Hydrogen Bond Detector

Programme Name: Hydrogen Bond Detector
Author: Deepak Patkar
Affiliation: Dr. Harisingh Gour Vishwavidyalaya
Date: December, 2023

Description

This Python script detects hydrogen bonds (H-bonds) in molecular clusters using atomic coordinates from an input .xyz file. It identifies potential H-bonds based on interatomic distances and geometric criteria such as angles between donor, hydrogen, and acceptor atoms.

The script:

• Parses an .xyz coordinate file
• Calculates interatomic distances
• Identifies covalent bonds
• Determines hydrogen bonds using user-defined thresholds
• Computes the angle (D-H...A) to confirm the geometric feasibility of hydrogen bonding

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How It Works

1. Input: A standard .xyz file containing atomic coordinates.
2. Bond Identification:
   • Covalent bond determination using atomic covalent radii with a tolerance margin.
   • Hydrogen bond detection based on:
     • Donor-H distance: between 1.2 and 2.5 Angstrom
     • Acceptor atoms: O, N, F, and S
     • Donor-H...Acceptor angle
3. Output: Printed list of potential hydrogen bonds with atom indices, elements, distances, and angles.

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Input File Format

Standard XYZ format:

10 H6O2F2 O 1.575496000 0.944747000 -0.095387000 H 0.685876000 1.352497000 -0.044309000 H 2.087610000 1.349081000 0.616396000 O -1.575497000 -0.944763000 -0.095205000 H -0.685876000 -1.352505000 -0.044066000 H -2.087602000 -1.348974000 0.616653000 F 1.080760000 -1.525644000 0.022481000 H 1.359119000 -0.597328000 -0.011120000 F -1.080760000 1.525648000 0.022230000 H -1.359119000 0.597325000 -0.011206000