plan-1  C2    0.020
 K8X  plan-1  C3    0.020
 K8X  plan-1  C4    0.020
 K8X  plan-1  C5    0.020
 K8X  plan-1  C6    0.020
 K8X  plan-1  I13   0.020
 K8X  plan-1  I15   0.020
 K8X  plan-1  I17   0.020
 K8X  plan-1  I19   0.020
 K8X  plan-1  N21   0.020
 K8X  plan-1  C23   0.020
 K8X  plan-1  N25   0.020
 K8X  plan-1  H23   0.020
 K8X  plan-1  HN21  0.020

