# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:11:03 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(5-methyl-1~{H}-benzimidazol-2-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4ccc(C)cc4n3)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
 AOK  AOK  ~{N}-[[3-chloranyl-4-(2-ethylphenyl)phenyl]methyl]-2-(5-methyl-1~{H}-benzimidazol-2-yl)ethanamine  ligand  55  29  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AOK
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
 AOK  CL   CL  CL    0  -0.130    3.7949  -2.0691  -0.6656
 AOK  C24  C   CR6   0  -0.095    3.2045  -0.5393  -0.0952
 AOK  C8   C   CR6   0   0.103    4.0941   0.3633   0.4831
 AOK  C7   C   CR6   0   0.022    5.5365   0.0631   0.6583
 AOK  C6   C   CR16  0  -0.270    5.9866  -0.3314   1.9158
 AOK  C5   C   CR16  0  -0.263    7.3275  -0.6072   2.1394
 AOK  C4   C   CR16  0  -0.248    8.2310  -0.4888   1.0932
 AOK  C3   C   CR16  0  -0.304    7.7858  -0.0944  -0.1603
 AOK  C2   C   CR6   0   0.108    6.4429   0.1879  -0.4013
 AOK  C1   C   CH2   0  -0.519    6.0174   0.6729  -1.7611
 AOK  C    C   CH3   0  -0.655    6.0260   2.1979  -1.8532
 AOK  C23  C   CR16  0  -0.236    1.8544  -0.2634  -0.2302
 AOK  C11  C   CR6   0   0.060    1.3447   0.9511   0.2188
 AOK  C10  C   CR16  0  -0.292    2.2146   1.8593   0.8103
 AOK  C9   C   CR16  0  -0.286    3.5643   1.5676   0.9371
 AOK  C12  C   CH2   0  -0.307   -0.1149   1.2766   0.0483
 AOK  N    N   NH1   0  -0.603   -0.9576   0.1312   0.3233
 AOK  C13  C   CH2   0  -0.246   -2.3647   0.4183   0.1217
 AOK  C14  C   CH2   0  -0.564   -3.1933  -0.8275   0.3920
 AOK  C15  C   CR5   0   0.470   -4.6536  -0.6040   0.2075
 AOK  N2   N   NR15  0  -0.704   -5.5337  -1.6388   0.1621
 AOK  C22  C   CR56  0   0.312   -6.7878  -1.1088   0.0055
 AOK  C16  C   CR56  0   0.149   -6.5820   0.2771  -0.0386
 AOK  N1   N   N     0  -0.487   -5.2410   0.5568   0.0891
 AOK  C21  C   CR16  0  -0.296   -8.0540  -1.6712  -0.1035
 AOK  C20  C   CR16  0  -0.314   -9.1143  -0.7962  -0.2564
 AOK  C18  C   CR6   0   0.083   -8.9415   0.6013  -0.3021
 AOK  C19  C   CH3   0  -0.723  -10.1439   1.4895  -0.4615
 AOK  C17  C   CR16  0  -0.394   -7.6683   1.1389  -0.1936
 AOK  H1   H   HCR6  0   0.249    5.2739  -0.4256   2.7260
 AOK  H2   H   HCR6  0   0.255    7.6619  -0.9146   3.1215
 AOK  H3   H   HCR6  0   0.254    9.2803  -0.7021   1.2514
 AOK  H4   H   HCR6  0   0.248    8.4965  -0.0041  -0.9736
 AOK  H5   H   HCH2  0   0.244    6.6938   0.2633  -2.5142
 AOK  H6   H   HCH2  0   0.239    5.0223   0.3007  -2.0083
 AOK  H7   H   HCH3  0   0.228    5.3244   2.6410  -1.1458
 AOK  H8   H   HCH3  0   0.226    7.0168   2.5984  -1.6355
 AOK  H9   H   HCH3  0   0.232    5.7429   2.5273  -2.8533
 AOK  H10  H   HCR6  0   0.269    1.1925  -0.9942  -0.6759
 AOK  H11  H   HCR6  0   0.256    1.8370   2.8044   1.1809
 AOK  H12  H   HCR6  0   0.259    4.2253   2.2862   1.4052
