data_50N
# 
_chem_comp.id                                    50N 
_chem_comp.name                                  "(1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H14 N3 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-07-08 
_chem_comp.pdbx_modified_date                    2015-08-07 
_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                        367.206 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     50N 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        5C7W 
_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 
50N P1   P1  P 0  1 N N N -7.182 -13.343 27.625 -4.484 -1.161 0.352  P1   50N 1  
50N C1   C1  C 0  1 Y N N -0.364 -11.267 27.572 3.141  1.208  0.900  C1   50N 2  
50N O1   O1  O 0  1 N N N 0.201  -10.159 28.154 3.219  2.453  1.434  O1   50N 3  
50N N1   N1  N 0  1 Y N N 0.307  -11.997 26.674 4.235  0.468  0.803  N1   50N 4  
50N C2   C2  C 0  1 Y N N -0.265 -13.069 26.091 4.201  -0.753 0.292  C2   50N 5  
50N C3   C3  C 0  1 Y N N -1.565 -13.468 26.399 3.006  -1.300 -0.161 C3   50N 6  
50N C4   C4  C 0  1 Y N N -2.296 -12.736 27.333 1.844  -0.552 -0.073 C4   50N 7  
50N OP1  O2  O 0  1 N N N -7.009 -14.336 26.527 -5.550 -0.575 -0.491 OP1  50N 8  
50N OP2  O3  O 0  1 N N N -8.455 -12.598 27.680 -3.921 -2.497 -0.348 OP2  50N 9  
50N O4   O4  O 0  1 N N N -5.960 -12.299 27.743 -3.287 -0.098 0.520  O4   50N 10 
50N C5   C5  C 0  1 N N N -5.975 -11.289 28.743 -2.618 0.503  -0.591 C5   50N 11 
50N C6   C6  C 0  1 N N R -4.667 -10.533 28.883 -1.539 1.460  -0.080 C6   50N 12 
50N O5   O5  O 0  1 N N N -3.564 -11.399 29.256 -0.491 0.730  0.594  O5   50N 13 
50N C7   C7  C 0  1 N N S -4.144 -9.769  27.669 -0.804 2.137  -1.265 C7   50N 14 
50N O6   O6  O 0  1 N N N -4.868 -8.574  27.404 -1.501 3.309  -1.694 O6   50N 15 
50N C8   C8  C 0  1 N N R -2.679 -9.530  28.036 0.560  2.505  -0.633 C8   50N 16 
50N O7   O7  O 0  1 N N N -2.532 -8.403  28.881 0.566  3.872  -0.217 O7   50N 17 
50N C9   C9  C 0  1 N N S -2.342 -10.815 28.827 0.676  1.570  0.587  C9   50N 18 
50N C10  C10 C 0  1 Y N N -1.676 -11.624 27.923 1.916  0.723  0.467  C10  50N 19 
50N N2   N2  N 0  1 N N N 0.403  -13.798 25.198 5.373  -1.496 0.208  N2   50N 20 
50N O8   O8  O -1 1 N N N -1.260 -15.261 24.740 2.249  -2.915 -1.675 O8   50N 21 
50N O9   O9  O 0  1 N N N -3.209 -15.205 26.316 3.678  -3.540 -0.255 O9   50N 22 
50N N3   N3  N 1  1 N N N -2.032 -14.581 25.800 2.976  -2.666 -0.731 N3   50N 23 
50N H1   H1  H 0  1 N N N -3.306 -13.015 27.594 0.903  -0.953 -0.417 H1   50N 24 
50N HOP2 H3  H 0  0 N N N -9.016 -12.875 26.965 -3.218 -2.936 0.151  HOP2 50N 25 
50N H4   H4  H 0  1 N N N -6.766 -10.567 28.492 -2.156 -0.274 -1.200 H4   50N 26 
50N H5   H5  H 0  1 N N N -6.205 -11.763 29.709 -3.339 1.056  -1.194 H5   50N 27 
50N H6   H6  H 0  1 N N N -4.805 -9.797  29.689 -1.974 2.208  0.583  H6   50N 28 
50N H7   H7  H 0  1 N N N -4.182 -10.434 26.793 -0.674 1.439  -2.092 H7   50N 29 
50N H8   H8  H 0  1 N N N -5.766 -8.790  27.183 -1.035 3.816  -2.373 H8   50N 30 
50N H9   H9  H 0  1 N N N -2.057 -9.461  27.131 1.370  2.316  -1.337 H9   50N 31 
50N H10  H10 H 0  1 N N N -1.613 -8.281  29.090 0.437  4.503  -0.938 H10  50N 32 
50N H11  H11 H 0  1 N N N -1.705 -10.556 29.686 0.714  2.159  1.503  H11  50N 33 
