data_5XI
#

_chem_comp.id                                   5XI
_chem_comp.name                                 "methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H28 N4 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-08-25
_chem_comp.pdbx_modified_date                   2022-05-06
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       372.461
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5XI
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7V6A
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
5XI  C14  C1   C  0  1  N  N  N  130.790  133.684  152.859  -1.678   1.758   0.010  C14  5XI   1  
5XI  C13  C2   C  0  1  N  N  N  129.907  133.894  149.624   1.899   2.910  -0.226  C13  5XI   2  
5XI  C12  C3   C  0  1  N  N  N  129.668  133.094  150.920   0.601   2.451   0.442  C12  5XI   3  
5XI  C16  C4   C  0  1  N  N  N  131.844  134.174  155.064  -4.064   1.198  -0.472  C16  5XI   4  
5XI  C17  C5   C  0  1  N  N  N  130.616  136.023  153.760  -2.900   0.213   1.545  C17  5XI   5  
5XI  C19  C6   C  0  1  N  N  N  131.733  136.627  156.057  -4.698  -0.998   0.407  C19  5XI   6  
5XI  C20  C7   C  0  1  N  N  N  131.216  138.760  157.030  -6.431  -2.297  -0.594  C20  5XI   7  
5XI  C11  C8   C  0  1  N  N  N  132.091  132.803  151.082   0.117   0.950  -1.397  C11  5XI   8  
5XI  C8   C9   C  0  1  N  N  N  129.880  134.504  144.231   3.360  -0.968   2.962  C8   5XI   9  
5XI  C6   C10  C  0  1  Y  N  N  131.901  135.261  147.150   3.047  -0.668  -0.675  C6   5XI  10  
5XI  C7   C11  C  0  1  N  N  N  130.347  133.833  146.574   2.860   0.641   1.110  C7   5XI  11  
5XI  C2   C12  C  0  1  Y  N  N  133.498  137.101  146.987   3.404  -2.595  -2.052  C2   5XI  12  
5XI  C5   C13  C  0  1  Y  N  N  131.537  135.509  145.869   3.303  -1.438   0.462  C5   5XI  13  
5XI  C4   C14  C  0  1  Y  N  N  132.133  136.550  145.125   3.609  -2.784   0.330  C4   5XI  14  
5XI  C3   C15  C  0  1  Y  N  N  133.120  137.353  145.694   3.658  -3.358  -0.925  C3   5XI  15  
5XI  C1   C16  C  0  1  Y  N  N  132.912  136.085  147.729   3.105  -1.253  -1.931  C1   5XI  16  
5XI  C10  C17  C  0  1  N  N  N  132.221  133.618  149.763   1.401   1.364  -2.120  C10  5XI  17  
5XI  C15  C18  C  0  1  N  N  N  131.943  133.377  153.746  -2.698   1.491  -1.099  C15  5XI  18  
5XI  C18  C19  C  0  1  N  N  N  130.773  135.154  152.511  -1.547   0.517   0.895  C18  5XI  19  
5XI  C9   C20  C  0  1  N  N  N  131.086  133.433  148.949   2.454   1.772  -1.086  C9   5XI  20  
5XI  N1   N1   N  0  1  N  N  N  130.567  134.604  145.534   3.177  -0.589   1.559  N1   5XI  21  
5XI  N2   N2   N  0  1  N  N  N  131.144  134.197  147.575   2.774   0.624  -0.234  N2   5XI  22  
5XI  N3   N3   N  0  1  N  N  N  130.818  132.913  151.732  -0.374   2.072  -0.588  N3   5XI  23  
5XI  N4   N4   N  0  1  N  N  N  131.682  135.736  154.873  -3.916   0.097   0.490  N4   5XI  24  
