data_RFJ
#

_chem_comp.id                                   RFJ
_chem_comp.name                                 "2'-O-methyl-5'-O-thiophosphonoguanosine"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H16 N5 O7 P S"
_chem_comp.mon_nstd_parent_comp_id              G
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-02-11
_chem_comp.pdbx_modified_date                   2020-04-24
_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                       393.313
_chem_comp.one_letter_code                      G
_chem_comp.three_letter_code                    RFJ
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_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
RFJ  C       C1   C  0  1  N  N  N  ?  ?  ?   1.933   3.263  -1.719  C       RFJ   1  
RFJ  "C1'"   C2   C  0  1  N  N  R  ?  ?  ?   0.718   0.553   0.477  "C1'"   RFJ   2  
RFJ  C2      C3   C  0  1  N  N  N  ?  ?  ?   5.173   0.203   0.783  C2      RFJ   3  
RFJ  "C2'"   C4   C  0  1  N  N  R  ?  ?  ?   0.558   1.638  -0.618  "C2'"   RFJ   4  
RFJ  "C3'"   C5   C  0  1  N  N  R  ?  ?  ?  -0.848   2.208  -0.306  "C3'"   RFJ   5  
RFJ  C4      C6   C  0  1  Y  N  N  ?  ?  ?   3.028  -0.441   0.216  C4      RFJ   6  
RFJ  "C4'"   C7   C  0  1  N  N  R  ?  ?  ?  -1.532   1.097   0.513  "C4'"   RFJ   7  
RFJ  C5      C8   C  0  1  Y  N  N  ?  ?  ?   3.518  -1.627  -0.343  C5      RFJ   8  
RFJ  "C5'"   C9   C  0  1  N  N  N  ?  ?  ?  -2.813   0.645  -0.191  "C5'"   RFJ   9  
RFJ  C6      C10  C  0  1  N  N  N  ?  ?  ?   4.912  -1.862  -0.318  C6      RFJ  10  
RFJ  C8      C11  C  0  1  Y  N  N  ?  ?  ?   1.364  -1.643  -0.588  C8      RFJ  11  
RFJ  N1      N1   N  0  1  N  N  N  ?  ?  ?   5.710  -0.931   0.250  N1      RFJ  12  
RFJ  N2      N2   N  0  1  N  N  N  ?  ?  ?   6.007   1.131   1.354  N2      RFJ  13  
RFJ  N3      N3   N  0  1  N  N  N  ?  ?  ?   3.879   0.435   0.762  N3      RFJ  14  
RFJ  N7      N4   N  0  1  Y  N  N  ?  ?  ?   2.452  -2.318  -0.818  N7      RFJ  15  
RFJ  N9      N5   N  0  1  Y  N  N  ?  ?  ?   1.670  -0.475   0.049  N9      RFJ  16  
RFJ  "O2'"   O1   O  0  1  N  N  N  ?  ?  ?   1.559   2.649  -0.484  "O2'"   RFJ  17  
RFJ  "O3'"   O2   O  0  1  N  N  N  ?  ?  ?  -0.745   3.407   0.464  "O3'"   RFJ  18  
RFJ  "O4'"   O3   O  0  1  N  N  N  ?  ?  ?  -0.608  -0.002   0.603  "O4'"   RFJ  19  
RFJ  "O5'"   O4   O  0  1  N  N  N  ?  ?  ?  -3.501  -0.300   0.631  "O5'"   RFJ  20  
RFJ  O6      O5   O  0  1  N  N  N  ?  ?  ?   5.383  -2.881  -0.794  O6      RFJ  21  
RFJ  OP2     O6   O  0  1  N  N  N  ?  ?  ?  -5.573  -1.673   1.490  OP2     RFJ  22  
RFJ  P       P1   P  0  1  N  N  N  ?  ?  ?  -4.893  -0.987   0.201  P       RFJ  23  
RFJ  S       S1   S  0  1  N  N  N  ?  ?  ?  -6.039   0.311  -0.489  S       RFJ  24  
RFJ  H1      H1   H  0  1  N  N  N  ?  ?  ?   1.059   3.733  -2.171  H1      RFJ  25  
RFJ  H2      H2   H  0  1  N  N  N  ?  ?  ?   2.696   4.018  -1.533  H2      RFJ  26  
RFJ  H3      H3   H  0  1  N  N  N  ?  ?  ?   2.329   2.506  -2.396  H3      RFJ  27  
RFJ  H4      H4   H  0  1  N  N  N  ?  ?  ?   1.037   1.002   1.418  H4      RFJ  28  
RFJ  H5      H5   H  0  1  N  N  N  ?  ?  ?   0.586   1.194  -1.613  H5      RFJ  29  
RFJ  H6      H6   H  0  1  N  N  N  ?  ?  ?  -1.395   2.393  -1.231  H6      RFJ  30  
RFJ  H7      H7   H  0  1  N  N  N  ?  ?  ?  -1.766   1.464   1.512  H7      RFJ  31  
RFJ  H8      H8   H  0  1  N  N  N  ?  ?  ?  -3.455   1.509  -0.367  H8      RFJ  32  
RFJ  H9      H9   H  0  1  N  N  N  ?  ?  ?  -2.560   0.181  -1.144  H9      RFJ  33  
