data_NP3
# 
_chem_comp.id                                    NP3 
_chem_comp.name                                  "1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5'-PHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H13 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-12-20 
_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                        308.182 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     NP3 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "Corina V3.40" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1DK6 
_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 
NP3 P      P    P 0  1 N N N -1.567 -8.712  11.284 4.322  -1.093 -0.031 P      NP3 1  
NP3 O1P    O1P  O 0  1 N N N -2.224 -9.789  10.510 4.047  -1.788 1.247  O1P    NP3 2  
NP3 O2P    O2P  O 0  1 N N N -0.226 -8.225  10.882 5.569  -0.093 0.160  O2P    NP3 3  
NP3 O3P    O3P  O 0  1 N Y N -1.527 -9.160  12.844 4.673  -2.178 -1.168 O3P    NP3 4  
NP3 "O5'"  O5*  O 0  1 N N N -2.575 -7.437  11.351 3.022  -0.252 -0.474 "O5'"  NP3 5  
NP3 "C5'"  C5*  C 0  1 N N N -3.863 -7.588  11.983 2.397  0.717  0.369  "C5'"  NP3 6  
NP3 "C4'"  C4*  C 0  1 N N R -4.528 -6.288  12.468 1.196  1.326  -0.356 "C4'"  NP3 7  
NP3 "O4'"  O4*  O 0  1 N N N -3.617 -5.643  13.367 0.166  0.334  -0.555 "O4'"  NP3 8  
NP3 "C1'"  C1*  C 0  1 N N R -3.220 -4.424  12.746 -1.068 1.044  -0.752 "C1'"  NP3 9  
NP3 N1     N1   N 0  1 Y N N -1.799 -4.211  12.866 -2.180 0.283  -0.177 N1     NP3 10 
NP3 C5     C5   C 0  1 Y N N -1.194 -3.301  13.677 -2.139 -0.424 0.989  C5     NP3 11 
NP3 C2     C2   C 0  1 Y N N -0.816 -4.830  12.195 -3.427 0.168  -0.715 C2     NP3 12 
NP3 C3     C3   C 0  1 Y N N 0.397  -4.386  12.501 -4.168 -0.609 0.101  C3     NP3 13 
NP3 C4     C4   C 0  1 Y N N 0.128  -3.409  13.456 -3.349 -0.985 1.184  C4     NP3 14 
NP3 N3     N3   N 1  1 N N N 1.542  -4.749  11.975 -5.583 -0.993 -0.102 N3     NP3 15 
NP3 ON1    ON1  O -1 1 N N N 1.966  -4.114  10.970 -6.187 -0.598 -1.084 ON1    NP3 16 
NP3 ON2    ON2  O 0  1 N N N 2.198  -5.707  12.458 -6.144 -1.704 0.712  ON2    NP3 17 
NP3 "C2'"  C2*  C 0  1 N N N -3.605 -4.566  11.280 -0.936 2.401  -0.035 "C2'"  NP3 18 
NP3 "C3'"  C3*  C 0  1 N N S -4.912 -5.273  11.379 0.505  2.392  0.531  "C3'"  NP3 19 
NP3 "O3'"  O3*  O 0  1 N N N -5.966 -4.392  11.819 1.125  3.670  0.370  "O3'"  NP3 20 
NP3 HOP2   2HOP H 0  0 N N N -0.196 -8.121  9.938  5.805  0.398  -0.639 HOP2   NP3 21 
NP3 HOP3   3HOP H 0  0 N N N -1.519 -10.108 12.902 5.446  -2.722 -0.967 HOP3   NP3 22 
NP3 "H5'1" 1H5* H 0  0 N N N -4.539 -8.049  11.247 2.062  0.237  1.288  "H5'1" NP3 23 
NP3 "H5'2" 2H5* H 0  0 N N N -3.688 -8.193  12.885 3.112  1.504  0.611  "H5'2" NP3 24 
NP3 "H4'"  H4*  H 0  1 N N N -5.478 -6.596  12.928 1.502  1.757  -1.309 "H4'"  NP3 25 
NP3 "H1'"  H1*  H 0  1 N N N -3.708 -3.562  13.224 -1.239 1.201  -1.817 "H1'"  NP3 26 
NP3 H5     H5   H 0  1 N N N -1.681 -2.624  14.364 -1.284 -0.518 1.642  H5     NP3 27 
NP3 H2     H2   H 0  1 N N N -0.994 -5.615  11.475 -3.764 0.621  -1.635 H2     NP3 28 
