data_HYJ
# 
_chem_comp.id                                    HYJ 
_chem_comp.name                                  "9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-2-oxidanyl-1~{H}-purin-6-one" 
_chem_comp.type                                  "L-RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H13 N4 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               G 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-02-07 
_chem_comp.pdbx_modified_date                    2023-01-20 
_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                        364.205 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     HYJ 
_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        7QTN 
_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 
HYJ N9     N1  N 0 1 Y N N -11.199 -2.006 -11.757 1.535  -0.315 -0.194 N9     HYJ 1  
HYJ C4     C1  C 0 1 Y N N -12.173 -2.888 -12.007 2.865  -0.258 0.126  C4     HYJ 2  
HYJ N3     N2  N 0 1 N N N -13.451 -2.681 -12.324 3.624  0.605  0.811  N3     HYJ 3  
HYJ C2     C2  C 0 1 N N N -14.228 -3.785 -12.490 4.911  0.403  0.964  C2     HYJ 4  
HYJ O2     O1  O 0 1 N N N -15.555 -3.602 -12.800 5.637  1.302  1.664  O2     HYJ 5  
HYJ N1     N3  N 0 1 N N N -13.780 -5.001 -12.357 5.538  -0.685 0.438  N1     HYJ 6  
HYJ C6     C3  C 0 1 N N N -12.487 -5.229 -12.117 4.838  -1.601 -0.267 C6     HYJ 7  
HYJ O6     O2  O 0 1 N N N -12.045 -6.498 -12.001 5.390  -2.579 -0.742 O6     HYJ 8  
HYJ C5     C4  C 0 1 Y N N -11.637 -4.140 -11.877 3.449  -1.397 -0.440 C5     HYJ 9  
HYJ N7     N4  N 0 1 Y N N -10.332 -3.982 -11.554 2.464  -2.084 -1.068 N7     HYJ 10 
HYJ C8     C5  C 0 1 Y N N -10.089 -2.680 -11.486 1.337  -1.450 -0.924 C8     HYJ 11 
HYJ "C1'"  C6  C 0 1 N N R -11.401 -0.546 -11.795 0.511  0.661  0.185  "C1'"  HYJ 12 
HYJ "C2'"  C7  C 0 1 N N R -12.201 -0.087 -10.576 0.422  1.785  -0.871 "C2'"  HYJ 13 
HYJ "C3'"  C8  C 0 1 N N S -11.074 0.125  -9.581  -1.087 2.107  -0.949 "C3'"  HYJ 14 
HYJ "C4'"  C9  C 0 1 N N R -10.028 0.792  -10.457 -1.731 1.140  0.069  "C4'"  HYJ 15 
HYJ "C5'"  C10 C 0 1 N N N -8.630  0.743  -9.935  -3.079 0.638  -0.452 "C5'"  HYJ 16 
HYJ "O2'"  O3  O 0 1 N N N -12.826 1.160  -10.865 1.158  2.933  -0.444 "O2'"  HYJ 17 
HYJ "O3'"  O4  O 0 1 N N N -11.423 0.917  -8.457  -1.329 3.465  -0.573 "O3'"  HYJ 18 
HYJ "O4'"  O5  O 0 1 N N N -10.122 0.052  -11.700 -0.796 0.046  0.181  "O4'"  HYJ 19 
HYJ "O5'"  O6  O 0 1 N N N -8.252  -0.609 -9.712  -3.710 -0.160 0.551  "O5'"  HYJ 20 
HYJ OP1    O7  O 0 1 N N N -6.412  -0.025 -8.082  -5.606 -1.561 1.715  OP1    HYJ 21 
HYJ OP2    O8  O 0 1 N N N -6.819  -2.375 -8.973  -6.142 0.175  -0.037 OP2    HYJ 22 
HYJ P      P1  P 0 1 N N N -6.795  -0.948 -9.195  -5.148 -0.854 0.343  P      HYJ 23 
HYJ HO2    H1  H 0 1 N N N -15.742 -2.672 -12.855 5.120  2.045  2.004  HO2    HYJ 24 
HYJ H1     H2  H 0 1 N N N -14.412 -5.772 -12.436 6.492  -0.803 0.570  H1     HYJ 25 
HYJ H8     H3  H 0 1 N N N -9.134  -2.236 -11.247 0.387  -1.774 -1.324 H8     HYJ 26 
HYJ "H1'"  H4  H 0 1 N N N -11.920 -0.249 -12.718 0.730  1.078  1.168  "H1'"  HYJ 27 
HYJ "H2'"  H5  H 0 1 N N N -12.906 -0.860 -10.237 0.787  1.432  -1.835 "H2'"  HYJ 28 
HYJ "H3'"  H6  H 0 1 N N N -10.695 -0.855 -9.256  -1.467 1.917  -1.953 "H3'"  HYJ 29 
