Development of Mm2cML Software to Facilitate the Preparation of a 3D File Applicable to Computational Analysis Using aMolecular Model Kit

Abstract

To perform molecular modeling or quantum chemistry calculations, a 3D file of a molecule of interest is required. The 3D file includes atomic types, coordinates, connectivity, and other structural data of a molecular model. A 3D file for a common molecule is available from existing data sources such as articles and databases in the web, or it can also be prepared using molecular modeling software. The use of computational chemistry techniques is expected to increase among researchers and students studying related subject matter if a molecular model built using a commercial molecular model kit can be directly subjected to computational analysis. Thus, we developed the Mm2cML software to facilitate the preparation of a 3D file from a real molecular model. Mm2cML is a web application based on structure from motion and multi-view stereo technologies in combination with a web interface. The effectiveness of the software was confirmed by evaluating the accuracy of vertical 3D models that were created using multiple 2D images. Further evaluation was performed through quantum chemistry calculations using 3D files obtained from vertical 3D models.