 AOK  H13  H   HCH2  0   0.219   -0.3622   2.1535   0.6654
 AOK  H14  H   HCH2  0   0.246   -0.2916   1.5821  -0.9886
 AOK  H15  H   HNH1  0   0.345   -0.8125  -0.1551   1.2851
 AOK  H17  H   HCH2  0   0.206   -2.7238   1.2467   0.7476
 AOK  H18  H   HCH2  0   0.230   -2.5068   0.7331  -0.9155
 AOK  H19  H   HCH2  0   0.265   -2.8625  -1.6401  -0.2603
 AOK  H20  H   HCH2  0   0.268   -3.0187  -1.1726   1.4173
 AOK  H21  H   HNR5  0   0.416   -5.2989  -2.6165   0.2272
 AOK  H23  H   HCR6  0   0.262   -8.2100  -2.7417  -0.0710
 AOK  H24  H   HCR6  0   0.245  -10.1166  -1.1991  -0.3445
 AOK  H25  H   HCH3  0   0.242  -10.8270   1.3889   0.3838
 AOK  H26  H   HCH3  0   0.241   -9.8590   2.5385  -0.5322
 AOK  H27  H   HCH3  0   0.241  -10.7095   1.2379  -1.3600
 AOK  H28  H   HCR6  0   0.243   -7.5164   2.2115  -0.2282

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
 AOK  C    C1   single    1.528  0.020  1.528
 AOK  C17  C16  aromatic  1.395  0.020  1.395
 AOK  C17  C18  aromatic  1.386  0.020  1.386
 AOK  N1   C16  aromatic  1.376  0.020  1.376
 AOK  N1   C15  aromatic  1.306  0.020  1.306
 AOK  C19  C18  single    1.503  0.020  1.503
 AOK  C16  C22  aromatic  1.402  0.020  1.402
 AOK  C18  C20  aromatic  1.409  0.020  1.409
 AOK  C14  C15  single    1.489  0.020  1.489
 AOK  C14  C13  single    1.520  0.020  1.520
 AOK  C15  N2   aromatic  1.359  0.020  1.359
 AOK  C1   C2   single    1.505  0.020  1.505
 AOK  C22  N2   aromatic  1.370  0.020  1.370
 AOK  C22  C21  aromatic  1.390  0.020  1.390
 AOK  C20  C21  aromatic  1.383  0.020  1.383
 AOK  C13  N    single    1.450  0.020  1.450
 AOK  N    C12  single    1.448  0.020  1.448
 AOK  C2   C3   aromatic  1.393  0.020  1.393
 AOK  C2   C7   aromatic  1.400  0.020  1.400
 AOK  C3   C4   aromatic  1.387  0.020  1.387
 AOK  CL   C24  single    1.736  0.020  1.736
 AOK  C23  C24  aromatic  1.385  0.020  1.385
 AOK  C23  C11  aromatic  1.392  0.020  1.392
 AOK  C12  C11  single    1.505  0.020  1.505
 AOK  C24  C8   aromatic  1.393  0.020  1.393
 AOK  C11  C10  aromatic  1.390  0.020  1.390
 AOK  C10  C9   aromatic  1.387  0.020  1.387
 AOK  C8   C9   aromatic  1.392  0.020  1.392
 AOK  C8   C7   single    1.484  0.020  1.484
 AOK  C7   C6   aromatic  1.393  0.020  1.393
 AOK  C4   C5   aromatic  1.387  0.020  1.387
 AOK  C6   C5   aromatic  1.387  0.020  1.387
 AOK  C6   H1   single    0.930  0.020  1.080
 AOK  C5   H2   single    0.930  0.020  1.080
 AOK  C4   H3   single    0.930  0.020  1.080
 AOK  C3   H4   single    0.930  0.020  1.080
 AOK  C1   H5   single    0.970  0.020  1.090
 AOK  C1   H6   single    0.970  0.020  1.090
 AOK  C    H7   single    0.970  0.020  1.090
 AOK  C    H8   single    0.970  0.020  1.090
 AOK  C    H9   single    0.970  0.020  1.090
 AOK  C23  H10  single    0.930  0.020  1.080
 AOK  C10  H11  single    0.930  0.020  1.080
