data_N5I
# 
_chem_comp.id                                    N5I 
_chem_comp.name                                  "1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-NITRO-1H-INDOLE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H15 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-MONOPHOSPHATE" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-03-21 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        358.241 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     N5I 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye OEToolkits" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
N5I O3P    O3P  O 0  1 N Y N -20.164 64.193 45.222 0.339  -0.227 -4.868 O3P    N5I 1  
N5I OR2    OR2  O 0  1 N N N -11.094 68.879 41.671 2.199  6.489  4.264  OR2    N5I 2  
N5I NRO    NRO  N 1  1 N N N -11.577 67.770 41.849 1.888  6.522  3.049  NRO    N5I 3  
N5I OR1    OR1  O -1 1 N N N -10.832 66.803 41.911 1.577  7.590  2.470  OR1    N5I 4  
N5I CZ3    CZ3  C 0  1 Y N N -13.021 67.604 41.987 1.888  5.311  2.306  CZ3    N5I 5  
N5I CE3    CE3  C 0  1 Y N N -13.527 66.329 42.191 1.543  5.334  0.950  CE3    N5I 6  
N5I CD2    CD2  C 0  1 Y N N -14.915 66.184 42.318 1.545  4.128  0.220  CD2    N5I 7  
N5I CH2    CH2  C 0  1 Y N N -13.844 68.740 41.911 2.232  4.116  2.935  CH2    N5I 8  
N5I CZ2    CZ2  C 0  1 Y N N -15.206 68.628 42.032 2.241  2.908  2.231  CZ2    N5I 9  
N5I CE2    CE2  C 0  1 Y N N -15.733 67.338 42.237 1.893  2.946  0.876  CE2    N5I 10 
N5I NE1    NE1  N 0  1 Y N N -17.026 66.918 42.395 1.818  1.923  -0.049 NE1    N5I 11 
N5I CD1    CD1  C 0  1 Y N N -17.046 65.558 42.568 1.433  2.429  -1.266 CD1    N5I 12 
N5I CG     CG   C 0  1 Y N N -15.780 65.064 42.539 1.257  3.787  -1.131 CG     N5I 13 
N5I "C1'"  C1*  C 0  1 N N R -18.261 67.759 42.392 2.101  0.516  0.211  "C1'"  N5I 14 
N5I "O4'"  O4*  O 0  1 N N N -19.381 66.974 42.806 2.678  -0.093 -0.958 "O4'"  N5I 15 
N5I "C4'"  C4*  C 0  1 N N R -20.259 66.740 41.703 2.156  -1.432 -1.088 "C4'"  N5I 16 
N5I "C3'"  C3*  C 0  1 N N S -19.515 67.224 40.464 1.309  -1.697 0.152  "C3'"  N5I 17 
N5I "O3'"  O3*  O 0  1 N N N -20.441 67.731 39.498 2.127  -2.250 1.180  "O3'"  N5I 18 
N5I "C2'"  C2*  C 0  1 N N N -18.637 68.330 41.029 0.878  -0.312 0.578  "C2'"  N5I 19 
N5I "C5'"  C5*  C 0  1 N N N -20.649 65.266 41.665 1.348  -1.500 -2.377 "C5'"  N5I 20 
N5I "O5'"  O5*  O 0  1 N N N -21.014 64.815 42.966 2.211  -1.232 -3.468 "O5'"  N5I 21 
N5I P      P    P 0  1 N N N -20.212 63.635 43.716 1.592  -1.245 -4.964 P      N5I 22 
N5I O2P    O2P  O 0  1 N N N -21.078 62.391 43.723 0.886  -2.697 -5.051 O2P    N5I 23 
N5I O1P    O1P  O 0  1 N N N -18.806 63.542 43.147 2.575  -0.951 -6.059 O1P    N5I 24 
N5I HOP3   3HOP H 0  0 N N N -20.155 63.463 45.830 -0.163 -0.014 -5.684 HOP3   N5I 25 
N5I HE3    HE3  H 0  1 N N N -12.871 65.473 42.250 1.274  6.266  0.460  HE3    N5I 26 
N5I HH2    HH2  H 0  1 N N N -13.400 69.712 41.756 2.499  4.107  3.990  HH2    N5I 27 
N5I HZ2    HZ2  H 0  1 N N N -15.848 69.494 41.972 2.510  1.980  2.725  HZ2    N5I 28 
N5I HD1    HD1  H 0  1 N N N -17.938 64.965 42.707 1.317  1.781  -2.124 HD1    N5I 29 
N5I HG     HG   H 0  1 N N N -15.485 64.032 42.659 0.954  4.461  -1.920 HG     N5I 30 
N5I "H1'"  H1*  H 0  1 N N N -18.031 68.592 43.072 2.853  0.503  1.007  "H1'"  N5I 31 
N5I "H4'"  H4*  H 0  1 N N N -21.211 67.286 41.777 3.008  -2.117 -1.157 "H4'"  N5I 32 
N5I "H3'"  H3*  H 0  1 N N N -18.944 66.442 39.943 0.475  -2.383 -0.018 "H3'"  N5I 33 
