data_6OP
# 
_chem_comp.id                                    6OP 
_chem_comp.name                                  "1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H21 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-05-13 
_chem_comp.pdbx_modified_date                    2016-07-15 
_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                        392.298 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6OP 
_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        5JS2 
_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 
6OP P      P1  P 0 1 N N N -18.447 30.666 29.630 5.126  0.069  0.038  P     6OP 1  
6OP OP1    O1  O 0 1 N N N -18.421 29.079 29.846 5.653  -1.418 -0.285 OP1   6OP 2  
6OP OP2    O2  O 0 1 N N N -17.121 31.169 29.204 5.901  0.633  1.166  OP2   6OP 3  
6OP OP3    O3  O 0 1 N Y N -18.773 31.355 30.969 5.316  1.000  -1.262 OP3   6OP 4  
6OP "C6'"  C1  C 0 1 N N N -19.645 31.071 28.374 3.369  0.004  0.483  "C6'" 6OP 5  
6OP "C5'"  C2  C 0 1 N N N -20.899 30.195 28.389 2.740  -1.145 0.502  "C5'" 6OP 6  
6OP "C4'"  C3  C 0 1 N N R -21.927 30.738 27.295 1.280  -1.199 0.872  "C4'" 6OP 7  
6OP "O4'"  O4  O 0 1 N N N -21.768 29.976 25.979 0.730  0.134  0.946  "O4'" 6OP 8  
6OP "C3'"  C4  C 0 1 N N R -23.091 30.565 27.637 0.469  -1.900 -0.241 "C3'" 6OP 9  
6OP "O3'"  O5  O 0 1 N N N -23.854 31.754 27.351 0.235  -3.269 0.096  "O3'" 6OP 10 
6OP "C2'"  C5  C 0 1 N N R -23.622 29.293 26.748 -0.862 -1.116 -0.285 "C2'" 6OP 11 
6OP "O2'"  O6  O 0 1 N N N -25.057 29.244 26.784 -1.960 -1.976 0.025  "O2'" 6OP 12 
6OP "C1'"  C6  C 0 1 N N R -23.166 29.506 25.622 -0.697 -0.035 0.806  "C1'" 6OP 13 
6OP "CB'"  C7  C 0 1 N N N -25.684 28.238 25.966 -2.557 -2.591 -1.119 "CB'" 6OP 14 
6OP "CG'"  C8  C 0 1 N N N -25.512 26.845 26.622 -3.716 -3.484 -0.671 "CG'" 6OP 15 
6OP "OD'"  O7  O 0 1 N N N -26.221 26.903 27.890 -4.745 -2.677 -0.096 "OD'" 6OP 16 
6OP "CE'"  C9  C 0 1 N N N -25.632 26.175 28.954 -5.880 -3.418 0.357  "CE'" 6OP 17 
6OP N1     N1  N 0 1 N N N -23.000 28.252 24.790 -1.319 1.221  0.379  N1    6OP 18 
6OP C2     C10 C 0 1 N N N -23.385 28.245 23.510 -0.866 1.848  -0.722 C2    6OP 19 
6OP O2     O8  O 0 1 N N N -23.883 29.230 23.030 0.059  1.368  -1.347 O2    6OP 20 
6OP N3     N2  N 0 1 N N N -23.247 27.163 22.732 -1.423 3.000  -1.140 N3    6OP 21 
6OP C4     C11 C 0 1 N N N -22.696 26.042 23.239 -2.451 3.545  -0.458 C4    6OP 22 
6OP O4     O9  O 0 1 N N N -22.554 25.021 22.534 -2.956 4.587  -0.837 O4    6OP 23 
6OP C5     C12 C 0 1 N N N -22.268 25.988 24.557 -2.937 2.895  0.702  C5    6OP 24 
6OP C7     C13 C 0 1 N N N -21.637 24.693 25.137 -4.084 3.484  1.483  C7    6OP 25 
6OP C6     C14 C 0 1 N N N -22.425 27.135 25.338 -2.360 1.741  1.099  C6    6OP 26 
6OP H1     H1  H 0 1 N N N -17.550 28.748 29.659 5.189  -1.850 -1.016 H1    6OP 27 
6OP HOP3   H2  H 0 0 N Y N -18.060 31.935 31.209 6.233  1.080  -1.558 H2    6OP 28 
6OP "H6'"  H3  H 0 1 N N N -19.498 31.869 27.661 2.841  0.912  0.734  H3    6OP 29 
6OP "H5'"  H5  H 0 1 N N N -21.063 29.346 29.036 3.267  -2.054 0.251  H5    6OP 30 
6OP "H4'"  H7  H 0 1 N N N -21.686 31.795 27.112 1.149  -1.719 1.821  H7    6OP 31 
6OP "H3'"  H8  H 0 1 N N N -23.203 30.295 28.697 0.988  -1.825 -1.196 H8    6OP 32 
6OP "HO3'" H9  H 0 0 N Y N -23.528 32.474 27.877 1.042  -3.792 0.194  H9    6OP 33 
6OP "H2'"  H10 H 0 1 N N N -23.212 28.383 27.211 -1.002 -0.656 -1.263 H10   6OP 34 
6OP "H1'"  H11 H 0 1 N N N -23.691 30.280 25.044 -1.133 -0.374 1.746  H11   6OP 35 
6OP H12    H12 H 0 1 N N N -25.216 28.233 24.971 -2.932 -1.819 -1.792 H12   6OP 36 
6OP H13    H13 H 0 1 N N N -26.756 28.465 25.866 -1.812 -3.194 -1.638 H13   6OP 37 
6OP H14    H14 H 0 1 N N N -25.945 26.065 25.979 -4.114 -4.021 -1.532 H14   6OP 38 
6OP H15    H15 H 0 1 N N N -24.446 26.632 26.791 -3.358 -4.199 0.069  H15   6OP 39 
6OP H16    H16 H 0 1 N N N -26.246 26.287 29.860 -5.567 -4.132 1.120  H16   6OP 40 
6OP H17    H17 H 0 1 N N N -25.572 25.111 28.681 -6.615 -2.734 0.781  H17   6OP 41 
6OP H18    H18 H 0 1 N N N -24.620 26.562 29.147 -6.323 -3.954 -0.482 H18   6OP 42 
