This menu contains all atom related properties such as charge, atom radicals, maps, and many more.
| Stereo > R/S > Off | Removes the absolute stereo configuration from a chiral atom along with the marking wedge bond. |
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| Stereo > R/S > R | Sets the absolute stereo configuration on a chiral atom to R, marking it with wedge bond. |
| Stereo > R/S > S | Sets the absolute stereo configuration on a chiral atom to S, marking it with wedge bond. |
| Stereo > Reaction > Off | Sets the stereo configuration of the atom not to be considered during the reaction. |
| Stereo > Reaction > Inversion | Sets the stereo configuration of the atom to be inverted during the reaction. |
| Stereo > Reaction > Retention | Sets the stereo configuration of the atom to be retained during the reaction. |
| Stereo > Enhanced | See Stereo documentation for details. |
| Charge | Allows you to change the charge of any atom between [-128, 128]. The number of implicit hydrogens will be adjusted if possible to accommodate the new charge. Valence errors will be highlighted in red. |
| Valence | Allows you to change the valence of any atom between [0, 8]. |
| Radical > Off | Removes the radical designation from an atom. |
| Radical > Monovalent | Sets Monovalent radical center. |
| Radical > Divalent | Sets Divalent radical center. |
| Radical > Divalent Singlet | Sets Divalent radical center with singlet electronic configuration. |
| Radical > Divalent Triplet | Sets Divalent radical center with triplet electronic configuration. |
| Radical > Trivalent | Sets Trivalent radical center. |
| Radical > Trivalent Doublet | Sets Trivalent radical center with doublet electronic configuration. |
| Radical > Trivalent Quartet | Sets Trivalent radical center with quartet electronic configuration. |
| Isotope | Sets or changes the isotope number of the selected element, or resets the default atom (no isotope) when it is set to Off. |
| Map | Sets map labels/identifiers on the selected atoms that do not change while altering the molecule. They are useful when dealing with reactions, and can be saved in SMILES and MDL formats. |
| R-group | Changes the selected atom to an R-group label. R-groups symbolize alternative substituents. |
| R-group Attachment | The selected atom becomes the attachment point for the substituent. |
| R-group Attachment Order | Changes the order (numbering) of the attachment points. |
| Link Node | Specifies query structures containing rings or chains of variable size. |
| Periodic Table | Shows Periodic Table and query/atom property drawing window. |
| Edit Properties | Specifies the property of an atom. |
| Add S-group attachment | Creates an attachment point on the selected atom of an S-group. |
| Remove S-group attachment | Removes the highest-numbered attachment point from an atom of an S-group. |