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. 2018 Nov 6;8:16380. doi: 10.1038/s41598-018-34622-1

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© The Author(s) 2018

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Collective variables (CVs) for calculating the binding Gibbs free energy change through ABMD. In each of the sub-figures, the smaller structure (with stripes) represents E64 (the ligand), while the bigger structure (with dotted grey shades) represents the FP2 (the protein). (a) The three CVs/reaction coordinates used for defining the three pairs of CVs are shown as CV1, CV2, and CV3. CV1 is the distance between L and P. L is the centre of mass of J and K, while and P is the centre of mass of M and N. CV2 is the angle formed by J, K, and P. CV3 is the torsion angle formed by J, K, M, and N. Examples of changes in the position of the E64 relative to FP2 when CV1 is sampled/explored is shown in (b); when CV2 is sampled is shown in (c); when CV3 is sampled is shown in (d). Panel (d) is made up by views from the top so as to easily demonstrate the effects of changes in the torsional angle (CV3) on the relative orientations of E64 to FP2. In each of the panels (a to d), the setup numbered “#1” depicts the initial E64-FP2 relative orientation before CV1, CV2, and/or CV3 is(are) explored³².