data_VPA
#

_chem_comp.id                                   VPA
_chem_comp.name                                 "2-phenyl-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)ethylamidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H28 N2 O9"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]e
thanimidamide
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-01-31
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       428.434
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VPA
_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       3WQ5
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
VPA  C1     C1     C  0  1  N  N  N  -29.216  12.631  -21.601  -3.257  -0.119   0.411  C1     VPA   1  
VPA  C2     C2     C  0  1  N  N  N  -29.025  12.387  -20.099  -4.243  -0.915   1.227  C2     VPA   2  
VPA  N2     N2     N  0  1  N  N  N  -30.400  12.493  -22.178  -2.914  -0.528  -0.767  N2     VPA   3  
VPA  C3     C3     C  0  1  Y  N  N  -29.867  11.204  -19.567  -4.673  -2.131   0.448  C3     VPA   4  
VPA  C4     C4     C  0  1  Y  N  N  -30.160  11.154  -18.206  -3.969  -3.315   0.571  C4     VPA   5  
VPA  C5     C5     C  0  1  Y  N  N  -30.912  10.109  -17.676  -4.364  -4.431  -0.143  C5     VPA   6  
VPA  C6     C6     C  0  1  Y  N  N  -31.378   9.098  -18.507  -5.463  -4.363  -0.980  C6     VPA   7  
VPA  C8     C8     C  0  1  Y  N  N  -30.336  10.180  -20.392  -5.775  -2.065  -0.384  C8     VPA   8  
VPA  C7     C7     C  0  1  Y  N  N  -31.093   9.137  -19.867  -6.166  -3.180  -1.102  C7     VPA   9  
VPA  N1     N1     N  0  1  N  N  N  -28.186  13.046  -22.322  -2.728   1.040   0.915  N1     VPA  10  
VPA  "C1'"  "C1'"  C  0  1  N  N  R  -28.304  13.275  -23.775  -1.769   1.813   0.122  "C1'"  VPA  11  
VPA  "O5'"  "O5'"  O  0  1  N  N  N  -29.705  13.511  -24.084  -0.439   1.447   0.493  "O5'"  VPA  12  
VPA  "C2'"  "C2'"  C  0  1  N  N  R  -27.614  12.067  -24.441  -1.978   3.307   0.383  "C2'"  VPA  13  
VPA  "O2'"  "O2'"  O  0  1  N  N  N  -26.216  12.348  -24.587  -3.289   3.687  -0.040  "O2'"  VPA  14  
VPA  "C3'"  "C3'"  C  0  1  N  N  S  -28.232  11.696  -25.793  -0.933   4.106  -0.403  "C3'"  VPA  15  
VPA  "O3'"  "O3'"  O  0  1  N  N  N  -27.812  10.390  -26.205  -1.074   5.497  -0.108  "O3'"  VPA  16  
VPA  "C4'"  "C4'"  C  0  1  N  N  S  -29.741  11.719  -25.643   0.466   3.634   0.004  "C4'"  VPA  17  
VPA  "O4'"  "O4'"  O  0  1  N  N  N  -30.362  11.208  -26.818   1.447   4.321  -0.775  "O4'"  VPA  18  
VPA  "C5'"  "C5'"  C  0  1  N  N  R  -30.183  13.147  -25.380   0.580   2.127  -0.243  "C5'"  VPA  19  
VPA  "C6'"  "C6'"  C  0  1  N  N  N  -31.689  13.203  -25.267   1.955   1.638   0.218  "C6'"  VPA  20  
VPA  "O6'"  "O6'"  O  0  1  N  N  N  -31.955  12.380  -24.116   2.106   0.257  -0.119  "O6'"  VPA  21  
VPA  C1A    C1A    C  0  1  N  N  S  -33.354  12.135  -23.952   3.362  -0.302   0.270  C1A    VPA  22  
VPA  O5A    O5A    O  0  1  N  N  N  -33.847  13.002  -22.899   4.412   0.329  -0.467  O5A    VPA  23  
VPA  C5A    C5A    C  0  1  N  N  N  -35.248  12.780  -22.631   5.721  -0.140  -0.135  C5A    VPA  24  
VPA  C4A    C4A    C  0  1  N  N  R  -35.453  11.337  -22.171   5.819  -1.636  -0.445  C4A    VPA  25  
VPA  O4A    O4A    O  0  1  N  N  N  -36.826  11.107  -21.849   7.108  -2.120  -0.061  O4A    VPA  26  
VPA  C3A    C3A    C  0  1  N  N  S  -35.011  10.402  -23.289   4.736  -2.384   0.338  C3A    VPA  27  
VPA  O3A    O3A    O  0  1  N  N  N  -35.204   9.047  -22.896   4.773  -3.772  -0.001  O3A    VPA  28  
