data_IC5
# 
_chem_comp.id                                    IC5 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H18 N5 O11 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2022-03-09 
_chem_comp.pdbx_modified_date                    2022-08-22 
_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                        458.235 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     IC5 
_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        7Z43 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
IC5 O6    O1  O 0 1 N N N -97.527  3.014  -22.669 5.875  3.159  0.546  O6    IC5 1  
IC5 N1    N1  N 0 1 N N N -99.310  3.907  -21.592 6.457  1.265  -0.491 N1    IC5 2  
IC5 N2    N2  N 0 1 N N N -101.189 4.652  -20.491 7.027  -0.751 -1.575 N2    IC5 3  
IC5 C2    C1  C 0 1 N N N -99.997  4.938  -21.026 6.087  0.040  -0.961 C2    IC5 4  
IC5 C4    C2  C 0 1 Y N N -98.323  6.337  -21.553 3.904  0.335  -0.248 C4    IC5 5  
IC5 C5    C3  C 0 1 Y N N -97.573  5.335  -22.146 4.235  1.595  0.259  C5    IC5 6  
IC5 C6    C4  C 0 1 N N N -98.069  4.006  -22.185 5.554  2.062  0.122  C6    IC5 7  
IC5 C8    C5  C 0 1 Y N N -96.410  7.181  -22.220 2.107  1.188  0.615  C8    IC5 8  
IC5 N3    N3  N 0 1 N N N -99.535  6.184  -20.985 4.858  -0.407 -0.843 N3    IC5 9  
IC5 N7    N4  N 0 1 Y N N -96.407  5.908  -22.599 3.074  2.110  0.800  N7    IC5 10 
IC5 N9    N5  N 1 1 Y N N -97.585  7.509  -21.679 2.599  0.142  0.006  N9    IC5 11 
IC5 "C1'" C6  C 0 1 N N R -98.065  8.849  -21.304 1.838  -1.056 -0.359 "C1'" IC5 12 
IC5 "O4'" O2  O 0 1 N N N -97.538  9.802  -22.207 0.422  -0.774 -0.371 "O4'" IC5 13 
IC5 "C2'" C7  C 0 1 N N R -97.637  9.278  -19.936 1.980  -2.146 0.733  "C2'" IC5 14 
IC5 "O2'" O3  O 0 1 N N N -98.554  8.722  -19.002 3.147  -2.941 0.511  "O2'" IC5 15 
IC5 "C3'" C8  C 0 1 N N S -97.759  10.780 -20.047 0.695  -2.983 0.526  "C3'" IC5 16 
IC5 "O3'" O4  O 0 1 N N N -99.073  11.251 -19.807 0.973  -4.140 -0.266 "O3'" IC5 17 
IC5 "C4'" C9  C 0 1 N N R -97.329  11.052 -21.498 -0.257 -2.032 -0.226 "C4'" IC5 18 
IC5 "C5'" C10 C 0 1 N N N -95.904  11.501 -21.721 -1.543 -1.840 0.581  "C5'" IC5 19 
IC5 "O5'" O5  O 0 1 N N N -95.198  11.474 -20.472 -2.459 -1.038 -0.168 "O5'" IC5 20 
IC5 PA    P1  P 0 1 N N N -93.886  10.566 -20.346 -3.919 -0.634 0.378  PA    IC5 21 
IC5 O1A   O6  O 0 1 N N N -92.793  11.224 -21.097 -3.787 0.029  1.695  O1A   IC5 22 
IC5 O2A   O7  O 0 1 N N N -94.257  9.166  -20.654 -4.821 -1.959 0.532  O2A   IC5 23 
IC5 O3A   O8  O 0 1 N N N -93.550  10.660 -18.787 -4.621 0.375  -0.663 O3A   IC5 24 
IC5 PB    P2  P 0 1 N N N -94.221  11.489 -17.549 -5.829 1.433  -0.553 PB    IC5 25 
IC5 O1B   O9  O 0 1 N N N -93.193  11.482 -16.440 -5.802 2.413  -1.830 O1B   IC5 26 
IC5 O2B   O10 O 0 1 N N N -95.479  10.734 -17.180 -7.232 0.643  -0.513 O2B   IC5 27 
IC5 O3B   O11 O 0 1 N N N -94.525  12.973 -18.112 -5.676 2.230  0.684  O3B   IC5 28 
IC5 CM    C11 C 0 1 N N N -95.348  5.241  -23.361 2.918  3.416  1.446  CM    IC5 29 
IC5 H1    H1  H 0 1 N N N -99.741  3.005  -21.576 7.374  1.564  -0.594 H1    IC5 30 
IC5 H2    H2  H 0 1 N N N -101.731 5.375  -20.061 7.939  -0.435 -1.669 H2    IC5 31 
IC5 H3    H3  H 0 1 N N N -101.539 3.716  -20.521 6.778  -1.625 -1.914 H3    IC5 32 
IC5 H4    H4  H 0 1 N N N -95.576  7.858  -22.334 1.081  1.293  0.933  H4    IC5 33 
IC5 H5    H5  H 0 1 N N N -99.164  8.861  -21.349 2.164  -1.436 -1.326 H5    IC5 34 
IC5 H6    H6  H 0 1 N N N -96.598  8.980  -19.732 1.999  -1.701 1.728  H6    IC5 35 
IC5 H7    H7  H 0 1 N N N -98.305  8.979  -18.122 3.280  -3.637 1.169  H7    IC5 36 
IC5 H8    H8  H 0 1 N N N -97.042  11.257 -19.363 0.269  -3.273 1.486  H8    IC5 37 
