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 
# 
