data_N5P
#

_chem_comp.id                                   N5P
_chem_comp.name                                 
;1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO
-1H-INDOLE
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H17 N2 O14 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2007-03-21
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       518.200
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    N5P
_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       ?
_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
N5P  OR2     OR2     O   0  1  N  N  N  -11.998  65.837  38.494  -9.522   2.250   1.175  OR2     N5P   1  
N5P  NRO     NRO     N   1  1  N  N  N  -12.083  64.841  39.197  -8.869   2.213   0.148  NRO     N5P   2  
N5P  OR1     OR1     O  -1  1  N  N  N  -11.065  64.372  39.684  -9.295   2.739  -0.865  OR1     N5P   3  
N5P  CZ3     CZ3     C   0  1  Y  N  N  -13.379  64.215  39.448  -7.553   1.535   0.131  CZ3     N5P   4  
N5P  CE3     CE3     C   0  1  Y  N  N  -13.435  63.087  40.255  -6.822   1.502  -1.023  CE3     N5P   5  
N5P  CD2     CD2     C   0  1  Y  N  N  -14.689  62.505  40.486  -5.581   0.862  -1.039  CD2     N5P   6  
N5P  CH2     CH2     C   0  1  Y  N  N  -14.522  64.788  38.877  -7.070   0.942   1.289  CH2     N5P   7  
N5P  CZ2     CZ2     C   0  1  Y  N  N  -15.762  64.242  39.088  -5.848   0.306   1.296  CZ2     N5P   8  
N5P  CE2     CE2     C   0  1  Y  N  N  -15.834  63.091  39.891  -5.089   0.255   0.130  CE2     N5P   9  
N5P  NE1     NE1     N   0  1  Y  N  N  -16.913  62.339  40.275  -3.863  -0.289  -0.179  NE1     N5P  10  
N5P  CD1     CD1     C   0  1  Y  N  N  -16.491  61.309  41.080  -3.566  -0.049  -1.493  CD1     N5P  11  
N5P  CG      CG      C   0  1  Y  N  N  -15.136  61.368  41.238  -4.563   0.642  -2.069  CG      N5P  12  
N5P  "C1'"   "C1'"   C   0  1  N  N  R  -18.346  62.553  39.911  -3.004  -1.017   0.758  "C1'"   N5P  13  
N5P  "O4'"   "O4'"   O   0  1  N  N  N  -19.140  61.497  40.459  -1.641  -0.977   0.304  "O4'"   N5P  14  
N5P  "C4'"   "C4'"   C   0  1  N  N  R  -19.839  60.808  39.424  -1.035  -2.233   0.679  "C4'"   N5P  15  
N5P  "C3'"   "C3'"   C   0  1  N  N  S  -19.933  61.809  38.279  -2.150  -3.271   0.398  "C3'"   N5P  16  
N5P  "O3'"   "O3'"   O   0  1  N  N  N  -21.050  62.687  38.470  -1.975  -4.438   1.204  "O3'"   N5P  17  
N5P  "C2'"   "C2'"   C   0  1  N  N  N  -18.617  62.561  38.407  -3.425  -2.498   0.813  "C2'"   N5P  18  
N5P  "C5'"   "C5'"   C   0  1  N  N  N  -19.116  59.497  39.113   0.196  -2.516  -0.185  "C5'"   N5P  19  
N5P  "O5'"   "O5'"   O   0  1  N  N  N  -19.882  58.704  38.212   1.212  -1.553   0.103  "O5'"   N5P  20  
N5P  PA      PA      P   0  1  N  N  N  -19.480  57.178  37.897   2.648  -1.549  -0.626  PA      N5P  21  
N5P  O1A     O1A     O   0  1  N  N  N  -18.003  57.138  37.578   3.289  -2.873  -0.459  O1A     N5P  22  
N5P  O2A     O2A     O   0  1  N  N  N  -20.008  56.330  39.030   2.453  -1.241  -2.194  O2A     N5P  23  
