# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:29:21 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: (2E,5R)-5-(2-cyclohexylethyl)-5-{[(1S,3R)-3-(cyclopentylamino)cyclohexyl]methyl}-2-imino-3-methylimidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@](CCC2CCCCC2)(C[C@H]3CCC[C@H](C3)NC4CCCC4)C1=O
#
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
 3KT  3KT  (2E,5R)-5-(2-cyclohexylethyl)-5-{[(1S,3R)-3-(cyclopentylamino)cyclohexyl]methyl}-2-imino-3-methylimidazolidin-4-one  ligand  71  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3KT
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
 3KT  C12  C  CH1   0  -0.060   3.4694   1.0233   0.1342
 3KT  C13  C  CH1   0  -0.229   1.0982   1.8538  -0.2855
 3KT  C3   C  CR5   0   0.547  -0.7576  -0.6449   0.6968
 3KT  C1   C  CR5   0   0.602  -0.5435  -1.3296  -1.4729
 3KT  C4   C  CR5   0  -0.008  -1.1646   0.5223  -0.1893
 3KT  C7   C  CH2   0  -0.395  -0.3745   1.8045   0.1185
 3KT  N2   N  NR5   0  -0.523  -0.4280  -1.6807  -0.1227
 3KT  C9   C  CH2   0  -0.411  -2.6654   0.7988   0.0239
 3KT  C11  C  CH3   0  -0.558   0.0095  -2.9822   0.3164
 3KT  N6   N  NR15  0  -0.658  -0.8781  -0.0138  -1.4987
 3KT  O8   O  O     0  -0.443  -0.7569  -0.6607   1.9073
 3KT  N10  N  NH1   0  -0.611   4.2289   0.0489   0.9042
 3KT  C14  C  CH2   0  -0.425   1.9942   0.9062   0.5125
 3KT  C15  C  CH2   0  -0.428  -3.5895  -0.3943  -0.1908
 3KT  C16  C  CR15  0  -0.045   5.5999  -0.1730   0.4678
 3KT  C17  C  CH1   0  -0.223  -5.0730  -0.0265  -0.1489
 3KT  C18  C  CH2   0  -0.433   3.0751   3.4184  -0.5353
 3KT  C19  C  CH2   0  -0.440   3.9471   2.4688   0.2775
 3KT  C20  C  CH2   0  -0.417   1.6074   3.2907  -0.1487
 3KT  C21  C  CH2   0  -0.457   5.6496  -0.8068  -0.9382
 3KT  C22  C  CH2   0  -0.462   6.3053  -1.1931   1.3924
 3KT  C23  C  CH2   0  -0.424  -5.5148   0.4624   1.2311
 3KT  C24  C  CH2   0  -0.413  -5.9340  -1.2133  -0.5845
 3KT  C25  C  CH2   0  -0.432  -7.4243  -0.8909  -0.5425
 3KT  C26  C  CH2   0  -0.445   6.7019  -1.9107  -0.8503
 3KT  C27  C  CH2   0  -0.437   6.4875  -2.4607   0.5560
 3KT  C28  C  CH2   0  -0.427  -7.0053   0.7869   1.2779
 3KT  C29  C  CH2   0  -0.429  -7.8484  -0.4055   0.8390
 3KT  H1   H  HCH1  0   0.219   3.5560   0.7422  -0.9230
 3KT  H2   H  HCH1  0   0.215   1.1716   1.5764  -1.3442
 3KT  H3   H  HCH2  0   0.233  -0.4754   2.0149   1.1878
 3KT  H4   H  HCH2  0   0.238  -0.8924   2.6217  -0.3950
 3KT  H5   H  HCH2  0   0.242  -2.7856   1.1974   1.0337
 3KT  H6   H  HCH2  0   0.241  -2.9499   1.6054  -0.6598
 3KT  H7   H  HCH3  0   0.263  -0.6686  -3.7591  -0.0354
 3KT  H8   H  HCH3  0   0.261   1.0148  -3.1940  -0.0466
 3KT  H9   H  HCH3  0   0.275   0.0208  -3.0000   1.4020
 3KT  H10  H  H     0   0.344  -0.1130  -3.0130  -2.2448
 3KT  H12  H  HNH1  0   0.328   4.2429   0.3523   1.8727
 3KT  H14  H  HCH2  0   0.226   1.7081  -0.1355   0.3585
 3KT  H15  H  HCH2  0   0.204   1.8763   1.1124   1.5843
 3KT  H16  H  HCH2  0   0.227  -3.3737  -0.8487  -1.1627
