# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:16:53 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2[nH]c(CCNC(=O)c3ccc(cc3)n4cnnc4)nc2cc1C
#
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
 4K6  4K6  N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide  ligand  47  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4K6
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
 4K6  O    O  O     0  -0.485   1.1950  -2.2273   0.8413
 4K6  C11  C  C     0   0.540   1.4812  -1.1352   0.3701
 4K6  C12  C  CR6   0  -0.036   2.9065  -0.6987   0.2464
 4K6  C17  C  CR16  0  -0.282   3.2877   0.6399   0.2792
 4K6  C16  C  CR16  0  -0.280   4.6218   0.9983   0.1791
 4K6  C15  C  CR6   0   0.370   5.5872   0.0088   0.0577
 4K6  N3   N  NR5   0  -0.541   6.9478   0.3658  -0.0430
 4K6  C19  C  CR15  0   0.078   7.9075  -0.2186  -0.8068
 4K6  N5   N  N     0  -0.320   9.0424   0.3881  -0.6401
 4K6  N4   N  N     0  -0.320   8.8457   1.3925   0.2542
 4K6  C18  C  CR15  0   0.078   7.5951   1.3721   0.6000
 4K6  C14  C  CR16  0  -0.283   5.2253  -1.3320   0.0412
 4K6  C13  C  CR16  0  -0.262   3.8895  -1.6784   0.1374
 4K6  N2   N  NH1   0  -0.662   0.5573  -0.2622  -0.0596
 4K6  C10  C  CH2   0  -0.233  -0.8601  -0.5511  -0.0095
 4K6  C9   C  CH2   0  -0.594  -1.6510   0.7296  -0.2287
 4K6  C8   C  CR5   0   0.475  -3.1194   0.4886  -0.1739
 4K6  N1   N  NR15  0  -0.708  -3.9933   1.4739   0.1600
 4K6  C3   C  CR56  0   0.333  -5.2548   0.9416   0.1035
 4K6  C2   C  CR16  0  -0.359  -6.5191   1.4631   0.3470
 4K6  N    N  N     0  -0.484  -3.7153  -0.6412  -0.4431
 4K6  C4   C  CR56  0   0.134  -5.0588  -0.3904  -0.2781
 4K6  C5   C  CR16  0  -0.392  -6.1613  -1.2302  -0.4283
 4K6  C6   C  CR6   0   0.060  -7.4323  -0.7308  -0.1920
 4K6  C7   C  CH3   0  -0.735  -8.6298  -1.6255  -0.3469
 4K6  C1   C  CR6   0   0.048  -7.6109   0.6205   0.1998
 4K6  C    C  CH3   0  -0.736  -8.9933   1.1427   0.4675
 4K6  H17  H  HCR6  0   0.272   2.5538   1.4263   0.3965
 4K6  H16  H  HCR6  0   0.291   4.8982   2.0445   0.1875
 4K6  H19  H  HCR5  0   0.317   7.7216  -1.0509  -1.4670
 4K6  H18  H  HCR5  0   0.317   7.1190   2.0300   1.3098
 4K6  H15  H  HCR6  0   0.290   5.9786  -2.1055  -0.0239
 4K6  H14  H  HCR6  0   0.272   3.6137  -2.7241   0.1324
 4K6  H13  H  HNH1  0   0.410   0.8518   0.5324  -0.6045
 4K6  H11  H  HCH2  0   0.247  -1.1312  -1.2954  -0.7619
 4K6  H12  H  HCH2  0   0.251  -1.1040  -0.9741   0.9651
 4K6  H9   H  HCH2  0   0.274  -1.3759   1.4731   0.5232
 4K6  H10  H  HCH2  0   0.281  -1.3979   1.1635  -1.2022
 4K6  H    H  HNR5  0   0.416  -3.7484   2.4175   0.4153
 4K6  H4   H  HCR6  0   0.256  -6.6562   2.4959   0.6439
 4K6  H5   H  HCR6  0   0.243  -6.0240  -2.2640  -0.7234
 4K6  H7   H  HCH3  0   0.239  -9.1860  -1.7218   0.5884
 4K6  H8   H  HCH3  0   0.239  -9.3317  -1.2394  -1.0892
 4K6  H6   H  HCH3  0   0.249  -8.3351  -2.6262  -0.6603
 4K6  H1   H  HCH3  0   0.240  -9.6421   1.0404  -0.4047
 4K6  H2   H  HCH3  0   0.241  -9.4765   0.5976   1.2816
 4K6  H3   H  HCH3  0   0.250  -8.9716   2.1964   0.7422

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
