# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:38:13 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1I)C(=O)Nc2ccc3nc(CN4CCCCC4)[nH]c3c2
#
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
 GKT  GKT  3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide  ligand  50  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GKT
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
 GKT  C1   C  CR6   0   0.152  -4.9915  -1.3628  -0.8372
 GKT  C2   C  CR16  0  -0.286  -4.1654  -2.3979  -1.2787
 GKT  C3   C  CR16  0  -0.249  -2.7980  -2.3843  -1.0764
 GKT  C4   C  CR6   0  -0.047  -2.2030  -1.3296  -0.3920
 GKT  C5   C  CR16  0  -0.256  -3.0015  -0.2809   0.0552
 GKT  C6   C  CR6   0  -0.266  -4.3696  -0.3069  -0.1704
 GKT  C7   C  C     0   0.529  -0.7185  -1.3385  -0.2191
 GKT  O    O  O     0  -0.463  -0.0001  -1.8988  -1.0301
 GKT  I    I  I     0   0.065  -5.5020   1.3302   0.5239
 GKT  C    C  CH3   0  -0.732  -6.4640  -1.4182  -1.0964
 GKT  N    N  NH1   0  -0.759  -0.2670  -0.6986   0.8849
 GKT  C8   C  CR6   0   0.365   1.0530  -0.4502   1.2872
 GKT  C20  C  CR16  0  -0.397   2.1715  -0.7986   0.5384
 GKT  C19  C  CR56  0   0.378   3.4043  -0.4508   1.0772
 GKT  C11  C  CR56  0   0.117   3.5631   0.2147   2.3023
 GKT  C10  C  CR16  0  -0.325   2.4295   0.5475   3.0401
 GKT  C9   C  CR16  0  -0.370   1.1948   0.2115   2.5258
 GKT  N3   N  NR15  0  -0.683   4.6795  -0.6246   0.6165
 GKT  C12  C  CR5   0   0.415   5.5224  -0.0707   1.5263
 GKT  N1   N  N     0  -0.477   4.8979   0.4406   2.5507
 GKT  C13  C  CH2   0  -0.360   7.0002  -0.1177   1.3224
 GKT  N2   N  NT    0  -0.429   7.3280  -0.0225  -0.0816
 GKT  C18  C  CH2   0  -0.277   8.6823  -0.4727  -0.3601
 GKT  C17  C  CH2   0  -0.438   8.9569  -0.4867  -1.8561
 GKT  C16  C  CH2   0  -0.441   8.7059   0.8855  -2.4696
 GKT  C15  C  CH2   0  -0.435   7.3093   1.3690  -2.1032
 GKT  C14  C  CH2   0  -0.288   7.0988   1.3188  -0.5987
 GKT  H1   H  HCR6  0   0.268  -4.6148  -3.2356  -1.7968
 GKT  H2   H  HCR6  0   0.268  -2.1957  -3.2039  -1.4446
 GKT  H3   H  HCR6  0   0.281  -2.5581   0.5726   0.5514
 GKT  H4   H  HCH3  0   0.260  -6.7883  -0.5865  -1.7242
 GKT  H5   H  HCH3  0   0.261  -6.7315  -2.3431  -1.6040
 GKT  H6   H  HCH3  0   0.259  -7.0379  -1.3667  -0.1701
 GKT  H7   H  HNH1  0   0.423  -0.9659  -0.3873   1.5421
 GKT  H8   H  HCR6  0   0.288   2.1004  -1.3087  -0.4081
 GKT  H9   H  HCR6  0   0.258   2.5080   1.0604   3.9898
 GKT  H10  H  HCR6  0   0.267   0.3032   0.4674   3.0861
 GKT  H11  H  HNR5  0   0.411   4.9725  -1.0336  -0.2577
 GKT  H13  H  HCH2  0   0.231   7.4657   0.6642   1.9413
 GKT  H14  H  HCH2  0   0.273   7.3678  -1.0762   1.7036
 GKT  H16  H  HCH2  0   0.190   9.4292   0.1677   0.1408
 GKT  H17  H  HCH2  0   0.238   8.8056  -1.4787   0.0485
 GKT  H18  H  HCH2  0   0.232   9.9869  -0.8073  -2.0272
 GKT  H19  H  HCH2  0   0.217   8.3080  -1.2286  -2.3309
 GKT  H20  H  HCH2  0   0.211   9.4476   1.5953  -2.0878
 GKT  H21  H  HCH2  0   0.232   8.8327   0.8517  -3.5538
 GKT  H22  H  HCH2  0   0.232   7.1449   2.3899  -2.4546
 GKT  H23  H  HCH2  0   0.217   6.5585   0.7381  -2.5883
 GKT  H24  H  HCH2  0   0.243   6.0770   1.6274  -0.3645
 GKT  H25  H  HCH2  0   0.195   7.7653   2.0489  -0.1065