 3KT  H17  H  HCH2  0   0.220  -3.4024  -1.1656   0.5650
 3KT  H18  H  HCR5  0   0.200   6.1874   0.7569   0.4615
 3KT  H19  H  HCH1  0   0.206  -5.2391   0.7887  -0.8672
 3KT  H20  H  HCH2  0   0.226   3.4097   4.4499  -0.4005
 3KT  H21  H  HCH2  0   0.210   3.1908   3.1932  -1.6014
 3KT  H22  H  HCH2  0   0.203   3.9078   2.7503   1.3375
 3KT  H23  H  HCH2  0   0.229   4.9919   2.5616  -0.0314
 3KT  H24  H  HCH2  0   0.226   0.9984   3.9574  -0.7657
 3KT  H25  H  HCH2  0   0.207   1.4745   3.6219   0.8884
 3KT  H26  H  HCH2  0   0.223   4.6754  -1.2559  -1.1525
 3KT  H27  H  HCH2  0   0.228   5.8499  -0.0790  -1.7261
 3KT  H28  H  HCH2  0   0.223   7.2831  -0.8058   1.6861
 3KT  H29  H  HCH2  0   0.228   5.7428  -1.3684   2.3121
 3KT  H30  H  HCH2  0   0.203  -5.2942  -0.3204   1.9681
 3KT  H31  H  HCH2  0   0.229  -4.9387   1.3411   1.5327
 3KT  H32  H  HCH2  0   0.223  -5.6468  -1.5269  -1.5925
 3KT  H33  H  HCH2  0   0.203  -5.7265  -2.0638   0.0766
 3KT  H34  H  HCH2  0   0.207  -7.6450  -0.1123  -1.2816
 3KT  H35  H  HCH2  0   0.224  -8.0069  -1.7682  -0.8350
 3KT  H36  H  HCH2  0   0.228   6.5938  -2.6612  -1.6350
 3KT  H37  H  HCH2  0   0.226   7.3050  -3.0906   0.9105
 3KT  H38  H  HCH2  0   0.224  -7.2861   1.1006   2.2864
 3KT  H39  H  HCH2  0   0.207  -7.2138   1.6375   0.6191
 3KT  H40  H  HCH2  0   0.224  -8.9093  -0.1431   0.8418
 3KT  H41  H  HCH2  0   0.207  -7.7262  -1.2198   1.5615
 3KT  H11  H  HNR5  0   0.394  -1.2590   0.3901  -2.3385
 3KT  H13  H  HCH2  0   0.215   7.7089  -1.4917  -0.9376
 3KT  H42  H  HCH2  0   0.216   5.5764  -3.0654   0.5774
 3KT  N5   N  N     0  -0.689  -0.3640  -2.0644  -2.4931

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
 3KT  C18  C20  single  1.523  0.020  1.523
 3KT  C18  C19  single  1.524  0.020  1.524
 3KT  C20  C13  single  1.531  0.020  1.531
 3KT  C19  C12  single  1.529  0.020  1.529
 3KT  C13  C7   single  1.528  0.020  1.528
 3KT  C13  C14  single  1.529  0.020  1.529
 3KT  C12  C14  single  1.527  0.020  1.527
 3KT  C12  N10  single  1.456  0.020  1.456
 3KT  C21  C16  single  1.543  0.020  1.543
 3KT  C21  C26  single  1.528  0.020  1.528
 3KT  C7   C4   single  1.537  0.020  1.537
 3KT  C16  N10  single  1.456  0.020  1.456
 3KT  C16  C22  single  1.547  0.020  1.547
 3KT  C26  C27  single  1.525  0.020  1.525
 3KT  C22  C27  single  1.530  0.020  1.530
 3KT  C4   C9   single  1.541  0.020  1.541
 3KT  C4   N6   single  1.444  0.020  1.444
 3KT  C4   C3   single  1.521  0.020  1.521
 3KT  C9   C15  single  1.524  0.020  1.524
 3KT  N6   C1   single  1.358  0.020  1.358
 3KT  C23  C28  single  1.526  0.020  1.526
 3KT  C23  C17  single  1.529  0.020  1.529
 3KT  C28  C29  single  1.525  0.020  1.525
 3KT  O8   C3   double  1.211  0.020  1.211
 3KT  C3   N2   single  1.361  0.020  1.361
 3KT  C17  C15  single  1.529  0.020  1.529
 3KT  C17  C24  single  1.530  0.020  1.530
 3KT  C1   N2   single  1.400  0.020  1.400
 3KT  C1   N5   double  1.270  0.020  1.270
