Molecule Sketcher

The molecule sketching tool includes basic features of molecular drawing, such as single and double bonds, erasers and translating tools, wedges to display stereochemistry and different elements.


Guide to the molecule sketcher



Single Bond

Click or drag to draw a single Carbon bond, click on existing bonds to make double and triple and crossed bonds.

Multi-node bond

Click and drag to draw an alkane chain of Carbon

Multi-atom rings

Multiple options for carbon ring systems

Above the plane bond

Draws a bond coming out of the plane

Below the plane bond

Draws a bond going into the plane

Charge modifiers

And positive or negative charge modifiers to atom nodes

Common Elements

Most commonly used elements, select your chosen element and paint it onto nodes that have been drawn

Other Elements

For other elements select this tool, then click on the atom node you want to change, from there type in the elemental abbreviation

SMILES editor

This field populates as you draw molecules, you can also type in this field to modify the SMILES string and see the resulting structure in the canvas

File upload

Click to upload a .sd or .smi containing a single compound


Deletes nodes and edges of the molecule graph as you click on the structure


Select this tool and click and drag on the canvas to change the scale of the structure


Click on drag on the canvas to draw around multiple atoms and bonds


Delete the structure on the canvas

Undo last step

Undo your last step

Beautify structure

Normalize bond lengths and angles, and fit the structure to the canvas.