data_U5M
# 
_chem_comp.id                                    U5M 
_chem_comp.name                                  "1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H14 F N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-08-18 
_chem_comp.pdbx_modified_date                    2016-06-24 
_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                        340.199 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     U5M 
_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        5D8T 
_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 
U5M O2    O1  O 0 1 N N N 6.729  -11.382 9.817  3.853  -1.557 -0.813 O2    U5M 1  
U5M C2    C1  C 0 1 N N N 6.650  -12.588 9.937  3.618  -0.437 -0.404 C2    U5M 2  
U5M N3    N1  N 0 1 N N N 5.479  -13.298 9.772  4.631  0.431  -0.225 N3    U5M 3  
U5M C4    C2  C 0 1 N N N 5.368  -14.625 9.917  4.387  1.677  0.228  C4    U5M 4  
U5M O4    O2  O 0 1 N N N 4.262  -15.151 9.676  5.304  2.462  0.391  O4    U5M 5  
U5M C5    C3  C 0 1 N N N 6.503  -15.336 10.350 3.056  2.064  0.513  C5    U5M 6  
U5M C6    C4  C 0 1 N N N 7.665  -14.689 10.556 2.058  1.174  0.323  C6    U5M 7  
U5M N1    N2  N 0 1 N N N 7.764  -13.357 10.333 2.347  -0.079 -0.143 N1    U5M 8  
U5M "C1'" C5  C 0 1 N N R 9.028  -12.573 10.484 1.264  -1.043 -0.353 "C1'" U5M 9  
U5M "O4'" O3  O 0 1 N N N 10.077 -13.530 10.548 0.245  -0.476 -1.204 "O4'" U5M 10 
U5M "C2'" C6  C 0 1 N N R 9.084  -11.791 11.745 0.544  -1.342 0.980  "C2'" U5M 11 
U5M "F2'" F1  F 0 1 N N N 9.964  -10.721 11.548 1.019  -2.534 1.538  "F2'" U5M 12 
U5M "C3'" C7  C 0 1 N N R 9.718  -12.765 12.713 -0.942 -1.486 0.581  "C3'" U5M 13 
U5M "O3'" O4  O 0 1 N N N 10.325 -12.113 13.816 -1.419 -2.796 0.891  "O3'" U5M 14 
U5M "C4'" C8  C 0 1 N N S 10.744 -13.395 11.814 -0.943 -1.257 -0.947 "C4'" U5M 15 
U5M "C5'" C9  C 0 1 N N S 11.145 -14.811 12.226 -2.192 -0.480 -1.368 "C5'" U5M 16 
U5M C5M   C10 C 0 1 N N N 11.975 -14.833 13.540 -2.076 -0.087 -2.842 C5M   U5M 17 
U5M "O5'" O5  O 0 1 N N N 11.982 -15.305 11.186 -2.312 0.699  -0.570 "O5'" U5M 18 
U5M P     P1  P 0 1 N N N 12.275 -16.878 11.019 -3.583 0.995  0.373  P     U5M 19 
U5M OP1   O6  O 0 1 N N N 13.607 -17.208 11.575 -3.785 -0.141 1.300  OP1   U5M 20 
U5M OP2   O7  O 0 1 N N N 11.150 -17.624 11.384 -3.322 2.339  1.220  OP2   U5M 21 
U5M H3    H1  H 0 1 N N N 4.655  -12.786 9.527  5.541  0.158  -0.422 H3    U5M 22 
U5M H5    H2  H 0 1 N N N 6.441  -16.401 10.517 2.841  3.058  0.877  H5    U5M 23 
U5M H6    H3  H 0 1 N N N 8.528  -15.238 10.903 1.036  1.452  0.535  H6    U5M 24 
U5M "H1'" H4  H 0 1 N N N 9.158  -11.904 9.620  1.655  -1.962 -0.790 "H1'" U5M 25 
U5M "H2'" H5  H 0 1 N N N 8.084  -11.479 12.081 0.675  -0.516 1.679  "H2'" U5M 26 
U5M "H3'" H6  H 0 1 N N N 8.981  -13.514 13.038 -1.547 -0.731 1.083  "H3'" U5M 27 
U5M H6N   H7  H 0 1 N N N 10.709 -12.761 14.395 -1.383 -3.016 1.832  H6N   U5M 28 
U5M "H4'" H8  H 0 1 N N N 11.635 -12.755 11.736 -0.892 -2.209 -1.474 "H4'" U5M 29 
U5M "H5'" H9  H 0 1 N N N 10.246 -15.434 12.348 -3.073 -1.105 -1.227 "H5'" U5M 30 
U5M H6L   H10 H 0 1 N N N 12.237 -15.871 13.791 -1.195 0.538  -2.984 H6L   U5M 31 
U5M H6M   H11 H 0 1 N N N 12.895 -14.246 13.402 -1.985 -0.987 -3.452 H6M   U5M 32 