 AOK  C9   H12  single    0.930  0.020  1.080
 AOK  C12  H13  single    0.970  0.020  1.090
 AOK  C12  H14  single    0.970  0.020  1.090
 AOK  N    H15  single    0.890  0.020  1.040
 AOK  C13  H17  single    0.970  0.020  1.090
 AOK  C13  H18  single    0.970  0.020  1.090
 AOK  C14  H19  single    0.970  0.020  1.090
 AOK  C14  H20  single    0.970  0.020  1.090
 AOK  N2   H21  single    0.860  0.020  1.020
 AOK  C21  H23  single    0.930  0.020  1.080
 AOK  C20  H24  single    0.930  0.020  1.080
 AOK  C19  H25  single    0.970  0.020  1.090
 AOK  C19  H26  single    0.970  0.020  1.090
 AOK  C19  H27  single    0.970  0.020  1.090
 AOK  C17  H28  single    0.930  0.020  1.080

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
 AOK  C23  C24  C8   122.28  3.000
 AOK  C8   C24  CL   119.35  3.000
 AOK  C23  C24  CL   118.36  3.000
 AOK  C9   C8   C7   120.44  3.000
 AOK  C7   C8   C24  122.59  3.000
 AOK  C9   C8   C24  116.94  3.000
 AOK  C2   C7   C6   119.96  3.000
 AOK  C6   C7   C8   118.56  3.000
 AOK  C2   C7   C8   121.47  3.000
 AOK  H1   C6   C5   119.88  3.000
 AOK  H1   C6   C7   119.16  3.000
 AOK  C5   C6   C7   120.95  3.000
 AOK  H2   C5   C4   120.49  3.000
 AOK  H2   C5   C6   120.10  3.000
 AOK  C4   C5   C6   119.41  3.000
 AOK  H3   C4   C3   119.95  3.000
 AOK  H3   C4   C5   120.28  3.000
 AOK  C3   C4   C5   119.77  3.000
 AOK  H4   C3   C2   119.04  3.000
 AOK  H4   C3   C4   119.42  3.000
 AOK  C2   C3   C4   121.55  3.000
 AOK  C1   C2   C3   119.61  3.000
 AOK  C3   C2   C7   118.37  3.000
 AOK  C1   C2   C7   121.97  3.000
 AOK  H6   C1   H5   106.30  3.000
 AOK  H6   C1   C    109.40  3.000
 AOK  H5   C1   C    109.23  3.000
 AOK  H6   C1   C2   110.65  3.000
 AOK  H5   C1   C2   109.09  3.000
 AOK  C    C1   C2   112.00  3.000
 AOK  H9   C    H8   107.94  3.000
 AOK  H9   C    H7   107.76  3.000
 AOK  H8   C    H7   107.81  3.000
 AOK  H9   C    C1   110.82  3.000
 AOK  H8   C    C1   111.08  3.000
 AOK  H7   C    C1   111.28  3.000
 AOK  H10  C23  C11  119.89  3.000
 AOK  H10  C23  C24  120.14  3.000
 AOK  C11  C23  C24  119.97  3.000
 AOK  C12  C11  C10  120.92  3.000
 AOK  C10  C11  C23  118.58  3.000
 AOK  C12  C11  C23  120.49  3.000
 AOK  H11  C10  C9   119.45  3.000
 AOK  H11  C10  C11  119.84  3.000
 AOK  C9   C10  C11  120.71  3.000
 AOK  H12  C9   C10  119.61  3.000
 AOK  H12  C9   C8   118.88  3.000
 AOK  C10  C9   C8   121.51  3.000
 AOK  H14  C12  H13  105.81  3.000
 AOK  H14  C12  N    107.84  3.000
 AOK  H13  C12  N    113.14  3.000
 AOK  H14  C12  C11  108.91  3.000
 AOK  H13  C12  C11  109.07  3.000
 AOK  N    C12  C11  111.82  3.000
 AOK  H15  N    C13  109.06  3.000
 AOK  H15  N    C12  108.67  3.000
 AOK  C13  N    C12  112.43  3.000
 AOK  H18  C13  H17  106.31  3.000
 AOK  H18  C13  C14  109.49  3.000
 AOK  H17  C13  C14  109.78  3.000
 AOK  H18  C13  N    108.36  3.000
 AOK  H17  C13  N    112.79  3.000
