data_BOE
# 
_chem_comp.id                                    BOE 
_chem_comp.name                                  
;2'-O-[2-(BENZYLOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C19 H25 N2 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-12-21 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        472.383 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     BOE 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1YBC 
_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 
BOE P      P      P 0 1 N N N -4.500 5.987  7.477  2.787  0.324  -4.407 P      BOE 1  
BOE OP1    O1P    O 0 1 N N N -5.715 6.689  6.969  3.659  1.172  -5.286 OP1    BOE 2  
BOE OP2    O2P    O 0 1 N N N -4.660 4.712  8.206  1.198  0.588  -4.548 OP2    BOE 3  
BOE "O5'"  O5*    O 0 1 N N N -3.573 5.777  6.211  3.063  0.476  -2.819 "O5'"  BOE 4  
BOE "C5'"  C5*    C 0 1 N N N -3.357 6.864  5.306  2.282  -0.292 -1.921 "C5'"  BOE 5  
BOE "C4'"  C4*    C 0 1 N N R -2.328 6.487  4.282  2.725  0.023  -0.498 "C4'"  BOE 6  
BOE "O4'"  O4*    O 0 1 N N N -1.039 6.300  4.928  2.470  1.422  -0.246 "O4'"  BOE 7  
BOE "C1'"  C1*    C 0 1 N N R -0.318 5.272  4.258  1.373  1.543  0.675  "C1'"  BOE 8  
BOE N1     N1     N 0 1 N N N -0.061 4.162  5.217  0.452  2.524  0.177  N1     BOE 9  
BOE C6     C6     C 0 1 N N N -0.850 3.927  6.327  0.309  2.663  -1.199 C6     BOE 10 
BOE C2     C2     C 0 1 N N N 1.021  3.366  4.929  -0.300 3.336  1.055  C2     BOE 11 
BOE O2     O2     O 0 1 N N N 1.733  3.570  3.961  -0.225 3.269  2.283  O2     BOE 12 
BOE N3     N3     N 0 1 N N N 1.234  2.326  5.808  -1.159 4.248  0.431  N3     BOE 13 
BOE C4     C4     C 0 1 N N N 0.473  2.017  6.921  -1.338 4.427  -0.932 C4     BOE 14 
BOE O4     O4     O 0 1 N N N 0.748  1.038  7.606  -2.112 5.251  -1.413 O4     BOE 15 
BOE C5     C5     C 0 1 N N N -0.643 2.906  7.176  -0.514 3.537  -1.792 C5     BOE 16 
BOE C5M    C5M    C 0 1 N N N -1.512 2.626  8.357  -0.651 3.669  -3.275 C5M    BOE 17 
BOE "C2'"  C2*    C 0 1 N N R -1.171 4.813  3.073  0.748  0.163  0.786  "C2'"  BOE 18 
BOE "O2'"  O2*    O 0 1 N N N -0.948 5.711  1.973  0.137  -0.058 2.041  "O2'"  BOE 19 
BOE "CB'"  "CB'"  C 0 1 N N N 0.361  5.685  1.432  -0.332 -1.396 2.174  "CB'"  BOE 20 
BOE "CC'"  "CC'"  C 0 1 N N N 0.346  6.681  0.289  -0.951 -1.569 3.547  "CC'"  BOE 21 
BOE "OD'"  "OD'"  O 0 1 N N N -0.793 6.285  -0.457 0.039  -1.320 4.537  "OD'"  BOE 22 
BOE "CE'"  "CE'"  C 0 1 N N N -0.877 6.743  -1.793 -0.494 -1.447 5.849  "CE'"  BOE 23 
BOE "CF'"  "CF'"  C 0 1 Y N N -2.013 5.991  -2.454 0.593  -1.175 6.847  "CF'"  BOE 24 
BOE "CG'"  "CG'"  C 0 1 Y N N -3.338 6.303  -2.174 1.381  -2.222 7.309  "CG'"  BOE 25 
BOE "CH'"  "CH'"  C 0 1 Y N N -4.362 5.584  -2.793 2.391  -1.969 8.237  "CH'"  BOE 26 
BOE "CI'"  "CI'"  C 0 1 Y N N -4.087 4.557  -3.689 2.606  -0.670 8.697  "CI'"  BOE 27 
