data_XTL
# 
_chem_comp.id                                    XTL 
_chem_comp.name                                  "[(1S,4R,6R)-6-HYDROXY-4-(THYMIN-9-YL)CYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H17 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-05-19 
_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                        332.246 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     XTL 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
XTL P      P    P 0 1 N N N -0.407 -5.216 23.991 -4.265 -0.636 -0.217 P      XTL 1  
XTL OP1    O1P  O 0 1 N N N -1.012 -4.789 25.244 -3.568 -1.930 -0.395 OP1    XTL 2  
XTL OP2    O2P  O 0 1 N N N 0.234  -6.531 23.924 -4.816 -0.527 1.291  OP2    XTL 3  
XTL "O5'"  O5*  O 0 1 N N N 0.744  -4.126 23.566 -3.237 0.570  -0.502 "O5'"  XTL 4  
XTL "C5'"  C5*  C 0 1 N N N 0.619  -2.739 23.950 -2.114 0.368  0.358  "C5'"  XTL 5  
XTL "C4'"  C4*  C 0 1 N N S 1.732  -1.908 23.379 -1.094 1.486  0.137  "C4'"  XTL 6  
XTL "C6'"  C6*  C 0 1 N N N 1.569  -1.904 21.931 -0.561 1.400  -1.263 "C6'"  XTL 7  
XTL "C7'"  C7*  C 0 1 N N N 2.488  -1.996 20.971 0.685  1.543  -1.573 "C7'"  XTL 8  
XTL "C3'"  C3*  C 0 1 N N R 3.108  -2.507 23.767 0.048  1.338  1.145  "C3'"  XTL 9  
XTL "O3'"  O3*  O 0 1 N N N 3.316  -2.075 25.097 -0.417 1.668  2.455  "O3'"  XTL 10 
XTL "C2'"  C2*  C 0 1 N N N 4.157  -1.875 22.864 1.178  2.294  0.742  "C2'"  XTL 11 
XTL "C1'"  C1*  C 0 1 N N R 3.954  -2.281 21.373 1.777  1.807  -0.578 "C1'"  XTL 12 
XTL C6     C6   C 0 1 N N N 3.646  -4.740 21.401 1.859  -0.584 -0.048 C6     XTL 13 
XTL C5     C5   C 0 1 N N N 4.084  -6.001 21.265 2.552  -1.723 0.168  C5     XTL 14 
XTL C5M    C5M  C 0 1 N N N 3.160  -7.177 21.475 1.831  -3.005 0.495  C5M    XTL 15 
XTL C4     C4   C 0 1 N N N 5.464  -6.235 20.912 3.965  -1.694 0.089  C4     XTL 16 
XTL O4     O4   O 0 1 N N N 5.973  -7.347 20.761 4.612  -2.708 0.280  O4     XTL 17 
XTL N3     N3   N 0 1 N N N 6.208  -5.097 20.747 4.588  -0.536 -0.209 N3     XTL 18 
XTL C2     C2   C 0 1 N N N 5.809  -3.797 20.874 3.872  0.584  -0.420 C2     XTL 19 
XTL O2     O2   O 0 1 N N N 6.551  -2.838 20.706 4.448  1.622  -0.684 O2     XTL 20 
XTL N1     N1   N 0 1 N N N 4.485  -3.674 21.211 2.529  0.572  -0.344 N1     XTL 21 
XTL OP3    O3P  O 0 1 N Y N -1.530 -5.309 23.127 -5.498 -0.545 -1.248 OP3    XTL 22 
XTL HOP2   2HOP H 0 0 N N N 0.373  -6.770 23.015 -5.262 0.329  1.364  HOP2   XTL 23 
XTL "H5'"  1H5* H 0 1 N N N 0.668  -2.677 25.047 -1.653 -0.594 0.134  "H5'"  XTL 24 
XTL "H5''" 2H5* H 0 0 N N N -0.340 -2.352 23.576 -2.445 0.378  1.397  "H5''" XTL 25 
XTL "H4'"  H4*  H 0 1 N N N 1.694  -0.883 23.776 -1.579 2.451  0.280  "H4'"  XTL 26 
XTL "H6'"  H6*  H 0 1 N N N 0.550  -1.813 21.584 -1.263 1.205  -2.061 "H6'"  XTL 27 
XTL "H7'"  H7*  H 0 1 N N N 2.215  -1.874 19.933 0.959  1.470  -2.615 "H7'"  XTL 28 
XTL "H3'"  H3*  H 0 1 N N N 3.159  -3.602 23.671 0.416  0.312  1.134  "H3'"  XTL 29 
XTL "HO3'" H3T  H 0 0 N Y N 3.363  -2.830 25.672 0.339  1.575  3.051  "HO3'" XTL 30 
XTL "H2'"  1H2* H 0 1 N N N 5.147  -2.230 23.186 1.947  2.298  1.515  "H2'"  XTL 31 
XTL "H2''" 2H2* H 0 0 N N N 4.081  -0.781 22.946 0.778  3.300  0.614  "H2''" XTL 32 
XTL "H1'"  H1*  H 0 1 N N N 4.526  -1.684 20.647 2.449  2.569  -0.974 "H1'"  XTL 33 
XTL H6     H6   H 0 1 N N N 2.614  -4.562 21.665 0.780  -0.586 0.011  H6     XTL 34 
