data_16B
#

_chem_comp.id                                   16B
_chem_comp.name                                 "N-hydroxycytidine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H14 N3 O9 P"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-10-18
_chem_comp.pdbx_modified_date                   2021-08-11
_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                       339.196
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    16B
_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       4HIB
_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
16B  OP1     OAA    O  0  1  N  N  N  3.588  14.113  29.523   3.702  -2.145   1.092  OP1     16B   1  
16B  P       PAE    P  0  1  N  N  N  3.724  13.339  30.931   4.165  -1.339  -0.060  P       16B   2  
16B  OP3     OAD    O  0  1  N  Y  N  2.220  12.934  31.347   5.481  -0.512   0.359  OP3     16B   3  
16B  OP2     OAF    O  0  1  N  N  N  4.472  14.140  31.917   4.515  -2.316  -1.291  OP2     16B   4  
16B  "O5'"   "O5'"  O  0  1  N  N  N  4.469  11.891  30.758   3.004  -0.315  -0.500  "O5'"   16B   5  
16B  "C5'"   "C5'"  C  0  1  N  N  N  4.217  10.720  29.889   2.401   0.613   0.405  "C5'"   16B   6  
16B  "C4'"   "C4'"  C  0  1  N  N  R  5.326   9.545  30.128   1.341   1.431  -0.336  "C4'"   16B   7  
16B  "O4'"   "O4'"  O  0  1  N  N  N  4.870   8.414  29.238   0.252   0.579  -0.728  "O4'"   16B   8  
16B  "C3'"   "C3'"  C  0  1  N  N  S  6.858   9.763  29.754   0.766   2.513   0.599  "C3'"   16B   9  
16B  "O3'"   "O3'"  O  0  1  N  N  N  7.839   9.173  30.669   0.998   3.815   0.059  "O3'"   16B  10  
16B  "C2'"   "C2'"  C  0  1  N  N  R  7.014   9.124  28.373  -0.751   2.207   0.645  "C2'"   16B  11  
16B  "O2'"   "O2'"  O  0  1  N  N  N  8.446   8.876  28.091  -1.517   3.413   0.598  "O2'"   16B  12  
16B  "C1'"   "C1'"  C  0  1  N  N  R  6.100   7.872  28.503  -0.953   1.370  -0.648  "C1'"   16B  13  
16B  N1      NAM    N  0  1  N  N  N  5.695   7.281  27.175  -2.132   0.509  -0.526  N1      16B  14  
16B  C2      CAL    C  0  1  N  N  N  4.969   6.105  27.001  -2.146  -0.480   0.387  C2      16B  15  
16B  O2      OAK    O  0  1  N  N  N  4.654   5.430  27.964  -1.175  -0.647   1.106  O2      16B  16  
16B  N3      NAG    N  0  1  N  N  N  4.621   5.685  25.761  -3.204  -1.277   0.520  N3      16B  17  
16B  C6      CAN    C  0  1  N  N  N  6.017   8.059  26.053  -3.209   0.715  -1.334  C6      16B  18  
16B  C5      CAI    C  0  1  N  N  N  5.654   7.627  24.793  -4.293  -0.088  -1.211  C5      16B  19  
16B  C4      CAH    C  0  1  N  N  N  4.962   6.426  24.673  -4.274  -1.117  -0.248  C4      16B  20  
16B  N4      NAB    N  0  1  N  N  N  4.624   6.111  23.454  -5.361  -1.948  -0.102  N4      16B  21  
16B  OAC     OAC    O  0  1  N  N  N  3.722   7.036  22.967  -5.338  -2.980   0.867  OAC     16B  22  
16B  HOP3    H1     H  0  0  N  Y  N  1.614  13.238  30.681   5.841   0.039  -0.349  HOP3    16B  23  
16B  HOP2    H2     H  0  0  N  N  N  4.730  14.966  31.524   5.208  -2.962  -1.097  HOP2    16B  24  
16B  "H5'"   H3     H  0  1  N  N  N  4.257  11.040  28.837   1.932   0.068   1.224  "H5'"   16B  25  
16B  "H5''"  H4     H  0  0  N  N  N  3.218  10.318  30.112   3.164   1.281   0.802  "H5''"  16B  26  
16B  "H4'"   H5     H  0  1  N  N  N  5.266   9.231  31.180   1.782   1.898  -1.216  "H4'"   16B  27  
16B  "H3'"   H6     H  0  1  N  N  N  7.037  10.845  29.667   1.205   2.429   1.594  "H3'"   16B  28  
16B  "HO3'"  H7     H  0  0  N  Y  N  7.747   9.566  31.529   0.657   4.535   0.608  "HO3'"  16B  29  