 3KT  N2   C11  single  1.442  0.020  1.442
 3KT  C29  C25  single  1.524  0.020  1.524
 3KT  C24  C25  single  1.525  0.020  1.525
 3KT  C12  H1   single  0.970  0.020  1.090
 3KT  C13  H2   single  0.970  0.020  1.090
 3KT  C7   H3   single  0.970  0.020  1.090
 3KT  C7   H4   single  0.970  0.020  1.090
 3KT  C9   H5   single  0.970  0.020  1.090
 3KT  C9   H6   single  0.970  0.020  1.090
 3KT  C11  H7   single  0.970  0.020  1.090
 3KT  C11  H8   single  0.970  0.020  1.090
 3KT  C11  H9   single  0.970  0.020  1.090
 3KT  N5   H10  single  0.890  0.020  1.040
 3KT  N10  H12  single  0.890  0.020  1.040
 3KT  C14  H14  single  0.970  0.020  1.090
 3KT  C14  H15  single  0.970  0.020  1.090
 3KT  C15  H16  single  0.970  0.020  1.090
 3KT  C15  H17  single  0.970  0.020  1.090
 3KT  C16  H18  single  0.970  0.020  1.090
 3KT  C17  H19  single  0.970  0.020  1.090
 3KT  C18  H20  single  0.970  0.020  1.090
 3KT  C18  H21  single  0.970  0.020  1.090
 3KT  C19  H22  single  0.970  0.020  1.090
 3KT  C19  H23  single  0.970  0.020  1.090
 3KT  C20  H24  single  0.970  0.020  1.090
 3KT  C20  H25  single  0.970  0.020  1.090
 3KT  C21  H26  single  0.970  0.020  1.090
 3KT  C21  H27  single  0.970  0.020  1.090
 3KT  C22  H28  single  0.970  0.020  1.090
 3KT  C22  H29  single  0.970  0.020  1.090
 3KT  C23  H30  single  0.970  0.020  1.090
 3KT  C23  H31  single  0.970  0.020  1.090
 3KT  C24  H32  single  0.970  0.020  1.090
 3KT  C24  H33  single  0.970  0.020  1.090
 3KT  C25  H34  single  0.970  0.020  1.090
 3KT  C25  H35  single  0.970  0.020  1.090
 3KT  C26  H36  single  0.970  0.020  1.090
 3KT  C27  H37  single  0.970  0.020  1.090
 3KT  C28  H38  single  0.970  0.020  1.090
 3KT  C28  H39  single  0.970  0.020  1.090
 3KT  C29  H40  single  0.970  0.020  1.090
 3KT  C29  H41  single  0.970  0.020  1.090
 3KT  N6   H11  single  0.890  0.020  1.040
 3KT  C26  H13  single  0.970  0.020  1.090
 3KT  C27  H42  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
 3KT  H1   C12  C19  107.92  3.000
 3KT  H1   C12  C14  107.16  3.000
 3KT  C19  C12  C14  110.55  3.000
 3KT  H1   C12  N10  107.28  3.000
 3KT  C14  C12  N10  108.76  3.000
 3KT  C19  C12  N10  114.85  3.000
 3KT  H2   C13  C20  107.54  3.000
 3KT  H2   C13  C14  107.92  3.000
 3KT  C20  C13  C14  109.89  3.000
 3KT  H2   C13  C7   108.15  3.000
 3KT  C14  C13  C7   114.01  3.000
 3KT  C20  C13  C7   109.11  3.000
 3KT  O8   C3   N2   126.29  3.000
 3KT  N2   C3   C4   107.33  3.000
 3KT  O8   C3   C4   126.35  3.000
 3KT  N6   C1   N5   125.47  3.000
 3KT  N5   C1   N2   128.17  3.000
 3KT  N6   C1   N2   106.36  3.000
 3KT  N6   C4   C9   112.67  3.000
 3KT  N6   C4   C7   112.91  3.000
 3KT  C9   C4   C7   108.86  3.000
 3KT  N6   C4   C3   100.97  3.000
 3KT  C9   C4   C3   108.53  3.000
 3KT  C7   C4   C3   112.70  3.000
 3KT  H4   C7   H3   105.72  3.000
 3KT  H4   C7   C4   106.58  3.000
 3KT  H3   C7   C4   107.97  3.000
 3KT  H4   C7   C13  107.93  3.000
