data_NBM
#

_chem_comp.id                                   NBM
_chem_comp.name                                 "6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H17 N5 O6 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-03-21
_chem_comp.pdbx_modified_date                   2019-06-28
_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                       419.412
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    NBM
_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       6OB6
_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
NBM  C01   C1   C   0  1  Y  N  N  11.111  30.019  31.673  -5.142  -0.690  -1.049  C01   NBM   1  
NBM  C02   C2   C   0  1  Y  N  N  12.219  29.215  31.773  -6.432  -0.225  -1.224  C02   NBM   2  
NBM  C03   C3   C   0  1  Y  N  N  12.947  29.155  32.974  -7.114   0.340  -0.162  C03   NBM   3  
NBM  C04   C4   C   0  1  Y  N  N  12.525  29.923  34.085  -6.505   0.440   1.075  C04   NBM   4  
NBM  C05   C5   C   0  1  Y  N  N  11.393  30.742  33.982  -5.215  -0.026   1.250  C05   NBM   5  
NBM  C06   C6   C   0  1  Y  N  N  10.685  30.807  32.799  -4.534  -0.590   0.188  C06   NBM   6  
NBM  C07   C7   C   0  1  N  N  N   9.413  31.724  32.688  -3.128  -1.097   0.380  C07   NBM   7  
NBM  C09   C8   C   0  1  Y  N  N   9.850  34.601  32.264  -0.436  -0.610   0.324  C09   NBM   8  
NBM  C11   C9   C   0  1  Y  N  N  10.116  35.780  34.278   0.704  -2.527   0.920  C11   NBM   9  
NBM  C13   C10  C   0  1  Y  N  N  10.205  36.994  32.256   1.973  -0.673   0.431  C13   NBM  10  
NBM  C14   C11  C   0  1  Y  N  N   9.999  35.827  31.520   0.796   0.052   0.178  C14   NBM  11  
NBM  C16   C12  C   0  1  Y  N  N  10.193  37.538  30.105   2.466   1.396  -0.149  C16   NBM  12  
NBM  C18   C13  C   0  1  N  N  R  10.545  39.398  31.791   4.436  -0.097   0.356  C18   NBM  13  
NBM  C19   C14  C   0  1  N  N  R  11.752  39.832  31.418   5.003  -0.679  -0.964  C19   NBM  14  
NBM  C20   C15  C   0  1  N  N  S  11.572  41.281  31.106   6.508  -0.329  -0.853  C20   NBM  15  
NBM  C21   C16  C   0  1  N  N  R  10.012  41.531  31.141   6.553   0.824   0.169  C21   NBM  16  
NBM  C23   C17  C   0  1  N  N  N   9.522  42.391  29.934   7.197   2.057  -0.468  C23   NBM  17  
NBM  N10   N1   N   0  1  Y  N  N   9.915  34.613  33.601  -0.428  -1.887   0.693  N10   NBM  18  
NBM  N12   N2   N   0  1  Y  N  N  10.255  36.926  33.627   1.880  -1.948   0.796  N12   NBM  19  
NBM  N15   N3   N   0  1  Y  N  N  10.000  36.197  30.178   1.168   1.307  -0.171  N15   NBM  20  
NBM  N17   N4   N   0  1  Y  N  N  10.325  38.031  31.388   3.009   0.201   0.217  N17   NBM  21  
NBM  N27   N5   N   1  1  N  N  N  14.129  28.279  33.064  -8.495   0.839  -0.350  N27   NBM  22  
NBM  O22   O1   O   0  1  N  N  N   9.487  40.370  31.069   5.196   1.116   0.543  O22   NBM  23  
NBM  O24   O2   O   0  1  N  N  N   8.121  42.451  29.999   7.341   3.082   0.518  O24   NBM  24  
NBM  O25   O3   O   0  1  N  N  N  12.200  42.057  32.052   7.248  -1.453  -0.371  O25   NBM  25  
NBM  O26   O4   O   0  1  N  N  N  12.715  39.668  32.533   4.812  -2.093  -1.022  O26   NBM  26  
NBM  O28   O5   O   0  1  N  N  N  14.783  28.209  34.116  -9.031   0.751  -1.441  O28   NBM  27  
NBM  O29   O6   O  -1  1  N  N  N  14.480  27.609  32.080  -9.095   1.337   0.585  O29   NBM  28  
NBM  S08   S1   S   0  1  N  N  N   9.590  32.999  31.416  -1.954   0.236   0.032  S08   NBM  29  
NBM  H011  H1   H   0  0  N  N  N  10.557  30.060  30.747  -4.612  -1.136  -1.877  H011  NBM  30  
NBM  H021  H2   H   0  0  N  N  N  12.533  28.625  30.924  -6.908  -0.302  -2.191  H021  NBM  31  
NBM  H041  H3   H   0  0  N  N  N  13.076  29.878  35.013  -7.037   0.881   1.904  H041  NBM  32  
NBM  H051  H4   H   0  0  N  N  N  11.073  31.325  34.833  -4.740   0.052   2.217  H051  NBM  33  
NBM  H071  H5   H   0  0  N  N  N   9.245  32.214  33.658  -3.000  -1.435   1.408  H071  NBM  34  
NBM  H072  H6   H   0  0  N  N  N   8.545  31.095  32.440  -2.945  -1.929  -0.301  H072  NBM  35  
NBM  H111  H7   H   0  0  N  N  N  10.162  35.770  35.357   0.665  -3.564   1.218  H111  NBM  36  