VPA  C2A    C2A    C  0  1  N  N  R  -33.539  10.663  -23.575   3.366  -1.804  -0.024  C2A    VPA  29  
VPA  O2A    O2A    O  0  1  N  N  N  -33.066   9.809  -24.625   2.354  -2.446   0.755  O2A    VPA  30  
VPA  H1     H1     H  0  1  N  N  N  -27.962  12.173  -19.911  -3.774  -1.227   2.160  H1     VPA  31  
VPA  H2     H2     H  0  1  N  N  N  -29.318  13.298  -19.556  -5.114  -0.298   1.447  H2     VPA  32  
VPA  H3     H3     H  0  1  N  N  N  -31.106  12.222  -21.524  -3.291  -1.347  -1.126  H3     VPA  33  
VPA  H4     H4     H  0  1  N  N  N  -29.799  11.936  -17.554  -3.111  -3.368   1.224  H4     VPA  34  
VPA  H5     H5     H  0  1  N  N  N  -31.133  10.084  -16.619  -3.814  -5.355  -0.048  H5     VPA  35  
VPA  H6     H6     H  0  1  N  N  N  -31.959   8.285  -18.098  -5.771  -5.235  -1.538  H6     VPA  36  
VPA  H7     H7     H  0  1  N  N  N  -30.109  10.197  -21.448  -6.325  -1.141  -0.480  H7     VPA  37  
VPA  H8     H8     H  0  1  N  N  N  -31.460   8.357  -20.517  -7.027  -3.128  -1.752  H8     VPA  38  
VPA  H9     H9     H  0  1  N  N  N  -27.308  13.208  -21.872  -2.988   1.348   1.797  H9     VPA  39  
VPA  H10    H10    H  0  1  N  N  N  -27.727  14.175  -24.035  -1.921   1.604  -0.937  H10    VPA  40  
VPA  H11    H11    H  0  1  N  N  N  -27.736  11.204  -23.770  -1.866   3.510   1.448  H11    VPA  41  
VPA  H12    H12    H  0  1  N  N  N  -25.848  12.576  -23.741  -4.001   3.216   0.414  H12    VPA  42  
VPA  H13    H13    H  0  1  N  N  N  -27.933  12.446  -26.540  -1.077   3.942  -1.471  H13    VPA  43  
VPA  H14    H14    H  0  1  N  N  N  -26.867  10.376  -26.299  -1.938   5.863  -0.340  H14    VPA  44  
VPA  H15    H15    H  0  1  N  N  N  -30.017  11.101  -24.776   0.628   3.843   1.062  H15    VPA  45  
VPA  H16    H16    H  0  1  N  N  N  -31.306  11.228  -26.712   1.429   5.283  -0.672  H16    VPA  46  
VPA  H17    H17    H  0  1  N  N  N  -29.819  13.824  -26.167   0.459   1.923  -1.306  H17    VPA  47  
VPA  H18    H18    H  0  1  N  N  N  -32.036  14.234  -25.105   2.732   2.219  -0.278  H18    VPA  48  
VPA  H19    H19    H  0  1  N  N  N  -32.169  12.792  -26.167   2.042   1.760   1.297  H19    VPA  49  
VPA  H20    H20    H  0  1  N  N  N  -33.892  12.335  -24.890   3.518  -0.140   1.336  H20    VPA  50  
VPA  H21    H21    H  0  1  N  N  N  -35.584  13.468  -21.842   6.461   0.403  -0.723  H21    VPA  51  
VPA  H22    H22    H  0  1  N  N  N  -35.830  12.960  -23.547   5.908   0.024   0.927  H22    VPA  52  
VPA  H23    H23    H  0  1  N  N  N  -34.823  11.155  -21.288   5.674  -1.797  -1.513  H23    VPA  53  
VPA  H24    H24    H  0  1  N  N  N  -37.091  11.695  -21.151   7.843  -1.686  -0.515  H24    VPA  54  
VPA  H25    H25    H  0  1  N  N  N  -35.596  10.625  -24.193   4.912  -2.266   1.408  H25    VPA  55  
VPA  H26    H26    H  0  1  N  N  N  -36.125   8.896  -22.720   5.616  -4.203   0.195  H26    VPA  56  
VPA  H27    H27    H  0  1  N  N  N  -32.967  10.468  -22.656   3.170  -1.968  -1.084  H27    VPA  57  
VPA  H28    H28    H  0  1  N  N  N  -33.188   8.901  -24.374   1.460  -2.123   0.580  H28    VPA  58  
#   #
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
VPA  "O4'"  "C4'"  SING  N  N   1  
VPA  "O3'"  "C3'"  SING  N  N   2  
VPA  "C3'"  "C4'"  SING  N  N   3  
VPA  "C3'"  "C2'"  SING  N  N   4  
VPA  "C4'"  "C5'"  SING  N  N   5  
VPA  "C5'"  "C6'"  SING  N  N   6  
VPA  "C5'"  "O5'"  SING  N  N   7  
VPA  "C6'"  "O6'"  SING  N  N   8  
VPA  O2A    C2A    SING  N  N   9  
VPA  "O2'"  "C2'"  SING  N  N  10  