 4K6  C9   C10  single    1.521  0.020  1.521
 4K6  C9   C8   single    1.489  0.020  1.489
 4K6  C10  N2   single    1.447  0.020  1.447
 4K6  N2   C11  single    1.342  0.020  1.342
 4K6  O    C11  double    1.223  0.020  1.223
 4K6  C11  C12  single    1.496  0.020  1.496
 4K6  C8   N    aromatic  1.305  0.020  1.305
 4K6  C8   N1   aromatic  1.359  0.020  1.359
 4K6  C17  C12  aromatic  1.392  0.020  1.392
 4K6  C17  C16  aromatic  1.385  0.020  1.385
 4K6  N    C4   aromatic  1.377  0.020  1.377
 4K6  C12  C13  aromatic  1.392  0.020  1.392
 4K6  N1   C3   aromatic  1.370  0.020  1.370
 4K6  C16  C15  aromatic  1.388  0.020  1.388
 4K6  C13  C14  aromatic  1.383  0.020  1.383
 4K6  C4   C3   aromatic  1.399  0.020  1.399
 4K6  C4   C5   aromatic  1.394  0.020  1.394
 4K6  C15  C14  aromatic  1.389  0.020  1.389
 4K6  C15  N3   single    1.410  0.020  1.410
 4K6  C3   C2   aromatic  1.389  0.020  1.389
 4K6  C18  N3   aromatic  1.358  0.020  1.358
 4K6  C18  N4   aromatic  1.298  0.020  1.298
 4K6  C5   C6   aromatic  1.386  0.020  1.386
 4K6  N3   C19  aromatic  1.359  0.020  1.359
 4K6  C2   C1   aromatic  1.387  0.020  1.387
 4K6  N4   N5   aromatic  1.359  0.020  1.359
 4K6  C6   C1   aromatic  1.418  0.020  1.418
 4K6  C6   C7   single    1.503  0.020  1.503
 4K6  C19  N5   aromatic  1.298  0.020  1.298
 4K6  C1   C    single    1.502  0.020  1.502
 4K6  C17  H17  single    0.930  0.020  1.080
 4K6  C16  H16  single    0.930  0.020  1.080
 4K6  C19  H19  single    0.930  0.020  1.080
 4K6  C18  H18  single    0.930  0.020  1.080
 4K6  C14  H15  single    0.930  0.020  1.080
 4K6  C13  H14  single    0.930  0.020  1.080
 4K6  N2   H13  single    0.860  0.020  1.020
 4K6  C10  H11  single    0.970  0.020  1.090
 4K6  C10  H12  single    0.970  0.020  1.090
 4K6  C9   H9   single    0.970  0.020  1.090
 4K6  C9   H10  single    0.970  0.020  1.090
 4K6  N1   H    single    0.860  0.020  1.020
 4K6  C2   H4   single    0.930  0.020  1.080
 4K6  C5   H5   single    0.930  0.020  1.080
 4K6  C7   H7   single    0.970  0.020  1.090
 4K6  C7   H8   single    0.970  0.020  1.090
 4K6  C7   H6   single    0.970  0.020  1.090
 4K6  C    H1   single    0.970  0.020  1.090
 4K6  C    H2   single    0.970  0.020  1.090
 4K6  C    H3   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
 4K6  N2   C11  C12  116.08  3.000
 4K6  C12  C11  O    121.02  3.000
 4K6  N2   C11  O    122.90  3.000
 4K6  C13  C12  C17  119.02  3.000
 4K6  C13  C12  C11  118.29  3.000
 4K6  C17  C12  C11  122.66  3.000
 4K6  H17  C17  C16  118.23  3.000
 4K6  H17  C17  C12  121.04  3.000
 4K6  C16  C17  C12  120.72  3.000
 4K6  H16  C16  C15  120.82  3.000
 4K6  H16  C16  C17  119.71  3.000
 4K6  C15  C16  C17  119.46  3.000
 4K6  C14  C15  N3   119.66  3.000
 4K6  N3   C15  C16  119.79  3.000
 4K6  C14  C15  C16  120.54  3.000
 4K6  C18  N3   C19  104.36  3.000
 4K6  C19  N3   C15  127.79  3.000
 4K6  C18  N3   C15  127.84  3.000
 4K6  H19  C19  N5   126.17  3.000
 4K6  H19  C19  N3   123.66  3.000
 4K6  N5   C19  N3   110.15  3.000
 4K6  N4   N5   C19  107.66  3.000
 4K6  C18  N4   N5   107.65  3.000
 4K6  H18  C18  N4   126.24  3.000
