Energy Calculations


The Energies tab of the Inspector menu contains main energies which are explained in detail below. The energies listed specifically pertain to the focused compound and the current protein that compound is associated with in the workspace. 

Types of Energy - Units in kcal/mol

van der Waals - London dispersion forces

Hydrogen bonds - Hydrogen bond energy

Interaction Score - Sum of "van der Waals" and "Hydrogen bonds"

Desolvation - Energy cost of desolvating both ligand and protein

Stress Delta - The internal energy required to take the compound from the unbound geometry configuration to the bound geometry configuration. 

Other electrostatics - Electrostatic energy besides hydrogen bonds

Static Energy

Static (a.k.a. Single Point) energy calculations are not currently available but are expected to become available in an upcoming release. If these energies are especially relevant to your research, please let us know so we can expedite their implementation. 

Energy Minimization

Energy minimization employs computational methods to optimize molecular geometry. This technique iteratively adjusts atomic coordinates to locate the minimum energy conformation, which represents the most stable arrangement for a given molecule on the potential energy surface. At present minimization is performed using Amber forcefield parameters.

If you bring in a precomputed protein, you may notice that compounds have already had their geometry minimized. If you however are dealing with a new or derivatives compound, you can minimize the compound by either right clicking the compound entry in the Compounds tab of the Selector menu and hit Minimize, or you can click the Calculate button under the name of the compound in the Energies tab of the Inspector menu. 

Note that if you have multiple compounds pinned in the workspace, you can select them all in the Compounds tab using shift+left click and minimize them at once through the right click menu option "Minimize Selected".

Energy Comparisons

A common task in drug design is to derivatize a hit molecule into a more strongly interacting lead compound. BMaps provides multiple state-of-the-art ways to do this, especially through our fragment simulations which you can learn about more in the Compound Design section.

To facilitate determining the impact of these compound changes, the Energies and Properties tabs can support up to 10 compounds shown side-by-side at once. To to this, simply pin all compounds you wish to compare into the workspace and then hit calculate in the Energies tab under each name or through shift-left-click selection followed by a right click to select "Minimize Selected" from the dropdown menu of the Compounds tab to minimize and calculate the energies of all of the compounds with respect to the protein at once. . 


Mol. Weight - Molecular Weight (a.u.)

LogP - XLogP calculated by OpenBabel

Energy Efficiency - Inverse of the energy score divided by the number of heavy atoms

PSA - Topological polar surface area

# of Heavy Atoms - Heavy atom count

Charge - Formal Charge

HB Donors - Hydrogen Bond Donors

HB  Acceptors - Hydrogen Bond Acceptors

# of Rotatable Bonds - Rotatable bond count

Note: N/A will be the value for Energy Efficiency if the energy has not been calculated yet. PSA will also be N/A if its value is less than 0.1