# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:14:32 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)ethyl-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(C[NH2+]CCc3[nH]c4ccccc4n3)cc2Cl
#
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
 AHK  AHK  2-(1~{H}-benzimidazol-2-yl)ethyl-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]azanium  ligand  53  28  .  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_AHK
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
 AHK  CL   CL  CL    0  -0.112    3.8297   2.2529   0.9582
 AHK  C23  C   CR6   0  -0.098    3.0077   0.7893   0.5354
 AHK  C8   C   CR6   0   0.115    3.6856  -0.2038  -0.1690
 AHK  C7   C   CR6   0   0.019    5.1026  -0.0613  -0.5849
 AHK  C6   C   CR16  0  -0.267    5.3753   0.2288  -1.9192
 AHK  C5   C   CR16  0  -0.262    6.6820   0.3552  -2.3671
 AHK  C4   C   CR16  0  -0.246    7.7282   0.1896  -1.4713
 AHK  C3   C   CR16  0  -0.304    7.4582  -0.1052  -0.1427
 AHK  C2   C   CR6   0   0.114    6.1524  -0.2370   0.3247
 AHK  C1   C   CH2   0  -0.522    5.9123  -0.6251   1.7588
 AHK  C    C   CH3   0  -0.654    5.7567  -2.1355   1.9278
 AHK  C22  C   CR16  0  -0.227    1.6828   0.6432   0.9129
 AHK  C11  C   CR6   0   0.060    0.9942  -0.5149   0.5724
 AHK  C10  C   CR16  0  -0.261    1.6451  -1.5104  -0.1454
 AHK  C9   C   CR16  0  -0.284    2.9728  -1.3517  -0.5062
 AHK  C12  C   CH2   0  -0.381   -0.4445  -0.6756   0.9559
 AHK  N    N   NT2   1  -0.667   -1.3373  -0.0291  -0.0541
 AHK  C13  C   CH2   0  -0.280   -2.7825  -0.2294   0.2342
 AHK  C14  C   CH2   0  -0.574   -3.6337   0.4958  -0.7900
 AHK  C15  C   CR5   0   0.485   -5.0802   0.2910  -0.5013
 AHK  N2   N   NR15  0  -0.704   -6.0411   1.0817  -1.0419
 AHK  C21  C   CR56  0   0.327   -7.2506   0.6222  -0.5914
 AHK  C16  C   CR56  0   0.138   -6.9298  -0.4681   0.2338
 AHK  N1   N   N     0  -0.483   -5.5655  -0.6450   0.2657
 AHK  C20  C   CR16  0  -0.306   -8.5588   1.0385  -0.8076
 AHK  C19  C   CR16  0  -0.279   -9.5528   0.3192  -0.1661
 AHK  C18  C   CR16  0  -0.271   -9.2512  -0.7739   0.6602
 AHK  C17  C   CR16  0  -0.335   -7.9452  -1.1801   0.8706
 AHK  H1   H   HCR6  0   0.252    4.5534   0.3589  -2.6125
 AHK  H2   H   HCR6  0   0.257    6.8790   0.5820  -3.4066
 AHK  H3   H   HCR6  0   0.256    8.7533   0.2886  -1.8044
 AHK  H4   H   HCR6  0   0.250    8.2800  -0.2374   0.5519
 AHK  H5   H   HCH2  0   0.247    6.7528  -0.2814   2.3653
 AHK  H6   H   HCH2  0   0.239    5.0285  -0.1225   2.1540
 AHK  H7   H   HCH3  0   0.234    5.5827  -2.3909   2.9734
 AHK  H8   H   HCH3  0   0.227    4.9158  -2.5162   1.3472
 AHK  H9   H   HCH3  0   0.227    6.6533  -2.6610   1.5978
 AHK  H10  H   HCR6  0   0.287    1.1897   1.4290   1.4715
 AHK  H11  H   HCR6  0   0.272    1.1197  -2.4173  -0.4173