50N H13  H13 H 0  1 N N N 1.318  -13.415 25.072 5.378  -2.343 -0.265 H13  50N 34 
50N H14  H14 H 0  1 N N N 0.478  -14.740 25.526 6.186  -1.168 0.623  H14  50N 35 
50N H15  H15 H 0  1 N N N 1.080  -10.037 27.816 3.091  2.478  2.392  H15  50N 36 
50N OP3  O10 O 0  1 N Y N ?      ?       ?      -5.085 -1.526 1.800  OP3  50N 37 
50N HOP3 H16 H 0  0 N Y N ?      ?       ?      -5.812 -2.163 1.775  HOP3 50N 38 
# 
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 
50N O8  N3   SING N N 1  
50N N2  C2   SING N N 2  
50N N3  O9   DOUB N N 3  
50N N3  C3   SING N N 4  
50N C2  C3   SING Y N 5  
50N C2  N1   DOUB Y N 6  
50N C3  C4   DOUB Y N 7  
50N OP1 P1   DOUB N N 8  
50N N1  C1   SING Y N 9  
50N C4  C10  SING Y N 10 
50N O6  C7   SING N N 11 
50N C1  C10  DOUB Y N 12 
50N C1  O1   SING N N 13 
50N P1  OP2  SING N N 14 
50N P1  O4   SING N N 15 
50N C7  C8   SING N N 16 
50N C7  C6   SING N N 17 
50N O4  C5   SING N N 18 
50N C10 C9   SING N N 19 
50N C8  C9   SING N N 20 
50N C8  O7   SING N N 21 
50N C5  C6   SING N N 22 
50N C9  O5   SING N N 23 
50N C6  O5   SING N N 24 
50N C4  H1   SING N N 25 
50N OP2 HOP2 SING N N 26 
50N C5  H4   SING N N 27 
50N C5  H5   SING N N 28 
50N C6  H6   SING N N 29 
50N C7  H7   SING N N 30 
50N O6  H8   SING N N 31 
50N C8  H9   SING N N 32 
50N O7  H10  SING N N 33 
50N C9  H11  SING N N 34 
50N N2  H13  SING N N 35 
50N N2  H14  SING N N 36 
50N O1  H15  SING N N 37 
50N P1  OP3  SING N N 38 
50N OP3 HOP3 SING N N 39 
# 
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 
50N SMILES           ACDLabs              12.01 "P(O)(OCC1OC(C(C1O)O)c2c(O)nc(c(c2)[N+]([O-])=O)N)(O)=O"                                                                                                    
50N InChI            InChI                1.03  "InChI=1S/C10H14N3O10P/c11-9-4(13(17)18)1-3(10(16)12-9)8-7(15)6(14)5(23-8)2-22-24(19,20)21/h1,5-8,14-15H,2H2,(H3,11,12,16)(H2,19,20,21)/t5-,6-,7-,8+/m1/s1" 
50N InChIKey         InChI                1.03  NFRHBMAHQZOVIK-XUTVFYLZSA-N                                                                                                                                 
50N SMILES_CANONICAL CACTVS               3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                    
50N SMILES           CACTVS               3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"                                                                                          
50N SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1c(c(nc(c1[N+](=O)[O-])N)O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                  
50N SMILES           "OpenEye OEToolkits" 1.9.2 "c1c(c(nc(c1[N+](=O)[O-])N)O)C2C(C(C(O2)COP(=O)(O)O)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 
50N "SYSTEMATIC NAME" ACDLabs              12.01 "(1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol"                                   
50N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5S)-5-(6-azanyl-5-nitro-2-oxidanyl-pyridin-3-yl)-3,4-bis(oxidanyl)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 
50N "Create component" 2015-07-08 RCSB 
50N "Modify name"      2015-07-17 RCSB 
50N "Initial release"  2015-08-12 RCSB 
# 