IC5 H9    H9  H 0 1 N N N -99.315  11.072 -18.906 1.613  -4.745 0.134  H9    IC5 38 
IC5 H10   H10 H 0 1 N N N -98.001  11.817 -21.913 -0.492 -2.443 -1.208 H10   IC5 39 
IC5 H11   H11 H 0 1 N N N -95.413  10.824 -22.436 -1.993 -2.811 0.785  H11   IC5 40 
IC5 H12   H12 H 0 1 N N N -95.900  12.525 -22.124 -1.310 -1.342 1.522  H12   IC5 41 
IC5 H13   H13 H 0 1 N N N -93.703  8.837  -21.352 -4.949 -2.445 -0.294 H13   IC5 42 
IC5 H14   H14 H 0 1 N N N -92.904  12.371 -16.270 -6.504 3.078  -1.830 H14   IC5 43 
IC5 H15   H15 H 0 1 N N N -96.238  11.280 -17.349 -7.399 0.098  -1.294 H15   IC5 44 
IC5 H16   H16 H 0 1 N N N -95.622  4.189  -23.527 3.107  3.318  2.515  H16   IC5 45 
IC5 H17   H17 H 0 1 N N N -95.222  5.744  -24.331 3.628  4.122  1.014  H17   IC5 46 
IC5 H18   H18 H 0 1 N N N -94.405  5.290  -22.797 1.903  3.780  1.288  H18   IC5 47 
# 
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 
IC5 CM    N7    SING N N 1  
IC5 O6    C6    DOUB N N 2  
IC5 N7    C8    SING Y N 3  
IC5 N7    C5    SING Y N 4  
IC5 C8    N9    DOUB Y N 5  
IC5 "O4'" "C4'" SING N N 6  
IC5 "O4'" "C1'" SING N N 7  
IC5 C6    C5    SING N N 8  
IC5 C6    N1    SING N N 9  
IC5 C5    C4    DOUB Y N 10 
IC5 "C5'" "C4'" SING N N 11 
IC5 "C5'" "O5'" SING N N 12 
IC5 N9    C4    SING Y N 13 
IC5 N9    "C1'" SING N N 14 
IC5 N1    C2    SING N N 15 
IC5 C4    N3    SING N N 16 
IC5 "C4'" "C3'" SING N N 17 
IC5 "C1'" "C2'" SING N N 18 
IC5 O1A   PA    DOUB N N 19 
IC5 C2    N3    DOUB N N 20 
IC5 C2    N2    SING N N 21 
IC5 O2A   PA    SING N N 22 
IC5 "O5'" PA    SING N N 23 
IC5 PA    O3A   SING N N 24 
IC5 "C3'" "C2'" SING N N 25 
IC5 "C3'" "O3'" SING N N 26 
IC5 "C2'" "O2'" SING N N 27 
IC5 O3A   PB    SING N N 28 
IC5 O3B   PB    DOUB N N 29 
IC5 PB    O2B   SING N N 30 
IC5 PB    O1B   SING N N 31 
IC5 N1    H1    SING N N 32 
IC5 N2    H2    SING N N 33 
IC5 N2    H3    SING N N 34 
IC5 C8    H4    SING N N 35 
IC5 "C1'" H5    SING N N 36 
IC5 "C2'" H6    SING N N 37 
IC5 "O2'" H7    SING N N 38 
IC5 "C3'" H8    SING N N 39 
IC5 "O3'" H9    SING N N 40 
IC5 "C4'" H10   SING N N 41 
IC5 "C5'" H11   SING N N 42 
IC5 "C5'" H12   SING N N 43 
IC5 O2A   H13   SING N N 44 
IC5 O1B   H14   SING N N 45 
IC5 O2B   H15   SING N N 46 
IC5 CM    H16   SING N N 47 
IC5 CM    H17   SING N N 48 
IC5 CM    H18   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 
IC5 InChI            InChI                1.06  "InChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1" 
IC5 InChIKey         InChI                1.06  SBASPRRECYVBRF-KQYNXXCUSA-O                                                                                                                                                                         
IC5 SMILES_CANONICAL CACTVS               3.385 "Cn1c[n+]([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13"                                                                                                                
IC5 SMILES           CACTVS               3.385 "Cn1c[n+]([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13"                                                                                                                      
IC5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cn1c[n+](c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                  
IC5 SMILES           "OpenEye OEToolkits" 2.0.7 "Cn1c[n+](c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           IC5 
_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        "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
IC5 "Create component"  2022-03-09 PDBE 
IC5 "Initial release"   2022-05-11 RCSB 
IC5 "Modify descriptor" 2022-08-22 RCSB 
# 