VPA  "C2'"  "C1'"  SING  N  N  11  
VPA  "O6'"  C1A    SING  N  N  12  
VPA  "O5'"  "C1'"  SING  N  N  13  
VPA  C1A    C2A    SING  N  N  14  
VPA  C1A    O5A    SING  N  N  15  
VPA  "C1'"  N1     SING  N  N  16  
VPA  C2A    C3A    SING  N  N  17  
VPA  C3A    O3A    SING  N  N  18  
VPA  C3A    C4A    SING  N  N  19  
VPA  O5A    C5A    SING  N  N  20  
VPA  C5A    C4A    SING  N  N  21  
VPA  N1     C1     SING  N  N  22  
VPA  N2     C1     DOUB  N  N  23  
VPA  C4A    O4A    SING  N  N  24  
VPA  C1     C2     SING  N  N  25  
VPA  C8     C7     DOUB  Y  N  26  
VPA  C8     C3     SING  Y  N  27  
VPA  C2     C3     SING  N  N  28  
VPA  C7     C6     SING  Y  N  29  
VPA  C3     C4     DOUB  Y  N  30  
VPA  C6     C5     DOUB  Y  N  31  
VPA  C4     C5     SING  Y  N  32  
VPA  C2     H1     SING  N  N  33  
VPA  C2     H2     SING  N  N  34  
VPA  N2     H3     SING  N  N  35  
VPA  C4     H4     SING  N  N  36  
VPA  C5     H5     SING  N  N  37  
VPA  C6     H6     SING  N  N  38  
VPA  C8     H7     SING  N  N  39  
VPA  C7     H8     SING  N  N  40  
VPA  N1     H9     SING  N  N  41  
VPA  "C1'"  H10    SING  N  N  42  
VPA  "C2'"  H11    SING  N  N  43  
VPA  "O2'"  H12    SING  N  N  44  
VPA  "C3'"  H13    SING  N  N  45  
VPA  "O3'"  H14    SING  N  N  46  
VPA  "C4'"  H15    SING  N  N  47  
VPA  "O4'"  H16    SING  N  N  48  
VPA  "C5'"  H17    SING  N  N  49  
VPA  "C6'"  H18    SING  N  N  50  
VPA  "C6'"  H19    SING  N  N  51  
VPA  C1A    H20    SING  N  N  52  
VPA  C5A    H21    SING  N  N  53  
VPA  C5A    H22    SING  N  N  54  
VPA  C4A    H23    SING  N  N  55  
VPA  O4A    H24    SING  N  N  56  
VPA  C3A    H25    SING  N  N  57  
VPA  O3A    H26    SING  N  N  58  
VPA  C2A    H27    SING  N  N  59  
VPA  O2A    H28    SING  N  N  60  
#   #
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
VPA  SMILES            ACDLabs               12.01  "O(CC2OC(NC(=[N@H])Cc1ccccc1)C(O)C(O)C2O)C3OCC(O)C(O)C3O"  
VPA  InChI             InChI                 1.03   "InChI=1S/C19H28N2O9/c20-12(6-9-4-2-1-3-5-9)21-18-16(26)15(25)14(24)11(30-18)8-29-19-17(27)13(23)10(22)7-28-19/h1-5,10-11,13-19,22-27H,6-8H2,(H2,20,21)/t10-,11-,13+,14-,15+,16-,17-,18-,19+/m1/s1"  
VPA  InChIKey          InChI                 1.03   SKGTWJNDCFMXKU-GZDQRYBESA-N  
VPA  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)Cc3ccccc3)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O"  
VPA  SMILES            CACTVS                3.385  "O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)Cc3ccccc3)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O"  
VPA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "[H]/N=C(\Cc1ccccc1)/N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)O"  
VPA  SMILES            "OpenEye OEToolkits"  1.7.6  "c1ccc(cc1)CC(=N)NC2C(C(C(C(O2)COC3C(C(C(CO3)O)O)O)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
VPA  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-[(1E)-2-phenylethanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine"  
VPA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]ethanimidamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VPA  "Create component"  2014-01-31  PDBJ  
VPA  "Modify name"       2014-02-18  PDBJ  
VPA  "Modify synonyms"   2014-02-18  PDBJ  
VPA  "Initial release"   2014-04-23  RCSB  
VPA  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VPA
_pdbx_chem_comp_synonyms.name        "2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]ethanimidamide"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
