data_U7B
#

_chem_comp.id                                   U7B
_chem_comp.name                                 "2'-deoxy-2'2'-difluorodeoxycytidine"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H12 F2 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-01-27
_chem_comp.pdbx_modified_date                   2021-04-02
_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                       343.178
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    U7B
_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       7NBK
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
U7B  P       P1   P  0  1  N  N  N  28.877  23.670  25.673   4.303   1.030   0.022  P       U7B   1  
U7B  "C5'"   C1   C  0  1  N  N  N  26.634  25.071  25.705   2.213  -0.595  -0.338  "C5'"   U7B   2  
U7B  "O5'"   O1   O  0  1  N  N  N  27.455  24.085  26.317   2.949   0.299   0.498  "O5'"   U7B   3  
U7B  "C4'"   C2   C  0  1  N  N  R  25.219  25.131  26.310   0.987  -1.109   0.419  "C4'"   U7B   4  
U7B  "O4'"   O2   O  0  1  N  N  N  24.468  23.932  26.099   0.026  -0.045   0.601  "O4'"   U7B   5  
U7B  "C3'"   C3   C  0  1  N  N  R  25.181  25.417  27.825   0.243  -2.173  -0.418  "C3'"   U7B   6  
U7B  "O3'"   O3   O  0  1  N  N  N  25.334  26.813  28.117   0.606  -3.488   0.007  "O3'"   U7B   7  
U7B  "C2'"   C4   C  0  1  N  N  N  23.813  24.782  28.179  -1.250  -1.903  -0.128  "C2'"   U7B   8  
U7B  "C1'"   C5   C  0  1  N  N  R  23.309  24.050  26.914  -1.233  -0.708   0.851  "C1'"   U7B   9  
U7B  N1      N1   N  0  1  N  N  N  22.642  22.730  27.186  -2.350   0.197   0.570  N1      U7B  10  
U7B  C2      C6   C  0  1  N  N  N  21.271  22.702  27.402  -2.434   0.806  -0.627  C2      U7B  11  
U7B  O2      O4   O  0  1  N  N  N  20.584  23.714  27.322  -1.575   0.597  -1.468  O2      U7B  12  
U7B  N3      N2   N  0  1  N  N  N  20.643  21.545  27.709  -3.439   1.633  -0.909  N3      U7B  13  
U7B  C4      C7   C  0  1  N  N  N  21.356  20.452  27.845  -4.386   1.878  -0.013  C4      U7B  14  
U7B  N4      N3   N  0  1  N  N  N  20.694  19.365  28.143  -5.420   2.734  -0.315  N4      U7B  15  
U7B  C5      C8   C  0  1  N  N  N  22.755  20.419  27.673  -4.327   1.256   1.252  C5      U7B  16  
U7B  C6      C9   C  0  1  N  N  N  23.367  21.584  27.347  -3.302   0.414   1.521  C6      U7B  17  
U7B  OP1     O5   O  0  1  N  N  N  29.504  24.890  25.120   4.049   1.770  -1.234  OP1     U7B  18  
U7B  OP2     O6   O  0  1  N  N  N  29.624  22.834  26.639   4.787   2.058   1.163  OP2     U7B  19  
U7B  F1      F1   F  0  1  N  N  N  22.842  25.706  28.513  -1.842  -3.020   0.472  F1      U7B  20  
U7B  F2      F2   F  0  1  N  N  N  24.002  23.893  29.221  -1.925  -1.566  -1.306  F2      U7B  21  
U7B  "H5''"  H1   H  0  0  N  N  N  26.548  24.840  24.633   1.890  -0.070  -1.237  "H5''"  U7B  22  
U7B  "H5'"   H2   H  0  1  N  N  N  27.112  26.054  25.831   2.846  -1.437  -0.617  "H5'"   U7B  23  
U7B  "H4'"   H3   H  0  1  N  N  N  24.693  25.960  25.814   1.283  -1.523   1.383  "H4'"   U7B  24  
U7B  "H3'"   H4   H  0  1  N  N  N  25.976  24.836  28.315   0.458  -2.043  -1.479  "H3'"   U7B  25  
