Molecular Modeling

small molecule graphics
An optimization of the MMFF94 test suite entry BUPSLB10, showing atom types.

Interact with your structures in real-time with advanced physical simulations

An expert molecular modeling engine is implemented in ChemDoodle 3D. In addition to calculating energies and generating 3D coordinates, you can interact with your structures in real-time to change conformations and see how your molecules would react to changes.

Generate 3D Coordinates

You can use ChemDoodle 3D to generate 3D coordinates for your molecule files and drawn structures. No more searching through databases to try to find the right conformation, simply build it in ChemDoodle 3D!

Universal Force Field (UFF)

An expert implementation of the Universal Force Field (UFF) is available, with several options to control the output.

Merck Molecular Force Field (MMFF94)

An accurate implementation of the Merck Molecular Force Field (MMFF94) and its static variant (MMFF94s) are available.

Optimization Functions

Choose from various optimization functions to minimize your energies. You can choose between steepest descent, conjugate gradients, and BFGS, with several line search options. A high quality system is provided in ChemDoodle 3D so you can confidently trust the output.

Atom Typing

Force field optimization in ChemDoodle 3D automatically atom types your structures for you. You can even view the specific mapped atom types.

Force Visualization

ChemDoodle 3D can render the optimization forces. This is helpful while you are optimizing to see where strain focuses in the molecule.

Real-time Interaction

Using the selection tools in ChemDoodle 3D, you can move individual atoms, bonds or selections while the optimization process is running. You can then see how movements affect the overall conformation of the structure, or change to a different local minimum. It is also a lot of fun!