Avogadro
An interactive molecular editor and visualization application for building geometries, preparing calculation inputs, and inspecting structures and electronic-structure outputs.
Where it fits
Learning molecular modeling and quickly preparing or checking structures.
Limits and practical considerations
Built-in geometry cleanup is not a substitute for validated quantum-chemical optimization.
Licensing and access
Avogadro 2 is free and open source under BSD 3-Clause; check plugin terms.