 AHK  H12  H   HCR6  0   0.271    3.4774  -2.1365  -1.0544
 AHK  H13  H   HCH2  0   0.322   -0.7313  -1.7242   1.0014
 AHK  H14  H   HCH2  0   0.323   -0.6698  -0.2101   1.9134
 AHK  H15  H   HNT2  0   0.471   -1.1282   0.9705  -0.0977
 AHK  H17  H   HCH2  0   0.306   -2.9627  -1.3015   0.2242
 AHK  H18  H   HCH2  0   0.305   -2.9617   0.1465   1.2390
 AHK  H19  H   HCH2  0   0.291   -3.4084   1.5650  -0.7849
 AHK  H20  H   HCH2  0   0.300   -3.4104   0.1310  -1.7972
 AHK  H21  H   HNR5  0   0.421   -5.8882   1.8680  -1.6542
 AHK  H23  H   HCR6  0   0.267   -8.7924   1.8839  -1.4413
 AHK  H24  H   HCR6  0   0.256  -10.5864   0.6083  -0.3032
 AHK  H25  H   HCR6  0   0.253  -10.0595  -1.3088   1.1415
 AHK  H26  H   HCR6  0   0.254   -7.7164  -2.0242   1.5084
 AHK  H16  H   HNT2  0   0.473   -1.1158  -0.3961  -0.9817

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
 AHK  C17  C18  aromatic  1.384  0.020  1.384
 AHK  C17  C16  aromatic  1.394  0.020  1.394
 AHK  C18  C19  aromatic  1.403  0.020  1.403
 AHK  N1   C16  aromatic  1.376  0.020  1.376
 AHK  N1   C15  aromatic  1.304  0.020  1.304
 AHK  C16  C21  aromatic  1.405  0.020  1.405
 AHK  C19  C20  aromatic  1.385  0.020  1.385
 AHK  C15  C14  single    1.489  0.020  1.489
 AHK  C15  N2   aromatic  1.357  0.020  1.357
 AHK  C21  C20  aromatic  1.390  0.020  1.390
 AHK  C21  N2   aromatic  1.370  0.020  1.370
 AHK  C14  C13  single    1.516  0.020  1.516
 AHK  C5   C6   aromatic  1.387  0.020  1.387
 AHK  C5   C4   aromatic  1.387  0.020  1.387
 AHK  C6   C7   aromatic  1.392  0.020  1.392
 AHK  C13  N    single    1.487  0.020  1.487
 AHK  N    C12  single    1.495  0.020  1.495
 AHK  C10  C9   aromatic  1.385  0.020  1.385
 AHK  C10  C11  aromatic  1.389  0.020  1.389
 AHK  C9   C8   aromatic  1.393  0.020  1.393
 AHK  C4   C3   aromatic  1.387  0.020  1.387
 AHK  C12  C11  single    1.498  0.020  1.498
 AHK  C7   C8   single    1.484  0.020  1.484
 AHK  C7   C2   aromatic  1.400  0.020  1.400
 AHK  C11  C22  aromatic  1.390  0.020  1.390
 AHK  C8   C23  aromatic  1.394  0.020  1.394
 AHK  C23  C22  aromatic  1.385  0.020  1.385
 AHK  C23  CL   single    1.731  0.020  1.731
 AHK  C3   C2   aromatic  1.393  0.020  1.393
 AHK  C2   C1   single    1.505  0.020  1.505
 AHK  C1   C    single    1.528  0.020  1.528
 AHK  C6   H1   single    0.930  0.020  1.080
 AHK  C5   H2   single    0.930  0.020  1.080
 AHK  C4   H3   single    0.930  0.020  1.080
 AHK  C3   H4   single    0.930  0.020  1.080
 AHK  C1   H5   single    0.970  0.020  1.090
 AHK  C1   H6   single    0.970  0.020  1.090
 AHK  C    H7   single    0.970  0.020  1.090
 AHK  C    H8   single    0.970  0.020  1.090
 AHK  C    H9   single    0.970  0.020  1.090
 AHK  C22  H10  single    0.930  0.020  1.080
 AHK  C10  H11  single    0.930  0.020  1.080
