data_D33 # _chem_comp.id D33 _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C8 H13 N2 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-07-09 _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 264.172 _chem_comp.one_letter_code N _chem_comp.three_letter_code D33 _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 2K69 _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 D33 C4 C4 C 0 1 Y N N -1.804 10.358 4.485 -4.883 1.770 0.034 C4 D33 1 D33 C5 C5 C 0 1 Y N N -2.687 10.974 3.630 -4.330 0.853 0.850 C5 D33 2 D33 C2 C2 C 0 1 Y N N -2.925 8.787 3.546 -2.997 1.205 -0.850 C2 D33 3 D33 N1 N1 N 0 1 Y N N -3.402 9.960 3.020 -3.134 0.494 0.289 N1 D33 4 D33 P P P 0 1 N N N -2.432 14.561 1.173 3.507 0.595 0.013 P D33 5 D33 OP1 OP1 O 0 1 N N N -2.939 15.744 0.442 4.373 -0.518 -0.434 OP1 D33 6 D33 OP2 OP2 O 0 1 N N N -1.669 14.739 2.428 3.297 1.633 -1.199 OP2 D33 7 D33 "O5'" "O5'" O 0 1 N N N -3.677 13.587 1.474 2.078 0.011 0.473 "O5'" D33 8 D33 "C5'" "C5'" C 0 1 N N N -4.618 13.285 0.443 1.262 -0.802 -0.371 "C5'" D33 9 D33 "C4'" "C4'" C 0 1 N N R -5.060 11.823 0.491 -0.020 -1.183 0.373 "C4'" D33 10 D33 "O4'" "O4'" O 0 1 N N N -3.977 11.010 0.949 -0.836 -0.016 0.611 "O4'" D33 11 D33 "C1'" "C1'" C 0 1 N N R -4.424 10.101 1.962 -2.179 -0.479 0.826 "C1'" D33 12 D33 N3 N3 N 0 1 Y N N -1.961 8.990 4.429 -4.050 1.962 -1.000 N3 D33 13 D33 "C2'" "C2'" C 0 1 N N N -5.740 10.653 2.513 -2.325 -1.821 0.083 "C2'" D33 14 D33 "C3'" "C3'" C 0 1 N N S -6.208 11.683 1.488 -0.921 -2.078 -0.516 "C3'" D33 15 D33 "O3'" "O3'" O 0 1 N N N -7.362 11.188 0.796 -0.557 -3.454 -0.390 "O3'" D33 16 D33 "H15'" "H15'" H 0 0 N N N -4.134 13.466 -0.528 1.007 -0.247 -1.274 "H15'" D33 17 D33 "H25'" "H25'" H 0 0 N N N -5.503 13.926 0.573 1.807 -1.707 -0.642 "H25'" D33 18 D33 "H4'" "H4'" H 0 1 N N N -5.375 11.507 -0.514 0.216 -1.685 1.311 "H4'" D33 19 D33 "H1'" "H1'" H 0 1 N N N -4.584 9.094 1.549 -2.356 -0.622 1.892 "H1'" D33 20 D33 H55 H55 H 0 1 N N N -2.799 12.036 3.468 -4.750 0.472 1.769 H55 D33 21 D33 H22 H22 H 0 1 N N N -3.294 7.810 3.271 -2.159 1.152 -1.529 H22 D33 22 D33 H44 H44 H 0 1 N N N -1.090 10.872 5.111 -5.833 2.262 0.183 H44 D33 23 D33 "H22'" "H22'" H 0 0 N N N -6.483 9.850 2.629 -2.594 -2.616 0.780 "H22'" D33 24 D33 "H12'" "H12'" H 0 0 N N N -5.609 11.100 3.509 -3.071 -1.740 -0.707 "H12'" D33 25 D33 "H3'" "H3'" H 0 1 N N N -6.469 12.639 1.966 -0.879 -1.760 -1.558 "H3'" D33 26 D33 HOP2 HOP2 H 0 0 N N N -0.740 14.777 2.232 2.737 2.390 -0.976 HOP2 D33 27 D33 "HO3'" "HO3'" H 0 0 N Y N -8.078 11.079 1.411 -1.092 -4.054 -0.927 "HO3'" D33 28 D33 OP3 OP3 O 0 1 N Y N -1.292 13.464 0.499 4.202 1.351 1.253 OP3 D33 29 D33 HOP3 HOP3 H 0 0 N Y N -1.538 13.262 -0.396 5.068 1.729 1.048 HOP3 D33 30 # 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 D33 C4 H44 SING N N 1 D33 C5 C4 DOUB Y N 2 D33 C2 N3 DOUB Y N 3 D33 N1 C5 SING Y N 4 D33 N1 C2 SING Y N 5 D33 P "O5'" SING N N 6 D33 P OP2 SING N N 7 D33 OP1 P DOUB N N 8 D33 OP2 HOP2 SING N N 9 D33 "C5'" "O5'" SING N N 10 D33 "C5'" "C4'" SING N N 11 D33 "C5'" "H25'" SING N N 12 D33 "C4'" "O4'" SING N N 13 D33 "C4'" "C3'" SING N N 14 D33 "O4'" "C1'" SING N N 15 D33 "C1'" N1 SING N N 16 D33 "C1'" "C2'" SING N N 17 D33 N3 C4 SING Y N 18 D33 "C2'" "H22'" SING N N 19 D33 "C2'" "H12'" SING N N 20 D33 "C3'" "C2'" SING N N 21 D33 "C3'" "H3'" SING N N 22 D33 "O3'" "C3'" SING N N 23 D33 "O3'" "HO3'" SING N N 24 D33 "H15'" "C5'" SING N N 25 D33 "H4'" "C4'" SING N N 26 D33 "H1'" "C1'" SING N N 27 D33 H55 C5 SING N N 28 D33 H22 C2 SING N N 29 D33 P OP3 SING N N 30 D33 OP3 HOP3 SING N N 31 # 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 D33 SMILES ACDLabs 10.04 "O=P(O)(O)OCC2OC(n1cncc1)CC2O" D33 SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccnc2" D33 SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccnc2" D33 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cn(cn1)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" D33 SMILES "OpenEye OEToolkits" 1.5.0 "c1cn(cn1)C2CC(C(O2)COP(=O)(O)O)O" D33 InChI InChI 1.03 "InChI=1S/C8H13N2O6P/c11-6-3-8(10-2-1-9-5-10)16-7(6)4-15-17(12,13)14/h1-2,5-8,11H,3-4H2,(H2,12,13,14)/t6-,7+,8+/m0/s1" D33 InChIKey InChI 1.03 YJJFDZQLJDAGPJ-XLPZGREQSA-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 D33 "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole" D33 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-imidazol-1-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 D33 "Create component" 2008-07-09 RCSB D33 "Modify aromatic_flag" 2011-06-04 RCSB D33 "Modify descriptor" 2011-06-04 RCSB #