RFJ  H10     H10  H  0  1  N  N  N  ?  ?  ?   0.368  -1.959  -0.861  H10     RFJ  34  
RFJ  H11     H11  H  0  1  N  N  N  ?  ?  ?   6.669  -1.069   0.279  H11     RFJ  35  
RFJ  H12     H12  H  0  1  N  N  N  ?  ?  ?   6.964   0.976   1.374  H12     RFJ  36  
RFJ  H13     H13  H  0  1  N  N  N  ?  ?  ?   5.639   1.943   1.737  H13     RFJ  37  
RFJ  "HO3'"  H14  H  0  0  N  Y  N  ?  ?  ?  -1.597   3.774   0.735  "HO3'"  RFJ  38  
RFJ  HOP2    H15  H  0  0  N  N  N  ?  ?  ?  -6.417  -2.107   1.304  HOP2    RFJ  39  
RFJ  OP3     O3P  O  0  1  N  Y  N  ?  ?  ?  -4.614  -2.108  -0.920  OP3     RFJ  40  
RFJ  HOP3    H16  H  0  0  N  Y  N  ?  ?  ?  -4.024  -2.817  -0.629  HOP3    RFJ  41  
#   #
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
RFJ  S      P       DOUB  N  N   1  
RFJ  OP2    P       SING  N  N   2  
RFJ  P      "O5'"   SING  N  N   3  
RFJ  "O3'"  "C3'"   SING  N  N   4  
RFJ  "C5'"  "O5'"   SING  N  N   5  
RFJ  "C5'"  "C4'"   SING  N  N   6  
RFJ  "C3'"  "C4'"   SING  N  N   7  
RFJ  "C3'"  "C2'"   SING  N  N   8  
RFJ  "C4'"  "O4'"   SING  N  N   9  
RFJ  "C2'"  "O2'"   SING  N  N  10  
RFJ  "C2'"  "C1'"   SING  N  N  11  
RFJ  "O4'"  "C1'"   SING  N  N  12  
RFJ  C8     N7      DOUB  Y  N  13  
RFJ  C8     N9      SING  Y  N  14  
RFJ  "O2'"  C       SING  N  N  15  
RFJ  N7     C5      SING  Y  N  16  
RFJ  "C1'"  N9      SING  N  N  17  
RFJ  N9     C4      SING  Y  N  18  
RFJ  C5     C4      DOUB  Y  N  19  
RFJ  C5     C6      SING  N  N  20  
RFJ  C4     N3      SING  N  N  21  
RFJ  O6     C6      DOUB  N  N  22  
RFJ  C6     N1      SING  N  N  23  
RFJ  N3     C2      DOUB  N  N  24  
RFJ  N1     C2      SING  N  N  25  
RFJ  C2     N2      SING  N  N  26  
RFJ  C      H1      SING  N  N  27  
RFJ  C      H2      SING  N  N  28  
RFJ  C      H3      SING  N  N  29  
RFJ  "C1'"  H4      SING  N  N  30  
RFJ  "C2'"  H5      SING  N  N  31  
RFJ  "C3'"  H6      SING  N  N  32  
RFJ  "C4'"  H7      SING  N  N  33  
RFJ  "C5'"  H8      SING  N  N  34  
RFJ  "C5'"  H9      SING  N  N  35  
RFJ  C8     H10     SING  N  N  36  
RFJ  N1     H11     SING  N  N  37  
RFJ  N2     H12     SING  N  N  38  
RFJ  N2     H13     SING  N  N  39  
RFJ  "O3'"  "HO3'"  SING  N  N  40  
RFJ  OP2    HOP2    SING  N  N  41  
RFJ  P      OP3     SING  N  N  42  
RFJ  OP3    HOP3    SING  N  N  43  
#   #
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
RFJ  SMILES            ACDLabs               12.01  "COC3C(n2c1N=C(N)NC(c1nc2)=O)OC(C3O)COP(O)(O)=S"  
RFJ  InChI             InChI                 1.03   "InChI=1S/C11H16N5O7PS/c1-21-7-6(17)4(2-22-24(19,20)25)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,25)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1"  
RFJ  InChIKey          InChI                 1.03   QUDYZWLGVZGRFN-KQYNXXCUSA-N  
RFJ  SMILES_CANONICAL  CACTVS                3.385  "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N"  
RFJ  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N"  
RFJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O"  
RFJ  SMILES            "OpenEye OEToolkits"  2.0.7  "COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(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
RFJ  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-O-methyl-5'-O-thiophosphonoguanosine"  
RFJ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "2-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RFJ  "Create component"  2020-02-11  RCSB  
RFJ  "Initial release"   2020-04-29  RCSB  
##
