data_VC7
#

_chem_comp.id                                   VC7
_chem_comp.name                                 "5'-O-[(R)-hydroxy(methyl)phosphoryl]guanosine"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H16 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              G
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-07-27
_chem_comp.pdbx_modified_date                   2020-12-18
_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                       361.248
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VC7
_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       7JJF
_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
VC7  "C1'"   C1   C  0  1  N  N  R  -13.397  14.581  -0.667   0.481   0.711   0.328  "C1'"  VC7   1  
VC7  C2      C2   C  0  1  N  N  N  -14.849  11.104  -2.492   4.944   0.486   0.619  C2     VC7   2  
VC7  "C2'"   C3   C  0  1  N  N  R  -13.159  14.195   0.791   0.328   1.681  -0.871  "C2'"  VC7   3  
VC7  "C3'"   C4   C  0  1  N  N  S  -11.802  14.794   1.001  -1.086   2.266  -0.636  "C3'"  VC7   4  
VC7  C4      C5   C  0  1  Y  N  N  -13.302  12.814  -2.297   2.807  -0.264   0.162  C4     VC7   5  
VC7  "C4'"   C6   C  0  1  N  N  R  -12.173  16.121   0.490  -1.774   1.235   0.280  "C4'"  VC7   6  
VC7  C5      C7   C  0  1  Y  N  N  -12.561  12.407  -3.343   3.316  -1.500  -0.255  C5     VC7   7  
VC7  "C5'"   C8   C  0  1  N  N  N  -10.943  16.988   0.311  -3.044   0.708  -0.392  "C5'"  VC7   8  
VC7  C6      C9   C  0  1  N  N  N  -12.937  11.300  -3.982   4.715  -1.703  -0.219  C6     VC7   9  
VC7  C8      C10  C  0  1  Y  N  N  -11.664  14.167  -2.526   1.161  -1.587  -0.467  C8     VC7  10  
VC7  CP2     C11  C  0  1  N  N  N   -8.772  16.378  -3.005  -5.597  -2.016   1.488  CP2    VC7  11  
VC7  N1      N1   N  0  1  N  N  N  -14.123  10.637  -3.581   5.499  -0.694   0.221  N1     VC7  12  
VC7  N2      N2   N  0  1  N  N  N  -15.942  10.486  -2.084   5.765   1.493   1.061  N2     VC7  13  
VC7  N3      N3   N  0  1  N  N  N  -14.423  12.202  -1.882   3.646   0.689   0.585  N3     VC7  14  
VC7  N7      N4   N  0  1  Y  N  N  -11.518  13.245  -3.481   2.260  -2.264  -0.627  N7     VC7  15  
VC7  N9      N5   N  0  1  Y  N  N  -12.736  13.887  -1.787   1.449  -0.344   0.018  N9     VC7  16  
VC7  "O2'"   O1   O  0  1  N  N  N  -14.157  14.874   1.619   1.319   2.709  -0.824  "O2'"  VC7  17  
VC7  "O3'"   O2   O  0  1  N  N  N  -11.500  14.925   2.412  -1.001   3.535   0.015  "O3'"  VC7  18  
VC7  "O4'"   O3   O  0  1  N  N  N  -12.777  15.876  -0.766  -0.844   0.159   0.486  "O4'"  VC7  19  
VC7  "O5'"   O4   O  0  1  N  N  N  -10.092  16.428  -0.699  -3.736  -0.158   0.511  "O5'"  VC7  20  
VC7  O6      O5   O  0  1  N  N  N  -12.303  10.890  -4.967   5.202  -2.762  -0.576  O6     VC7  21  
VC7  OP1     O6   O  0  1  N  N  N   -8.167  18.054  -1.171  -4.939  -1.671  -1.112  OP1    VC7  22  
VC7  P       P1   P  0  1  N  N  N   -9.376  17.410  -1.765  -5.118  -0.893   0.134  P      VC7  23  
VC7  "H1'"   H1   H  0  1  N  N  N  -14.479  14.654  -0.853   0.780   1.253   1.225  "H1'"  VC7  24  
VC7  "H2'"   H2   H  0  1  N  N  N  -13.159  13.104   0.931   0.373   1.141  -1.816  "H2'"  VC7  25  
VC7  "H3'"   H3   H  0  1  N  N  N  -11.013  14.299   0.416  -1.623   2.358  -1.580  "H3'"  VC7  26  
VC7  "H4'"   H4   H  0  1  N  N  N  -12.876  16.613   1.179  -2.025   1.697   1.235  "H4'"  VC7  27  
VC7  "H5'"   H5   H  0  1  N  N  N  -10.393  17.041   1.262  -3.689   1.546  -0.658  "H5'"  VC7  28  
VC7  "H5''"  H6   H  0  0  N  N  N  -11.251  18.000   0.008  -2.776   0.155  -1.292  H5S    VC7  29  
VC7  H8      H7   H  0  1  N  N  N  -11.010  15.013  -2.375   0.169  -1.953  -0.687  H8     VC7  30  
VC7  HCP2    H8   H  0  0  N  N  N   -9.611  15.863  -3.495  -4.816  -2.763   1.634  HP2    VC7  31  
