NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

Area of Science:

• Computational chemistry
• Chemoinformatics
• Bioinformatics

Background:

• Partial atomic charges are crucial in various scientific fields, including chemistry and bioinformatics.
• The electronegativity equalization method (EEM) is a widely used approach for calculating these charges due to its speed and comparable accuracy to quantum mechanical methods.
• Existing EEM parameter sets are limited, and a dedicated tool for parameterization and validation was previously unavailable.

Purpose of the Study:

• To develop and introduce NEEMP, a novel software tool for the parameterization and validation of EEM.
• To provide a solution for the ongoing need for new and improved EEM parameter sets.
• To assess the quality and coverage of existing EEM parameter sets.

Main Methods:

• EEM parameterization using linear regression (LR) and differential evolution with local minimization (DE-MIN).
• Validation of EEM parameter sets for coverage and quality.
• Demonstration of NEEMP functionalities through case studies.

Main Results:

• NEEMP offers functionalities for EEM parameterization, validation, and charge calculation.
• LR is suitable for smaller datasets, while DE-MIN is effective for larger, heterogeneous datasets.
• Validation revealed that EEM parameter set coverage and quality can be problematic, highlighting the need for verification.

Conclusions:

• NEEMP is the first software package enabling both EEM parameterization and validation.
• The DE-MIN method represents an innovative approach to EEM parameterization.
• Four high-quality EEM parameter sets for ligand molecules were developed and are provided.