NBM  H161  H8   H   0  0  N  N  N  10.236  38.121  29.197   3.030   2.286  -0.386  H161  NBM  37  
NBM  H181  H9   H   0  0  N  N  N  10.401  39.494  32.877   4.605  -0.787   1.183  H181  NBM  38  
NBM  H191  H10  H   0  0  N  N  N  12.122  39.305  30.526   4.554  -0.191  -1.829  H191  NBM  39  
NBM  H201  H11  H   0  0  N  N  N  11.942  41.495  30.093   6.895  -0.001  -1.817  H201  NBM  40  
NBM  H211  H12  H   0  0  N  N  N   9.765  42.059  32.074   7.123   0.519   1.046  H211  NBM  41  
NBM  H231  H13  H   0  0  N  N  N   9.834  41.923  28.989   8.178   1.792  -0.862  H231  NBM  42  
NBM  H232  H14  H   0  0  N  N  N   9.945  43.404  29.999   6.566   2.420  -1.279  H232  NBM  43  
NBM  H241  H15  H   0  0  N  N  N   7.792  42.970  29.274   7.744   3.895   0.185  H241  NBM  44  
NBM  H251  H16  H   0  0  N  N  N  13.136  41.898  32.022   8.187  -1.273  -0.227  H251  NBM  45  
NBM  H261  H17  H   0  0  N  N  N  12.824  38.744  32.725   5.150  -2.503  -1.830  H261  NBM  46  
#   #
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
NBM  C23  O24   SING  N  N   1  
NBM  C23  C21   SING  N  N   2  
NBM  C16  N15   DOUB  Y  N   3  
NBM  C16  N17   SING  Y  N   4  
NBM  N15  C14   SING  Y  N   5  
NBM  O22  C21   SING  N  N   6  
NBM  O22  C18   SING  N  N   7  
NBM  C20  C21   SING  N  N   8  
NBM  C20  C19   SING  N  N   9  
NBM  C20  O25   SING  N  N  10  
NBM  N17  C18   SING  N  N  11  
NBM  N17  C13   SING  Y  N  12  
NBM  S08  C09   SING  N  N  13  
NBM  S08  C07   SING  N  N  14  
NBM  C19  C18   SING  N  N  15  
NBM  C19  O26   SING  N  N  16  
NBM  C14  C13   DOUB  Y  N  17  
NBM  C14  C09   SING  Y  N  18  
NBM  C01  C02   DOUB  Y  N  19  
NBM  C01  C06   SING  Y  N  20  
NBM  C02  C03   SING  Y  N  21  
NBM  O29  N27   SING  N  N  22  
NBM  C13  N12   SING  Y  N  23  
NBM  C09  N10   DOUB  Y  N  24  
NBM  C07  C06   SING  N  N  25  
NBM  C06  C05   DOUB  Y  N  26  
NBM  C03  N27   SING  N  N  27  
NBM  C03  C04   DOUB  Y  N  28  
NBM  N27  O28   DOUB  N  N  29  
NBM  N10  C11   SING  Y  N  30  
NBM  N12  C11   DOUB  Y  N  31  
NBM  C05  C04   SING  Y  N  32  
NBM  C01  H011  SING  N  N  33  
NBM  C02  H021  SING  N  N  34  
NBM  C04  H041  SING  N  N  35  
NBM  C05  H051  SING  N  N  36  
NBM  C07  H071  SING  N  N  37  
NBM  C07  H072  SING  N  N  38  
NBM  C11  H111  SING  N  N  39  
NBM  C16  H161  SING  N  N  40  
NBM  C18  H181  SING  N  N  41  
NBM  C19  H191  SING  N  N  42  
NBM  C20  H201  SING  N  N  43  
NBM  C21  H211  SING  N  N  44  
NBM  C23  H231  SING  N  N  45  
NBM  C23  H232  SING  N  N  46  
NBM  O24  H241  SING  N  N  47  
NBM  O25  H251  SING  N  N  48  
NBM  O26  H261  SING  N  N  49  
#   #
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
NBM  SMILES            ACDLabs               12.01  "c1cc([N+](=O)[O-])ccc1CSc2ncnc3c2ncn3C4C(O)C(C(CO)O4)O"  
NBM  InChI             InChI                 1.03   "InChI=1S/C17H17N5O6S/c23-5-11-13(24)14(25)17(28-11)21-8-20-12-15(21)18-7-19-16(12)29-6-9-1-3-10(4-2-9)22(26)27/h1-4,7-8,11,13-14,17,23-25H,5-6H2/t11-,13-,14-,17-/m1/s1"  
NBM  InChIKey          InChI                 1.03   DYCJFJRCWPVDHY-LSCFUAHRSA-N  
NBM  SMILES_CANONICAL  CACTVS                3.385  "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(SCc4ccc(cc4)[N+]([O-])=O)ncnc23"  
NBM  SMILES            CACTVS                3.385  "OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(SCc4ccc(cc4)[N+]([O-])=O)ncnc23"  
NBM  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(ccc1CSc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)[N+](=O)[O-]"  
NBM  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(ccc1CSc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O)[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
NBM  "SYSTEMATIC NAME"  ACDLabs               12.01  "6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine"  
NBM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-5-[6-[(4-nitrophenyl)methylsulfanyl]purin-9-yl]oxolane-3,4-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NBM  "Create component"  2019-03-21  RCSB  
NBM  "Initial release"   2019-07-03  RCSB  
##