XTL H71    1H5M H 0 1 N N N 2.225  -6.830 21.940 1.601  -3.538 -0.428 H71    XTL 35 
XTL H72    2H5M H 0 1 N N N 3.646  -7.912 22.133 2.465  -3.627 1.126  H72    XTL 36 
XTL H73    3H5M H 0 1 N N N 2.935  -7.645 20.505 0.905  -2.777 1.023  H73    XTL 37 
XTL HN3    HN3  H 0 1 N N N 7.167  -5.236 20.502 5.556  -0.509 -0.268 HN3    XTL 38 
XTL HOP3   3HOP H 0 0 N N N -2.327 -5.330 23.644 -6.088 -1.283 -1.044 HOP3   XTL 39 
# 
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 
XTL P     OP1    DOUB N N 1  
XTL P     OP2    SING N N 2  
XTL P     "O5'"  SING N N 3  
XTL P     OP3    SING N N 4  
XTL OP2   HOP2   SING N N 5  
XTL "O5'" "C5'"  SING N N 6  
XTL "C5'" "C4'"  SING N N 7  
XTL "C5'" "H5'"  SING N N 8  
XTL "C5'" "H5''" SING N N 9  
XTL "C4'" "C6'"  SING N N 10 
XTL "C4'" "C3'"  SING N N 11 
XTL "C4'" "H4'"  SING N N 12 
XTL "C6'" "C7'"  DOUB N N 13 
XTL "C6'" "H6'"  SING N N 14 
XTL "C7'" "C1'"  SING N N 15 
XTL "C7'" "H7'"  SING N N 16 
XTL "C3'" "O3'"  SING N N 17 
XTL "C3'" "C2'"  SING N N 18 
XTL "C3'" "H3'"  SING N N 19 
XTL "O3'" "HO3'" SING N N 20 
XTL "C2'" "C1'"  SING N N 21 
XTL "C2'" "H2'"  SING N N 22 
XTL "C2'" "H2''" SING N N 23 
XTL "C1'" N1     SING N N 24 
XTL "C1'" "H1'"  SING N N 25 
XTL C6    C5     DOUB N N 26 
XTL C6    N1     SING N N 27 
XTL C6    H6     SING N N 28 
XTL C5    C5M    SING N N 29 
XTL C5    C4     SING N N 30 
XTL C5M   H71    SING N N 31 
XTL C5M   H72    SING N N 32 
XTL C5M   H73    SING N N 33 
XTL C4    O4     DOUB N N 34 
XTL C4    N3     SING N N 35 
XTL N3    C2     SING N N 36 
XTL N3    HN3    SING N N 37 
XTL C2    O2     DOUB N N 38 
XTL C2    N1     SING N N 39 
XTL OP3   HOP3   SING N N 40 
# 
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 
XTL SMILES           ACDLabs              10.04 "O=P(O)(O)OCC2C=CC(N1C=C(C(=O)NC1=O)C)CC2O"                                                                                                               
XTL SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O"                                                                                             
XTL SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O"                                                                                                  
XTL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](C=C2)COP(=O)(O)O)O"                                                                                               
XTL SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(C=C2)COP(=O)(O)O)O"                                                                                                             
XTL InChI            InChI                1.03  "InChI=1S/C12H17N2O7P/c1-7-5-14(12(17)13-11(7)16)9-3-2-8(10(15)4-9)6-21-22(18,19)20/h2-3,5,8-10,15H,4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9-,10+/m0/s1" 
XTL InChIKey         InChI                1.03  PIQIDTLVJACCCC-LPEHRKFASA-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 
XTL "SYSTEMATIC NAME" ACDLabs              10.04 "[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate" 
XTL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-1-cyclohex-2-enyl]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 
XTL "Create component"  2006-05-19 RCSB 
XTL "Modify descriptor" 2011-06-04 RCSB 
# 