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
 GKT  C    C1   single    1.496  0.020  1.496
 GKT  C2   C1   aromatic  1.396  0.020  1.396
 GKT  C2   C3   aromatic  1.382  0.020  1.382
 GKT  C1   C6   aromatic  1.395  0.020  1.395
 GKT  C3   C4   aromatic  1.391  0.020  1.391
 GKT  C6   I    single    2.108  0.020  2.108
 GKT  C6   C5   aromatic  1.387  0.020  1.387
 GKT  O    C7   double    1.220  0.020  1.220
 GKT  C4   C5   aromatic  1.392  0.020  1.392
 GKT  C4   C7   single    1.495  0.020  1.495
 GKT  C7   N    single    1.354  0.020  1.354
 GKT  N    C8   single    1.402  0.020  1.402
 GKT  C20  C8   aromatic  1.390  0.020  1.390
 GKT  C20  C19  aromatic  1.390  0.020  1.390
 GKT  C8   C9   aromatic  1.411  0.020  1.411
 GKT  N3   C19  aromatic  1.367  0.020  1.367
 GKT  N3   C12  aromatic  1.358  0.020  1.358
 GKT  C19  C11  aromatic  1.403  0.020  1.403
 GKT  C9   C10  aromatic  1.379  0.020  1.379
 GKT  C12  C13  single    1.493  0.020  1.493
 GKT  C12  N1   aromatic  1.304  0.020  1.304
 GKT  C11  C10  aromatic  1.393  0.020  1.393
 GKT  C11  N1   aromatic  1.376  0.020  1.376
 GKT  C13  N2   single    1.445  0.020  1.445
 GKT  N2   C18  single    1.454  0.020  1.454
 GKT  N2   C14  single    1.456  0.020  1.456
 GKT  C18  C17  single    1.521  0.020  1.521
 GKT  C17  C16  single    1.524  0.020  1.524
 GKT  C14  C15  single    1.520  0.020  1.520
 GKT  C16  C15  single    1.523  0.020  1.523
 GKT  C2   H1   single    0.930  0.020  1.080
 GKT  C3   H2   single    0.930  0.020  1.080
 GKT  C5   H3   single    0.930  0.020  1.080
 GKT  C    H4   single    0.970  0.020  1.090
 GKT  C    H5   single    0.970  0.020  1.090
 GKT  C    H6   single    0.970  0.020  1.090
 GKT  N    H7   single    0.860  0.020  1.020
 GKT  C20  H8   single    0.930  0.020  1.080
 GKT  C10  H9   single    0.930  0.020  1.080
 GKT  C9   H10  single    0.930  0.020  1.080
 GKT  N3   H11  single    0.860  0.020  1.020
 GKT  C13  H13  single    0.970  0.020  1.090
 GKT  C13  H14  single    0.970  0.020  1.090
 GKT  C18  H16  single    0.970  0.020  1.090
 GKT  C18  H17  single    0.970  0.020  1.090
 GKT  C17  H18  single    0.970  0.020  1.090
 GKT  C17  H19  single    0.970  0.020  1.090
 GKT  C16  H20  single    0.970  0.020  1.090
 GKT  C16  H21  single    0.970  0.020  1.090
 GKT  C15  H22  single    0.970  0.020  1.090
 GKT  C15  H23  single    0.970  0.020  1.090
 GKT  C14  H24  single    0.970  0.020  1.090
 GKT  C14  H25  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
 GKT  C    C1   C6   123.33  3.000
 GKT  C6   C1   C2   116.65  3.000
 GKT  C    C1   C2   120.01  3.000
 GKT  H1   C2   C3   119.22  3.000
 GKT  H1   C2   C1   118.65  3.000
 GKT  C3   C2   C1   122.13  3.000
 GKT  H2   C3   C4   120.25  3.000
 GKT  H2   C3   C2   119.57  3.000
 GKT  C4   C3   C2   120.17  3.000
 GKT  C7   C4   C5   122.49  3.000
 GKT  C7   C4   C3   118.51  3.000
 GKT  C5   C4   C3   118.95  3.000
 GKT  H3   C5   C6   119.57  3.000
 GKT  H3   C5   C4   120.43  3.000
 GKT  C6   C5   C4   119.97  3.000
 GKT  I    C6   C5   117.50  3.000
 GKT  C5   C6   C1   122.12  3.000
 GKT  I    C6   C1   120.38  3.000
 GKT  N    C7   O    124.26  3.000
 GKT  N    C7   C4   115.02  3.000
