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. 2022 Sep 30;12:16453. doi: 10.1038/s41598-022-20509-9

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Shows the MD simulation trajectories analysis of both Mevalonate kinase complexed with R-Mevalonate (MEV) and Caprylic acid (CA). (A,B) Shows the RMSD result of a protein (left Y-axis) and ligand (right Y-axis). The RMSD of a ligand is calculated by aligning the protein–ligand complex on the reference protein backbone and then measuring the RMSD of the ligand heavy atoms (Lig_wrt_protein). If the observed values are significantly greater than the protein's RMSD, the ligand has most likely diffused away from its original binding site. The RMSD of a ligand aligned and measured only on its reference conformation is shown in 'Lig fit Lig.' Internal ligand atom fluctuations are measured by this RMSD value. (C,D) The RMSF plot depicts the distribution of alpha helixes (red colour) and beta sheets (blue colour) as well as local fluctuations for a protein chain throughout the simulation. The ligand contacts points with specific residues are shown in green bars. (E,F) The interaction fraction of individual protein residues with ligand via H-bonds (green), Salt bridge (blue), hydrophobic (purple), and ionic (pink) interactions is shown in the protein–ligand contacts plot. Due to the involvement of a particular residue in multiple types of interactions, the total value of interaction fraction may be greater than 1.