Demonstrating π-π and π-cation Interactions with Pseudoatoms in PyMOL

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Key Insights

The text provides a guide on demonstrating pi-pi and pi-cation interactions in molecular models. For pi-pi interactions, use wizard->measurement->Distances to Rings, which is straightforward and doesn't require hiding pseudoatoms. However, for pi-cation interactions, Distances to Rings is insufficient since it only measures distances between rings. Instead, use pseudoatoms. The procedure involves coloring the model, selecting and renaming ligands and interactive residues, hiding valence, and removing hydrogen. For pi-cation interactions, create pseudoatoms by selecting ring atoms, then measure the distance using wizard->measurement. Hide the pseudoatoms afterwards. Discussions note that pi-cation interaction distances should be less than 6.6 angstroms, while pi-pi interactions should be less than 7 angstroms, with pi-pi interactions typically shown in blue and pi-cation in green. References include a video and a scholarly work on evaluating π-π interactions in proteins.

Intro

You can demonstrate π-π interactions with wizard->measurement->Distances to Rings; it's easy to do and you don't need to hide the pseudoatom.

However, Distances to Rings doesn't work for π-cation interactions because it only measures the distance between two rings. You can do it with a pseudoatom instead.

Detailed procedure

Preprocessing

Color the model grey, then color by element for clarity.
Select the ligand and rename the object to 'ligand', then color it magenta (or whatever color you like).
Select the interacting residues: select the ligand, choose actions->around->residues with..., rename the object to 'active', then show the residues as sticks via show->side chain->sticks.
Hide valences with hide->valence, and remove hydrogens with remove hydrogen.
Find polar contacts: select the ligand, then choose action->find->polar contacts->to others excluding solvent.

Demonstrate π-cation interactions

Create pseudoatoms
1. Switch the selection mode to 'Atoms', then click the atoms of each ring one by one to generate a center; the selection is stored as sele.
2. Run pseudatom $NameOftheCenter, sele in the command line.
Measure the distance with wizard->measurement.
Hide the pseudoatoms with hide->everything.

Discussion

π-cation interaction distances should be less than 6.6 angstroms, and π-cation interactions are generally shown in green.
π-π interaction distances should be less than 7 angstroms [2], and π-π interactions are generally shown in blue.

References

https://www.bilibili.com/video/BV1ZK4y1j7AW/
Shao, Jinfeng. / Evaluation of π-π interactions in proteins using Trp analogs : From protein labeling to quantitating the energies involved. [Groningen] : University of Groningen, 2016. 127 p.