data_D3
# 
_chem_comp.id                                    D3 
_chem_comp.name                                  "1-(2-DEOXY-BETA-D-RIBOFURANOSYL)-4-(3-BENZAMIDO)PHENYLIMIDAZOLE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H22 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        459.389 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     D3 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1WAN 
_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 
D3 P      P    P 0 1 N N N -10.037 2.022  -9.988  -1.567 -0.326 -6.763 P      D3 1  
D3 OP1    O1P  O 0 1 N N N -9.856  1.452  -8.634  -2.286 -1.305 -5.918 OP1    D3 2  
D3 OP2    O2P  O 0 1 N N N -11.133 1.533  -10.855 -2.606 0.775  -7.309 OP2    D3 3  
D3 OP3    O3P  O 0 1 N Y N -10.184 3.619  -9.850  -0.888 -1.087 -8.008 OP3    D3 4  
D3 "O5'"  O5*  O 0 1 N N N -8.651  1.864  -10.793 -0.425 0.399  -5.890 "O5'"  D3 5  
D3 "C5'"  C5*  C 0 1 N N N -8.166  0.570  -11.164 0.460  -0.625 -5.436 "C5'"  D3 6  
D3 "C4'"  C4*  C 0 1 N N R -6.866  0.665  -11.955 1.575  0.000  -4.595 "C4'"  D3 7  
D3 "O4'"  O4*  O 0 1 N N N -5.809  1.257  -11.148 1.021  0.655  -3.431 "O4'"  D3 8  
D3 "C3'"  C3*  C 0 1 N N S -6.388  -0.726 -12.387 2.506  -1.092 -4.025 "C3'"  D3 9  
D3 "O3'"  O3*  O 0 1 N N N -6.155  -0.796 -13.801 3.681  -1.218 -4.828 "O3'"  D3 10 
D3 "C2'"  C2*  C 0 1 N N N -5.111  -0.928 -11.631 2.869  -0.581 -2.612 "C2'"  D3 11 
D3 "C1'"  C1*  C 0 1 N N R -4.627  0.462  -11.310 2.115  0.762  -2.495 "C1'"  D3 12 
D3 N1A    N1A  N 0 1 Y N N -3.787  0.426  -10.109 1.608  0.945  -1.132 N1A    D3 13 
D3 C2A    C2A  C 0 1 Y N N -4.098  0.178  -8.833  2.260  1.541  -0.110 C2A    D3 14 
D3 N3A    N3A  N 0 1 Y N N -3.114  0.142  -7.986  1.499  1.520  0.947  N3A    D3 15 
D3 C4A    C4A  C 0 1 Y N N -2.003  0.396  -8.775  0.334  0.911  0.644  C4A    D3 16 
D3 C5A    C5A  C 0 1 Y N N -2.446  0.568  -10.060 0.387  0.548  -0.664 C5A    D3 17 
D3 C1B    C1B  C 0 1 Y N N -0.604  0.398  -8.214  -0.801 0.684  1.570  C1B    D3 18 
D3 C2B    C2B  C 0 1 Y N N -0.368  0.415  -6.817  -0.562 0.307  2.889  C2B    D3 19 
D3 C3B    C3B  C 0 1 Y N N 0.953   0.374  -6.337  -1.629 0.101  3.751  C3B    D3 20 
D3 C4B    C4B  C 0 1 Y N N 2.029   0.316  -7.246  -2.931 0.261  3.294  C4B    D3 21 
D3 C5B    C5B  C 0 1 Y N N 1.785   0.300  -8.616  -3.168 0.629  1.983  C5B    D3 22 
D3 C6B    C6B  C 0 1 Y N N 0.489   0.339  -9.102  -2.112 0.841  1.120  C6B    D3 23 
D3 N      N    N 0 1 N N N 1.187   0.379  -4.946  -1.394 -0.271 5.078  N      D3 24 
D3 C      C    C 0 1 N N N 1.849   1.357  -4.357  -0.304 0.187  5.724  C      D3 25 
D3 O      O    O 0 1 N N N 2.294   2.303  -4.984  0.420  1.004  5.189  O      D3 26 
D3 C1C    C1C  C 0 1 Y N N 2.034   1.256  -2.840  0.010  -0.300 7.083  C1C    D3 27 
D3 C2C    C2C  C 0 1 Y N N 3.301   1.431  -2.253  1.138  0.173  7.755  C2C    D3 28 