BOE "CJ'"  "CJ'"  C 0 1 Y N N -2.759 4.250  -3.968 1.811  0.376  8.228  "CJ'"  BOE 28 
BOE "CK'"  "CK'"  C 0 1 Y N N -1.732 4.965  -3.352 0.801  0.123  7.300  "CK'"  BOE 29 
BOE "C3'"  C3*    C 0 1 N N R -2.563 5.165  3.567  1.940  -0.742 0.560  "C3'"  BOE 30 
BOE "O3'"  O3*    O 0 1 N N N -3.500 5.245  2.514  2.742  -0.809 1.739  "O3'"  BOE 31 
BOE OP3    O3P    O 0 1 N Y N ?      ?      ?      2.921  -1.270 -4.647 OP3    BOE 32 
BOE HOP2   2HOP   H 0 0 N N N -3.887 4.265  8.529  0.799  0.616  -5.443 HOP2   BOE 33 
BOE "H5'"  1H5*   H 0 1 N N N -3.088 7.805  5.841  1.229  -0.035 -2.051 "H5'"  BOE 34 
BOE "H5''" 2H5*   H 0 0 N N N -4.307 7.209  4.835  2.428  -1.352 -2.133 "H5''" BOE 35 
BOE "H4'"  H4*    H 0 1 N N N -2.380 7.323  3.546  3.804  -0.139 -0.410 "H4'"  BOE 36 
BOE "H1'"  H1*    H 0 1 N N N 0.669  5.629  3.881  1.754  1.910  1.633  "H1'"  BOE 37 
BOE H6     H6     H 0 1 N N N -1.698 4.596  6.549  0.928  1.995  -1.790 H6     BOE 38 
BOE HN3    HN3    H 0 1 N N N 2.035  1.725  5.616  -1.709 4.843  1.045  HN3    BOE 39 
BOE H71    1H5M   H 0 1 N N N -2.559 2.537  7.983  -1.057 2.748  -3.690 H71    BOE 40 
BOE H72    2H5M   H 0 1 N N N -1.340 1.779  9.061  0.324  3.866  -3.719 H72    BOE 41 
BOE H73    3H5M   H 0 1 N N N -1.552 3.559  8.966  -1.320 4.497  -3.510 H73    BOE 42 
BOE "H2'"  H2*    H 0 1 N N N -0.984 3.757  2.768  -0.000 0.004  -0.000 "H2'"  BOE 43 
BOE "HB'1" "1HB'" H 0 0 N N N 0.703  4.666  1.135  -1.066 -1.580 1.383  "HB'1" BOE 44 
BOE "HB'2" "2HB'" H 0 0 N N N 1.161  5.878  2.184  0.520  -2.071 2.050  "HB'2" BOE 45 
BOE "HC'1" "1HC'" H 0 0 N N N 1.293  6.733  -0.297 -1.324 -2.588 3.686  "HC'1" BOE 46 
BOE "HC'2" "2HC'" H 0 0 N N N 0.350  7.751  0.602  -1.768 -0.855 3.691  "HC'2" BOE 47 
BOE "HE'1" "1HE'" H 0 0 N N N 0.087  6.653  -2.347 -0.897 -2.458 5.974  "HE'1" BOE 48 
BOE "HE'2" "2HE'" H 0 0 N N N -0.984 7.850  -1.869 -1.320 -0.738 5.971  "HE'2" BOE 49 
BOE "HG'"  "HG'"  H 0 1 N N N -3.575 7.115  -1.466 1.221  -3.238 6.957  "HG'"  BOE 50 
BOE "HH'"  "HH'"  H 0 1 N N N -5.413 5.833  -2.569 3.011  -2.783 8.602  "HH'"  BOE 51 
BOE "HI'"  "HI'"  H 0 1 N N N -4.907 3.997  -4.169 3.393  -0.473 9.419  "HI'"  BOE 52 
BOE "HJ'"  "HJ'"  H 0 1 N N N -2.520 3.440  -4.677 1.979  1.388  8.586  "HJ'"  BOE 53 
BOE "HK'"  "HK'"  H 0 1 N N N -0.682 4.715  -3.578 0.187  0.944  6.941  "HK'"  BOE 54 
BOE "H3'"  H3*    H 0 1 N N N -3.015 4.395  4.234  1.675  -1.764 0.277  "H3'"  BOE 55 
BOE "HO3'" H3T    H 0 0 N Y N -3.647 4.419  2.068  3.447  -0.153 1.628  "HO3'" BOE 56 
BOE HOP3   3HOP   H 0 0 N N N 0.773  -0.447 0.323  2.886  -1.617 -5.563 HOP3   BOE 57 
# 
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 
BOE P     OP1    DOUB N N 1  
BOE P     OP2    SING N N 2  
BOE P     "O5'"  SING N N 3  
BOE P     OP3    SING N N 4  