N5P  O3A     O3A     O   0  1  N  N  N  -20.269  56.735  36.564   3.581  -0.414   0.033  O3A     N5P  24  
N5P  PB      PB      P   0  1  N  N  N  -21.441  57.639  35.922   5.159  -0.101  -0.008  PB      N5P  25  
N5P  O1B     O1B     O   0  1  N  N  N  -20.892  58.294  34.677   5.649  -0.216  -1.400  O1B     N5P  26  
N5P  O2B     O2B     O   0  1  N  N  N  -22.078  58.503  36.990   5.940  -1.156   0.924  O2B     N5P  27  
N5P  O3B     O3B     O   0  1  N  N  N  -22.512  56.523  35.471   5.425   1.392   0.532  O3B     N5P  28  
N5P  PG      PG      P   0  1  N  N  N  -23.685  56.000  36.449   6.640   2.437   0.380  PG      N5P  29  
N5P  O3G     O3G     O   0  1  N  N  N  -23.759  54.517  36.153   6.146   3.903   0.824  O3G     N5P  30  
N5P  O2G     O2G     O   0  1  N  N  N  -23.229  56.314  37.860   7.864   1.977   1.319  O2G     N5P  31  
N5P  O1G     O1G     O   0  1  N  N  N  -24.900  56.779  35.998   7.087   2.472  -1.030  O1G     N5P  32  
N5P  HE3     HE3     H   0  1  N  N  N  -12.539  62.670  40.692  -7.203   1.969  -1.919  HE3     N5P  33  
N5P  HH2     HH2     H   0  1  N  N  N  -14.426  65.671  38.263  -7.657   0.980   2.195  HH2     N5P  34  
N5P  HZ2     HZ2     H   0  1  N  N  N  -16.649  64.680  38.654  -5.480  -0.152   2.202  HZ2     N5P  35  
N5P  HD1     HD1     H   0  1  N  N  N  -17.135  60.563  41.522  -2.663  -0.368  -1.993  HD1     N5P  36  
N5P  HG      HG      H   0  1  N  N  N  -14.522  60.692  41.815  -4.606   0.973  -3.096  HG      N5P  37  
N5P  "H1'"   "H1'"   H   0  1  N  N  N  -18.602  63.544  40.315  -3.079  -0.573   1.751  "H1'"   N5P  38  
N5P  "H4'"   "H4'"   H   0  1  N  N  N  -20.859  60.488  39.683  -0.770  -2.230   1.737  "H4'"   N5P  39  
N5P  "H3'"   "H3'"   H   0  1  N  N  N  -20.084  61.350  37.291  -2.181  -3.532  -0.660  "H3'"   N5P  40  
N5P  "HO3'"  "HO3'"  H   0  0  N  N  N  -21.095  63.304  37.749  -2.649  -5.117   1.064  "HO3'"  N5P  41  
N5P  "H2'1"  "H2'1"  H   0  0  N  N  N  -18.699  63.586  38.017  -3.725  -2.772   1.825  "H2'1"  N5P  42  
N5P  "H2'2"  "H2'2"  H   0  0  N  N  N  -17.811  62.061  37.849  -4.235  -2.691   0.109  "H2'2"  N5P  43  
N5P  "H5'1"  "H5'1"  H   0  0  N  N  N  -18.142  59.723  38.655   0.571  -3.516   0.034  "H5'1"  N5P  44  
N5P  "H5'2"  "H5'2"  H   0  0  N  N  N  -18.968  58.937  40.048  -0.077  -2.453  -1.238  "H5'2"  N5P  45  
N5P  HO2A    HO2A    H   0  0  N  N  N  -19.292  55.846  39.424   2.038  -0.387  -2.378  HO2A    N5P  46  
N5P  HO2B    HO2B    H   0  0  N  N  N  -22.049  59.414  36.721   5.670  -1.137   1.852  HO2B    N5P  47  
N5P  HOG3    HOG3    H   0  0  N  N  N  -24.582  54.321  35.721   6.828   4.585   0.758  HOG3    N5P  48  
N5P  HOG2    HOG2    H   0  0  N  N  N  -23.801  56.970  38.240   7.643   1.931   2.260  HOG2    N5P  49  
#   #
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
N5P  OR2    NRO     DOUB  N  N   1  
N5P  NRO    CZ3     SING  N  N   2  
N5P  NRO    OR1     SING  N  N   3  
N5P  CZ3    CH2     SING  Y  N   4  
N5P  CZ3    CE3     DOUB  Y  N   5  
N5P  CE3    CD2     SING  Y  N   6  