 3KT  H3   C7   C13  109.94  3.000
 3KT  C4   C7   C13  118.00  3.000
 3KT  C11  N2   C1   123.04  3.000
 3KT  C11  N2   C3   125.24  3.000
 3KT  C1   N2   C3   111.71  3.000
 3KT  H6   C9   H5   106.25  3.000
 3KT  H6   C9   C15  109.33  3.000
 3KT  H5   C9   C15  110.44  3.000
 3KT  H6   C9   C4   107.39  3.000
 3KT  H5   C9   C4   107.49  3.000
 3KT  C15  C9   C4   115.50  3.000
 3KT  H9   C11  H8   108.69  3.000
 3KT  H9   C11  H7   108.52  3.000
 3KT  H8   C11  H7   109.15  3.000
 3KT  H9   C11  N2   108.81  3.000
 3KT  H8   C11  N2   110.73  3.000
 3KT  H7   C11  N2   110.88  3.000
 3KT  H11  N6   C4   122.18  3.000
 3KT  H11  N6   C1   119.86  3.000
 3KT  C4   N6   C1   113.05  3.000
 3KT  H12  N10  C16  108.57  3.000
 3KT  H12  N10  C12  108.17  3.000
 3KT  C16  N10  C12  115.77  3.000
 3KT  H15  C14  H14  106.79  3.000
 3KT  H15  C14  C13  109.28  3.000
 3KT  H14  C14  C13  111.37  3.000
 3KT  H15  C14  C12  109.34  3.000
 3KT  H14  C14  C12  106.95  3.000
 3KT  C13  C14  C12  112.91  3.000
 3KT  H17  C15  H16  106.66  3.000
 3KT  H17  C15  C17  108.42  3.000
 3KT  H16  C15  C17  108.40  3.000
 3KT  H17  C15  C9   110.50  3.000
 3KT  H16  C15  C9   109.30  3.000
 3KT  C17  C15  C9   113.33  3.000
 3KT  H18  C16  C22  108.51  3.000
 3KT  H18  C16  C21  108.95  3.000
 3KT  C22  C16  C21  105.01  3.000
 3KT  H18  C16  N10  112.08  3.000
 3KT  C22  C16  N10  110.53  3.000
 3KT  C21  C16  N10  111.48  3.000
 3KT  H19  C17  C24  107.71  3.000
 3KT  H19  C17  C23  108.00  3.000
 3KT  C24  C17  C23  110.02  3.000
 3KT  H19  C17  C15  107.89  3.000
 3KT  C24  C17  C15  110.59  3.000
 3KT  C23  C17  C15  112.46  3.000
 3KT  H21  C18  H20  106.36  3.000
 3KT  H21  C18  C20  109.36  3.000
 3KT  H20  C18  C20  110.06  3.000
 3KT  H21  C18  C19  109.29  3.000
 3KT  H20  C18  C19  110.31  3.000
 3KT  C20  C18  C19  111.33  3.000
 3KT  H23  C19  H22  106.58  3.000
 3KT  H23  C19  C18  110.07  3.000
 3KT  H22  C19  C18  109.56  3.000
 3KT  H23  C19  C12  110.63  3.000
 3KT  H22  C19  C12  108.77  3.000
 3KT  C18  C19  C12  111.12  3.000
 3KT  H25  C20  H24  106.37  3.000
 3KT  H25  C20  C18  109.36  3.000
 3KT  H24  C20  C18  110.01  3.000
 3KT  H25  C20  C13  109.13  3.000
 3KT  H24  C20  C13  109.67  3.000
 3KT  C18  C20  C13  112.13  3.000
 3KT  H27  C21  H26  107.20  3.000
 3KT  H27  C21  C26  113.40  3.000
 3KT  H26  C21  C26  109.16  3.000
 3KT  H27  C21  C16  112.95  3.000
 3KT  H26  C21  C16  108.57  3.000
 3KT  C26  C21  C16  105.46  3.000
 3KT  H29  C22  H28  106.95  3.000
 3KT  H29  C22  C27  112.88  3.000
 3KT  H28  C22  C27  109.53  3.000
 3KT  H29  C22  C16  111.98  3.000
 3KT  H28  C22  C16  109.58  3.000
 3KT  C27  C22  C16  105.90  3.000
 3KT  H31  C23  H30  106.38  3.000
 3KT  H31  C23  C28  109.59  3.000
 3KT  H30  C23  C28  109.11  3.000
 3KT  H31  C23  C17  110.71  3.000
 3KT  H30  C23  C17  108.66  3.000
 3KT  C28  C23  C17  112.20  3.000
 3KT  H33  C24  H32  106.46  3.000
 3KT  H33  C24  C25  109.39  3.000
