FMODB

FMODB provides a repository of fragment molecular orbital (FMO) calculation datasets and associated quantum mechanical interaction metrics to analyze biomacromolecular interactions.

Key Features:

• Extensive Data Collection: Contains over 13,600 FMO calculation datasets with compilation metadata and computed total energies for each molecular system.
• Interfragment Interaction Energy (IFIE): Includes interfragment interaction energy values to quantify pairwise interactions between molecular fragments.
• Pair Interaction Energy Decomposition Analysis (PIEDA): Provides PIEDA values to decompose and interpret interaction energy contributions.
• Methodological Rigor: Documents selection and preprocessing of target proteins and experimental structures used for calculations.

Scientific Applications:

• Drug Discovery: Supplies standard reference values for interaction types such as hydrogen bonds, ion-pairs, and XH/π interactions to assess relative interaction strengths in ligand–target systems.
• Molecular Recognition Studies: Enables quantum mechanical analysis of biomolecular recognition and binding that complements classical mechanics approaches.
• Quantitative Analysis of Halogen Interactions: Has been used to analyze halogen-containing inhibitors, for example studying human cathepsin L where PIEDA electrostatic terms correlated with binding affinities.

Methodology:

Computations use the fragment molecular orbital (FMO) method with datasets produced by fragmenting biomolecules and calculating total energies, interfragment interaction energies (IFIE), and pair interaction energy decomposition analysis (PIEDA); dataset entries record selection and preprocessing of target proteins and experimental structures.