N5P  CE3    HE3     SING  N  N   7  
N5P  CD2    CE2     DOUB  Y  N   8  
N5P  CD2    CG      SING  Y  N   9  
N5P  CH2    CZ2     DOUB  Y  N  10  
N5P  CH2    HH2     SING  N  N  11  
N5P  CZ2    CE2     SING  Y  N  12  
N5P  CZ2    HZ2     SING  N  N  13  
N5P  CE2    NE1     SING  Y  N  14  
N5P  NE1    "C1'"   SING  N  N  15  
N5P  NE1    CD1     SING  Y  N  16  
N5P  CD1    CG      DOUB  Y  N  17  
N5P  CD1    HD1     SING  N  N  18  
N5P  CG     HG      SING  N  N  19  
N5P  "C1'"  "C2'"   SING  N  N  20  
N5P  "C1'"  "O4'"   SING  N  N  21  
N5P  "C1'"  "H1'"   SING  N  N  22  
N5P  "O4'"  "C4'"   SING  N  N  23  
N5P  "C4'"  "C3'"   SING  N  N  24  
N5P  "C4'"  "C5'"   SING  N  N  25  
N5P  "C4'"  "H4'"   SING  N  N  26  
N5P  "C3'"  "C2'"   SING  N  N  27  
N5P  "C3'"  "O3'"   SING  N  N  28  
N5P  "C3'"  "H3'"   SING  N  N  29  
N5P  "O3'"  "HO3'"  SING  N  N  30  
N5P  "C2'"  "H2'1"  SING  N  N  31  
N5P  "C2'"  "H2'2"  SING  N  N  32  
N5P  "C5'"  "O5'"   SING  N  N  33  
N5P  "C5'"  "H5'1"  SING  N  N  34  
N5P  "C5'"  "H5'2"  SING  N  N  35  
N5P  "O5'"  PA      SING  N  N  36  
N5P  PA     O3A     SING  N  N  37  
N5P  PA     O1A     DOUB  N  N  38  
N5P  PA     O2A     SING  N  N  39  
N5P  O2A    HO2A    SING  N  N  40  
N5P  O3A    PB      SING  N  N  41  
N5P  PB     O1B     DOUB  N  N  42  
N5P  PB     O3B     SING  N  N  43  
N5P  PB     O2B     SING  N  N  44  
N5P  O2B    HO2B    SING  N  N  45  
N5P  O3B    PG      SING  N  N  46  
N5P  PG     O1G     DOUB  N  N  47  
N5P  PG     O3G     SING  N  N  48  
N5P  PG     O2G     SING  N  N  49  
N5P  O3G    HOG3    SING  N  N  50  
N5P  O2G    HOG2    SING  N  N  51  
#   #
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
N5P  SMILES            ACDLabs               12.01  "[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"  
N5P  InChI             InChI                 1.03   "InChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1"  
N5P  InChIKey          InChI                 1.03   JJJBDAFRCKSXDR-YNEHKIRRSA-N  
N5P  SMILES_CANONICAL  CACTVS                3.370  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O"  
N5P  SMILES            CACTVS                3.370  "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O"  
N5P  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.2  "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]"  
N5P  SMILES            "OpenEye OEToolkits"  1.7.2  "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=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
N5P  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole"  
N5P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.2  "[[5-(5-nitroindol-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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
N5P  "Create component"   2007-03-21  RCSB  
N5P  "Modify descriptor"  2011-06-04  RCSB  
N5P  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     N5P
_pdbx_chem_comp_synonyms.name        "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
