Normal-Coordinate Structural Decomposition is an analysis method, originally developed by Walter Jentzen and John Shelnutt, to quantify out-of-plane distortions of heme using vibrational normal coordiantes. Heme out-of-plane deformations can be described in terms of six distinct displacements from idealized D4h symmetry. The most common, and energetically-accessible, out-of-plane distortions are doming (a2u), saddling (b2u), and ruffling (b1u). In several cases, these distortions have been correlated to biochemical function.
This analysis method can be applied to any set of Cartesian coordinates describing the three-dimensional structure of a molecule with a porphine moiety. This includes X-ray crystal structure data derived from the Protein Data Bank and molecular structures predicted by electronic structure calculations.
The original derivation of this method was described by Jentzen, Song, and Shelnutt in 1997.
The current version of this method was described by Graves, Graves, and Liptak in 2016.
Please cite both manuscripts if you use this program.
Click here for an online version of the normal-mode structural decomposition script: