data_6OO
# 
_chem_comp.id                                    6OO 
_chem_comp.name                                  "2'-O-methyl-5'-O-thiophosphonocytidine" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N3 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               C 
_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                        353.289 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6OO 
_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 
6OO C2    C1  C 0 1 N N N -31.350 24.700 38.316 -2.465 1.068  -0.540 C2    6OO 1  
6OO C4    C2  C 0 1 N N N -29.178 24.622 37.520 -4.483 2.098  -0.087 C4    6OO 2  
6OO C5    C3  C 0 1 N N N -28.708 24.473 38.810 -4.661 1.254  1.028  C5    6OO 3  
6OO C6    C4  C 0 1 N N N -29.669 24.438 39.858 -3.711 0.331  1.310  C6    6OO 4  
6OO O2    O1  O 0 1 N N N -32.499 24.810 38.037 -1.469 0.980  -1.239 O2    6OO 5  
6OO P     P1  P 0 1 N N N -27.546 25.691 42.946 3.898  1.098  0.002  P     6OO 6  
6OO SP1   S1  S 0 1 N N N -27.861 25.811 44.845 5.463  -0.297 -0.305 SP1   6OO 7  
6OO OP2   O2  O 0 1 N N N -26.378 24.839 42.448 3.572  1.764  -1.280 OP2   6OO 8  
6OO "O5'" O3  O 0 1 N N N -28.936 25.407 42.387 2.595  0.330  0.554  "O5'" 6OO 9  
6OO "C5'" C5  C 0 1 N N N -29.786 24.640 43.280 1.877  -0.637 -0.214 "C5'" 6OO 10 
6OO "C4'" C6  C 0 1 N N R -31.022 24.243 42.718 0.700  -1.168 0.605  "C4'" 6OO 11 
6OO "O4'" O4  O 0 1 N N N -31.516 25.186 41.677 -0.261 -0.120 0.817  "O4'" 6OO 12 
6OO "C3'" C7  C 0 1 N N R -30.971 22.844 41.974 -0.011 -2.296 -0.168 "C3'" 6OO 13 
6OO "O3'" O5  O 0 1 N N N -31.146 21.650 42.864 0.023  -3.514 0.579  "O3'" 6OO 14 
6OO "C2'" C8  C 0 1 N N R -31.767 22.934 41.050 -1.467 -1.794 -0.318 "C2'" 6OO 15 
6OO "O2'" O6  O 0 1 N N N -33.098 22.336 41.154 -2.398 -2.858 -0.109 "O2'" 6OO 16 
6OO "C1'" C9  C 0 1 N N R -31.858 24.505 40.639 -1.566 -0.738 0.818  "C1'" 6OO 17 
6OO "CM'" C10 C 0 1 N N N -33.555 21.881 39.893 -2.767 -3.550 -1.304 "CM'" 6OO 18 
6OO N1    N1  N 0 1 N N N -30.943 24.564 39.564 -2.606 0.248  0.518  N1    6OO 19 
6OO N3    N2  N 0 1 N N N -30.478 24.732 37.303 -3.393 1.978  -0.834 N3    6OO 20 
6OO N4    N3  N 0 1 N N N -28.274 24.664 36.419 -5.432 3.045  -0.397 N4    6OO 21 
6OO O1    O7  O 0 1 N Y N -27.302 27.211 42.604 4.366  2.202  1.076  O1    6OO 22 
6OO H1    H1  H 0 1 N N N -27.651 24.386 39.015 -5.543 1.340  1.646  H1    6OO 23 
6OO H2    H2  H 0 1 N N N -29.355 24.309 40.883 -3.824 -0.327 2.159  H2    6OO 24 
6OO H3    H3  H 0 1 N N N -26.912 25.063 45.324 5.651  -0.817 0.921  H3    6OO 25 
6OO H4    H4  H 0 1 N N N -29.239 23.734 43.581 1.504  -0.172 -1.127 H4    6OO 26 
6OO H5    H5  H 0 1 N N N -29.994 25.255 44.168 2.542  -1.462 -0.473 H5    6OO 27 
6OO H6    H6  H 0 1 N N N -31.781 24.167 43.511 1.056  -1.544 1.565  H6    6OO 28 
6OO H7    H7  H 0 1 N N N -29.949 22.773 41.574 0.449  -2.437 -1.146 H7    6OO 29 
6OO H8    H8  H 0 1 N N N -30.487 21.665 43.548 0.916  -3.843 0.754  H8    6OO 30 
6OO H9    H9  H 0 1 N N N -31.314 22.465 40.165 -1.620 -1.331 -1.293 H9    6OO 31 
6OO H10   H10 H 0 1 N N N -32.883 24.714 40.300 -1.760 -1.222 1.776  H10   6OO 32 
6OO H11   H11 H 0 1 N N N -34.556 21.438 40.003 -3.229 -2.851 -2.001 H11   6OO 33 
6OO H12   H12 H 0 1 N N N -33.605 22.728 39.194 -1.878 -3.985 -1.761 H12   6OO 34 
6OO H13   H13 H 0 1 N N N -32.859 21.124 39.503 -3.475 -4.342 -1.060 H13   6OO 35 
6OO H14   H14 H 0 1 N N N -28.624 24.776 35.489 -6.226 3.133  0.153  H14   6OO 36 
6OO H15   H15 H 0 1 N N N -27.290 24.581 36.577 -5.307 3.624  -1.165 H15   6OO 37 
6OO H16   H16 H 0 1 N N N -26.472 27.305 42.152 5.147  2.705  0.808  H16   6OO 38 
# 
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 
6OO N4    C4    SING N N 1  
6OO N3    C4    DOUB N N 2  
6OO N3    C2    SING N N 3  
6OO C4    C5    SING N N 4  
6OO O2    C2    DOUB N N 5  
6OO C2    N1    SING N N 6  
6OO C5    C6    DOUB N N 7  
6OO N1    C6    SING N N 8  
6OO N1    "C1'" SING N N 9  
6OO "CM'" "O2'" SING N N 10 
6OO "C1'" "C2'" SING N N 11 
6OO "C1'" "O4'" SING N N 12 
6OO "C2'" "O2'" SING N N 13 
6OO "C2'" "C3'" SING N N 14 
6OO "O4'" "C4'" SING N N 15 
6OO "C3'" "C4'" SING N N 16 
6OO "C3'" "O3'" SING N N 17 
6OO "O5'" P     SING N N 18 
6OO "O5'" "C5'" SING N N 19 
6OO OP2   P     DOUB N N 20 
6OO "C4'" "C5'" SING N N 21 
6OO P     SP1   SING N N 22 
6OO P     O1    SING N N 23 
6OO C5    H1    SING N N 24 
6OO C6    H2    SING N N 25 
6OO SP1   H3    SING N N 26 
6OO "C5'" H4    SING N N 27 
6OO "C5'" H5    SING N N 28 
6OO "C4'" H6    SING N N 29 
6OO "C3'" H7    SING N N 30 
6OO "O3'" H8    SING N N 31 
6OO "C2'" H9    SING N N 32 
6OO "C1'" H10   SING N N 33 
6OO "CM'" H11   SING N N 34 
6OO "CM'" H12   SING N N 35 
6OO "CM'" H13   SING N N 36 
6OO N4    H14   SING N N 37 
6OO N4    H15   SING N N 38 
6OO O1    H16   SING N N 39 
# 
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 
6OO InChI            InChI                1.03  "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1" 
6OO InChIKey         InChI                1.03  JKIZWHJBBPPNBB-ZOQUXTDFSA-N                                                                                                                                 
6OO SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N"                                                                                              
6OO SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N"                                                                                                    
6OO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O"                                                                                                
6OO SMILES           "OpenEye OEToolkits" 2.0.5 "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)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 
6OO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic 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 
6OO "Create component"   2016-05-13 RCSB 
6OO "Other modification" 2016-06-21 RCSB 
6OO "Initial release"    2016-07-20 RCSB 
# 
