VMap

VMap is a computational chemistry application developed by VeraChem LLC for superimposing related ligands — such as those sharing a common scaffold with varying R-groups — onto a reference molecule. It is designed for medicinal chemists and computational scientists working with congeneric ligand series, and is particularly useful when the reference structure is a co-crystallized ligand extracted from a protein PDB file, providing high-quality starting structures for downstream VM2 binding free energy calculations or molecular docking workflows.

VMap automatically identifies the maximum common substructure (MCS) shared between a reference molecule and each ligand in a series, then uses this information to superimpose each ligand onto the reference by maximizing structural overlap through dihedral rotations. The tool is part of VeraChem's broader suite of small molecule tools and integrates directly with VDisplay for molecular visualization of results.

Core Capabilities

• Congeneric ligand superimposition: Identifies the maximum common substructure between the reference molecule and each ligand in a series, then superimposes each ligand onto the reference by maximizing overlap via dihedral rotations.
• Multiple input format support: The reference molecule can be provided in PDB (e.g., a co-crystallized ligand), SDF, MOL, or CRD format. The ligand series is supplied as an SDF file.
• Automatic atom mapping: Handles arbitrary atom numbering and ordering — equivalent atoms are mapped automatically with no manual atom reordering required.
• Output and visualization: Superimposed structures can be sent directly to VeraChem's VDisplay molecular visualization tool with a single click. Atom mappings of the maximum common substructures are also exported in a CSV file format.

Graphical User Interface and User Options

• Ability to select which molecule serves as the reference from a multi-molecule input file.
• Option to include or exclude hydrogen atoms in the atom mapping when using an all-atom reference structure.
• Control over whether RMSD calculations include hydrogen atoms or are restricted to heavy atoms only.
• Choice between rigid superposition and overlap maximization through dihedral rotations.

Workflow Integration

• VMap is well-suited as a preparatory step for VM2 protein-ligand binding free energy calculations or molecular docking, by generating accurately superimposed ligand starting structures based on a known co-crystallized reference.
• Seamless interfacing with VDisplay enables immediate visual inspection of superimposed molecular structures produced by VMap.
• VMap is available for Microsoft Windows and comes with a dedicated user manual to support installation and use.

VMap is part of VeraChem LLC's suite of small molecule tools, which also includes VConf, VDraw, VCharge, VFilter, Vrms, and VDisplay, all designed to support computational chemistry workflows in drug discovery and molecular design.