 GKT  O    C7   C4   120.72  3.000
 GKT  H6   C    H5   107.87  3.000
 GKT  H6   C    H4   107.23  3.000
 GKT  H5   C    H4   107.84  3.000
 GKT  H6   C    C1   111.65  3.000
 GKT  H5   C    C1   110.73  3.000
 GKT  H4   C    C1   111.34  3.000
 GKT  H7   N    C8   114.25  3.000
 GKT  H7   N    C7   116.50  3.000
 GKT  C8   N    C7   129.19  3.000
 GKT  C9   C8   C20  120.62  3.000
 GKT  C9   C8   N    115.43  3.000
 GKT  C20  C8   N    123.94  3.000
 GKT  H8   C20  C19  121.17  3.000
 GKT  H8   C20  C8   122.59  3.000
 GKT  C19  C20  C8   116.24  3.000
 GKT  N3   C19  C11  104.41  3.000
 GKT  C11  C19  C20  123.89  3.000
 GKT  N3   C19  C20  131.69  3.000
 GKT  N1   C11  C10  130.88  3.000
 GKT  N1   C11  C19  110.19  3.000
 GKT  C10  C11  C19  118.92  3.000
 GKT  H9   C10  C9   120.51  3.000
 GKT  H9   C10  C11  121.27  3.000
 GKT  C9   C10  C11  118.23  3.000
 GKT  H10  C9   C10  119.10  3.000
 GKT  H10  C9   C8   118.80  3.000
 GKT  C10  C9   C8   122.10  3.000
 GKT  H11  N3   C12  124.44  3.000
 GKT  H11  N3   C19  127.92  3.000
 GKT  C12  N3   C19  107.54  3.000
 GKT  C13  C12  N1   126.42  3.000
 GKT  N1   C12  N3   112.88  3.000
 GKT  C13  C12  N3   120.67  3.000
 GKT  C12  N1   C11  104.97  3.000
 GKT  H14  C13  H13  106.51  3.000
 GKT  H14  C13  N2   108.65  3.000
 GKT  H13  C13  N2   113.81  3.000
 GKT  H14  C13  C12  108.20  3.000
 GKT  H13  C13  C12  108.64  3.000
 GKT  N2   C13  C12  110.81  3.000
 GKT  C14  N2   C18  111.34  3.000
 GKT  C14  N2   C13  111.72  3.000
 GKT  C18  N2   C13  112.14  3.000
 GKT  H17  C18  H16  106.74  3.000
 GKT  H17  C18  C17  109.81  3.000
 GKT  H16  C18  C17  109.23  3.000
 GKT  H17  C18  N2   108.58  3.000
 GKT  H16  C18  N2   111.32  3.000
 GKT  C17  C18  N2   111.06  3.000
 GKT  H19  C17  H18  107.00  3.000
 GKT  H19  C17  C16  109.77  3.000
 GKT  H18  C17  C16  110.88  3.000
 GKT  H19  C17  C18  109.03  3.000
 GKT  H18  C17  C18  109.09  3.000
 GKT  C16  C17  C18  110.98  3.000
 GKT  H21  C16  H20  106.71  3.000
 GKT  H21  C16  C15  110.80  3.000
 GKT  H20  C16  C15  109.35  3.000
 GKT  H21  C16  C17  110.65  3.000
 GKT  H20  C16  C17  109.37  3.000
 GKT  C15  C16  C17  109.88  3.000
 GKT  H23  C15  H22  107.04  3.000
 GKT  H23  C15  C14  108.96  3.000
 GKT  H22  C15  C14  109.18  3.000
 GKT  H23  C15  C16  109.85  3.000
 GKT  H22  C15  C16  110.94  3.000
 GKT  C14  C15  C16  110.78  3.000
 GKT  H25  C14  H24  106.38  3.000
 GKT  H25  C14  C15  109.62  3.000
 GKT  H24  C14  C15  109.41  3.000
 GKT  H25  C14  N2   110.85  3.000
 GKT  H24  C14  N2   109.35  3.000
 GKT  C15  C14  N2   111.11  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
 GKT  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 GKT  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 GKT  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 GKT  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 GKT  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 GKT  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 GKT  CONST_07  N3   C19  C20  C8    180.00   0.0  0
 GKT  CONST_08  C11  C19  C20  C8      0.00   0.0  0
 GKT  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 GKT  CONST_10  C10  C9   C8   C20     0.00   0.0  0
