data_VDM
#

_chem_comp.id                                   VDM
_chem_comp.name                                 "(1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H25 N O8"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        VALIDOXYLAMINE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2007-01-25
_chem_comp.pdbx_modified_date                   2021-03-01
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       335.350
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VDM
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       2JF4
_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
VDM  O7      O7    O  0  1  N  N  N  29.348  51.117  15.007   6.214   2.855  -2.249  O7      VDM   1  
VDM  C7      C7    C  0  1  N  N  N  30.453  51.070  14.108   5.686   1.726  -1.579  C7      VDM   2  
VDM  C5      C5    C  0  1  N  N  N  30.173  52.166  13.119   4.709   1.019  -2.477  C5      VDM   3  
VDM  C6      C6    C  0  1  N  N  N  29.647  51.840  11.917   3.422   0.870  -2.115  C6      VDM   4  
VDM  C4      C4    C  0  1  N  N  S  30.406  53.598  13.560   5.233   0.518  -3.805  C4      VDM   5  
VDM  O4      O4    O  0  1  N  N  N  31.681  53.801  14.150   6.403  -0.279  -3.608  O4      VDM   6  
VDM  C3      C3    C  0  1  N  N  R  30.282  54.586  12.422   4.236  -0.345  -4.599  C3      VDM   7  
VDM  O3      O3    O  0  1  N  N  N  30.203  55.886  13.020   4.595  -0.293  -5.983  O3      VDM   8  
VDM  C2      C2    C  0  1  N  N  S  29.053  54.227  11.579   2.809   0.181  -4.455  C2      VDM   9  
VDM  O2      O2    O  0  1  N  N  N  28.716  55.302  10.696   1.921  -0.644  -5.210  O2      VDM  10  
VDM  C1      C1    C  0  1  N  N  S  29.327  52.889  10.854   2.371   0.231  -2.979  C1      VDM  11  
VDM  "N1'"   N1*   N  0  1  N  N  N  30.438  52.957   9.893   2.062  -1.106  -2.458  "N1'"   VDM  12  
VDM  "C1'"   C1*   C  0  1  N  N  S  31.198  51.748   9.526   1.557  -1.019  -1.083  "C1'"   VDM  13  
VDM  "C2'"   C2*   C  0  1  N  N  S  32.695  51.999   9.340   1.288  -2.416  -0.504  "C2'"   VDM  14  
VDM  "O2'"   O2*   O  0  1  N  N  N  33.203  52.878  10.348   2.463  -3.221  -0.597  "O2'"   VDM  15  
VDM  "C6'"   C6*   C  0  1  N  N  N  30.573  50.945   8.363   0.274  -0.181  -1.048  "C6'"   VDM  16  
VDM  "C5'"   C5*   C  0  1  N  N  R  31.063  51.304   6.955  -0.897  -0.864  -1.772  "C5'"   VDM  17  
VDM  "C7'"   C7*   C  0  1  N  N  N  30.546  50.300   5.924  -2.159  -0.002  -1.662  "C7'"   VDM  18  
VDM  "O7'"   O7*   O  0  1  N  N  N  29.105  50.280   5.932  -3.206  -0.659  -2.348  "O7'"   VDM  19  
VDM  "C4'"   C4*   C  0  1  N  N  R  32.591  51.464   6.910  -1.143  -2.281  -1.223  "C4'"   VDM  20  
VDM  "O4'"   O4*   O  0  1  N  N  N  33.027  51.816   5.589  -2.116  -2.921  -2.050  "O4'"   VDM  21  
VDM  "C3'"   C3*   C  0  1  N  N  S  33.017  52.518   7.934   0.131  -3.135  -1.203  "C3'"   VDM  22  
VDM  "O3'"   O3*   O  0  1  N  N  N  34.416  52.777   7.798  -0.132  -4.339  -0.474  "O3'"   VDM  23  