D3 C3C    C3C  C 0 1 Y N N 3.447   1.333  -0.864  1.425  -0.287 9.024  C3C    D3 29 
D3 C4C    C4C  C 0 1 Y N N 2.337   1.061  -0.059  0.598  -1.216 9.630  C4C    D3 30 
D3 C5C    C5C  C 0 1 Y N N 1.078   0.888  -0.639  -0.520 -1.690 8.969  C5C    D3 31 
D3 C6C    C6C  C 0 1 Y N N 0.925   0.985  -2.027  -0.823 -1.233 7.703  C6C    D3 32 
D3 HOP2   2HOP H 0 0 N N N -11.249 1.898  -11.724 -3.272 0.300  -7.825 HOP2   D3 33 
D3 HOP3   3HOP H 0 0 N N N -10.300 3.984  -10.719 -0.431 -0.414 -8.532 HOP3   D3 34 
D3 "H5'"  1H5* H 0 1 N N N -8.919  0.069  -11.774 0.896  -1.135 -6.295 "H5'"  D3 35 
D3 "H5''" 2H5* H 0 0 N N N -7.991  -0.016 -10.261 -0.092 -1.341 -4.829 "H5''" D3 36 
D3 "H4'"  H4*  H 0 1 N N N -7.028  1.279  -12.841 2.147  0.710  -5.193 "H4'"  D3 37 
D3 "H3'"  H3*  H 0 1 N N N -7.119  -1.480 -12.091 1.983  -2.046 -3.963 "H3'"  D3 38 
D3 "HO3'" *HO3 H 0 0 N Y N -5.858  -1.658 -14.068 4.236  -1.890 -4.409 "HO3'" D3 39 
D3 "H2'"  1H2* H 0 1 N N N -5.308  -1.478 -10.709 2.522  -1.281 -1.852 "H2'"  D3 40 
D3 "H2''" 2H2* H 0 0 N N N -4.377  -1.453 -12.241 3.944  -0.424 -2.527 "H2''" D3 41 
D3 "H1'"  H1*  H 0 1 N N N -4.047  0.840  -12.153 2.770  1.589  -2.769 "H1'"  D3 42 
D3 H2A    H2A  H 0 1 N N N -5.135  0.007  -8.526  3.252  1.966  -0.161 H2A    D3 43 
D3 H5A    H5A  H 0 1 N N N -1.814  0.790  -10.925 -0.383 0.040  -1.223 H5A    D3 44 
D3 H2B    H2B  H 0 1 N N N -1.200  0.451  -6.109  0.450  0.183  3.241  H2B    D3 45 
D3 H4B    H4B  H 0 1 N N N 3.047   0.277  -6.895  -3.761 0.097  3.966  H4B    D3 46 
D3 H5B    H5B  H 0 1 N N N 2.606   0.254  -9.307  -4.182 0.753  1.633  H5B    D3 47 
D3 H6B    H6B  H 0 1 N N N 0.331   0.316  -10.174 -2.300 1.130  0.097  H6B    D3 48 
D3 HN     HN   H 0 1 N N N 0.846   -0.361 -4.402  -2.015 -0.860 5.534  HN     D3 49 
D3 H2C    H2C  H 0 1 N N N 4.162   1.644  -2.866  1.784  0.897  7.283  H2C    D3 50 
D3 H3C    H3C  H 0 1 N N N 4.421   1.466  -0.414  2.298  0.078  9.544  H3C    D3 51 
D3 H4C    H4C  H 0 1 N N N 2.455   0.987  1.013   0.828  -1.573 10.623 H4C    D3 52 
D3 H5C    H5C  H 0 1 N N N 0.221   0.679  -0.016  -1.162 -2.415 9.448  H5C    D3 53 
D3 H6C    H6C  H 0 1 N N N -0.050  0.853  -2.472  -1.697 -1.604 7.189  H6C    D3 54 
# 
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 
D3 P     OP1    DOUB N N 1  
D3 P     OP2    SING N N 2  
D3 P     OP3    SING N N 3  
D3 P     "O5'"  SING N N 4  
D3 OP2   HOP2   SING N N 5  
D3 OP3   HOP3   SING N N 6  
D3 "O5'" "C5'"  SING N N 7  
D3 "C5'" "C4'"  SING N N 8  
D3 "C5'" "H5'"  SING N N 9  
D3 "C5'" "H5''" SING N N 10 
D3 "C4'" "O4'"  SING N N 11 
D3 "C4'" "C3'"  SING N N 12 
D3 "C4'" "H4'"  SING N N 13 
D3 "O4'" "C1'"  SING N N 14 
D3 "C3'" "O3'"  SING N N 15 
D3 "C3'" "C2'"  SING N N 16 
D3 "C3'" "H3'"  SING N N 17 
D3 "O3'" "HO3'" SING N N 18 
D3 "C2'" "C1'"  SING N N 19 
D3 "C2'" "H2'"  SING N N 20 
D3 "C2'" "H2''" SING N N 21 
