data_A1H3G # _chem_comp.id A1H3G _chem_comp.name ;2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (protonated at N1) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2024-02-05 _chem_comp.pdbx_modified_date 2024-03-08 _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 332.230 _chem_comp.one_letter_code A _chem_comp.three_letter_code A1H3G _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 8RW2 _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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1H3G N1 N1 N 1 1 Y N N N N N 32.259 30.746 32.957 -5.824 -0.285 -0.597 N1 A1H3G 1 A1H3G N3 N2 N 0 1 Y N N N N N 31.368 31.660 35.030 -3.910 0.891 -1.142 N3 A1H3G 2 A1H3G C6 C1 C 0 1 Y N N N N N 33.357 30.173 33.577 -5.156 -1.118 0.195 C6 A1H3G 3 A1H3G C5 C2 C 0 1 Y N N N N N 33.495 30.415 34.973 -3.769 -0.941 0.334 C5 A1H3G 4 A1H3G C4 C3 C 0 1 Y N N N N N 32.488 31.120 35.600 -3.159 0.109 -0.373 C4 A1H3G 5 A1H3G C8 C4 C 0 1 Y N N N N N 34.037 30.524 37.031 -1.651 -0.993 0.799 C8 A1H3G 6 A1H3G P P1 P 0 1 N N N N N N 32.445 28.294 42.045 4.752 -0.903 -0.187 P A1H3G 7 A1H3G OP3 O1 O 0 1 N Y N N N N 31.263 28.357 42.941 5.285 -1.611 -1.531 OP3 A1H3G 8 A1H3G OP1 O2 O 0 1 N N N N N N 32.699 27.041 41.292 5.776 0.042 0.312 OP1 A1H3G 9 A1H3G "O5'" O3 O 0 1 N N N N N N 32.334 29.503 40.990 3.392 -0.103 -0.504 "O5'" A1H3G 10 A1H3G "O3'" O4 O 0 1 N N N N N N 29.709 32.758 39.594 1.271 3.558 0.836 "O3'" A1H3G 11 A1H3G C2 C5 C 0 1 Y N N N N N 31.336 31.446 33.716 -5.207 0.688 -1.242 C2 A1H3G 12 A1H3G N7 N3 N 0 1 Y N N N N N 34.479 30.051 35.896 -2.793 -1.574 1.029 N7 A1H3G 13 A1H3G N9 N4 N 0 1 Y N N N N N 32.828 31.164 36.936 -1.825 0.051 -0.060 N9 A1H3G 14 A1H3G N6 N5 N 0 1 N N N N N N 34.170 29.425 32.820 -5.812 -2.134 0.867 N6 A1H3G 15 A1H3G "C1'" C6 C 0 1 N N R N N N 32.042 31.774 38.033 -0.778 0.947 -0.558 "C1'" A1H3G 16 A1H3G "O4'" O5 O 0 1 N N N N N N 32.787 31.768 39.235 0.503 0.301 -0.467 "O4'" A1H3G 17 A1H3G "C4'" C7 C 0 1 N N R N N N 31.865 31.822 40.316 1.473 1.327 -0.167 "C4'" A1H3G 18 A1H3G "C3'" C8 C 0 1 N N S N N N 30.461 31.553 39.747 0.738 2.233 0.853 "C3'" A1H3G 19 A1H3G "C2'" C9 C 0 1 N N N N N N 30.784 30.982 38.370 -0.714 2.215 0.316 "C2'" A1H3G 20 A1H3G "C5'" C10 C 0 1 N N N N N N 32.263 30.852 41.435 2.727 0.716 0.460 "C5'" A1H3G 21 A1H3G OP2 O6 O 0 1 N Y N N N N 33.745 28.647 42.936 4.466 -2.025 0.932 OP2 A1H3G 22 A1H3G H1 H1 H 0 1 N N N N N N 32.134 30.655 31.969 -6.781 -0.396 -0.706 H1 A1H3G 23 A1H3G H8 H2 H 0 1 N N N N N N 34.576 30.420 37.961 -0.706 -1.294 1.226 H8 A1H3G 24 A1H3G HOP3 H3 H 0 0 N Y N N N N 30.797 27.530 42.909 6.103 -2.112 -1.414 HOP3 A1H3G 25 A1H3G "HO3'" H4 H 0 0 N Y N N N N 29.506 33.116 40.450 0.844 4.162 1.459 "HO3'" A1H3G 26 A1H3G H2 H5 H 0 1 N N N N N N 30.496 31.865 33.182 -5.788 1.343 -1.875 H2 A1H3G 27 A1H3G H62 H6 H 0 1 N N N N N N 