U5M H5M   H12 H 0 1 N N N 11.380 -14.397 14.356 -2.966 0.466  -3.142 H5M   U5M 33 
U5M H1    H14 H 0 1 N N N 11.406 -18.306 11.994 -4.049 2.578  1.811  H1    U5M 34 
U5M OP3   O8  O 0 1 N Y N 12.496 -16.937 9.393  -4.896 1.183  -0.540 O1    U5M 35 
U5M H2    H15 H 0 1 N Y N 13.399 -17.162 9.204  -4.834 1.911  -1.173 H2    U5M 36 
# 
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 
U5M O2    C2    DOUB N N 1  
U5M C2    N3    SING N N 2  
U5M C2    N1    SING N N 3  
U5M N3    C4    SING N N 4  
U5M C4    O4    DOUB N N 5  
U5M C4    C5    SING N N 6  
U5M C5    C6    DOUB N N 7  
U5M C6    N1    SING N N 8  
U5M N1    "C1'" SING N N 9  
U5M "C1'" "O4'" SING N N 10 
U5M "C1'" "C2'" SING N N 11 
U5M "O4'" "C4'" SING N N 12 
U5M "C2'" "F2'" SING N N 13 
U5M "C2'" "C3'" SING N N 14 
U5M "C3'" "O3'" SING N N 15 
U5M "C3'" "C4'" SING N N 16 
U5M "C4'" "C5'" SING N N 17 
U5M "C5'" C5M   SING N N 18 
U5M "C5'" "O5'" SING N N 19 
U5M "O5'" P     SING N N 20 
U5M P     OP1   DOUB N N 21 
U5M P     OP2   SING N N 22 
U5M N3    H3    SING N N 23 
U5M C5    H5    SING N N 24 
U5M C6    H6    SING N N 25 
U5M "C1'" "H1'" SING N N 26 
U5M "C2'" "H2'" SING N N 27 
U5M "C3'" "H3'" SING N N 28 
U5M "O3'" H6N   SING N N 29 
U5M "C4'" "H4'" SING N N 30 
U5M "C5'" "H5'" SING N N 31 
U5M C5M   H6L   SING N N 32 
U5M C5M   H6M   SING N N 33 
U5M C5M   H5M   SING N N 34 
U5M OP2   H1    SING N N 35 
U5M P     OP3   SING N N 36 
U5M OP3   H2    SING N N 37 
# 
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 
U5M SMILES           ACDLabs              12.01 "O=C1NC(=O)C=CN1C2OC(C(C2F)O)C(C)OP(=O)(O)O"                                                                                                            
U5M InChI            InChI                1.03  "InChI=1S/C10H14FN2O8P/c1-4(21-22(17,18)19)8-7(15)6(11)9(20-8)13-3-2-5(14)12-10(13)16/h2-4,6-9,15H,1H3,(H,12,14,16)(H2,17,18,19)/t4-,6+,7-,8+,9+/m0/s1" 
U5M InChIKey         InChI                1.03  AVNIYVQWHJOOLV-VEMNEOHVSA-N                                                                                                                             
U5M SMILES_CANONICAL CACTVS               3.385 "C[C@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](F)[C@@H]1O)N2C=CC(=O)NC2=O"                                                                                     
U5M SMILES           CACTVS               3.385 "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](F)[CH]1O)N2C=CC(=O)NC2=O"                                                                                           
U5M SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)F)O)OP(=O)(O)O"                                                                                   
U5M SMILES           "OpenEye OEToolkits" 1.9.2 "CC(C1C(C(C(O1)N2C=CC(=O)NC2=O)F)O)OP(=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 
U5M "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione"                                        
U5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1S)-1-[(2S,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]ethyl] 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 
U5M "Create component" 2015-08-18 RCSB 
U5M "Initial release"  2016-06-29 RCSB 
# 
