Using the Molecule Structure tool, create bonds between atoms and build molecules. There are four fixed-colour atoms to choose from. Select a colour to use, as shown:

To create a molecule, drag out the number of atoms required. Click inside each atom to label it. Finally, click the outer edge of an atom and drag to another. This will create a bond between them. A water molecule is shown below:

Once the atoms have been bonded, they will move as one. Click a bond to break it and move the atom independently again.