data_3R2
# 
_chem_comp.id                                    3R2 
_chem_comp.name                                  "2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H28 N2 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-10-10 
_chem_comp.pdbx_modified_date                    2015-01-23 
_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                        530.357 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     3R2 
_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        4RIF 
_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 
3R2 O4    O4    O 0 1 N N N -3.176 12.918 4.907  7.043  3.547  1.674  O4    3R2 1  
3R2 C4    C4    C 0 1 N N N -2.952 11.917 4.227  6.460  2.704  1.016  C4    3R2 2  
3R2 N3    N3    N 0 1 N N N -2.543 11.989 2.907  6.032  1.564  1.596  N3    3R2 3  
3R2 C2    C2    C 0 1 N N N -2.228 10.947 2.067  5.384  0.635  0.869  C2    3R2 4  
3R2 O2    O2    O 0 1 N N N -1.897 11.148 0.902  5.004  -0.388 1.406  O2    3R2 5  
3R2 C5    C5    C 0 1 N N N -3.079 10.535 4.762  6.219  2.914  -0.363 C5    3R2 6  
3R2 C5M   C5M   C 0 1 N N N -3.533 10.306 6.155  6.682  4.181  -1.035 C5M   3R2 7  
3R2 C6    C6    C 0 1 N N N -2.761 9.524  3.939  5.571  1.963  -1.069 C6    3R2 8  
3R2 N1    N1    N 0 1 N N N -2.341 9.697  2.627  5.148  0.823  -0.442 N1    3R2 9  
3R2 C1C   C1C   C 0 1 N N R -2.036 8.534  1.802  4.440  -0.206 -1.207 C1C   3R2 10 
3R2 O4C   O4C   O 0 1 N N N -2.591 7.329  2.351  3.187  -0.534 -0.567 O4C   3R2 11 
3R2 C2C   C2C   C 0 1 N N N -0.540 8.299  1.751  5.242  -1.526 -1.204 C2C   3R2 12 
3R2 C3C   C3C   C 0 1 N N S -0.463 6.822  1.466  4.157  -2.624 -1.117 C3C   3R2 13 
3R2 O3C   O3C   O 0 1 N N N -0.722 6.640  0.071  4.206  -3.468 -2.269 O3C   3R2 14 
3R2 C4C   C4C   C 0 1 N N R -1.663 6.249  2.214  2.829  -1.837 -1.077 C4C   3R2 15 
3R2 C5C   C5C   C 0 1 N N N -1.253 5.819  3.621  1.832  -2.520 -0.139 C5C   3R2 16 
3R2 O5C   O5C   O 0 1 N N N -0.688 4.528  3.516  0.575  -1.845 -0.206 O5C   3R2 17 
3R2 PA    PA    P 0 1 N N N 0.422  3.988  4.586  -0.710 -2.296 0.653  PA    3R2 18 
3R2 O1A   O1A   O 0 1 N N N 1.566  3.301  3.888  -1.004 -3.722 0.389  O1A   3R2 19 
3R2 O2A   O2A   O 0 1 N N N 0.778  5.189  5.602  -0.405 -2.093 2.221  O2A   3R2 20 
3R2 O3A   O3A   O 0 1 N N N -0.333 2.940  5.548  -1.979 -1.399 0.233  O3A   3R2 21 
3R2 PB    PB    P 0 1 N N N -1.816 2.353  5.768  -3.567 -1.529 0.465  PB    3R2 22 
3R2 O1B   O1B   O 0 1 N N N -1.906 1.903  7.207  -4.161 -2.665 -0.509 O1B   3R2 23 
3R2 O2B   O2B   O 0 1 N N N -2.871 3.494  5.354  -3.830 -1.900 1.874  O2B   3R2 24 
3R2 O3B   O3B   O 0 1 N N N -1.945 1.195  4.629  -4.274 -0.120 0.141  O3B   3R2 25 
3R2 "C1'" "C1'" C 0 1 N N S -1.903 -0.207 4.913  -5.667 0.119  0.352  "C1'" 3R2 26 
3R2 "C2'" "C2'" C 0 1 N N N -0.577 -0.631 5.552  -6.328 0.489  -0.978 "C2'" 3R2 27 
3R2 "C3'" "C3'" C 0 1 N N R 0.622  -0.421 4.641  -5.673 1.753  -1.538 "C3'" 3R2 28 
3R2 "O3'" "O3'" O 0 1 N N N 1.797  -0.931 5.270  -6.290 2.099  -2.780 "O3'" 3R2 29 
3R2 "C4'" "C4'" C 0 1 N N R 0.427  -1.089 3.293  -5.849 2.903  -0.544 "C4'" 3R2 30 