BOE OP2   HOP2   SING N N 5  
BOE "O5'" "C5'"  SING N N 6  
BOE "C5'" "C4'"  SING N N 7  
BOE "C5'" "H5'"  SING N N 8  
BOE "C5'" "H5''" SING N N 9  
BOE "C4'" "O4'"  SING N N 10 
BOE "C4'" "C3'"  SING N N 11 
BOE "C4'" "H4'"  SING N N 12 
BOE "O4'" "C1'"  SING N N 13 
BOE "C1'" N1     SING N N 14 
BOE "C1'" "C2'"  SING N N 15 
BOE "C1'" "H1'"  SING N N 16 
BOE N1    C6     SING N N 17 
BOE N1    C2     SING N N 18 
BOE C6    C5     DOUB N N 19 
BOE C6    H6     SING N N 20 
BOE C2    O2     DOUB N N 21 
BOE C2    N3     SING N N 22 
BOE N3    C4     SING N N 23 
BOE N3    HN3    SING N N 24 
BOE C4    O4     DOUB N N 25 
BOE C4    C5     SING N N 26 
BOE C5    C5M    SING N N 27 
BOE C5M   H71    SING N N 28 
BOE C5M   H72    SING N N 29 
BOE C5M   H73    SING N N 30 
BOE "C2'" "O2'"  SING N N 31 
BOE "C2'" "C3'"  SING N N 32 
BOE "C2'" "H2'"  SING N N 33 
BOE "O2'" "CB'"  SING N N 34 
BOE "CB'" "CC'"  SING N N 35 
BOE "CB'" "HB'1" SING N N 36 
BOE "CB'" "HB'2" SING N N 37 
BOE "CC'" "OD'"  SING N N 38 
BOE "CC'" "HC'1" SING N N 39 
BOE "CC'" "HC'2" SING N N 40 
BOE "OD'" "CE'"  SING N N 41 
BOE "CE'" "CF'"  SING N N 42 
BOE "CE'" "HE'1" SING N N 43 
BOE "CE'" "HE'2" SING N N 44 
BOE "CF'" "CG'"  DOUB Y N 45 
BOE "CF'" "CK'"  SING Y N 46 
BOE "CG'" "CH'"  SING Y N 47 
BOE "CG'" "HG'"  SING N N 48 
BOE "CH'" "CI'"  DOUB Y N 49 
BOE "CH'" "HH'"  SING N N 50 
BOE "CI'" "CJ'"  SING Y N 51 
BOE "CI'" "HI'"  SING N N 52 
BOE "CJ'" "CK'"  DOUB Y N 53 
BOE "CJ'" "HJ'"  SING N N 54 
BOE "CK'" "HK'"  SING N N 55 
BOE "C3'" "O3'"  SING N N 56 
BOE "C3'" "H3'"  SING N N 57 
BOE "O3'" "HO3'" SING N N 58 
BOE OP3   HOP3   SING N N 59 
# 
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 
BOE SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C3OC(C(O)C3OCCOCc2ccccc2)COP(=O)(O)O" 
BOE InChI            InChI                1.02b 
"InChI=1/C19H25N2O10P/c1-12-9-21(19(24)20-17(12)23)18-16(15(22)14(31-18)11-30-32(25,26)27)29-8-7-28-10-13-5-3-2-4-6-13/h2-6,9,14-16,18,22H,7-8,10-11H2,1H3,(H,20,23,24)(H2,25,26,27)/t14-,15-,16-,18-/m1/s1/f/h20,25-26H" 
BOE InChIKey         InChI                1.02b LZEOXHFYJVFRES-AVJNBRAIDM 
BOE SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OCCOCc3ccccc3)C(=O)NC1=O" 
BOE SMILES           CACTVS               3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OCCOCc3ccccc3)C(=O)NC1=O" 
BOE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOCc3ccccc3" 
BOE SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOCc3ccccc3" 
# 
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 
BOE "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-[2-(benzyloxy)ethyl]-5-methyluridine 5'-(dihydrogen phosphate)
;
BOE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-(2-phenylmethoxyethoxy)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
