data_C6T
# 
_chem_comp.id                                    C6T 
_chem_comp.name                                  "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H20 N3 O12 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-11-13 
_chem_comp.pdbx_modified_date                    2015-06-26 
_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                        479.211 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     C6T 
_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        4RT3 
_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 
C6T O4    O4    O 0 1 N N N 10.754 7.723  11.003 -8.155 2.112  -0.957 O4    C6T 1  
C6T C4    C4    C 0 1 N N N 9.384  7.705  10.780 -7.258 1.376  -0.589 C4    C6T 2  
C6T C5    C5    C 0 1 N N N 8.547  7.268  11.820 -7.322 0.750  0.679  C5    C6T 3  
C6T C7    C7    C 0 1 N N N 9.110  6.812  13.164 -8.501 0.986  1.588  C7    C6T 4  
C6T C6    C6    C 0 1 N N N 7.164  7.233  11.554 -6.314 -0.062 1.063  C6    C6T 5  
C6T N3    N3    N 0 1 N N N 8.882  8.098  9.590  -6.196 1.145  -1.388 N3    C6T 6  
C6T C2    C2    C 0 1 N N N 7.569  8.049  9.417  -5.205 0.331  -0.980 C2    C6T 7  
C6T O2    O2    O 0 1 N N N 7.123  8.389  8.343  -4.254 0.131  -1.711 O2    C6T 8  
C6T N1    N1    N 0 1 N N N 6.715  7.640  10.355 -5.252 -0.266 0.225  N1    C6T 9  
C6T "C1'" "C1'" C 0 1 N N R 5.290  7.559  10.078 -4.158 -1.148 0.641  "C1'" C6T 10 
C6T "C2'" "C2'" C 0 1 N N N 5.002  6.340  9.705  -4.045 -2.354 -0.318 "C2'" C6T 11 
C6T "C3'" "C3'" C 0 1 N N S 4.459  5.606  10.934 -2.524 -2.599 -0.435 "C3'" C6T 12 
C6T "O3'" "O3'" O 0 1 N N N 3.689  4.474  10.648 -2.188 -3.902 0.046  "O3'" C6T 13 
C6T "O4'" "O4'" O 0 1 N N N 4.464  7.784  11.413 -2.891 -0.465 0.526  "O4'" C6T 14 
C6T "C4'" "C4'" C 0 1 N N R 3.688  6.764  11.583 -1.898 -1.512 0.467  "C4'" C6T 15 
C6T "C5'" "C5'" C 0 1 N N N 3.441  6.503  13.113 -0.603 -0.985 -0.155 "C5'" C6T 16 
C6T "O5'" "O5'" O 0 1 N N N 4.709  6.516  13.769 0.019  -0.067 0.747  "O5'" C6T 17 
C6T PA    PA    P 0 1 N N N 5.045  5.344  14.797 1.405  0.683  0.417  PA    C6T 18 
C6T O1A   O1A   O 0 1 N N N 3.908  5.301  15.811 1.674  1.823  1.521  O1A   C6T 19 
C6T O2A   O2A   O 0 1 N N N 6.359  5.684  15.458 1.323  1.304  -0.924 O2A   C6T 20 
C6T N3A   N3A   N 0 1 N N N 5.154  3.920  13.908 2.666  -0.431 0.443  N3A   C6T 21 
C6T PB    PB    P 0 1 N N N 4.004  2.684  13.800 4.136  0.313  0.103  PB    C6T 22 
C6T O1B   O1B   O 0 1 N N N 3.959  2.232  12.267 4.406  1.359  1.115  O1B   C6T 23 
C6T O2B   O2B   O 0 1 N N N 2.611  3.117  14.379 4.071  0.985  -1.359 O2B   C6T 24 
C6T C3B   C3B   C 0 1 N N N 4.634  1.243  14.744 5.470  -0.929 0.142  C3B   C6T 25 
C6T PG    PG    P 0 1 N N N 4.129  1.154  16.500 7.062  -0.122 -0.227 PG    C6T 26 
C6T O2G   O2G   O 0 1 N N N 2.892  0.309  16.573 7.003  0.496  -1.571 O2G   C6T 27 
C6T O1G   O1G   O 0 1 N N N 5.205  0.547  17.365 7.356  1.016  0.874  O1G   C6T 28 
C6T O3G   O3G   O 0 1 N N N 3.808  2.583  16.904 8.241  -1.219 -0.193 O3G   C6T 29 
C6T H1    H1    H 0 1 N N N 8.284  6.514  13.826 -9.203 1.665  1.104  H1    C6T 30 
C6T H2    H2    H 0 1 N N N 9.782  5.955  13.008 -8.996 0.037  1.795  H2    C6T 31 
C6T H3    H3    H 0 1 N N N 9.671  7.638  13.626 -8.155 1.426  2.524  H3    C6T 32 
C6T H4    H4    H 0 1 N N N 6.472  6.883  12.306 -6.346 -0.549 2.027  H4    C6T 33 
C6T H5    H5    H 0 1 N N N 9.485  8.417  8.859  -6.147 1.568  -2.259 H5    C6T 34 
C6T H6    H6    H 0 1 N N N 4.992  8.320  9.341  -4.314 -1.488 1.664  H6    C6T 35 
C6T H7    H7    H 0 1 N N N 4.241  6.359  8.911  -4.541 -3.227 0.106  H7    C6T 36 
C6T H8    H8    H 0 1 N N N 5.907  5.836  9.334  -4.468 -2.108 -1.292 H8    C6T 37 
C6T H9    H9    H 0 1 N N N 5.305  5.340  11.586 -2.195 -2.475 -1.467 H9    C6T 38 
C6T H10   H10   H 0 1 N N N 3.884  3.790  11.278 -2.604 -4.622 -0.448 H10   C6T 39 
C6T H11   H11   H 0 1 N N N 2.715  6.876  11.082 -1.707 -1.910 1.464  H11   C6T 40 