 4K6  H18  C18  N3   123.58  3.000
 4K6  N4   C18  N3   110.17  3.000
 4K6  H15  C14  C13  119.85  3.000
 4K6  H15  C14  C15  120.63  3.000
 4K6  C13  C14  C15  119.50  3.000
 4K6  H14  C13  C14  119.21  3.000
 4K6  H14  C13  C12  120.05  3.000
 4K6  C14  C13  C12  120.74  3.000
 4K6  H13  N2   C10  117.54  3.000
 4K6  H13  N2   C11  119.02  3.000
 4K6  C10  N2   C11  122.23  3.000
 4K6  H12  C10  H11  107.20  3.000
 4K6  H12  C10  C9   109.83  3.000
 4K6  H11  C10  C9   110.21  3.000
 4K6  H12  C10  N2   109.12  3.000
 4K6  H11  C10  N2   110.80  3.000
 4K6  C9   C10  N2   109.64  3.000
 4K6  H10  C9   H9   106.49  3.000
 4K6  H10  C9   C8   108.94  3.000
 4K6  H9   C9   C8   109.46  3.000
 4K6  H10  C9   C10  109.96  3.000
 4K6  H9   C9   C10  110.05  3.000
 4K6  C8   C9   C10  111.79  3.000
 4K6  N    C8   N1   112.62  3.000
 4K6  N1   C8   C9   121.73  3.000
 4K6  N    C8   C9   125.64  3.000
 4K6  H    N1   C3   126.72  3.000
 4K6  H    N1   C8   125.80  3.000
 4K6  C3   N1   C8   107.47  3.000
 4K6  C4   C3   C2   122.18  3.000
 4K6  C2   C3   N1   133.21  3.000
 4K6  C4   C3   N1   104.60  3.000
 4K6  H4   C2   C1   120.57  3.000
 4K6  H4   C2   C3   121.41  3.000
 4K6  C1   C2   C3   118.02  3.000
 4K6  C4   N    C8   105.25  3.000
 4K6  C5   C4   N    130.48  3.000
 4K6  C5   C4   C3   119.48  3.000
 4K6  N    C4   C3   110.05  3.000
 4K6  H5   C5   C6   120.42  3.000
 4K6  H5   C5   C4   120.25  3.000
 4K6  C6   C5   C4   119.33  3.000
 4K6  C1   C6   C7   119.69  3.000
 4K6  C7   C6   C5   119.92  3.000
 4K6  C1   C6   C5   120.39  3.000
 4K6  H6   C7   H8   107.65  3.000
 4K6  H6   C7   H7   107.64  3.000
 4K6  H8   C7   H7   106.61  3.000
 4K6  H6   C7   C6   111.16  3.000
 4K6  H8   C7   C6   111.82  3.000
 4K6  H7   C7   C6   111.71  3.000
 4K6  C    C1   C6   119.77  3.000
 4K6  C    C1   C2   119.63  3.000
 4K6  C6   C1   C2   120.60  3.000
 4K6  H3   C    H2   107.67  3.000
 4K6  H3   C    H1   107.69  3.000
 4K6  H2   C    H1   106.60  3.000
 4K6  H3   C    C1   111.29  3.000
 4K6  H2   C    C1   111.50  3.000
 4K6  H1   C    C1   111.84  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
 4K6  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 4K6  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 4K6  CONST_03  C14  C13  C12  C17     0.00   0.0  0
 4K6  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 4K6  CONST_05  N3   C15  C16  C17   180.00   0.0  0
 4K6  CONST_06  C13  C12  C17  C16     0.00   0.0  0
 4K6  CONST_07  C13  C14  C15  C16     0.00   0.0  0
 4K6  CONST_10  N4   C18  N3   C15   180.00   0.0  0
 4K6  CONST_11  N5   C19  N3   C15   180.00   0.0  0
 4K6  CONST_12  C13  C14  C15  N3    180.00   0.0  0
 4K6  CONST_13  N5   N4   C18  N3      0.00   0.0  0
 4K6  CONST_14  N4   N5   C19  N3      0.00   0.0  0
 4K6  CONST_16  N4   C18  N3   C19     0.00   0.0  0
 4K6  CONST_17  C18  N4   N5   C19     0.00   0.0  0
 4K6  CONST_18  C18  N3   C19  N5      0.00   0.0  0
 4K6  CONST_20  C3   C4   N    C8      0.00   0.0  0
 4K6  CONST_21  C5   C4   N    C8    180.00   0.0  0
 4K6  CONST_22  C4   C3   N1   C8      0.00   0.0  0
 4K6  CONST_23  C2   C3   N1   C8    180.00   0.0  0