HYJ "H4'"  H7  H 0 1 N N N -10.317 1.840  -10.623 -1.858 1.634  1.033  "H4'"  HYJ 30 
HYJ "H5'2" H8  H 0 0 N N N -7.949  1.197  -10.669 -3.716 1.489  -0.693 "H5'2" HYJ 31 
HYJ "H5'1" H9  H 0 0 N N N -8.573  1.300  -8.988  -2.921 0.038  -1.348 "H5'1" HYJ 32 
HYJ "HO2'" H10 H 0 0 N N N -13.324 1.448  -10.109 1.135  3.669  -1.070 "HO2'" HYJ 33 
HYJ H2     H11 H 0 1 N N N -10.670 1.004  -7.884  -0.897 4.114  -1.144 H2     HYJ 34 
HYJ H3     H12 H 0 1 N N N -6.216  -0.532 -7.303  -6.466 -2.000 1.663  H3     HYJ 35 
HYJ OP3    OP3 O 0 1 N Y N -5.823  -0.570 -10.425 -5.048 -1.959 -0.823 OP3    HYJ 36 
HYJ H6     H15 H 0 1 N N N -5.440  -1.363 -10.782 -4.414 -2.666 -0.641 H6     HYJ 37 
# 
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 
HYJ O2    C2     SING N N 1  
HYJ C2    N1     SING N N 2  
HYJ C2    N3     DOUB N N 3  
HYJ N1    C6     SING N N 4  
HYJ N3    C4     SING N N 5  
HYJ C6    O6     DOUB N N 6  
HYJ C6    C5     SING N N 7  
HYJ C4    C5     DOUB Y N 8  
HYJ C4    N9     SING Y N 9  
HYJ C5    N7     SING Y N 10 
HYJ "C1'" N9     SING N N 11 
HYJ "C1'" "O4'"  SING N N 12 
HYJ "C1'" "C2'"  SING N N 13 
HYJ N9    C8     SING Y N 14 
HYJ "O4'" "C4'"  SING N N 15 
HYJ N7    C8     DOUB Y N 16 
HYJ "O2'" "C2'"  SING N N 17 
HYJ "C2'" "C3'"  SING N N 18 
HYJ "C4'" "C5'"  SING N N 19 
HYJ "C4'" "C3'"  SING N N 20 
HYJ "C5'" "O5'"  SING N N 21 
HYJ "O5'" P      SING N N 22 
HYJ "C3'" "O3'"  SING N N 23 
HYJ P     OP2    DOUB N N 24 
HYJ P     OP1    SING N N 25 
HYJ O2    HO2    SING N N 26 
HYJ N1    H1     SING N N 27 
HYJ C8    H8     SING N N 28 
HYJ "C1'" "H1'"  SING N N 29 
HYJ "C2'" "H2'"  SING N N 30 
HYJ "C3'" "H3'"  SING N N 31 
HYJ "C4'" "H4'"  SING N N 32 
HYJ "C5'" "H5'2" SING N N 33 
HYJ "C5'" "H5'1" SING N N 34 
HYJ "O2'" "HO2'" SING N N 35 
HYJ "O3'" H2     SING N N 36 
HYJ OP1   H3     SING N N 37 
HYJ P     OP3    SING N N 38 
HYJ OP3   H6     SING N N 39 
# 
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 
HYJ InChI            InChI                1.06  "InChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1" 
HYJ InChIKey         InChI                1.06  DCTLYFZHFGENCW-UUOKFMHZSA-N                                                                                                                                          
HYJ SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)O"                                                                                                 
HYJ SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)O"                                                                                                        
HYJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)O"                                                                                                  
HYJ SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)O"                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           HYJ 
_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})-3,4-bis(oxidanyl)-5-(2-oxidanyl-6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methyl dihydrogen 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 
HYJ "Create component"  2022-02-07 PDBE 
HYJ "Modify descriptor" 2022-08-22 RCSB 
HYJ "Initial release"   2023-01-25 RCSB 
# 
