data_Y5U
# 
_chem_comp.id                                    Y5U 
_chem_comp.name                                  "(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H16 N8 Se" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_chem_comp.pdbx_modified_date                    2024-06-07 
_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                        447.355 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y5U 
_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        8T4N 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
Y5U C1  C1  C  0 1 N N N N N N 14.473 26.552 0.361  8.505   1.281  -0.004 C1  Y5U 1  
Y5U C2  C2  C  0 1 Y N N N N N 13.439 26.669 1.432  7.285   0.446  -0.003 C2  Y5U 2  
Y5U C3  C3  C  0 1 Y N N N N N 12.699 27.857 1.544  7.395   -0.950 -0.001 C3  Y5U 3  
Y5U C4  C4  C  0 1 Y N N N N N 11.733 28.023 2.505  6.280   -1.733 -0.000 C4  Y5U 4  
Y5U C5  C5  C  0 1 Y N N N N N 11.512 26.985 3.411  5.008   -1.143 -0.001 C5  Y5U 5  
Y5U C6  C6  C  0 1 Y N N N N N 10.818 25.657 5.027  2.882   -0.669 -0.002 C6  Y5U 6  
Y5U C7  C7  C  0 1 Y N N N N N 10.071 25.141 6.164  1.428   -0.839 -0.002 C7  Y5U 7  
Y5U C8  C8  C  0 1 Y N N N N N 8.843  25.566 6.689  0.694   -1.988 0.000  C8  Y5U 8  
Y5U C9  C9  C  0 1 Y N N N N N 8.374  24.854 7.811  -0.685  -1.989 -0.000 C9  Y5U 9  
Y5U C10 C10 C  0 1 Y N N N N N 9.205  23.840 8.269  -1.420  -0.840 -0.002 C10 Y5U 10 
Y5U C11 C11 C  0 1 Y N N N N N 9.007  22.970 9.414  -2.874  -0.672 -0.002 C11 Y5U 11 
Y5U C12 C12 C  0 1 Y N N N N N 8.046  21.937 11.086 -4.999  -1.148 0.000  C12 Y5U 12 
Y5U C13 C13 C  0 1 Y N N N N N 7.164  21.433 12.038 -6.271  -1.739 -0.001 C13 Y5U 13 
Y5U C14 C14 C  0 1 Y N N N N N 7.662  20.588 12.994 -7.386  -0.958 -0.002 C14 Y5U 14 
Y5U C15 C15 C  0 1 Y N N N N N 9.018  20.251 13.042 -7.278  0.439  -0.001 C15 Y5U 15 
Y5U C16 C16 C  0 1 N N N N N N 9.468  19.341 14.125 -8.498  1.274  -0.002 C16 Y5U 16 
Y5U C17 C17 C  0 1 Y N N N N N 9.902  20.746 12.090 -6.023  1.043  -0.000 C17 Y5U 17 
Y5U C18 C18 C  0 1 Y N N N N N 9.400  21.586 11.116 -4.884  0.256  0.001  C18 Y5U 18 
Y5U C19 C19 C  0 1 Y N N N N N 12.255 25.806 3.320  4.891   0.261  -0.002 C19 Y5U 19 
Y5U C20 C20 C  0 1 Y N N N N N 13.223 25.632 2.338  6.029   1.049  0.002  C20 Y5U 20 
Y5U SE1 SE1 SE 0 0 Y N N N N N 10.733 23.738 7.205  0.004   0.540  0.005  SE1 Y5U 21 
Y5U N1  N1  N  0 1 N N N N N N 15.175 27.554 -0.063 8.404   2.581  -0.006 N1  Y5U 22 
Y5U N2  N2  N  0 1 N N N N N N 14.645 25.353 -0.246 9.748   0.686  0.003  N2  Y5U 23 
Y5U N3  N3  N  0 1 Y N N N N N 10.606 26.900 4.457  3.760   -1.649 -0.001 N3  Y5U 24 
Y5U N4  N4  N  0 1 Y N N N N N 7.799  22.809 10.039 -3.751  -1.653 0.001  N4  Y5U 25 
Y5U N5  N5  N  0 1 N N N N N N 8.638  18.561 14.727 -8.399  2.573  -0.001 N5  Y5U 26 
Y5U N6  N6  N  0 1 N N N N N N 10.745 19.439 14.529 -9.741  0.677  -0.003 N6  Y5U 27 
Y5U N7  N7  N  0 1 Y N N N N N 9.977  22.267 10.074 -3.530  0.534  0.002  N7  Y5U 28 
Y5U N8  N8  N  0 1 Y N N N N N 11.795 24.997 4.339  3.537   0.537  -0.003 N8  Y5U 29 
Y5U H4  H1  H  0 1 N N N N N N 12.896 28.664 0.854  8.372   -1.411 -0.000 H4  Y5U 30 
Y5U H5  H2  H  0 1 N N N N N N 11.158 28.935 2.559  6.376   -2.809 0.000  H5  Y5U 31 
Y5U H6  H3  H  0 1 N N N N N N 8.290  26.389 6.260  1.214   -2.935 0.002  H6  Y5U 32 
Y5U H7  H4  H  0 1 N N N N N N 7.430  25.082 8.284  -1.203  -2.936 0.001  H7  Y5U 33 
Y5U H8  H5  H  0 1 N N N N N N 6.118  21.700 12.023 -6.366  -2.815 -0.002 H8  Y5U 34 
Y5U H9  H6  H  0 1 N N N N N N 6.990  20.171 13.730 -8.363  -1.419 -0.003 H9  Y5U 35 
Y5U H13 H7  H  0 1 N N N N N N 10.949 20.482 12.112 -5.939  2.120  -0.000 H13 Y5U 36 
Y5U H16 H8  H  0 1 N N N N N N 13.793 24.717 2.278  5.944   2.126  0.006  H16 Y5U 37 
Y5U H1  H9  H  0 1 N N N N N N 14.940 28.403 0.411  7.529   3.000  -0.006 H1  Y5U 38 
