data_2DF # _chem_comp.id 2DF _chem_comp.name "N-(2-DEOXY-BETA-D-ERYTHO-PENTOFURANOSYL-5-PHOSPHATE) FORMAMIDE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C6 H12 N O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-03-24 _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 241.136 _chem_comp.one_letter_code N _chem_comp.three_letter_code 2DF _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1OSR _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 2DF P P P 0 1 N N N 9.795 2.818 3.055 6.400 1.685 0.524 P 2DF 1 2DF O1P O1P O 0 1 N N N 10.477 3.886 2.289 6.992 3.020 0.180 O1P 2DF 2 2DF O2P O2P O 0 1 N N N 9.139 3.152 4.337 7.021 0.426 -0.280 O2P 2DF 3 2DF O3P O3P O 0 1 N Y N ? ? ? 6.553 1.249 2.073 O3P 2DF 4 2DF "O5'" O5* O 0 1 N N N 10.882 1.651 3.369 4.807 1.557 0.268 "O5'" 2DF 5 2DF "C5'" C5* C 0 1 N N N 12.057 1.451 2.596 4.172 0.325 0.569 "C5'" 2DF 6 2DF "C4'" C4* C 0 1 N N R 11.762 0.696 1.297 2.692 0.445 0.250 "C4'" 2DF 7 2DF "O4'" O4* O 0 1 N N N 12.953 0.601 0.522 2.523 0.722 -1.151 "O4'" 2DF 8 2DF "C1'" C1* C 0 1 N N R 12.884 -0.578 -0.251 1.407 -0.038 -1.638 "C1'" 2DF 9 2DF N1 N1 N 0 1 N N N 14.219 -1.004 -0.651 1.898 -1.016 -2.572 N1 2DF 10 2DF C2 C2 C 0 1 N N N 14.507 -1.572 -1.831 1.175 -1.464 -3.658 C2 2DF 11 2DF O2 O2 O 0 1 N N N 13.672 -1.787 -2.706 0.048 -1.127 -3.998 O2 2DF 12 2DF "C3'" C3* C 0 1 N N S 11.279 -0.739 1.561 1.910 -0.829 0.525 "C3'" 2DF 13 2DF "C2'" C2* C 0 1 N N N 12.272 -1.577 0.741 0.748 -0.678 -0.431 "C2'" 2DF 14 2DF "O3'" O3* O 0 1 N N N 9.946 -0.929 1.120 1.469 -0.911 1.864 "O3'" 2DF 15 2DF HOP2 2HOP H 0 0 N N N 8.701 2.466 4.828 7.996 0.328 -0.328 HOP2 2DF 16 2DF HOP3 3HOP H 0 0 N N N -0.437 -0.685 0.491 7.429 1.331 2.506 HOP3 2DF 17 2DF "H5'1" 1H5* H 0 0 N N N 12.539 2.405 2.375 4.627 -0.466 -0.033 "H5'1" 2DF 18 2DF "H5'2" 2H5* H 0 0 N N N 12.756 0.857 3.186 4.315 0.100 1.628 "H5'2" 2DF 19 2DF "H4'" H4* H 0 1 N N N 11.017 1.254 0.740 2.281 1.291 0.813 "H4'" 2DF 20 2DF "H1'" H1* H 0 1 N N N 12.268 -0.392 -1.148 0.725 0.620 -2.184 "H1'" 2DF 21 2DF H1 H1 H 0 1 N N N 14.962 -0.869 0.018 2.831 -1.397 -2.423 H1 2DF 22 2DF H2 H2 H 0 1 N N N 15.541 -1.843 -2.008 1.752 -2.209 -4.230 H2 2DF 23 2DF "H3'" H3* H 0 1 N N N 11.353 -0.986 2.626 2.495 -1.724 0.283 "H3'" 2DF 24 2DF "H2'1" 1H2* H 0 0 N N N 13.000 -1.951 1.469 0.242 -1.625 -0.643 "H2'1" 2DF 25 2DF "H2'2" 2H2* H 0 0 N N N 11.837 -2.426 0.212 -0.000 0.000 0.000 "H2'2" 2DF 26 2DF H3T H3T H 0 1 N Y N 9.647 -1.816 1.283 1.038 -0.065 2.078 H3T 2DF 27 # 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 2DF P O1P DOUB N N 1 2DF P O2P SING N N 2 2DF P O3P SING N N 3 2DF P "O5'" SING N N 4 2DF O2P HOP2 SING N N 5 2DF O3P HOP3 SING N N 6 2DF "O5'" "C5'" SING N N 7 2DF "C5'" "C4'" SING N N 8 2DF "C5'" "H5'1" SING N N 9 2DF "C5'" "H5'2" SING N N 10 2DF "C4'" "O4'" SING N N 11 2DF "C4'" "C3'" SING N N 12 2DF "C4'" "H4'" SING N N 13 2DF "O4'" "C1'" SING N N 14 2DF "C1'" N1 SING N N 15 2DF "C1'" "C2'" SING N N 16 2DF "C1'" "H1'" SING N N 17 2DF N1 C2 SING N N 18 2DF N1 H1 SING N N 19 2DF C2 O2 DOUB N N 20 2DF C2 H2 SING N N 21 2DF "C3'" "C2'" SING N N 22 2DF "C3'" "O3'" SING N N 23 2DF "C3'" "H3'" SING N N 24 2DF "C2'" "H2'1" SING N N 25 2DF "C2'" "H2'2" SING N N 26 2DF "O3'" H3T SING N N 27 # 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 2DF SMILES ACDLabs 10.04 "O=CNC1OC(C(O)C1)COP(=O)(O)O" 2DF SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@H](NC=O)O[C@@H]1CO[P](O)(O)=O" 2DF SMILES CACTVS 3.341 "O[CH]1C[CH](NC=O)O[CH]1CO[P](O)(O)=O" 2DF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1NC=O)COP(=O)(O)O)O" 2DF SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1NC=O)COP(=O)(O)O)O" 2DF InChI InChI 1.03 "InChI=1S/C6H12NO7P/c8-3-7-6-1-4(9)5(14-6)2-13-15(10,11)12/h3-6,9H,1-2H2,(H,7,8)(H2,10,11,12)/t4-,5+,6+/m0/s1" 2DF InChIKey InChI 1.03 CLIXLSFJUCMEGR-KVQBGUIXSA-N # 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 2DF "SYSTEMATIC NAME" ACDLabs 10.04 2-deoxy-N-formyl-5-O-phosphono-beta-D-erythro-pentofuranosylamine 2DF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-formamido-3-hydroxy-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 2DF "Create component" 2003-03-24 RCSB 2DF "Modify descriptor" 2011-06-04 RCSB #