VDM  H7      H7    H  0  1  N  N  N  29.525  50.424  15.632   6.808   2.524  -2.945  H7      VDM  24  
VDM  H7C1    1H7C  H  0  0  N  N  N  30.623  50.070  13.645   6.497   1.053  -1.310  H7C1    VDM  25  
VDM  H7C2    2H7C  H  0  0  N  N  N  31.449  51.146  14.604   5.173   2.056  -0.679  H7C2    VDM  26  
VDM  H6      H6    H  0  1  N  N  N  29.484  50.755  11.807   3.099   1.240  -1.144  H6      VDM  27  
VDM  H4      H4    H  0  1  N  N  N  29.607  53.776  14.317   5.542   1.381  -4.407  H4      VDM  28  
VDM  H1      H1    H  0  1  N  N  N  28.417  52.629  10.264   1.449   0.821  -2.918  H1      VDM  29  
VDM  HA      HA    H  0  1  N  N  N  31.827  54.698  14.426   6.122  -1.060  -3.108  HA      VDM  30  
VDM  H3      H3    H  0  1  N  N  N  31.153  54.564  11.726   4.298  -1.401  -4.310  H3      VDM  31  
VDM  HB      HB    H  0  1  N  N  N  30.125  56.507  12.305   4.603  -1.210  -6.299  HB      VDM  32  
VDM  H2      H2    H  0  1  N  N  N  28.156  54.082  12.225   2.741   1.183  -4.897  H2      VDM  33  
VDM  HC      HC    H  0  1  N  N  N  28.548  56.124  11.141   1.924  -0.293  -6.113  HC      VDM  34  
VDM  "H1'"   H1*   H  0  1  N  N  N  31.100  53.660  10.223   1.351  -1.544  -3.038  "H1'"   VDM  35  
VDM  HD      HD    H  0  1  N  N  N  31.114  51.085  10.418   2.335  -0.528  -0.489  HD      VDM  36  
VDM  "H2'"   H2*   H  0  1  N  N  N  33.210  51.017   9.453   1.067  -2.327   0.568  "H2'"   VDM  37  
VDM  "H6'1"  1H6*  H  0  0  N  N  N  29.461  51.020   8.407   0.459   0.805  -1.494  "H6'1"  VDM  38  
VDM  "H6'2"  2H6*  H  0  0  N  N  N  30.708  49.853   8.543  -0.002   0.001  -0.001  "H6'2"  VDM  39  
VDM  HE      HE    H  0  1  N  N  N  34.133  53.034  10.232   2.194  -4.125  -0.377  HE      VDM  40  
VDM  "H3'"   H3*   H  0  1  N  N  N  32.465  53.471   7.762   0.410  -3.451  -2.215  "H3'"   VDM  41  
VDM  "H5'"   H5*   H  0  1  N  N  N  30.638  52.298   6.684  -0.670  -0.938  -2.844  "H5'"   VDM  42  
VDM  "H7'1"  1H7*  H  0  0  N  N  N  30.978  49.284   6.078  -1.977   0.969  -2.117  "H7'1"  VDM  43  
VDM  "H7'2"  2H7*  H  0  0  N  N  N  30.955  50.499   4.906  -2.428   0.120  -0.616  "H7'2"  VDM  44  
VDM  "H4'"   H4*   H  0  1  N  N  N  33.073  50.493   7.170  -1.572  -2.230  -0.215  "H4'"   VDM  45  
VDM  "H7'"   H7*   H  0  1  N  N  N  28.784  49.656   5.292  -2.807  -1.124  -3.104  "H7'"   VDM  46  
VDM  HF      HF    H  0  1  N  N  N  32.763  51.162   4.953  -1.684  -3.086  -2.901  HF      VDM  47  
VDM  HG      HG    H  0  1  N  N  N  34.616  53.099   6.927   0.123  -4.160   0.443  HG      VDM  48  
#   #
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
VDM  O7     C7      SING  N  N   1  
VDM  O7     H7      SING  N  N   2  
VDM  C7     C5      SING  N  N   3  
VDM  C7     H7C1    SING  N  N   4  
VDM  C7     H7C2    SING  N  N   5  
VDM  C5     C6      DOUB  N  N   6  
VDM  C5     C4      SING  N  N   7  
VDM  C6     C1      SING  N  N   8  
VDM  C6     H6      SING  N  N   9  