 AOK  C14  C13  N    109.99  3.000
 AOK  H20  C14  H19  106.02  3.000
 AOK  H20  C14  C15  108.63  3.000
 AOK  H19  C14  C15  109.54  3.000
 AOK  H20  C14  C13  109.72  3.000
 AOK  H19  C14  C13  109.76  3.000
 AOK  C15  C14  C13  112.93  3.000
 AOK  N1   C15  N2   112.47  3.000
 AOK  N2   C15  C14  121.67  3.000
 AOK  N1   C15  C14  125.86  3.000
 AOK  H21  N2   C22  126.57  3.000
 AOK  H21  N2   C15  125.85  3.000
 AOK  C22  N2   C15  107.58  3.000
 AOK  C21  C22  C16  122.10  3.000
 AOK  C21  C22  N2   133.33  3.000
 AOK  C16  C22  N2   104.57  3.000
 AOK  C17  C16  N1   130.07  3.000
 AOK  N1   C16  C22  109.95  3.000
 AOK  C17  C16  C22  119.99  3.000
 AOK  C16  N1   C15  105.43  3.000
 AOK  H23  C21  C20  121.23  3.000
 AOK  H23  C21  C22  121.96  3.000
 AOK  C20  C21  C22  116.81  3.000
 AOK  H24  C20  C18  118.66  3.000
 AOK  H24  C20  C21  118.86  3.000
 AOK  C18  C20  C21  122.48  3.000
 AOK  C17  C18  C19  120.92  3.000
 AOK  C19  C18  C20  119.43  3.000
 AOK  C17  C18  C20  119.66  3.000
 AOK  H27  C19  H26  107.71  3.000
 AOK  H27  C19  H25  106.98  3.000
 AOK  H26  C19  H25  107.62  3.000
 AOK  H27  C19  C18  111.45  3.000
 AOK  H26  C19  C18  111.51  3.000
 AOK  H25  C19  C18  111.35  3.000
 AOK  H28  C17  C18  120.67  3.000
 AOK  H28  C17  C16  120.37  3.000
 AOK  C18  C17  C16  118.96  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
 AOK  CONST_01  C10  C11  C23  C24     0.00   0.0  0
 AOK  CONST_02  C10  C9   C8   C24     0.00   0.0  0
 AOK  CONST_05  C11  C23  C24  C8      0.00   0.0  0
 AOK  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 AOK  CONST_07  C3   C2   C7   C8    180.00   0.0  0
 AOK  CONST_08  C5   C6   C7   C8    180.00   0.0  0
 AOK  CONST_09  C4   C3   C2   C7      0.00   0.0  0
 AOK  CONST_10  C23  C24  C8   C7    180.00   0.0  0
 AOK  CONST_11  C10  C9   C8   C7    180.00   0.0  0
 AOK  CONST_12  C4   C5   C6   C7      0.00   0.0  0
 AOK  CONST_13  C3   C2   C7   C6      0.00   0.0  0
 AOK  CONST_15  C3   C4   C5   C6      0.00   0.0  0
 AOK  CONST_16  C2   C3   C4   C5      0.00   0.0  0
 AOK  CONST_17  C2   C7   C6   C5      0.00   0.0  0
 AOK  CONST_19  C9   C8   C24  C23     0.00   0.0  0
 AOK  CONST_20  C9   C10  C11  C23     0.00   0.0  0
 AOK  CONST_21  C17  C16  N1   C15   180.00   0.0  0
 AOK  CONST_22  C22  C16  N1   C15     0.00   0.0  0
 AOK  CONST_23  C16  C22  N2   C15     0.00   0.0  0
 AOK  CONST_24  C21  C22  N2   C15   180.00   0.0  0
 AOK  CONST_25  C16  N1   C15  N2      0.00   0.0  0
 AOK  CONST_26  C17  C16  C22  N2    180.00   0.0  0
 AOK  CONST_27  N1   C16  C22  N2      0.00   0.0  0
 AOK  CONST_28  C20  C21  C22  N2    180.00   0.0  0
 AOK  CONST_29  C18  C17  C16  C22     0.00   0.0  0
 AOK  CONST_30  N1   C15  N2   C22     0.00   0.0  0
 AOK  CONST_31  C18  C20  C21  C22     0.00   0.0  0
 AOK  CONST_32  C20  C18  C17  C16     0.00   0.0  0
 AOK  CONST_33  C20  C21  C22  C16     0.00   0.0  0
