We developed the world’s first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.

The bond energies of ${\mathrm{C}}_{32}$ and ${\mathrm{C}}_{60}$ fullerenes have been calculated by a self-consistent molecular-orbital method based on nonlocal-density-functional theory with the generalized gradient approximation (GGA). These results were compared with those obtained with use of the local-density approximation (LDA). The bond energies calculated with the GGA (${\mathrm{C}}_{60}$, 7.24 eV/atom; ${\mathrm{C}}_{32}$, 6.88 eV/atom) were about 1.3 eV/atom (15%) smaller than those calculated with the LDA, and the GGA result for ${\mathrm{C}}_{60}$ was found to be in good agreement with the evaluated value from the experimental formation energy. The differences in bond lengths, force constants, and orbital energies for the same molecular structure —except for the core orbitals—between the LDA and GGA were small, compared with the difference in bond energies.