16B  "H2'"   H8     H  0  1  N  N  N  6.592   9.797  27.612  -1.003   1.623   1.530  "H2'"   16B  30  
16B  "HO2'"  H9     H  0  0  N  N  N  8.906   9.705  28.033  -1.424   3.970   1.383  "HO2'"  16B  31  
16B  "H1'"   H10    H  0  1  N  N  N  6.601   7.112  29.121  -1.041   2.022  -1.517  "H1'"   16B  32  
16B  H6      H11    H  0  1  N  N  N  6.547   8.992  26.174  -3.199   1.511  -2.064  H6      16B  33  
16B  H5      H12    H  0  1  N  N  N  5.902   8.210  23.918  -5.158   0.059  -1.841  H5      16B  34  
16B  H41     H13    H  0  1  N  N  N  4.966   5.319  22.948  -6.143  -1.826  -0.663  H41     16B  35  
16B  H14     H14    H  0  1  N  N  N  3.478   6.804  22.079  -6.146  -3.511   0.895  H14     16B  36  
#   #
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
16B  OAC    N4      SING  N  N   1  
16B  N4     C4      SING  N  N   2  
16B  C4     C5      SING  N  N   3  
16B  C4     N3      DOUB  N  N   4  
16B  C5     C6      DOUB  N  N   5  
16B  N3     C2      SING  N  N   6  
16B  C6     N1      SING  N  N   7  
16B  C2     N1      SING  N  N   8  
16B  C2     O2      DOUB  N  N   9  
16B  N1     "C1'"   SING  N  N  10  
16B  "O2'"  "C2'"   SING  N  N  11  
16B  "C2'"  "C1'"   SING  N  N  12  
16B  "C2'"  "C3'"   SING  N  N  13  
16B  "C1'"  "O4'"   SING  N  N  14  
16B  "O4'"  "C4'"   SING  N  N  15  
16B  OP1    P       DOUB  N  N  16  
16B  "C3'"  "C4'"   SING  N  N  17  
16B  "C3'"  "O3'"   SING  N  N  18  
16B  "C5'"  "C4'"   SING  N  N  19  
16B  "C5'"  "O5'"   SING  N  N  20  
16B  "O5'"  P       SING  N  N  21  
16B  P      OP3     SING  N  N  22  
16B  P      OP2     SING  N  N  23  
16B  OP3    HOP3    SING  N  N  24  
16B  OP2    HOP2    SING  N  N  25  
16B  "C5'"  "H5'"   SING  N  N  26  
16B  "C5'"  "H5''"  SING  N  N  27  
16B  "C4'"  "H4'"   SING  N  N  28  
16B  "C3'"  "H3'"   SING  N  N  29  
16B  "O3'"  "HO3'"  SING  N  N  30  
16B  "C2'"  "H2'"   SING  N  N  31  
16B  "O2'"  "HO2'"  SING  N  N  32  
16B  "C1'"  "H1'"   SING  N  N  33  
16B  C6     H6      SING  N  N  34  
16B  C5     H5      SING  N  N  35  
16B  N4     H41     SING  N  N  36  
16B  OAC    H14     SING  N  N  37  
#   #
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
16B  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC1OC(N2C=CC(=NC2=O)NO)C(O)C1O"  
16B  InChI             InChI                 1.03   "InChI=1S/C9H14N3O9P/c13-6-4(3-20-22(17,18)19)21-8(7(6)14)12-2-1-5(11-16)10-9(12)15/h1-2,4,6-8,13-14,16H,3H2,(H,10,11,15)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1"  
16B  InChIKey          InChI                 1.03   DYOUVDKCXLKHKY-XVFCMESISA-N  
16B  SMILES_CANONICAL  CACTVS                3.385  "ONC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"  
16B  SMILES            CACTVS                3.385  "ONC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"  
16B  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1NO)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
16B  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1NO)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
16B  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-hydroxycytidine 5'-(dihydrogen phosphate)"  
16B  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[4-(oxidanylamino)-2-oxidanylidene-pyrimidin-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
16B  "Create component"  2012-10-18  RCSB  
16B  "Initial release"   2012-11-09  RCSB  
16B  "Modify atom id"    2021-07-27  RCSB  
16B  "Modify atom id"    2021-08-11  PDBE  
##