 AHK  C9   H12  single    0.930  0.020  1.080
 AHK  C12  H13  single    0.970  0.020  1.090
 AHK  C12  H14  single    0.970  0.020  1.090
 AHK  N    H15  single    0.890  0.020  1.040
 AHK  C13  H17  single    0.970  0.020  1.090
 AHK  C13  H18  single    0.970  0.020  1.090
 AHK  C14  H19  single    0.970  0.020  1.090
 AHK  C14  H20  single    0.970  0.020  1.090
 AHK  N2   H21  single    0.860  0.020  1.020
 AHK  C20  H23  single    0.930  0.020  1.080
 AHK  C19  H24  single    0.930  0.020  1.080
 AHK  C18  H25  single    0.930  0.020  1.080
 AHK  C17  H26  single    0.930  0.020  1.080
 AHK  N    H16  single    0.890  0.020  1.040

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
 AHK  C22  C23  C8   121.86  3.000
 AHK  C22  C23  CL   118.48  3.000
 AHK  C8   C23  CL   119.66  3.000
 AHK  C9   C8   C7   120.01  3.000
 AHK  C7   C8   C23  122.54  3.000
 AHK  C9   C8   C23  117.44  3.000
 AHK  C2   C7   C6   120.12  3.000
 AHK  C2   C7   C8   121.47  3.000
 AHK  C6   C7   C8   118.40  3.000
 AHK  H1   C6   C5   119.82  3.000
 AHK  H1   C6   C7   119.32  3.000
 AHK  C5   C6   C7   120.86  3.000
 AHK  H2   C5   C4   120.53  3.000
 AHK  H2   C5   C6   120.05  3.000
 AHK  C4   C5   C6   119.41  3.000
 AHK  H3   C4   C3   119.90  3.000
 AHK  H3   C4   C5   120.30  3.000
 AHK  C3   C4   C5   119.79  3.000
 AHK  H4   C3   C2   118.95  3.000
 AHK  H4   C3   C4   119.46  3.000
 AHK  C2   C3   C4   121.59  3.000
 AHK  C1   C2   C3   119.58  3.000
 AHK  C1   C2   C7   122.13  3.000
 AHK  C3   C2   C7   118.23  3.000
 AHK  H6   C1   H5   106.10  3.000
 AHK  H6   C1   C    109.44  3.000
 AHK  H5   C1   C    109.15  3.000
 AHK  H6   C1   C2   110.84  3.000
 AHK  H5   C1   C2   108.99  3.000
 AHK  C    C1   C2   112.12  3.000
 AHK  H9   C    H8   107.74  3.000
 AHK  H9   C    H7   107.97  3.000
 AHK  H8   C    H7   107.81  3.000
 AHK  H9   C    C1   111.05  3.000
 AHK  H8   C    C1   111.40  3.000
 AHK  H7   C    C1   110.73  3.000
 AHK  H10  C22  C11  120.36  3.000
 AHK  H10  C22  C23  119.97  3.000
 AHK  C11  C22  C23  119.67  3.000
 AHK  C12  C11  C10  120.37  3.000
 AHK  C12  C11  C22  120.18  3.000
 AHK  C10  C11  C22  119.44  3.000
 AHK  H11  C10  C9   119.72  3.000
 AHK  H11  C10  C11  120.17  3.000
 AHK  C9   C10  C11  120.11  3.000
 AHK  H12  C9   C10  119.73  3.000
 AHK  H12  C9   C8   118.80  3.000
 AHK  C10  C9   C8   121.47  3.000
 AHK  H14  C12  H13  108.72  3.000
 AHK  H14  C12  N    106.61  3.000
 AHK  H13  C12  N    106.71  3.000
 AHK  H14  C12  C11  112.23  3.000
 AHK  H13  C12  C11  111.55  3.000
 AHK  N    C12  C11  110.75  3.000
 AHK  H16  N    H15  105.55  3.000
 AHK  H16  N    C13  109.76  3.000
 AHK  H15  N    C13  109.80  3.000
 AHK  H16  N    C12  109.18  3.000
 AHK  H15  N    C12  109.24  3.000
 AHK  C13  N    C12  113.02  3.000
 AHK  H18  C13  H17  108.78  3.000