5XI  O1   O1   O  0  1  N  N  N  129.563  132.939  146.614   2.678   1.618   1.812  O1   5XI  25  
5XI  O2   O2   O  0  1  N  N  N  131.753  136.166  157.130  -4.567  -1.901   1.209  O2   5XI  26  
5XI  O3   O3   O  0  1  N  N  N  131.741  138.049  155.895  -5.625  -1.090  -0.565  O3   5XI  27  
5XI  H1   H1   H  0  1  N  N  N  129.870  133.470  153.422  -2.013   2.602   0.615  H1   5XI  28  
5XI  H2   H2   H  0  1  N  N  N  130.028  134.958  149.875   1.698   3.777  -0.855  H2   5XI  29  
5XI  H3   H3   H  0  1  N  N  N  129.040  133.770  148.959   2.628   3.177   0.540  H3   5XI  30  
5XI  H4   H4   H  0  1  N  N  N  128.910  133.625  151.515   0.805   1.592   1.082  H4   5XI  31  
5XI  H5   H5   H  0  1  N  N  N  129.286  132.100  150.643   0.195   3.264   1.045  H5   5XI  32  
5XI  H6   H6   H  0  1  N  N  N  130.973  133.804  155.625  -4.428   2.087   0.043  H6   5XI  33  
5XI  H7   H7   H  0  1  N  N  N  132.760  133.992  155.646  -4.770   0.912  -1.251  H7   5XI  34  
5XI  H8   H8   H  0  1  N  N  N  130.703  137.078  153.461  -2.838  -0.725   2.097  H8   5XI  35  
5XI  H9   H9   H  0  1  N  N  N  129.617  135.843  154.183  -3.171   1.020   2.226  H9   5XI  36  
5XI  H10  H10  H  0  1  N  N  N  131.253  139.842  156.835  -7.137  -2.243  -1.424  H10  5XI  37  
5XI  H11  H11  H  0  1  N  N  N  130.174  138.455  157.204  -5.783  -3.164  -0.724  H11  5XI  38  
5XI  H12  H12  H  0  1  N  N  N  131.819  138.527  157.920  -6.980  -2.391   0.343  H12  5XI  39  
5XI  H13  H13  H  0  1  N  N  N  132.266  131.742  150.848  -0.639   0.672  -2.131  H13  5XI  40  
5XI  H14  H14  H  0  1  N  N  N  132.864  133.156  151.780   0.324   0.098  -0.749  H14  5XI  41  
5XI  H15  H15  H  0  1  N  N  N  129.151  133.681  144.262   4.404  -0.828   3.243  H15  5XI  42  
5XI  H16  H16  H  0  1  N  N  N  129.357  135.448  144.019   2.727  -0.344   3.592  H16  5XI  43  
5XI  H17  H17  H  0  1  N  N  N  130.620  134.309  143.441   3.085  -2.014   3.094  H17  5XI  44  
5XI  H18  H18  H  0  1  N  N  N  134.269  137.707  147.439   3.450  -3.050  -3.030  H18  5XI  45  
5XI  H19  H19  H  0  1  N  N  N  131.822  136.726  144.106   3.807  -3.382   1.207  H19  5XI  46  
5XI  H20  H20  H  0  1  N  N  N  133.575  138.154  145.130   3.896  -4.406  -1.027  H20  5XI  47  
5XI  H21  H21  H  0  1  N  N  N  133.223  135.917  148.750   2.913  -0.660  -2.813  H21  5XI  48  
5XI  H22  H22  H  0  1  N  N  N  133.115  133.282  149.218   1.774   0.525  -2.708  H22  5XI  49  
5XI  H23  H23  H  0  1  N  N  N  132.320  134.686  150.007   1.192   2.206  -2.780  H23  5XI  50  
5XI  H24  H24  H  0  1  N  N  N  131.947  132.301  153.974  -2.773   2.367  -1.743  H24  5XI  51  
5XI  H25  H25  H  0  1  N  N  N  132.877  133.646  153.231  -2.376   0.632  -1.689  H25  5XI  52  
5XI  H26  H26  H  0  1  N  N  N  131.718  135.414  152.011  -1.236  -0.333   0.287  H26  5XI  53  
5XI  H27  H27  H  0  1  N  N  N  129.931  135.351  151.830  -0.804   0.700   1.671  H27  5XI  54  
