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
#