 AHK  H18  C13  C14  111.48  3.000
 AHK  H17  C13  C14  111.86  3.000
 AHK  H18  C13  N    107.01  3.000
 AHK  H17  C13  N    106.99  3.000
 AHK  C14  C13  N    110.50  3.000
 AHK  H20  C14  H19  106.76  3.000
 AHK  H20  C14  C15  109.31  3.000
 AHK  H19  C14  C15  109.51  3.000
 AHK  H20  C14  C13  110.35  3.000
 AHK  H19  C14  C13  110.43  3.000
 AHK  C15  C14  C13  110.40  3.000
 AHK  N1   C15  N2   112.90  3.000
 AHK  N2   C15  C14  122.04  3.000
 AHK  N1   C15  C14  125.06  3.000
 AHK  H21  N2   C21  126.52  3.000
 AHK  H21  N2   C15  126.09  3.000
 AHK  C21  N2   C15  107.38  3.000
 AHK  C20  C21  C16  122.61  3.000
 AHK  C20  C21  N2   132.80  3.000
 AHK  C16  C21  N2   104.59  3.000
 AHK  C17  C16  N1   130.23  3.000
 AHK  N1   C16  C21  109.87  3.000
 AHK  C17  C16  C21  119.90  3.000
 AHK  C16  N1   C15  105.26  3.000
 AHK  H23  C20  C19  121.48  3.000
 AHK  H23  C20  C21  121.89  3.000
 AHK  C19  C20  C21  116.62  3.000
 AHK  H24  C19  C18  119.22  3.000
 AHK  H24  C19  C20  119.22  3.000
 AHK  C18  C19  C20  121.55  3.000
 AHK  H25  C18  C17  119.48  3.000
 AHK  H25  C18  C19  119.11  3.000
 AHK  C17  C18  C19  121.41  3.000
 AHK  H26  C17  C18  121.20  3.000
 AHK  H26  C17  C16  120.89  3.000
 AHK  C18  C17  C16  117.91  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
 AHK  CONST_01  C10  C9   C8   C23     0.00   0.0  0
 AHK  CONST_04  C10  C11  C22  C23     0.00   0.0  0
 AHK  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 AHK  CONST_06  C5   C6   C7   C8    180.00   0.0  0
 AHK  CONST_07  C3   C2   C7   C8    180.00   0.0  0
 AHK  CONST_08  C11  C22  C23  C8      0.00   0.0  0
 AHK  CONST_09  C4   C5   C6   C7      0.00   0.0  0
 AHK  CONST_10  C10  C9   C8   C7    180.00   0.0  0
 AHK  CONST_11  C22  C23  C8   C7    180.00   0.0  0
 AHK  CONST_12  C4   C3   C2   C7      0.00   0.0  0
 AHK  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 AHK  CONST_15  C3   C2   C7   C6      0.00   0.0  0
 AHK  CONST_16  C2   C7   C6   C5      0.00   0.0  0
 AHK  CONST_17  C2   C3   C4   C5      0.00   0.0  0
 AHK  CONST_19  C9   C10  C11  C22     0.00   0.0  0
 AHK  CONST_20  C9   C8   C23  C22     0.00   0.0  0
 AHK  CONST_21  C17  C16  N1   C15   180.00   0.0  0
 AHK  CONST_22  C21  C16  N1   C15     0.00   0.0  0
 AHK  CONST_23  C16  C21  N2   C15     0.00   0.0  0
 AHK  CONST_24  C20  C21  N2   C15   180.00   0.0  0
 AHK  CONST_25  C16  N1   C15  N2      0.00   0.0  0
 AHK  CONST_26  C17  C16  C21  N2    180.00   0.0  0
 AHK  CONST_27  N1   C16  C21  N2      0.00   0.0  0
 AHK  CONST_28  C19  C20  C21  N2    180.00   0.0  0
 AHK  CONST_29  C18  C17  C16  C21     0.00   0.0  0
 AHK  CONST_30  C18  C19  C20  C21     0.00   0.0  0
 AHK  CONST_31  N1   C15  N2   C21     0.00   0.0  0
 AHK  CONST_32  C19  C18  C17  C16     0.00   0.0  0
