Double Click to draw a site.
Click on one site, keep the left click on and pull it over another to connect two sites.
Click on a site or a bond to select it (purple shadow will mark it) and edit "Selected site/coupling energy" box and press enter to change energy values.
Grab sites to move them around.
Double Click on a site to make it a lead site.
Click on a site or bond to delete it.
You can Pan by clicking once on the background area and move the mouse and you can Zoom with the mouse scroll wheel.
In the plot the X axis is the energy, Y axis is Log10 T(E)