Y5U H2  H10 H  0 1 N N N N N N 14.085 24.570 0.026  9.823   -0.281 0.008  H2  Y5U 39 
Y5U H3  H11 H  0 1 N N N N N N 15.332 25.251 -0.966 10.548  1.234  0.002  H3  Y5U 40 
Y5U H10 H14 H  0 1 N N N N N N 9.066  18.075 15.489 -9.200  3.121  -0.002 H10 Y5U 41 
Y5U H12 H15 H  0 1 N N N N N N 11.065 18.901 15.309 -9.815  -0.290 -0.003 H12 Y5U 42 
Y5U H11 H16 H  0 1 N N N N N N 11.376 20.050 14.050 -10.542 1.225  -0.003 H11 Y5U 43 
Y5U H14 H17 H  0 1 N N N N N N 10.948 22.252 9.836  -3.121  1.413  0.005  H14 Y5U 44 
Y5U H15 H18 H  0 1 N N N N N N 12.125 24.075 4.541  3.127   1.416  -0.004 H15 Y5U 45 
# 
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 
Y5U N2  C1  SING N N 1  
Y5U N1  C1  DOUB N N 2  
Y5U C1  C2  SING N N 3  
Y5U C2  C3  DOUB Y N 4  
Y5U C2  C20 SING Y N 5  
Y5U C3  C4  SING Y N 6  
Y5U C20 C19 DOUB Y N 7  
Y5U C4  C5  DOUB Y N 8  
Y5U C19 C5  SING Y N 9  
Y5U C19 N8  SING Y N 10 
Y5U C5  N3  SING Y N 11 
Y5U N8  C6  SING Y N 12 
Y5U N3  C6  DOUB Y N 13 
Y5U C6  C7  SING N N 14 
Y5U C7  C8  DOUB Y N 15 
Y5U C7  SE1 SING Y N 16 
Y5U C8  C9  SING Y N 17 
Y5U SE1 C10 SING Y N 18 
Y5U C9  C10 DOUB Y N 19 
Y5U C10 C11 SING N N 20 
Y5U C11 N4  DOUB Y N 21 
Y5U C11 N7  SING Y N 22 
Y5U N4  C12 SING Y N 23 
Y5U N7  C18 SING Y N 24 
Y5U C12 C18 DOUB Y N 25 
Y5U C12 C13 SING Y N 26 
Y5U C18 C17 SING Y N 27 
Y5U C13 C14 DOUB Y N 28 
Y5U C17 C15 DOUB Y N 29 
Y5U C14 C15 SING Y N 30 
Y5U C15 C16 SING N N 31 
Y5U C16 N6  SING N N 32 
Y5U C16 N5  DOUB N N 33 
Y5U C3  H4  SING N N 34 
Y5U C4  H5  SING N N 35 
Y5U C8  H6  SING N N 36 
Y5U C9  H7  SING N N 37 
Y5U C13 H8  SING N N 38 
Y5U C14 H9  SING N N 39 
Y5U C17 H13 SING N N 40 
Y5U C20 H16 SING N N 41 
Y5U N1  H1  SING N N 42 
Y5U N2  H2  SING N N 43 
Y5U N2  H3  SING N N 44 
Y5U N5  H10 SING N N 45 
Y5U N6  H12 SING N N 46 
Y5U N6  H11 SING N N 47 
Y5U N7  H14 SING N N 48 
Y5U N8  H15 SING N N 49 
# 
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 
Y5U SMILES           ACDLabs              12.01 "N=C(N)c1ccc2nc([NH]c2c1)c1ccc([se]1)c1[NH]c2cc(ccc2n1)C(=N)N"                                                                                                  
Y5U InChI            InChI                1.06  "InChI=1S/C20H16N8Se/c21-17(22)9-1-3-11-13(7-9)27-19(25-11)15-5-6-16(29-15)20-26-12-4-2-10(18(23)24)8-14(12)28-20/h1-8H,(H3,21,22)(H3,23,24)(H,25,27)(H,26,28)" 
Y5U InChIKey         InChI                1.06  NXECULIQZLOKFU-UHFFFAOYSA-N                                                                                                                                     
Y5U SMILES_CANONICAL CACTVS               3.385 "NC(=N)c1ccc2nc([nH]c2c1)c3[se]c(cc3)c4[nH]c5cc(ccc5n4)C(N)=N"                                                                                                  
Y5U SMILES           CACTVS               3.385 "NC(=N)c1ccc2nc([nH]c2c1)c3[se]c(cc3)c4[nH]c5cc(ccc5n4)C(N)=N"                                                                                                  
Y5U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\N)/c1cc2[nH]c(nc2cc1)c3[se]c(cc3)c4nc5c([nH]4)cc(cc5)/C(=N\[H])/N"                                                                                    
Y5U SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1C(=N)N)[nH]c(n2)c3ccc([se]3)c4[nH]c5cc(ccc5n4)C(=N)N"                                                                                                
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
Y5U "SYSTEMATIC NAME" ACDLabs              12.01 "(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)"                           
Y5U "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[5-(6-carbamimidoyl-1~{H}-benzimidazol-2-yl)selenophen-2-yl]-3~{H}-benzimidazole-5-carboximidamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y5U "Create component" 2023-06-12 RCSB 
Y5U "Initial release"  2024-06-12 RCSB 
# 