C6T H12   H12   H 0 1 N N N 2.797  7.292  13.528 0.072  -1.818 -0.349 H12   C6T 41 
C6T H13   H13   H 0 1 N N N 2.958  5.525  13.252 -0.831 -0.475 -1.091 H13   C6T 42 
C6T H14   H14   H 0 1 N N N 4.247  5.499  16.676 1.739  1.488  2.426  H14   C6T 43 
C6T H15   H15   H 0 1 N N N 5.981  3.471  14.246 2.489  -1.192 -0.195 H15   C6T 44 
C6T H16   H16   H 0 1 N N N 1.948  3.037  13.703 3.897  0.357  -2.073 H16   C6T 45 
C6T H17   H17   H 0 1 N N N 4.277  0.331  14.244 5.514  -1.384 1.131  H17   C6T 46 
C6T H18   H18   H 0 1 N N N 5.733  1.273  14.711 5.271  -1.699 -0.604 H18   C6T 47 
C6T H19   H19   H 0 1 N N N 4.874  -0.243 17.775 7.408  0.682  1.780  H19   C6T 48 
C6T H20   H20   H 0 1 N N N 2.886  2.651  17.122 9.118  -0.859 -0.381 H20   C6T 49 
# 
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 
C6T O2    C2    DOUB N N 1  
C6T C2    N3    SING N N 2  
C6T C2    N1    SING N N 3  
C6T N3    C4    SING N N 4  
C6T "C2'" "C1'" SING N N 5  
C6T "C2'" "C3'" SING N N 6  
C6T "C1'" N1    SING N N 7  
C6T "C1'" "O4'" SING N N 8  
C6T N1    C6    SING N N 9  
C6T "O3'" "C3'" SING N N 10 
C6T C4    O4    DOUB N N 11 
C6T C4    C5    SING N N 12 
C6T "C3'" "C4'" SING N N 13 
C6T "O4'" "C4'" SING N N 14 
C6T C6    C5    DOUB N N 15 
C6T "C4'" "C5'" SING N N 16 
C6T C5    C7    SING N N 17 
C6T O1B   PB    DOUB N N 18 
C6T "C5'" "O5'" SING N N 19 
C6T "O5'" PA    SING N N 20 
C6T PB    N3A   SING N N 21 
C6T PB    O2B   SING N N 22 
C6T PB    C3B   SING N N 23 
C6T N3A   PA    SING N N 24 
C6T C3B   PG    SING N N 25 
C6T PA    O2A   DOUB N N 26 
C6T PA    O1A   SING N N 27 
C6T PG    O2G   DOUB N N 28 
C6T PG    O3G   SING N N 29 
C6T PG    O1G   SING N N 30 
C6T C7    H1    SING N N 31 
C6T C7    H2    SING N N 32 
C6T C7    H3    SING N N 33 
C6T C6    H4    SING N N 34 
C6T N3    H5    SING N N 35 
C6T "C1'" H6    SING N N 36 
C6T "C2'" H7    SING N N 37 
C6T "C2'" H8    SING N N 38 
C6T "C3'" H9    SING N N 39 
C6T "O3'" H10   SING N N 40 
C6T "C4'" H11   SING N N 41 
C6T "C5'" H12   SING N N 42 
C6T "C5'" H13   SING N N 43 
C6T O1A   H14   SING N N 44 
C6T N3A   H15   SING N N 45 
C6T O2B   H16   SING N N 46 
C6T C3B   H17   SING N N 47 
C6T C3B   H18   SING N N 48 
C6T O1G   H19   SING N N 49 
C6T O3G   H20   SING N N 50 
# 
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 
C6T SMILES           ACDLabs              12.01 "O=P(O)(O)CP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O"                                                                                                                                   
C6T InChI            InChI                1.03  "InChI=1S/C11H20N3O12P3/c1-6-3-14(11(17)12-10(6)16)9-2-7(15)8(26-9)4-25-29(23,24)13-27(18,19)5-28(20,21)22/h3,7-9,15H,2,4-5H2,1H3,(H,12,16,17)(H2,20,21,22)(H3,13,18,19,23,24)/t7-,8+,9+/m0/s1" 
C6T InChIKey         InChI                1.03  ARKIPWDBYLJBIH-DJLDLDEBSA-N                                                                                                                                                                     
C6T SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                
C6T SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                    
C6T SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(CP(=O)(O)O)O)O)O"                                                                                                                      
C6T SMILES           "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(CP(=O)(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 
C6T "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine"                                                            
C6T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]amino]-oxidanyl-phosphoryl]methylphosphonic 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 
C6T "Create component" 2014-11-13 RCSB 
C6T "Initial release"  2015-07-01 RCSB 
# 