5XI  H28  H28  H  0  1  N  N  N  130.972  132.363  148.722   3.356   2.109  -1.598  H28  5XI  55  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
5XI  C8   N1   SING  N  N   1  
5XI  C4   C3   DOUB  Y  N   2  
5XI  C4   C5   SING  Y  N   3  
5XI  N1   C5   SING  N  N   4  
5XI  N1   C7   SING  N  N   5  
5XI  C3   C2   SING  Y  N   6  
5XI  C5   C6   DOUB  Y  N   7  
5XI  C7   O1   DOUB  N  N   8  
5XI  C7   N2   SING  N  N   9  
5XI  C2   C1   DOUB  Y  N  10  
5XI  C6   N2   SING  N  N  11  
5XI  C6   C1   SING  Y  N  12  
5XI  N2   C9   SING  N  N  13  
5XI  C9   C13  SING  N  N  14  
5XI  C9   C10  SING  N  N  15  
5XI  C13  C12  SING  N  N  16  
5XI  C10  C11  SING  N  N  17  
5XI  C12  N3   SING  N  N  18  
5XI  C11  N3   SING  N  N  19  
5XI  N3   C14  SING  N  N  20  
5XI  C18  C14  SING  N  N  21  
5XI  C18  C17  SING  N  N  22  
5XI  C14  C15  SING  N  N  23  
5XI  C15  C16  SING  N  N  24  
5XI  C17  N4   SING  N  N  25  
5XI  N4   C16  SING  N  N  26  
5XI  N4   C19  SING  N  N  27  
5XI  O3   C19  SING  N  N  28  
5XI  O3   C20  SING  N  N  29  
5XI  C19  O2   DOUB  N  N  30  
5XI  C14  H1   SING  N  N  31  
5XI  C13  H2   SING  N  N  32  
5XI  C13  H3   SING  N  N  33  
5XI  C12  H4   SING  N  N  34  
5XI  C12  H5   SING  N  N  35  
5XI  C16  H6   SING  N  N  36  
5XI  C16  H7   SING  N  N  37  
5XI  C17  H8   SING  N  N  38  
5XI  C17  H9   SING  N  N  39  
5XI  C20  H10  SING  N  N  40  
5XI  C20  H11  SING  N  N  41  
5XI  C20  H12  SING  N  N  42  
5XI  C11  H13  SING  N  N  43  
5XI  C11  H14  SING  N  N  44  
5XI  C8   H15  SING  N  N  45  
5XI  C8   H16  SING  N  N  46  
5XI  C8   H17  SING  N  N  47  
5XI  C2   H18  SING  N  N  48  
5XI  C4   H19  SING  N  N  49  
5XI  C3   H20  SING  N  N  50  
5XI  C1   H21  SING  N  N  51  
5XI  C10  H22  SING  N  N  52  
5XI  C10  H23  SING  N  N  53  
5XI  C15  H24  SING  N  N  54  
5XI  C15  H25  SING  N  N  55  
5XI  C18  H26  SING  N  N  56  
5XI  C18  H27  SING  N  N  57  
5XI  C9   H28  SING  N  N  58  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
5XI  InChI             InChI                 1.03   "InChI=1S/C20H28N4O3/c1-21-17-5-3-4-6-18(17)24(19(21)25)16-9-11-22(12-10-16)15-7-13-23(14-8-15)20(26)27-2/h3-6,15-16H,7-14H2,1-2H3"  
5XI  InChIKey          InChI                 1.03   LFVHMTNJDWYMGD-UHFFFAOYSA-N  
5XI  SMILES_CANONICAL  CACTVS                3.385  "COC(=O)N1CCC(CC1)N2CCC(CC2)N3C(=O)N(C)c4ccccc34"  
5XI  SMILES            CACTVS                3.385  "COC(=O)N1CCC(CC1)N2CCC(CC2)N3C(=O)N(C)c4ccccc34"  
5XI  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN1c2ccccc2N(C1=O)C3CCN(CC3)C4CCN(CC4)C(=O)OC"  
5XI  SMILES            "OpenEye OEToolkits"  2.0.7  "CN1c2ccccc2N(C1=O)C3CCN(CC3)C4CCN(CC4)C(=O)OC"  
#
_pdbx_chem_comp_identifier.comp_id          5XI
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5XI  "Create component"  2021-08-25  PDBJ  
5XI  "Initial release"   2022-05-11  RCSB  
##