VC7  HCP3    H9   H  0  0  N  N  N   -8.226  16.978  -3.748  -5.728  -1.444   2.406  H8L    VC7  32  
VC7  HCP1    H10  H  0  0  N  N  N   -8.092  15.634  -2.564  -6.532  -2.514   1.233  H8M    VC7  33  
VC7  H1      H11  H  0  1  N  N  N  -14.438   9.831  -4.083   6.462  -0.810   0.254  H1     VC7  34  
VC7  H21     H12  H  0  1  N  N  N  -16.459  10.845  -1.307   5.385   2.340   1.344  H21    VC7  35  
VC7  H22     H13  H  0  1  N  N  N  -16.253   9.659  -2.552   6.725   1.358   1.091  H22    VC7  36  
VC7  "HO2'"  H14  H  0  0  N  N  N  -14.022  14.644   2.531   1.264   3.341  -1.554  H8O    VC7  37  
VC7  "HO3'"  H15  H  0  0  N  Y  N  -11.257  14.077   2.764  -0.525   4.207  -0.493  H2     VC7  38  
VC7  OP3     OP3  O  0  1  N  Y  N  -10.534  18.190  -2.466  -6.271   0.209  -0.082  OP3    VC7  39  
VC7  HOP3    H16  H  0  0  N  Y  N  -10.344  19.121  -2.451  -6.442   0.757   0.697  H3     VC7  40  
#   #
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
VC7  O6     C6      DOUB  N  N   1  
VC7  C6     N1      SING  N  N   2  
VC7  C6     C5      SING  N  N   3  
VC7  N1     C2      SING  N  N   4  
VC7  N7     C5      SING  Y  N   5  
VC7  N7     C8      DOUB  Y  N   6  
VC7  C5     C4      DOUB  Y  N   7  
VC7  CP2    P       SING  N  N   8  
VC7  C8     N9      SING  Y  N   9  
VC7  C2     N2      SING  N  N  10  
VC7  C2     N3      DOUB  N  N  11  
VC7  C4     N3      SING  N  N  12  
VC7  C4     N9      SING  Y  N  13  
VC7  N9     "C1'"   SING  N  N  14  
VC7  P      OP1     DOUB  N  N  15  
VC7  P      "O5'"   SING  N  N  16  
VC7  "O4'"  "C1'"   SING  N  N  17  
VC7  "O4'"  "C4'"   SING  N  N  18  
VC7  "O5'"  "C5'"   SING  N  N  19  
VC7  "C1'"  "C2'"   SING  N  N  20  
VC7  "C5'"  "C4'"   SING  N  N  21  
VC7  "C4'"  "C3'"   SING  N  N  22  
VC7  "C2'"  "C3'"   SING  N  N  23  
VC7  "C2'"  "O2'"   SING  N  N  24  
VC7  "C3'"  "O3'"   SING  N  N  25  
VC7  "C1'"  "H1'"   SING  N  N  26  
VC7  "C2'"  "H2'"   SING  N  N  27  
VC7  "C3'"  "H3'"   SING  N  N  28  
VC7  "C4'"  "H4'"   SING  N  N  29  
VC7  "C5'"  "H5'"   SING  N  N  30  
VC7  "C5'"  "H5''"  SING  N  N  31  
VC7  C8     H8      SING  N  N  32  
VC7  CP2    HCP2    SING  N  N  33  
VC7  CP2    HCP3    SING  N  N  34  
VC7  CP2    HCP1    SING  N  N  35  
VC7  N1     H1      SING  N  N  36  
VC7  N2     H21     SING  N  N  37  
VC7  N2     H22     SING  N  N  38  
VC7  "O2'"  "HO2'"  SING  N  N  39  
VC7  "O3'"  "HO3'"  SING  N  N  40  
VC7  P      OP3     SING  N  N  41  
VC7  OP3    HOP3    SING  N  N  42  
#   #
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
VC7  SMILES            ACDLabs               12.01  "C1(C(C(O)C(COP(C)(=O)O)O1)O)n3c2N=C(N)NC(c2nc3)=O"  
VC7  InChI             InChI                 1.03   "InChI=1S/C11H16N5O7P/c1-24(20,21)22-2-4-6(17)7(18)10(23-4)16-3-13-5-8(16)14-11(12)15-9(5)19/h3-4,6-7,10,17-18H,2H2,1H3,(H,20,21)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1"  
VC7  InChIKey          InChI                 1.03   ZRTURURJQQBKIB-KQYNXXCUSA-N  
VC7  SMILES_CANONICAL  CACTVS                3.385  "C[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N"  
VC7  SMILES            CACTVS                3.385  "C[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=Nc23)N"  
VC7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2N=C(NC3=O)N)O)O"  
VC7  SMILES            "OpenEye OEToolkits"  2.0.7  "CP(=O)(O)OCC1C(C(C(O1)n2cnc3c2N=C(NC3=O)N)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
VC7  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(R)-hydroxy(methyl)phosphoryl]guanosine"  
VC7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-methyl-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
VC7  "Create component"  2020-07-27  RCSB  
VC7  "Initial release"   2020-12-23  RCSB  
##