VDM  C4     O4      SING  N  N  10  
VDM  C4     C3      SING  N  N  11  
VDM  C4     H4      SING  N  N  12  
VDM  O4     HA      SING  N  N  13  
VDM  C3     O3      SING  N  N  14  
VDM  C3     C2      SING  N  N  15  
VDM  C3     H3      SING  N  N  16  
VDM  O3     HB      SING  N  N  17  
VDM  C2     O2      SING  N  N  18  
VDM  C2     C1      SING  N  N  19  
VDM  C2     H2      SING  N  N  20  
VDM  O2     HC      SING  N  N  21  
VDM  C1     "N1'"   SING  N  N  22  
VDM  C1     H1      SING  N  N  23  
VDM  "N1'"  "C1'"   SING  N  N  24  
VDM  "N1'"  "H1'"   SING  N  N  25  
VDM  "C1'"  HD      SING  N  N  26  
VDM  "C1'"  "C2'"   SING  N  N  27  
VDM  "C1'"  "C6'"   SING  N  N  28  
VDM  "C2'"  "H2'"   SING  N  N  29  
VDM  "C2'"  "O2'"   SING  N  N  30  
VDM  "C2'"  "C3'"   SING  N  N  31  
VDM  "O2'"  HE      SING  N  N  32  
VDM  "C6'"  "H6'1"  SING  N  N  33  
VDM  "C6'"  "H6'2"  SING  N  N  34  
VDM  "C6'"  "C5'"   SING  N  N  35  
VDM  "C5'"  "H5'"   SING  N  N  36  
VDM  "C5'"  "C7'"   SING  N  N  37  
VDM  "C5'"  "C4'"   SING  N  N  38  
VDM  "C7'"  "H7'1"  SING  N  N  39  
VDM  "C7'"  "H7'2"  SING  N  N  40  
VDM  "C7'"  "O7'"   SING  N  N  41  
VDM  "O7'"  "H7'"   SING  N  N  42  
VDM  "C4'"  "H4'"   SING  N  N  43  
VDM  "C4'"  "O4'"   SING  N  N  44  
VDM  "C4'"  "C3'"   SING  N  N  45  
VDM  "O4'"  HF      SING  N  N  46  
VDM  "C3'"  "H3'"   SING  N  N  47  
VDM  "C3'"  "O3'"   SING  N  N  48  
VDM  "O3'"  HG      SING  N  N  49  
#   #
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
VDM  SMILES            ACDLabs               10.04  "OC2C(NC1C=C(CO)C(O)C(O)C1O)CC(C(O)C2O)CO"  
VDM  SMILES_CANONICAL  CACTVS                3.341  "OC[C@H]1C[C@H](N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O"  
VDM  SMILES            CACTVS                3.341  "OC[CH]1C[CH](N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O"  
VDM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)CO"  
VDM  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(C(C(C1NC2C=C(C(C(C2O)O)O)CO)O)O)O)CO"  
VDM  InChI             InChI                 1.03   "InChI=1S/C14H25NO8/c16-3-5-1-7(11(20)13(22)9(5)18)15-8-2-6(4-17)10(19)14(23)12(8)21/h1,6-23H,2-4H2/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1"  
VDM  InChIKey          InChI                 1.03   YCJYNBLLJHFIIW-MBABXGOBSA-N  
#   #
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
VDM  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol"  
VDM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(1S,2S,3R,6S)-4-(hydroxymethyl)-6-[[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino]cyclohex-4-ene-1,2,3-triol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VDM  "Create component"   2007-01-25  PDBJ  
VDM  "Modify descriptor"  2011-06-04  RCSB  
VDM  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VDM
_pdbx_chem_comp_synonyms.name        VALIDOXYLAMINE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