34.962 28.974 33.232 -6.769 -2.245 0.763 H62 A1H3G 28 A1H3G H61 H7 H 0 1 N N N N N N 33.985 29.317 31.843 -5.313 -2.736 1.442 H61 A1H3G 29 A1H3G "H1'" H8 H 0 1 N N N N N N 31.758 32.801 37.758 -0.985 1.220 -1.592 "H1'" A1H3G 30 A1H3G "H4'" H9 H 0 1 N N N N N N 31.864 32.838 40.739 1.729 1.888 -1.067 "H4'" A1H3G 31 A1H3G "H3'" H10 H 0 1 N N N N N N 29.932 30.809 40.362 0.787 1.808 1.856 "H3'" A1H3G 32 A1H3G "H2'" H11 H 0 1 N N N N N N 29.976 31.176 37.649 -0.909 3.103 -0.285 "H2'" A1H3G 33 A1H3G "H2''" H12 H 0 0 N N N N N N 30.984 29.901 38.415 -1.425 2.147 1.140 "H2''" A1H3G 34 A1H3G "H5''" H13 H 0 0 N N N N N N 33.249 31.147 41.823 2.445 0.109 1.319 "H5''" A1H3G 35 A1H3G "H5'" H14 H 0 1 N N N N N N 31.517 30.918 42.241 3.397 1.513 0.783 "H5'" A1H3G 36 A1H3G HOP2 H15 H 0 0 N N N N N N 34.412 27.984 42.801 3.803 -2.680 0.673 HOP2 A1H3G 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 A1H3G N6 C6 SING N N 1 A1H3G N1 C6 DOUB Y N 2 A1H3G N1 C2 SING Y N 3 A1H3G C6 C5 SING Y N 4 A1H3G C2 N3 DOUB Y N 5 A1H3G C5 C4 DOUB Y N 6 A1H3G C5 N7 SING Y N 7 A1H3G N3 C4 SING Y N 8 A1H3G C4 N9 SING Y N 9 A1H3G N7 C8 DOUB Y N 10 A1H3G N9 C8 SING Y N 11 A1H3G N9 "C1'" SING N N 12 A1H3G "C1'" "C2'" SING N N 13 A1H3G "C1'" "O4'" SING N N 14 A1H3G "C2'" "C3'" SING N N 15 A1H3G "O4'" "C4'" SING N N 16 A1H3G "O3'" "C3'" SING N N 17 A1H3G "C3'" "C4'" SING N N 18 A1H3G "C4'" "C5'" SING N N 19 A1H3G "O5'" "C5'" SING N N 20 A1H3G "O5'" P SING N N 21 A1H3G OP1 P DOUB N N 22 A1H3G P OP3 SING N N 23 A1H3G P OP2 SING N N 24 A1H3G N1 H1 SING N N 25 A1H3G C8 H8 SING N N 26 A1H3G OP3 HOP3 SING N N 27 A1H3G "O3'" "HO3'" SING N N 28 A1H3G C2 H2 SING N N 29 A1H3G N6 H62 SING N N 30 A1H3G N6 H61 SING N N 31 A1H3G "C1'" "H1'" SING N N 32 A1H3G "C4'" "H4'" SING N N 33 A1H3G "C3'" "H3'" SING N N 34 A1H3G "C2'" "H2'" SING N N 35 A1H3G "C2'" "H2''" SING N N 36 A1H3G "C5'" "H5''" SING N N 37 A1H3G "C5'" "H5'" SING N N 38 A1H3G OP2 HOP2 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 A1H3G InChI InChI 1.06 "InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/p+1/t5-,6+,7+/m0/s1" A1H3G InChIKey InChI 1.06 KHWCHTKSEGGWEX-RRKCRQDMSA-O A1H3G SMILES_CANONICAL CACTVS 3.385 "Nc1[nH+]cnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" A1H3G SMILES CACTVS 3.385 "Nc1[nH+]cnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" A1H3G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1[nH+]c(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N" A1H3G SMILES "OpenEye OEToolkits" 2.0.7 "c1[nH+]c(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N" # _pdbx_chem_comp_identifier.comp_id A1H3G _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},5~{R})-5-(6-azanylpurin-1-ium-9-yl)-3-oxidanyl-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 A1H3G "Create component" 2024-02-08 PDBE A1H3G "Initial release" 2024-03-13 RCSB #