 3KT  H32  C24  C25  110.02  3.000
 3KT  H33  C24  C17  108.87  3.000
 3KT  H32  C24  C17  109.70  3.000
 3KT  C25  C24  C17  112.22  3.000
 3KT  H35  C25  H34  106.40  3.000
 3KT  H35  C25  C29  110.48  3.000
 3KT  H34  C25  C29  109.21  3.000
 3KT  H35  C25  C24  110.11  3.000
 3KT  H34  C25  C24  109.16  3.000
 3KT  C29  C25  C24  111.35  3.000
 3KT  H13  C26  H36  107.29  3.000
 3KT  H13  C26  C27  109.94  3.000
 3KT  H36  C26  C27  113.65  3.000
 3KT  H13  C26  C21  110.65  3.000
 3KT  H36  C26  C21  112.79  3.000
 3KT  C27  C26  C21  102.52  3.000
 3KT  H42  C27  H37  107.36  3.000
 3KT  H42  C27  C26  109.55  3.000
 3KT  H37  C27  C26  113.73  3.000
 3KT  H42  C27  C22  110.39  3.000
 3KT  H37  C27  C22  112.95  3.000
 3KT  C26  C27  C22  102.83  3.000
 3KT  H39  C28  H38  106.45  3.000
 3KT  H39  C28  C29  109.20  3.000
 3KT  H38  C28  C29  110.37  3.000
 3KT  H39  C28  C23  109.41  3.000
 3KT  H38  C28  C23  109.89  3.000
 3KT  C29  C28  C23  111.40  3.000
 3KT  H41  C29  H40  106.56  3.000
 3KT  H41  C29  C28  109.26  3.000
 3KT  H40  C29  C28  110.37  3.000
 3KT  H41  C29  C25  109.27  3.000
 3KT  H40  C29  C25  110.41  3.000
 3KT  C28  C29  C25  110.85  3.000
 3KT  H10  N5   C1   112.35  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
 3KT  CONST_01  N6   C1   N2   C3      0.00   0.0  0
 3KT  CONST_02  C4   C3   N2   C1      0.00   0.0  0
 3KT  CONST_03  N2   C1   N6   C4      0.00   0.0  0
 3KT  CONST_04  N5   C1   N2   C3    180.00   0.0  0
 3KT  CONST_05  O8   C3   N2   C1    180.00   0.0  0
 3KT  CONST_06  N5   C1   N6   C4    180.00   0.0  0
 3KT  CONST_07  C11  N2   C3   C4    180.00   0.0  0
 3KT  CONST_08  N6   C1   N2   C11   180.00   0.0  0
 3KT  CONST_10  O8   C3   N2   C11     0.00   0.0  0
 3KT  CONST_11  N5   C1   N2   C11     0.00   0.0  0
 3KT  CONST_12  H10  N5   C1   N2      0.00   0.0  0
 3KT  Var_01    C20  C18  C19  C12    55.87  30.0  1
 3KT  Var_02    C19  C18  C20  C13   -55.89  30.0  1
 3KT  Var_03    C27  C26  C21  C16    36.70  30.0  1
 3KT  Var_04    C26  C27  C22  C16    33.09  30.0  1
 3KT  Var_05    C29  C28  C23  C17    55.54  30.0  1
 3KT  Var_06    C29  C25  C24  C17   -55.68  30.0  1
 3KT  Var_07    C22  C27  C26  C21   -42.87  30.0  1
 3KT  Var_08    C25  C29  C28  C23   -55.16  30.0  1
 3KT  Var_09    C28  C29  C25  C24    55.22  30.0  1
 3KT  Var_10    C17  C15  C9   C4   -172.38  30.0  3
 3KT  Var_11    H7   C11  N2   C3    119.91  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3KT  chir_01  C12  C19  C14  N10  positiv
 3KT  chir_02  C13  C14  C7   C20  negativ
 3KT  chir_03  C4   C3   N6   C7   positiv
 3KT  chir_04  C16  N10  C21  C22  positiv
 3KT  chir_05  C17  C23  C15  C24  negativ

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
 3KT  plan-1  C3   0.020
 3KT  plan-1  C1   0.020
 3KT  plan-1  C4   0.020
 3KT  plan-1  N2   0.020
 3KT  plan-1  C11  0.020
 3KT  plan-1  N6   0.020
 3KT  plan-1  O8   0.020
 3KT  plan-1  H10  0.020
 3KT  plan-1  H11  0.020
 3KT  plan-1  N5   0.020