3R2 "O4'" "O4'" O 0 1 N N N 1.538  -0.723 2.480  -5.237 4.083  -1.068 "O4'" 3R2 31 
3R2 "C5'" "C5'" C 0 1 N N S -0.877 -0.621 2.651  -5.188 2.533  0.785  "C5'" 3R2 32 
3R2 "C6'" "C6'" C 0 1 N N N -1.101 -1.226 1.282  -5.363 3.682  1.780  "C6'" 3R2 33 
3R2 "C7'" "C7'" C 0 1 N N N -2.074 -0.895 3.562  -5.843 1.268  1.346  "C7'" 3R2 34 
3R2 H1    H1    H 0 1 N N N -2.468 12.907 2.518  6.194  1.413  2.540  H1    3R2 35 
3R2 H2    H2    H 0 1 N N N -3.736 11.273 6.639  7.181  4.818  -0.304 H2    3R2 36 
3R2 H3    H3    H 0 1 N N N -4.451 9.700  6.146  7.377  3.935  -1.837 H3    3R2 37 
3R2 H4    H4    H 0 1 N N N -2.748 9.774  6.713  5.822  4.708  -1.448 H4    3R2 38 
3R2 H5    H5    H 0 1 N N N -2.836 8.516  4.320  5.378  2.106  -2.122 H5    3R2 39 
3R2 H6    H6    H 0 1 N N N -2.410 8.693  0.780  4.267  0.133  -2.228 H6    3R2 40 
3R2 H7    H7    H 0 1 N N N -0.064 8.546  2.711  5.814  -1.628 -2.125 H7    3R2 41 
3R2 H8    H8    H 0 1 N N N -0.071 8.886  0.948  5.902  -1.570 -0.338 H8    3R2 42 
3R2 H9    H9    H 0 1 N N N 0.486  6.378  1.802  4.280  -3.211 -0.206 H9    3R2 43 
3R2 H10   H10   H 0 1 N N N -0.680 5.715  -0.141 5.043  -3.940 -2.375 H10   3R2 44 
3R2 H11   H11   H 0 1 N N N -2.095 5.402  1.661  2.409  -1.750 -2.080 H11   3R2 45 
3R2 H12   H12   H 0 1 N N N -0.512 6.522  4.029  1.703  -3.560 -0.441 H12   3R2 46 
3R2 H13   H13   H 0 1 N N N -2.134 5.792  4.279  2.211  -2.483 0.882  H13   3R2 47 
3R2 H14   H14   H 0 1 N N N 1.719  5.313  5.629  -0.203 -1.180 2.467  H14   3R2 48 
3R2 H15   H15   H 0 1 N N N -2.596 2.385  7.647  -4.024 -2.487 -1.449 H15   3R2 49 
3R2 H16   H16   H 0 1 N N N -2.733 -0.494 5.575  -6.134 -0.781 0.751  H16   3R2 50 
3R2 H17   H17   H 0 1 N N N -0.638 -1.699 5.808  -6.203 -0.330 -1.686 H17   3R2 51 
3R2 H18   H18   H 0 1 N N N -0.427 -0.042 6.469  -7.391 0.671  -0.817 H18   3R2 52 
3R2 H19   H19   H 0 1 N N N 0.739  0.660  4.474  -4.610 1.571  -1.699 H19   3R2 53 
3R2 H20   H20   H 0 1 N N N 1.914  -0.509 6.113  -6.218 1.414  -3.459 H20   3R2 54 
3R2 H21   H21   H 0 1 N N N 0.391  -2.180 3.430  -6.911 3.085  -0.383 H21   3R2 55 
3R2 H22   H22   H 0 1 N N N 2.342  -1.019 2.890  -5.607 4.377  -1.912 H22   3R2 56 
3R2 H23   H23   H 0 1 N N N -0.806 0.469  2.523  -4.125 2.350  0.624  H23   3R2 57 
3R2 H24   H24   H 0 1 N N N -2.051 -0.856 0.868  -6.426 3.864  1.940  H24   3R2 58 
3R2 H25   H25   H 0 1 N N N -0.274 -0.940 0.615  -4.892 3.418  2.727  H25   3R2 59 
3R2 H26   H26   H 0 1 N N N -1.141 -2.322 1.368  -4.897 4.582  1.380  H26   3R2 60 
3R2 H27   H27   H 0 1 N N N -2.987 -0.517 3.079  -6.905 1.451  1.507  H27   3R2 61 
3R2 H28   H28   H 0 1 N N N -2.165 -1.980 3.720  -5.372 1.005  2.293  H28   3R2 62 
# 
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 
3R2 O3C   C3C   SING N N 1  
3R2 O2    C2    DOUB N N 2  
3R2 "C6'" "C5'" SING N N 3  
3R2 C3C   C2C   SING N N 4  
3R2 C3C   C4C   SING N N 5  
3R2 C2C   C1C   SING N N 6  
3R2 C1C   O4C   SING N N 7  
3R2 C1C   N1    SING N N 8  
3R2 C2    N1    SING N N 9  
3R2 C2    N3    SING N N 10 
3R2 C4C   O4C   SING N N 11 
