data_AP7 # _chem_comp.id AP7 _chem_comp.name ;N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2004-08-10 _chem_comp.pdbx_modified_date 2011-06-04 _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 348.229 _chem_comp.one_letter_code A _chem_comp.three_letter_code AP7 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1U6P _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.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 AP7 "C1'" "C1'" C 0 1 N N R 83.398 19.268 -15.697 -0.717 0.818 -0.421 "C1'" AP7 1 AP7 N1 N1 N 1 1 Y N N 81.627 20.963 -11.167 -5.765 -0.407 -0.380 N1 AP7 2 AP7 C2 C2 C 0 1 Y N N 81.943 21.604 -12.315 -5.190 0.712 -0.782 C2 AP7 3 AP7 N3 N3 N 0 1 Y N N 82.404 21.094 -13.472 -3.887 0.893 -0.738 N3 AP7 4 AP7 C4 C4 C 0 1 Y N N 82.532 19.744 -13.355 -3.086 -0.063 -0.277 C4 AP7 5 AP7 C5 C5 C 0 1 Y N N 82.257 18.967 -12.274 -3.649 -1.272 0.163 C5 AP7 6 AP7 C6 C6 C 0 1 Y N N 81.778 19.612 -11.115 -5.045 -1.418 0.095 C6 AP7 7 AP7 N6 N6 N 0 1 N N N 81.459 18.977 -9.958 -5.656 -2.586 0.515 N6 AP7 8 AP7 N7 N7 N 0 1 Y N N 82.513 17.648 -12.539 -2.628 -2.061 0.575 N7 AP7 9 AP7 C8 C8 C 0 1 Y N N 82.945 17.653 -13.796 -1.501 -1.428 0.420 C8 AP7 10 AP7 N9 N9 N 0 1 Y N N 82.975 18.891 -14.332 -1.731 -0.191 -0.103 N9 AP7 11 AP7 "C2'" "C2'" C 0 1 N N R 84.896 19.529 -15.819 -0.550 1.814 0.754 "C2'" AP7 12 AP7 "O2'" "O2'" O 0 1 N N N 85.266 20.498 -16.774 -1.497 2.879 0.659 "O2'" AP7 13 AP7 "C3'" "C3'" C 0 1 N N S 85.352 18.246 -16.458 0.891 2.335 0.536 "C3'" AP7 14 AP7 "O3'" "O3'" O 0 1 N N N 86.613 18.403 -17.106 0.871 3.588 -0.151 "O3'" AP7 15 AP7 "C4'" "C4'" C 0 1 N N R 84.286 17.911 -17.496 1.556 1.253 -0.336 "C4'" AP7 16 AP7 "O4'" "O4'" O 0 1 N N N 83.197 18.207 -16.604 0.587 0.209 -0.535 "O4'" AP7 17 AP7 "C5'" "C5'" C 0 1 N N N 84.228 16.451 -17.884 2.786 0.691 0.379 "C5'" AP7 18 AP7 "O5'" "O5'" O 0 1 N N N 83.813 15.664 -16.770 3.462 -0.226 -0.484 "O5'" AP7 19 AP7 OP1 O1P O 0 1 N N N 83.394 13.586 -18.082 4.562 -1.745 1.206 OP1 AP7 20 AP7 OP2 O2P O 0 1 N N N 82.620 13.766 -15.680 5.210 -2.049 -1.215 OP2 AP7 21 AP7 P P P 0 1 N N N 82.836 14.417 -16.992 4.802 -1.008 -0.056 P AP7 22 AP7 OP3 O3P O 0 1 N Y N ? ? ? 5.996 0.051 0.160 OP3 AP7 23 AP7 "H1'" "H1'" H 0 1 N N N 82.803 20.168 -15.913 -0.978 1.347 -1.338 "H1'" AP7 24 AP7 H1 H1 H 0 1 N N N 81.290 21.471 -10.374 -6.730 -0.491 -0.430 H1 AP7 25 AP7 H2 H2 H 0 1 N N N 81.806 22.675 -12.301 -5.812 1.509 -1.162 H2 AP7 26 AP7 H61 H61 H 0 1 N N N 81.559 17.984 -9.889 -6.621 -2.674 0.463 H61 AP7 27 AP7 H62 H62 H 0 1 N N N 81.124 19.502 -9.175 -5.120 -3.317 0.860 H62 AP7 28 AP7 H8 H8 H 0 1 N N N 83.240 16.762 -14.331 -0.528 -1.825 0.669 H8 AP7 29 AP7 "H2'" "H2'" H 0 1 N N N 85.293 19.850 -14.845 -0.638 1.303 1.713 "H2'" AP7 30 AP7 "HO2'" "HO'2" H 0 0 N N N 86.211 20.593 -16.780 -1.433 3.529 1.372 "HO2'" AP7 31 AP7 "H3'" "H3'" H 0 1 N N N 85.478 17.456 -15.703 1.411 2.432 1.489 "H3'" AP7 32 AP7 "HO3'" H3T H 0 0 N Y N 86.873 17.578 -17.499 0.413 4.292 0.328 "HO3'" AP7 33 AP7 "H4'" "H4'" H 0 1 N N N 84.376 18.415 -18.470 1.845 1.677 -1.298 "H4'" AP7 34 AP7 "H5''" "H5'2" H 0 0 N N N 83.509 16.323 -18.707 3.460 1.508 0.639 "H5''" AP7 35 AP7 "H5'" "H5'1" H 0 1 N N N 85.226 16.122 -18.209 2.475 0.174 1.286 "H5'" AP7 36 AP7 HOP2 HOP2 H 0 0 N N N 82.886 12.855 -15.730 6.011 -2.556 -1.024 HOP2 AP7 37 AP7 HOP3 HOP3 H 0 0 N N N -0.580 -0.741 -0.132 6.208 0.570 -0.628 HOP3 AP7 38 # 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 AP7 "C1'" N9 SING N N 1 AP7 "C1'" "C2'" SING N N 2 AP7 "C1'" "O4'" SING N N 3 AP7 "C1'" "H1'" SING N N 4 AP7 N1 C2 SING Y N 5 AP7 N1 C6 DOUB Y N 6 AP7 N1 H1 SING N N 7 AP7 C2 N3 DOUB Y N 8 AP7 C2 H2 SING N N 9 AP7 N3 C4 SING Y N 10 AP7 C4 C5 DOUB Y N 11 AP7 C4 N9 SING Y N 12 AP7 C5 C6 SING Y N 13 AP7 C5 N7 SING Y N 14 AP7 C6 N6 SING N N 15 AP7 N6 H61 SING N N 16 AP7 N6 H62 SING N N 17 AP7 N7 C8 DOUB Y N 18 AP7 C8 N9 SING Y N 19 AP7 C8 H8 SING N N 20 AP7 "C2'" "O2'" SING N N 21 AP7 "C2'" "C3'" SING N N 22 AP7 "C2'" "H2'" SING N N 23 AP7 "O2'" "HO2'" SING N N 24 AP7 "C3'" "O3'" SING N N 25 AP7 "C3'" "C4'" SING N N 26 AP7 "C3'" "H3'" SING N N 27 AP7 "O3'" "HO3'" SING N N 28 AP7 "C4'" "O4'" SING N N 29 AP7 "C4'" "C5'" SING N N 30 AP7 "C4'" "H4'" SING N N 31 AP7 "C5'" "O5'" SING N N 32 AP7 "C5'" "H5''" SING N N 33 AP7 "C5'" "H5'" SING N N 34 AP7 "O5'" P SING N N 35 AP7 OP1 P DOUB N N 36 AP7 OP2 P SING N N 37 AP7 OP2 HOP2 SING N N 38 AP7 P OP3 SING N N 39 AP7 OP3 HOP3 SING N N 40 # 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 AP7 SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n2cnc1c(N)[nH+]cnc12)C(O)C3O" AP7 SMILES_CANONICAL CACTVS 3.370 "Nc1[nH+]cnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" AP7 SMILES CACTVS 3.370 "Nc1[nH+]cnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" AP7 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1[nH+]c(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N" AP7 SMILES "OpenEye OEToolkits" 1.7.0 "c1[nH+]c(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N" AP7 InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p+1/t4-,6-,7-,10-/m1/s1" AP7 InChIKey InChI 1.03 UDMBCSSLTHHNCD-KQYNXXCUSA-O # 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 AP7 "SYSTEMATIC NAME" ACDLabs 12.01 ;5'-adenylic acid ; AP7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4R,5R)-5-(6-azanylpurin-1-ium-9-yl)-3,4-dihydroxy-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 AP7 "Create component" 2004-08-10 RCSB AP7 "Modify descriptor" 2011-06-04 RCSB #