 4K6  CONST_24  C4   N    C8   N1      0.00   0.0  0
 4K6  CONST_25  N    C4   C3   N1      0.00   0.0  0
 4K6  CONST_26  C5   C4   C3   N1    180.00   0.0  0
 4K6  CONST_27  C1   C2   C3   N1    180.00   0.0  0
 4K6  CONST_28  N    C8   N1   C3      0.00   0.0  0
 4K6  CONST_29  C6   C5   C4   C3      0.00   0.0  0
 4K6  CONST_30  C6   C1   C2   C3      0.00   0.0  0
 4K6  CONST_31  N    C4   C3   C2    180.00   0.0  0
 4K6  CONST_32  C5   C4   C3   C2      0.00   0.0  0
 4K6  CONST_33  C5   C6   C1   C2      0.00   0.0  0
 4K6  CONST_34  C6   C5   C4   N     180.00   0.0  0
 4K6  CONST_35  C1   C2   C3   C4      0.00   0.0  0
 4K6  CONST_36  C1   C6   C5   C4      0.00   0.0  0
 4K6  CONST_37  C16  C17  C12  C11   180.00   0.0  0
 4K6  CONST_38  C14  C13  C12  C11   180.00   0.0  0
 4K6  CONST_39  C4   N    C8   C9    180.00   0.0  0
 4K6  CONST_40  C3   N1   C8   C9    180.00   0.0  0
 4K6  CONST_41  C    C1   C2   C3    180.00   0.0  0
 4K6  CONST_42  C7   C6   C1   C2    180.00   0.0  0
 4K6  CONST_43  C7   C6   C5   C4    180.00   0.0  0
 4K6  CONST_44  C    C1   C6   C5    180.00   0.0  0
 4K6  CONST_45  H16  C16  C17  C12   180.00   0.0  0
 4K6  CONST_46  H15  C14  C13  C12   180.00   0.0  0
 4K6  CONST_47  H14  C13  C12  C17   180.00   0.0  0
 4K6  CONST_48  H17  C17  C16  C15   180.00   0.0  0
 4K6  CONST_49  H18  C18  N3   C15     0.00   0.0  0
 4K6  CONST_50  H19  C19  N3   C15     0.00   0.0  0
 4K6  CONST_51  H4   C2   C3   N1      0.00   0.0  0
 4K6  CONST_52  H5   C5   C4   C3    180.00   0.0  0
 4K6  CONST_53  H    N1   C3   C2      0.00   0.0  0
 4K6  CONST_54  C10  N2   C11  C12   180.00   0.0  0
 4K6  CONST_55  H13  N2   C11  C12     0.00   0.0  0
 4K6  CONST_56  C10  N2   C11  O       0.00   0.0  0
 4K6  Var_01    C17  C12  C11  O    -151.70  30.0  2
 4K6  Var_02    N    C8   C9   C10   -26.07  30.0  2
 4K6  Var_03    H1   C    C1   C2    121.83  30.0  2
 4K6  Var_04    H7   C7   C6   C5    119.51  30.0  2
 4K6  Var_05    C8   C9   C10  N2   -179.48  30.0  1
 4K6  Var_06    C9   C10  N2   C11   165.90  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
 4K6  plan-1  C15  0.020
 4K6  plan-1  N3   0.020
 4K6  plan-1  C19  0.020
 4K6  plan-1  N5   0.020
 4K6  plan-1  N4   0.020
 4K6  plan-1  C18  0.020
 4K6  plan-1  H19  0.020
 4K6  plan-1  H18  0.020
 4K6  plan-2  C11  0.020
 4K6  plan-2  C12  0.020
 4K6  plan-2  C17  0.020
 4K6  plan-2  C16  0.020
 4K6  plan-2  C15  0.020
 4K6  plan-2  N3   0.020
 4K6  plan-2  C14  0.020
 4K6  plan-2  C13  0.020
 4K6  plan-2  H17  0.020
 4K6  plan-2  H16  0.020
 4K6  plan-2  H15  0.020
 4K6  plan-2  H14  0.020
 4K6  plan-3  C9   0.020
 4K6  plan-3  C8   0.020
 4K6  plan-3  N1   0.020
 4K6  plan-3  C3   0.020
 4K6  plan-3  C2   0.020
 4K6  plan-3  N    0.020
 4K6  plan-3  C4   0.020
 4K6  plan-3  C5   0.020
 4K6  plan-3  C6   0.020
 4K6  plan-3  C7   0.020
 4K6  plan-3  C1   0.020
 4K6  plan-3  C    0.020
 4K6  plan-3  H    0.020
 4K6  plan-3  H4   0.020
 4K6  plan-3  H5   0.020
 4K6  plan-4  O    0.020
 4K6  plan-4  C11  0.020
 4K6  plan-4  C12  0.020
 4K6  plan-4  N2   0.020
 4K6  plan-4  C10  0.020
 4K6  plan-4  H13  0.020

