data_4BD
# 
_chem_comp.id                                    4BD 
_chem_comp.name                                  "5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 F2 N2 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-03-20 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        516.176 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     4BD 
_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        3GDX 
_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 
4BD PA     PA     P 0 1 N N S 5.188  5.440 14.944 1.242  -1.081 -0.575 PA     4BD 1  
4BD O1A    O1A    O 0 1 N N N 4.011  5.447 15.857 1.028  -0.290 -1.960 O1A    4BD 2  
4BD O2A    O2A    O 0 1 N N N 6.451  6.054 15.428 1.777  -2.432 -0.855 O2A    4BD 3  
4BD C3A    C3A    C 0 1 N N N 5.517  3.763 14.364 2.421  -0.166 0.472  C3A    4BD 4  
4BD F1A    F1A    F 0 1 N N N 6.343  3.831 13.327 1.915  1.111  0.737  F1A    4BD 5  
4BD F2A    F2A    F 0 1 N N N 6.162  3.123 15.344 2.607  -0.853 1.676  F2A    4BD 6  
4BD "O5'"  "O5'"  O 0 1 N N N 4.723  6.377 13.733 -0.168 -1.211 0.192  "O5'"  4BD 7  
4BD PB     PB     P 0 1 N N S 4.116  2.756 13.879 4.017  -0.019 -0.396 PB     4BD 8  
4BD O1B    O1B    O 0 1 N N N 4.281  2.314 12.471 3.820  0.708  -1.670 O1B    4BD 9  
4BD O2B    O2B    O 0 1 N N N 2.841  3.387 14.282 4.599  -1.489 -0.702 O2B    4BD 10 
4BD O3B    O3B    O 0 1 N N N 4.232  1.484 14.684 5.058  0.789  0.528  O3B    4BD 11 
4BD PG     PG     P 0 1 N N N 4.000  1.277 16.169 6.593  1.244  0.350  PG     4BD 12 
4BD O1G    O1G    O 0 1 N N N 5.193  0.557 16.685 7.231  1.556  1.794  O1G    4BD 13 
4BD O2G    O2G    O 0 1 N N N 2.662  0.674 16.372 7.357  0.158  -0.303 O2G    4BD 14 
4BD O3G    O3G    O 0 1 N N N 4.002  2.615 16.825 6.657  2.569  -0.563 O3G    4BD 15 
4BD "C5'"  "C5'"  C 0 1 N N N 3.512  6.143 13.017 -1.267 -1.965 -0.322 "C5'"  4BD 16 
4BD "C4'"  "C4'"  C 0 1 N N R 3.713  6.378 11.538 -2.445 -1.878 0.651  "C4'"  4BD 17 
4BD "O4'"  "O4'"  O 0 1 N N N 4.547  7.541 11.279 -2.989 -0.541 0.673  "O4'"  4BD 18 
4BD "C1'"  "C1'"  C 0 1 N N R 5.290  7.337 10.088 -4.333 -0.643 1.171  "C1'"  4BD 19 
4BD N1     N1     N 0 1 N N N 6.737  7.470 10.390 -5.182 0.358  0.520  N1     4BD 20 
4BD C6     C6     C 0 1 N N N 7.219  7.163 11.645 -5.921 1.220  1.284  C6     4BD 21 
4BD C2     C2     C 0 1 N N N 7.594  7.874 9.378  -5.223 0.426  -0.823 C2     4BD 22 
4BD O2     O2     O 0 1 N N N 7.218  8.202 8.265  -4.555 -0.346 -1.483 O2     4BD 23 
4BD N3     N3     N 0 1 N N N 8.923  7.877 9.724  -5.995 1.336  -1.447 N3     4BD 24 
4BD C4     C4     C 0 1 N N N 9.471  7.531 10.942 -6.742 2.199  -0.729 C4     4BD 25 
4BD O4     O4     O 0 1 N N N 10.688 7.526 11.079 -7.440 3.023  -1.293 O4     4BD 26 
4BD C5     C5     C 0 1 N N N 8.517  7.174 11.973 -6.703 2.143  0.685  C5     4BD 27 
4BD C5M    C5M    C 0 1 N N N 9.022  6.573 13.247 -7.525 3.100  1.510  C5M    4BD 28 
4BD "C2'"  "C2'"  C 0 1 N N N 4.921  5.943 9.563  -4.840 -2.059 0.833  "C2'"  4BD 29 
4BD "C3'"  "C3'"  C 0 1 N N S 4.436  5.252 10.837 -3.629 -2.746 0.153  "C3'"  4BD 30 
4BD "O3'"  "O3'"  O 0 1 N N N 3.492  4.222 10.594 -3.497 -4.099 0.594  "O3'"  4BD 31 
4BD HO1A   HO1A   H 0 0 N N N 4.309  5.448 16.759 0.678  0.605  -1.852 HO1A   4BD 32 
4BD HO2B   HO2B   H 0 0 N N N 2.837  3.522 15.222 4.753  -2.023 0.090  HO2B   4BD 33 
4BD HO1G   HO1G   H 0 0 N N N 5.803  0.403 15.973 8.156  1.836  1.763  HO1G   4BD 34 
4BD HO3G   HO3G   H 0 0 N N N 4.002  2.506 17.769 6.176  3.323  -0.195 HO3G   4BD 35 
4BD "H5'"  "H5'"  H 0 1 N N N 3.196  5.101 13.176 -1.565 -1.561 -1.289 "H5'"  4BD 36 
4BD "H5'A" "H5'A" H 0 0 N N N 2.743  6.838 13.385 -0.970 -3.007 -0.440 "H5'A" 4BD 37 
4BD "H4'"  "H4'"  H 0 1 N N N 2.686  6.491 11.162 -2.138 -2.185 1.651  "H4'"  4BD 38 
4BD "H1'"  "H1'"  H 0 1 N N N 5.057  8.083 9.314  -4.342 -0.491 2.250  "H1'"  4BD 39 
4BD H6     H6     H 0 1 N N N 6.505  6.897 12.411 -5.879 1.162  2.362  H6     4BD 40 
4BD HN3    HN3    H 0 1 N N N 9.566  8.162 9.013  -6.013 1.370  -2.416 HN3    4BD 41 