6OP H3     H19 H 0 1 N N N -23.551 27.187 21.780 -1.084 3.439  -1.936 H19   6OP 43 
6OP H20    H20 H 0 1 N N N -21.367 24.856 26.191 -4.410 4.409  1.007  H20   6OP 44 
6OP H21    H21 H 0 1 N N N -22.363 23.869 25.068 -4.911 2.775  1.504  H21   6OP 45 
6OP H22    H22 H 0 1 N N N -20.735 24.436 24.563 -3.759 3.694  2.502  H22   6OP 46 
6OP H6     H23 H 0 1 N N N -22.096 27.142 26.367 -2.720 1.229  1.979  H23   6OP 47 
# 
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 
6OP O4    C4     DOUB N N 1  
6OP N3    C4     SING N N 2  
6OP N3    C2     SING N N 3  
6OP O2    C2     DOUB N N 4  
6OP C4    C5     SING N N 5  
6OP C2    N1     SING N N 6  
6OP C5    C7     SING N N 7  
6OP C5    C6     DOUB N N 8  
6OP N1    C6     SING N N 9  
6OP N1    "C1'"  SING N N 10 
6OP "C1'" "O4'"  SING N N 11 
6OP "C1'" "C2'"  SING N N 12 
6OP "CB'" "CG'"  SING N N 13 
6OP "CB'" "O2'"  SING N N 14 
6OP "O4'" "C4'"  SING N N 15 
6OP "CG'" "OD'"  SING N N 16 
6OP "C2'" "O2'"  SING N N 17 
6OP "C2'" "C3'"  SING N N 18 
6OP "C4'" "C3'"  SING N N 19 
6OP "C4'" "C5'"  SING N N 20 
6OP "O3'" "C3'"  SING N N 21 
6OP "OD'" "CE'"  SING N N 22 
6OP "C6'" "C5'"  DOUB N E 23 
6OP "C6'" P      SING N N 24 
6OP OP2   P      DOUB N N 25 
6OP P     OP1    SING N N 26 
6OP P     OP3    SING N N 27 
6OP OP1   H1     SING N N 28 
6OP OP3   HOP3   SING N N 29 
6OP "C6'" "H6'"  SING N N 30 
6OP "C5'" "H5'"  SING N N 31 
6OP "C4'" "H4'"  SING N N 32 
6OP "C3'" "H3'"  SING N N 33 
6OP "O3'" "HO3'" SING N N 34 
6OP "C2'" "H2'"  SING N N 35 
6OP "C1'" "H1'"  SING N N 36 
6OP "CB'" H12    SING N N 37 
6OP "CB'" H13    SING N N 38 
6OP "CG'" H14    SING N N 39 
6OP "CG'" H15    SING N N 40 
6OP "CE'" H16    SING N N 41 
6OP "CE'" H17    SING N N 42 
6OP "CE'" H18    SING N N 43 
6OP N3    H3     SING N N 44 
6OP C7    H20    SING N N 45 
6OP C7    H21    SING N N 46 
6OP C7    H22    SING N N 47 
6OP C6    H6     SING N N 48 
# 
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 
6OP SMILES           ACDLabs              12.01 "P(O)(O)(=O)C=[C@H]C1C(O)C(OCCOC)C(O1)N2C=C(C(NC2=O)=O)C"                                                                                                                              
6OP InChI            InChI                1.03  "InChI=1S/C14H21N2O9P/c1-8-7-16(14(19)15-12(8)18)13-11(24-5-4-23-2)10(17)9(25-13)3-6-26(20,21)22/h3,6-7,9-11,13,17H,4-5H2,1-2H3,(H,15,18,19)(H2,20,21,22)/b6-3+/t9-,10-,11-,13-/m1/s1" 
6OP InChIKey         InChI                1.03  MIWMWNWNEZHLGC-PSDJLLRUSA-N                                                                                                                                                            
6OP SMILES_CANONICAL CACTVS               3.385 "COCCO[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=C(C)C(=O)NC2=O)/C=C/[P](O)(O)=O"                                                                                                                 
6OP SMILES           CACTVS               3.385 "COCCO[CH]1[CH](O)[CH](O[CH]1N2C=C(C)C(=O)NC2=O)C=C[P](O)(O)=O"                                                                                                                        
6OP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)/C=C/P(=O)(O)O)O)OCCOC"                                                                                                                
6OP SMILES           "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)C=CP(=O)(O)O)O)OCCOC"                                                                                                                                    
# 
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 
6OP "SYSTEMATIC NAME" ACDLabs              12.01 "1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione"                                  
6OP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(~{E})-2-[(2~{R},3~{R},4~{R},5~{R})-4-(2-methoxyethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]ethenyl]phosphonic 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 
6OP "Create component" 2016-05-13 RCSB 
6OP "Initial release"  2016-07-20 RCSB 
# 