D3 "C1'" N1A    SING N N 22 
D3 "C1'" "H1'"  SING N N 23 
D3 N1A   C2A    SING Y N 24 
D3 N1A   C5A    SING Y N 25 
D3 C2A   N3A    DOUB Y N 26 
D3 C2A   H2A    SING N N 27 
D3 N3A   C4A    SING Y N 28 
D3 C4A   C5A    DOUB Y N 29 
D3 C4A   C1B    SING Y N 30 
D3 C5A   H5A    SING N N 31 
D3 C1B   C2B    DOUB Y N 32 
D3 C1B   C6B    SING Y N 33 
D3 C2B   C3B    SING Y N 34 
D3 C2B   H2B    SING N N 35 
D3 C3B   C4B    DOUB Y N 36 
D3 C3B   N      SING N N 37 
D3 C4B   C5B    SING Y N 38 
D3 C4B   H4B    SING N N 39 
D3 C5B   C6B    DOUB Y N 40 
D3 C5B   H5B    SING N N 41 
D3 C6B   H6B    SING N N 42 
D3 N     C      SING N N 43 
D3 N     HN     SING N N 44 
D3 C     O      DOUB N N 45 
D3 C     C1C    SING N N 46 
D3 C1C   C2C    DOUB Y N 47 
D3 C1C   C6C    SING Y N 48 
D3 C2C   C3C    SING Y N 49 
D3 C2C   H2C    SING N N 50 
D3 C3C   C4C    DOUB Y N 51 
D3 C3C   H3C    SING N N 52 
D3 C4C   C5C    SING Y N 53 
D3 C4C   H4C    SING N N 54 
D3 C5C   C6C    DOUB Y N 55 
D3 C5C   H5C    SING N N 56 
D3 C6C   H6C    SING N N 57 
# 
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 
D3 SMILES           ACDLabs              10.04 "O=C(c1ccccc1)Nc4cccc(c2ncn(c2)C3OC(C(O)C3)COP(=O)(O)O)c4"                                                                                                                                        
D3 SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3"                                                                                                                          
D3 SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3"                                                                                                                               
D3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O"                                                                                                                         
D3 SMILES           "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)C4CC(C(O4)COP(=O)(O)O)O"                                                                                                                                      
D3 InChI            InChI                1.03  "InChI=1S/C21H22N3O7P/c25-18-10-20(31-19(18)12-30-32(27,28)29)24-11-17(22-13-24)15-7-4-8-16(9-15)23-21(26)14-5-2-1-3-6-14/h1-9,11,13,18-20,25H,10,12H2,(H,23,26)(H2,27,28,29)/t18-,19+,20+/m0/s1" 
D3 InChIKey         InChI                1.03  OCVGIISTWVVLJA-XUVXKRRUSA-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 
D3 "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-{3-[(phenylcarbonyl)amino]phenyl}-1H-imidazole" 
D3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[4-(3-benzamidophenyl)imidazol-1-yl]-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 
D3 "Create component"     1999-07-08 RCSB 
D3 "Modify aromatic_flag" 2011-06-04 RCSB 
D3 "Modify descriptor"    2011-06-04 RCSB 
# 
