Using the 3D Ligand Editor - what do the green colored values on each atom in the ligand represent?

[Andrew Orry]

Q.

Using the 3D Ligand Editor - what do the green colored values on each atom in the ligand represent?

A.

When you setup the ligand and receptor in the ligand editor you can display energy circles around each atom in the ligand that you are editing.

Good ligand-receptor interactions are highlighted by green spheres and low values. Poor energy interactions are displayed as orange-->red stars - red being a major clash and a very poor energy contribution. Each atom is given an energy value relating to its contribution to the total receptor-ligand interaction energy. Low values colored green are considered favorable. The green values on each atom are per-atom contribution to the total energy in the receptor grid ('show energy atom' command). The score/energy can not be partitioned into per-atomic contributions because several terms/contributions are not pairwise (in particular solvation-related, as well as the strain). However, grid-based approximate interaction energy is calculated per-atom and reflects, to an extent, favorable/unfavorable contributions from things like van der waals, hydrogen bonds, coulomb part of electrostatics and some approximation of lipophilicity.