N5I H3T    H3T  H 0  1 N Y N -21.293 67.843 39.904 2.928  -1.706 1.218  H3T    N5I 34 
N5I "H2'1" 1H2* H 0  0 N N N -19.176 69.285 41.114 0.008  0.008  -0.009 "H2'1" N5I 35 
N5I "H2'2" 2H2* H 0  0 N N N -17.771 68.576 40.397 0.635  -0.225 1.641  "H2'2" N5I 36 
N5I "H5'1" 1H5* H 0  0 N N N -21.504 65.136 40.985 0.551  -0.756 -2.359 "H5'1" N5I 37 
N5I "H5'2" 2H5* H 0  0 N N N -19.789 64.678 41.311 0.917  -2.495 -2.497 "H5'2" N5I 38 
N5I HOP2   2HOP H 0  0 N N N -21.259 62.126 42.829 0.508  -2.990 -5.907 HOP2   N5I 39 
# 
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 
N5I O3P   P      SING N N 1  
N5I O3P   HOP3   SING N N 2  
N5I OR2   NRO    DOUB N N 3  
N5I NRO   OR1    SING N N 4  
N5I NRO   CZ3    SING N N 5  
N5I CZ3   CH2    DOUB Y N 6  
N5I CZ3   CE3    SING Y N 7  
N5I CE3   CD2    DOUB Y N 8  
N5I CE3   HE3    SING N N 9  
N5I CD2   CE2    SING Y N 10 
N5I CD2   CG     SING Y N 11 
N5I CH2   CZ2    SING Y N 12 
N5I CH2   HH2    SING N N 13 
N5I CZ2   CE2    DOUB Y N 14 
N5I CZ2   HZ2    SING N N 15 
N5I CE2   NE1    SING Y N 16 
N5I NE1   "C1'"  SING N N 17 
N5I NE1   CD1    SING Y N 18 
N5I CD1   CG     DOUB Y N 19 
N5I CD1   HD1    SING N N 20 
N5I CG    HG     SING N N 21 
N5I "C1'" "C2'"  SING N N 22 
N5I "C1'" "O4'"  SING N N 23 
N5I "C1'" "H1'"  SING N N 24 
N5I "O4'" "C4'"  SING N N 25 
N5I "C4'" "C3'"  SING N N 26 
N5I "C4'" "C5'"  SING N N 27 
N5I "C4'" "H4'"  SING N N 28 
N5I "C3'" "O3'"  SING N N 29 
N5I "C3'" "C2'"  SING N N 30 
N5I "C3'" "H3'"  SING N N 31 
N5I "O3'" H3T    SING N N 32 
N5I "C2'" "H2'1" SING N N 33 
N5I "C2'" "H2'2" SING N N 34 
N5I "C5'" "O5'"  SING N N 35 
N5I "C5'" "H5'1" SING N N 36 
N5I "C5'" "H5'2" SING N N 37 
N5I "O5'" P      SING N N 38 
N5I P     O1P    DOUB N N 39 
N5I P     O2P    SING N N 40 
N5I O2P   HOP2   SING N N 41 
# 
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 
N5I SMILES           ACDLabs              10.04 "[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)O"                                                                                                          
N5I InChI            InChI                1.02b "InChI=1/C13H15N2O8P/c16-11-6-13(23-12(11)7-22-24(19,20)21)14-4-3-8-5-9(15(17)18)1-2-10(8)14/h1-5,11-13,16H,6-7H2,(H2,19,20,21)/t11-,12+,13+/m0/s1/f/h19-20H" 
N5I InChIKey         InChI                1.02b FQCJFJRLZCIFHB-ORXCSARQDN                                                                                                                                     
N5I SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O"                                                                                            
N5I SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O"                                                                                                 
N5I SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc2c(ccn2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)cc1[N+](=O)[O-]"                                                                                             
N5I SMILES           "OpenEye OEToolkits" 1.5.0 "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)O)O)cc1[N+](=O)[O-]"                                                                                                          
# 
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 
N5I "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-nitro-1H-indole"          
N5I "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-nitroindol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