4BD H5M    H5M    H 0 1 N N N 9.146  5.488 13.117 -6.941 3.997  1.714  H5M    4BD 42 
4BD H5MA   H5MA   H 0 0 N N N 9.991  7.024 13.506 -8.427 3.371  0.961  H5MA   4BD 43 
4BD H5MB   H5MB   H 0 0 N N N 8.300  6.765 14.054 -7.801 2.624  2.451  H5MB   4BD 44 
4BD "H2'"  "H2'"  H 0 1 N N N 4.140  5.984 8.790  -5.117 -2.592 1.743  "H2'"  4BD 45 
4BD "H2'A" "H2'A" H 0 0 N N N 5.752  5.422 9.064  -5.686 -2.007 0.148  "H2'A" 4BD 46 
4BD "H3'"  "H3'"  H 0 1 N N N 5.267  4.779 11.381 -3.714 -2.698 -0.932 "H3'"  4BD 47 
4BD "HO3'" "HO3'" H 0 0 N N N 3.281  4.197 9.668  -4.258 -4.657 0.382  "HO3'" 4BD 48 
# 
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 
4BD "O5'" PA     SING N N 1  
4BD C3A   PA     SING N N 2  
4BD PA    O2A    DOUB N N 3  
4BD PA    O1A    SING N N 4  
4BD O1A   HO1A   SING N N 5  
4BD F1A   C3A    SING N N 6  
4BD PB    C3A    SING N N 7  
4BD C3A   F2A    SING N N 8  
4BD "C5'" "O5'"  SING N N 9  
4BD O1B   PB     DOUB N N 10 
4BD PB    O2B    SING N N 11 
4BD PB    O3B    SING N N 12 
4BD O2B   HO2B   SING N N 13 
4BD O3B   PG     SING N N 14 
4BD PG    O2G    DOUB N N 15 
4BD PG    O1G    SING N N 16 
4BD PG    O3G    SING N N 17 
4BD O1G   HO1G   SING N N 18 
4BD O3G   HO3G   SING N N 19 
4BD "C4'" "C5'"  SING N N 20 
4BD "C5'" "H5'"  SING N N 21 
4BD "C5'" "H5'A" SING N N 22 
4BD "C3'" "C4'"  SING N N 23 
4BD "O4'" "C4'"  SING N N 24 
4BD "C4'" "H4'"  SING N N 25 
4BD "C1'" "O4'"  SING N N 26 
4BD "C2'" "C1'"  SING N N 27 
4BD "C1'" N1     SING N N 28 
4BD "C1'" "H1'"  SING N N 29 
4BD C2    N1     SING N N 30 
4BD N1    C6     SING N N 31 
4BD C6    C5     DOUB N N 32 
4BD C6    H6     SING N N 33 
4BD O2    C2     DOUB N N 34 
4BD C2    N3     SING N N 35 
4BD N3    C4     SING N N 36 
4BD N3    HN3    SING N N 37 
4BD C4    O4     DOUB N N 38 
4BD C4    C5     SING N N 39 
4BD C5    C5M    SING N N 40 
4BD C5M   H5M    SING N N 41 
4BD C5M   H5MA   SING N N 42 
4BD C5M   H5MB   SING N N 43 
4BD "C2'" "C3'"  SING N N 44 
4BD "C2'" "H2'"  SING N N 45 
4BD "C2'" "H2'A" SING N N 46 
4BD "O3'" "C3'"  SING N N 47 
4BD "C3'" "H3'"  SING N N 48 
4BD "O3'" "HO3'" 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 
4BD SMILES           ACDLabs              10.04 "O=P(O)(O)OP(=O)(O)C(F)(F)P(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O"                                                                                                                                  
4BD SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)C(F)(F)[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                            
4BD SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                   
4BD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(C(F)(F)[P@](=O)(O)OP(=O)(O)O)O)O"                                                                                                               
4BD SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(C(F)(F)P(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                  
4BD InChI            InChI                1.03  "InChI=1S/C11H17F2N2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-29(19,20)11(12,13)30(21,22)28-31(23,24)25/h3,6-8,16H,2,4H2,1H3,(H,19,20)(H,21,22)(H,14,17,18)(H2,23,24,25)/t6-,7+,8+/m0/s1" 
4BD InChIKey         InChI                1.03  WQZXQECPJNOPSV-XLPZGREQSA-N                                                                                                                                                                          
# 
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 
4BD "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine"                                                       
4BD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[difluoro-(hydroxy-phosphonooxy-phosphoryl)methyl]-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphinic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
4BD "Create component"  2009-03-20 RCSB 
4BD "Modify descriptor" 2011-06-04 RCSB 
# 