U7B  H1      H5   H  0  1  N  N  N  25.305  26.945  29.057   0.169  -4.196  -0.486  H1      U7B  26  
U7B  "H1'"   H6   H  0  1  N  N  N  22.580  24.707  26.416  -1.279  -1.059   1.882  "H1'"   U7B  27  
U7B  H42     H7   H  0  1  N  N  N  19.701  19.399  28.254  -5.458   3.160  -1.186  H42     U7B  28  
U7B  H41     H8   H  0  1  N  N  N  21.181  18.499  28.260  -6.111   2.911   0.342  H41     U7B  29  
U7B  H5      H9   H  0  1  N  N  N  23.316  19.504  27.796  -5.090   1.446   1.992  H5      U7B  30  
U7B  H6      H10  H  0  1  N  N  N  24.438  21.606  27.213  -3.237  -0.078   2.480  H6      U7B  31  
U7B  H3      H12  H  0  1  N  N  N  30.480  23.217  26.794   5.599   2.535   0.943  H3      U7B  32  
U7B  OP3     O7   O  0  1  N  Y  N  28.395  22.735  24.436   5.449  -0.073  -0.227  OP3     U7B  33  
U7B  H2      H13  H  0  1  N  N  N  28.612  23.159  23.614   5.667  -0.597   0.555  H2      U7B  34  
#   #
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
U7B  OP1    P       DOUB  N  N   1  
U7B  P      "O5'"   SING  N  N   2  
U7B  P      OP2     SING  N  N   3  
U7B  "C5'"  "C4'"   SING  N  N   4  
U7B  "C5'"  "O5'"   SING  N  N   5  
U7B  "O4'"  "C4'"   SING  N  N   6  
U7B  "O4'"  "C1'"   SING  N  N   7  
U7B  "C4'"  "C3'"   SING  N  N   8  
U7B  "C1'"  N1      SING  N  N   9  
U7B  "C1'"  "C2'"   SING  N  N  10  
U7B  N1     C6      SING  N  N  11  
U7B  N1     C2      SING  N  N  12  
U7B  O2     C2      DOUB  N  N  13  
U7B  C6     C5      DOUB  N  N  14  
U7B  C2     N3      SING  N  N  15  
U7B  C5     C4      SING  N  N  16  
U7B  N3     C4      DOUB  N  N  17  
U7B  "C3'"  "O3'"   SING  N  N  18  
U7B  "C3'"  "C2'"   SING  N  N  19  
U7B  C4     N4      SING  N  N  20  
U7B  "C2'"  F1      SING  N  N  21  
U7B  "C2'"  F2      SING  N  N  22  
U7B  "C5'"  "H5''"  SING  N  N  23  
U7B  "C5'"  "H5'"   SING  N  N  24  
U7B  "C4'"  "H4'"   SING  N  N  25  
U7B  "C3'"  "H3'"   SING  N  N  26  
U7B  "O3'"  H1      SING  N  N  27  
U7B  "C1'"  "H1'"   SING  N  N  28  
U7B  N4     H42     SING  N  N  29  
U7B  N4     H41     SING  N  N  30  
U7B  C5     H5      SING  N  N  31  
U7B  C6     H6      SING  N  N  32  
U7B  OP2    H3      SING  N  N  33  
U7B  P      OP3     SING  N  N  34  
U7B  OP3    H2      SING  N  N  35  
#   #
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
U7B  InChI             InChI                 1.03   "InChI=1S/C9H12F2N3O7P/c10-9(11)6(15)4(3-20-22(17,18)19)21-7(9)14-2-1-5(12)13-8(14)16/h1-2,4,6-7,15H,3H2,(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1"  
U7B  InChIKey          InChI                 1.03   KNTREFQOVSMROS-QPPQHZFASA-N  
U7B  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)C2(F)F"  
U7B  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)C2(F)F"  
U7B  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)O)O)(F)F"  
U7B  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)(F)F"  
#
_pdbx_chem_comp_identifier.comp_id          U7B
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     U7B
_pdbx_chem_comp_synonyms.name        "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
U7B  "Create component"  2021-01-27  PDBE  
U7B  "Modify synonyms"   2021-03-13  RCSB  
U7B  "Initial release"   2021-04-07  RCSB  
##