 AHK  CONST_33  C19  C20  C21  C16     0.00   0.0  0
 AHK  CONST_34  C18  C17  C16  N1    180.00   0.0  0
 AHK  CONST_35  C20  C21  C16  N1    180.00   0.0  0
 AHK  CONST_36  C17  C18  C19  C20     0.00   0.0  0
 AHK  CONST_37  C17  C16  C21  C20     0.00   0.0  0
 AHK  CONST_38  C9   C8   C23  CL    180.00   0.0  0
 AHK  CONST_39  C7   C8   C23  CL      0.00   0.0  0
 AHK  CONST_40  C11  C22  C23  CL    180.00   0.0  0
 AHK  CONST_41  C12  C11  C22  C23   180.00   0.0  0
 AHK  CONST_42  C1   C2   C7   C8      0.00   0.0  0
 AHK  CONST_43  C1   C2   C7   C6    180.00   0.0  0
 AHK  CONST_44  C1   C2   C3   C4    180.00   0.0  0
 AHK  CONST_45  C12  C11  C10  C9    180.00   0.0  0
 AHK  CONST_46  C16  N1   C15  C14   180.00   0.0  0
 AHK  CONST_47  C21  N2   C15  C14   180.00   0.0  0
 AHK  CONST_48  H12  C9   C8   C23   180.00   0.0  0
 AHK  CONST_49  H11  C10  C9   C8    180.00   0.0  0
 AHK  CONST_50  H1   C6   C7   C8      0.00   0.0  0
 AHK  CONST_51  H10  C22  C23  C8    180.00   0.0  0
 AHK  CONST_52  H2   C5   C6   C7    180.00   0.0  0
 AHK  CONST_53  H4   C3   C2   C7    180.00   0.0  0
 AHK  CONST_54  H3   C4   C5   C6    180.00   0.0  0
 AHK  CONST_55  H23  C20  C21  N2      0.00   0.0  0
 AHK  CONST_56  H26  C17  C16  C21   180.00   0.0  0
 AHK  CONST_57  H24  C19  C20  C21   180.00   0.0  0
 AHK  CONST_58  H25  C18  C17  C16   180.00   0.0  0
 AHK  CONST_59  H21  N2   C21  C16   180.00   0.0  0
 AHK  Var_01    C    C1   C2   C7     84.10  30.0  2
 AHK  Var_02    N    C12  C11  C22    84.53  30.0  2
 AHK  Var_03    N1   C15  C14  C13   -17.47  30.0  2
 AHK  Var_04    C13  N    C12  C11   176.52  30.0  1
 AHK  Var_05    C15  C14  C13  N     179.86  30.0  1
 AHK  Var_06    H7   C    C1   C2   -179.93  30.0  3
 AHK  Var_07    C14  C13  N    C12   177.66  30.0  1

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
 AHK  plan-1  C8   0.020
 AHK  plan-1  C7   0.020
 AHK  plan-1  C6   0.020
 AHK  plan-1  C5   0.020
 AHK  plan-1  C4   0.020
 AHK  plan-1  C3   0.020
 AHK  plan-1  C2   0.020
 AHK  plan-1  C1   0.020
 AHK  plan-1  H1   0.020
 AHK  plan-1  H2   0.020
 AHK  plan-1  H3   0.020
 AHK  plan-1  H4   0.020
 AHK  plan-2  CL   0.020
 AHK  plan-2  C23  0.020
 AHK  plan-2  C8   0.020
 AHK  plan-2  C7   0.020
 AHK  plan-2  C22  0.020
 AHK  plan-2  C11  0.020
 AHK  plan-2  C10  0.020
 AHK  plan-2  C9   0.020
 AHK  plan-2  C12  0.020
 AHK  plan-2  H10  0.020
 AHK  plan-2  H11  0.020
 AHK  plan-2  H12  0.020
 AHK  plan-3  C14  0.020
 AHK  plan-3  C15  0.020
 AHK  plan-3  N2   0.020
 AHK  plan-3  C21  0.020
 AHK  plan-3  C16  0.020
 AHK  plan-3  N1   0.020
 AHK  plan-3  C20  0.020
 AHK  plan-3  C19  0.020
 AHK  plan-3  C18  0.020
 AHK  plan-3  C17  0.020
 AHK  plan-3  H21  0.020
 AHK  plan-3  H23  0.020
 AHK  plan-3  H24  0.020
 AHK  plan-3  H25  0.020
 AHK  plan-3  H26  0.020