3R2 C4C   C5C   SING N N 12 
3R2 "O4'" "C4'" SING N N 13 
3R2 N1    C6    SING N N 14 
3R2 "C5'" "C4'" SING N N 15 
3R2 "C5'" "C7'" SING N N 16 
3R2 N3    C4    SING N N 17 
3R2 "C4'" "C3'" SING N N 18 
3R2 O5C   C5C   SING N N 19 
3R2 O5C   PA    SING N N 20 
3R2 "C7'" "C1'" SING N N 21 
3R2 O1A   PA    DOUB N N 22 
3R2 C6    C5    DOUB N N 23 
3R2 C4    C5    SING N N 24 
3R2 C4    O4    DOUB N N 25 
3R2 PA    O3A   SING N N 26 
3R2 PA    O2A   SING N N 27 
3R2 O3B   "C1'" SING N N 28 
3R2 O3B   PB    SING N N 29 
3R2 "C3'" "O3'" SING N N 30 
3R2 "C3'" "C2'" SING N N 31 
3R2 C5    C5M   SING N N 32 
3R2 "C1'" "C2'" SING N N 33 
3R2 O2B   PB    DOUB N N 34 
3R2 O3A   PB    SING N N 35 
3R2 PB    O1B   SING N N 36 
3R2 N3    H1    SING N N 37 
3R2 C5M   H2    SING N N 38 
3R2 C5M   H3    SING N N 39 
3R2 C5M   H4    SING N N 40 
3R2 C6    H5    SING N N 41 
3R2 C1C   H6    SING N N 42 
3R2 C2C   H7    SING N N 43 
3R2 C2C   H8    SING N N 44 
3R2 C3C   H9    SING N N 45 
3R2 O3C   H10   SING N N 46 
3R2 C4C   H11   SING N N 47 
3R2 C5C   H12   SING N N 48 
3R2 C5C   H13   SING N N 49 
3R2 O2A   H14   SING N N 50 
3R2 O1B   H15   SING N N 51 
3R2 "C1'" H16   SING N N 52 
3R2 "C2'" H17   SING N N 53 
3R2 "C2'" H18   SING N N 54 
3R2 "C3'" H19   SING N N 55 
3R2 "O3'" H20   SING N N 56 
3R2 "C4'" H21   SING N N 57 
3R2 "O4'" H22   SING N N 58 
3R2 "C5'" H23   SING N N 59 
3R2 "C6'" H24   SING N N 60 
3R2 "C6'" H25   SING N N 61 
3R2 "C6'" H26   SING N N 62 
3R2 "C7'" H27   SING N N 63 
3R2 "C7'" H28   SING N N 64 
# 
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 
3R2 SMILES           ACDLabs              12.01 "O=P(OC1CC(C)C(O)C(O)C1)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O" 
3R2 InChI            InChI                1.03  
"InChI=1S/C17H28N2O13P2/c1-8-3-10(4-12(21)15(8)22)31-34(27,28)32-33(25,26)29-7-13-11(20)5-14(30-13)19-6-9(2)16(23)18-17(19)24/h6,8,10-15,20-22H,3-5,7H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t8-,10-,11-,12+,13+,14+,15+/m0/s1" 
3R2 InChIKey         InChI                1.03  CWVOKCJHBPKJQP-PVMIAKCWSA-N 
3R2 SMILES_CANONICAL CACTVS               3.385 "C[C@H]1C[C@@H](C[C@@H](O)[C@@H]1O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O" 
3R2 SMILES           CACTVS               3.385 "C[CH]1C[CH](C[CH](O)[CH]1O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O" 
3R2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H]1C[C@@H](C[C@H]([C@@H]1O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O" 
3R2 SMILES           "OpenEye OEToolkits" 1.7.6 "CC1CC(CC(C1O)O)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)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 
3R2 "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine"                                            
3R2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1S,3S,4R,5R)-3-methyl-4,5-bis(oxidanyl)cyclohexyl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen 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 
3R2 "Create component" 2014-10-10 RCSB 
3R2 "Initial release"  2015-01-28 RCSB 
# 