 AOK  CONST_34  C18  C17  C16  N1    180.00   0.0  0
 AOK  CONST_35  C21  C22  C16  N1    180.00   0.0  0
 AOK  CONST_36  C17  C16  C22  C21     0.00   0.0  0
 AOK  CONST_37  C17  C18  C20  C21     0.00   0.0  0
 AOK  CONST_38  C11  C23  C24  CL    180.00   0.0  0
 AOK  CONST_39  C9   C8   C24  CL    180.00   0.0  0
 AOK  CONST_40  C7   C8   C24  CL      0.00   0.0  0
 AOK  CONST_41  C12  C11  C23  C24   180.00   0.0  0
 AOK  CONST_42  C1   C2   C7   C8      0.00   0.0  0
 AOK  CONST_43  C1   C2   C7   C6    180.00   0.0  0
 AOK  CONST_44  C1   C2   C3   C4    180.00   0.0  0
 AOK  CONST_45  C12  C11  C10  C9    180.00   0.0  0
 AOK  CONST_46  C16  N1   C15  C14   180.00   0.0  0
 AOK  CONST_47  C22  N2   C15  C14   180.00   0.0  0
 AOK  CONST_48  C19  C18  C17  C16   180.00   0.0  0
 AOK  CONST_49  C19  C18  C20  C21   180.00   0.0  0
 AOK  CONST_50  H12  C9   C8   C24   180.00   0.0  0
 AOK  CONST_51  H10  C23  C24  C8    180.00   0.0  0
 AOK  CONST_52  H11  C10  C9   C8    180.00   0.0  0
 AOK  CONST_53  H1   C6   C7   C8      0.00   0.0  0
 AOK  CONST_54  H4   C3   C2   C7    180.00   0.0  0
 AOK  CONST_55  H2   C5   C6   C7    180.00   0.0  0
 AOK  CONST_56  H3   C4   C5   C6    180.00   0.0  0
 AOK  CONST_57  H23  C21  C22  N2      0.00   0.0  0
 AOK  CONST_58  H28  C17  C16  C22   180.00   0.0  0
 AOK  CONST_59  H24  C20  C21  C22   180.00   0.0  0
 AOK  CONST_60  H21  N2   C22  C16   180.00   0.0  0
 AOK  Var_01    C    C1   C2   C7     85.63  30.0  2
 AOK  Var_02    N    C12  C11  C23    40.93  30.0  3
 AOK  Var_03    N1   C15  C14  C13   -13.03  30.0  2
 AOK  Var_04    H25  C19  C18  C20    62.69  30.0  2
 AOK  Var_05    C13  N    C12  C11  -178.16  30.0  1
 AOK  Var_06    C15  C14  C13  N     179.83  30.0  1
 AOK  Var_07    H7   C    C1   C2    -61.74  30.0  3
 AOK  Var_08    C14  C13  N    C12   178.62  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
 AOK  plan-1  C8   0.020
 AOK  plan-1  C7   0.020
 AOK  plan-1  C6   0.020
 AOK  plan-1  C5   0.020
 AOK  plan-1  C4   0.020
 AOK  plan-1  C3   0.020
 AOK  plan-1  C2   0.020
 AOK  plan-1  C1   0.020
 AOK  plan-1  H1   0.020
 AOK  plan-1  H2   0.020
 AOK  plan-1  H3   0.020
 AOK  plan-1  H4   0.020
 AOK  plan-2  CL   0.020
 AOK  plan-2  C24  0.020
 AOK  plan-2  C8   0.020
 AOK  plan-2  C7   0.020
 AOK  plan-2  C23  0.020
 AOK  plan-2  C11  0.020
 AOK  plan-2  C10  0.020
 AOK  plan-2  C9   0.020
 AOK  plan-2  C12  0.020
 AOK  plan-2  H10  0.020
 AOK  plan-2  H11  0.020
 AOK  plan-2  H12  0.020
 AOK  plan-3  C14  0.020
 AOK  plan-3  C15  0.020
 AOK  plan-3  N2   0.020
 AOK  plan-3  C22  0.020
 AOK  plan-3  C16  0.020
 AOK  plan-3  N1   0.020
 AOK  plan-3  C21  0.020
 AOK  plan-3  C20  0.020
 AOK  plan-3  C18  0.020
 AOK  plan-3  C19  0.020
 AOK  plan-3  C17  0.020
 AOK  plan-3  H21  0.020
 AOK  plan-3  H23  0.020
 AOK  plan-3  H24  0.020
 AOK  plan-3  H28  0.020