 GKT  CONST_11  C12  N3   C19  C20   180.00   0.0  0
 GKT  CONST_12  C10  C11  C19  C20     0.00   0.0  0
 GKT  CONST_13  N1   C11  C19  C20   180.00   0.0  0
 GKT  CONST_14  C9   C8   C20  C19     0.00   0.0  0
 GKT  CONST_15  N1   C12  N3   C19     0.00   0.0  0
 GKT  CONST_16  C9   C10  C11  C19     0.00   0.0  0
 GKT  CONST_17  C12  N1   C11  C19     0.00   0.0  0
 GKT  CONST_18  C12  N3   C19  C11     0.00   0.0  0
 GKT  CONST_19  N3   C12  N1   C11     0.00   0.0  0
 GKT  CONST_20  N3   C19  C11  C10   180.00   0.0  0
 GKT  CONST_21  C12  N1   C11  C10   180.00   0.0  0
 GKT  CONST_22  N1   C11  C10  C9    180.00   0.0  0
 GKT  CONST_23  N1   C11  C19  N3      0.00   0.0  0
 GKT  CONST_24  I    C6   C1   C2    180.00   0.0  0
 GKT  CONST_25  C7   C4   C3   C2    180.00   0.0  0
 GKT  CONST_26  C    C1   C2   C3    180.00   0.0  0
 GKT  CONST_27  I    C6   C5   C4    180.00   0.0  0
 GKT  CONST_28  C    C1   C6   C5    180.00   0.0  0
 GKT  CONST_29  C7   C4   C5   C6    180.00   0.0  0
 GKT  CONST_30  C19  C20  C8   N     180.00   0.0  0
 GKT  CONST_31  C10  C9   C8   N     180.00   0.0  0
 GKT  CONST_32  C13  C12  N3   C19   180.00   0.0  0
 GKT  CONST_33  C13  C12  N1   C11   180.00   0.0  0
 GKT  CONST_34  H2   C3   C2   C1    180.00   0.0  0
 GKT  CONST_35  H3   C5   C6   C1    180.00   0.0  0
 GKT  CONST_36  H1   C2   C3   C4    180.00   0.0  0
 GKT  CONST_37  H9   C10  C9   C8    180.00   0.0  0
 GKT  CONST_38  H10  C9   C8   C20   180.00   0.0  0
 GKT  CONST_39  H11  N3   C19  C20     0.00   0.0  0
 GKT  CONST_40  H8   C20  C19  C11   180.00   0.0  0
 GKT  CONST_41  C8   N    C7   C4    180.00   0.0  0
 GKT  CONST_42  C20  C8   N    C7      0.00   0.0  0
 GKT  CONST_43  C9   C8   N    C7    180.00   0.0  0
 GKT  CONST_44  H7   N    C8   C20   180.00   0.0  0
 GKT  CONST_45  C8   N    C7   O       0.00   0.0  0
 GKT  Var_01    C16  C17  C18  N2     56.28  30.0  1
 GKT  Var_02    C16  C15  C14  N2    -56.67  30.0  1
 GKT  Var_03    C15  C14  N2   C18    59.62  30.0  1
 GKT  Var_04    C15  C16  C17  C18   -53.12  30.0  1
 GKT  Var_05    C14  N2   C18  C17   -59.34  30.0  1
 GKT  Var_06    C14  C15  C16  C17    53.25  30.0  1
 GKT  Var_07    N2   C13  C12  N3     34.27  30.0  2
 GKT  Var_08    C18  N2   C13  C12  -162.16  30.0  3
 GKT  Var_09    O    C7   C4   C3     27.95  30.0  2
 GKT  Var_10    H4   C    C1   C2   -117.86  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
 GKT  plan-1  C1   0.020
 GKT  plan-1  C2   0.020
 GKT  plan-1  C3   0.020
 GKT  plan-1  C4   0.020
 GKT  plan-1  C5   0.020
 GKT  plan-1  C6   0.020
 GKT  plan-1  C7   0.020
 GKT  plan-1  I    0.020
 GKT  plan-1  C    0.020
 GKT  plan-1  H1   0.020
 GKT  plan-1  H2   0.020
 GKT  plan-1  H3   0.020
 GKT  plan-2  N    0.020
 GKT  plan-2  C8   0.020
 GKT  plan-2  C20  0.020
 GKT  plan-2  C19  0.020
 GKT  plan-2  C11  0.020
 GKT  plan-2  C10  0.020
 GKT  plan-2  C9   0.020
 GKT  plan-2  N3   0.020
 GKT  plan-2  C12  0.020
 GKT  plan-2  N1   0.020
 GKT  plan-2  C13  0.020
 GKT  plan-2  H8   0.020
 GKT  plan-2  H9   0.020
 GKT  plan-2  H10  0.020
 GKT  plan-2  H11  0.020
 GKT  plan-3  C4   0.020
 GKT  plan-3  C7   0.020
 GKT  plan-3  O    0.020
 GKT  plan-3  N    0.020
 GKT  plan-3  C8   0.020
 GKT  plan-3  H7   0.020