NP3 H4     H4   H 0  1 N N N 0.881  -2.816  13.953 -3.638 -1.607 2.018  H4     NP3 29 
NP3 "H2'1" 1H2* H 0  0 N N N -3.698 -3.591  10.779 -1.063 3.221  -0.742 "H2'1" NP3 30 
NP3 "H2'2" 2H2* H 0  0 N N N -2.857 -5.099  10.674 -1.663 2.478  0.774  "H2'2" NP3 31 
NP3 "H3'"  H3*  H 0  1 N N N -5.305 -5.694  10.442 0.510  2.089  1.578  "H3'"  NP3 32 
NP3 H3T    H3T  H 0  1 N Y N -5.853 -4.198  12.742 0.727  4.370  0.905  H3T    NP3 33 
# 
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 
NP3 P     O1P    DOUB N N 1  
NP3 P     O2P    SING N N 2  
NP3 P     O3P    SING N N 3  
NP3 P     "O5'"  SING N N 4  
NP3 O2P   HOP2   SING N N 5  
NP3 O3P   HOP3   SING N N 6  
NP3 "O5'" "C5'"  SING N N 7  
NP3 "C5'" "C4'"  SING N N 8  
NP3 "C5'" "H5'1" SING N N 9  
NP3 "C5'" "H5'2" SING N N 10 
NP3 "C4'" "O4'"  SING N N 11 
NP3 "C4'" "C3'"  SING N N 12 
NP3 "C4'" "H4'"  SING N N 13 
NP3 "O4'" "C1'"  SING N N 14 
NP3 "C1'" N1     SING N N 15 
NP3 "C1'" "C2'"  SING N N 16 
NP3 "C1'" "H1'"  SING N N 17 
NP3 N1    C5     SING Y N 18 
NP3 N1    C2     SING Y N 19 
NP3 C5    C4     DOUB Y N 20 
NP3 C5    H5     SING N N 21 
NP3 C2    C3     DOUB Y N 22 
NP3 C2    H2     SING N N 23 
NP3 C3    C4     SING Y N 24 
NP3 C3    N3     SING N N 25 
NP3 C4    H4     SING N N 26 
NP3 N3    ON1    SING N N 27 
NP3 N3    ON2    DOUB N N 28 
NP3 "C2'" "C3'"  SING N N 29 
NP3 "C2'" "H2'1" SING N N 30 
NP3 "C2'" "H2'2" SING N N 31 
NP3 "C3'" "O3'"  SING N N 32 
NP3 "C3'" "H3'"  SING N N 33 
NP3 "O3'" H3T    SING N N 34 
# 
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 
NP3 SMILES           ACDLabs              10.04 "[O-][N+](=O)c1ccn(c1)C2OC(C(O)C2)COP(=O)(O)O"                                                                                    
NP3 SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccc(c2)[N+]([O-])=O"                                                                      
NP3 SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccc(c2)[N+]([O-])=O"                                                                           
NP3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cn(cc1[N+](=O)[O-])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                       
NP3 SMILES           "OpenEye OEToolkits" 1.5.0 "c1cn(cc1[N+](=O)[O-])C2CC(C(O2)COP(=O)(O)O)O"                                                                                    
NP3 InChI            InChI                1.03  "InChI=1S/C9H13N2O8P/c12-7-3-9(10-2-1-6(4-10)11(13)14)19-8(7)5-18-20(15,16)17/h1-2,4,7-9,12H,3,5H2,(H2,15,16,17)/t7-,8+,9+/m0/s1" 
NP3 InChIKey         InChI                1.03  RZUPPTSNKSBSQO-DJLDLDEBSA-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 
NP3 "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-nitro-1H-pyrrole"          
NP3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(3-nitropyrrol-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 
NP3 "Create component"  1999-12-20 RCSB 
NP3 "Modify descriptor" 2011-06-04 RCSB 
# 
