There are four ways of adding molecules to the structure database (see screenshots):

1. Draw a molecule on a "three-dimensional" drawing board using an intuitive graphical tool set, or

2. Import an externally created MOL-datafile of a molecule onto the graphical input window, or

3. Import an SDF-datafile containing a set of molecules directly into the structure database, or

4. Import a list of externally created MOL-datafiles directly into the structure database.

You can draw a molecule on the "three-dimensional" drawing board "from scratch" or you can start drawing with a fragment selected from a fragment list (and optionally add further fragments) or you may even use a molecule from the structure database itself as a starting point, e. g. by calling the molecule's datasheet and doubleclicking on its graphics screen.

Since in most cases externally created molecule datafiles only contain planar structures, occasionally with inclusion of some conformational information, ChemBrain immediately translates these data into a real 3-dimensional structure by means of a fast force-field algorithm.

A very helpful program feature prevents involuntary duplications of molecules in the database: before saving an input molecule via the drawing board, the program always checks for an identical configuration in the database and - if yes - requests confirmation to continue. On the other hand, if a whole set of molecules (using SDF-files or a list of MOL-files) is being imported the program simply ignores molecules with identical configuration. Consequently, configurationally identical but conformationally different molecules, e. g. enantiomers or stable cis-trans isomers, must always be entered "manually" via the drawing board. Of course, identical file or molecule names for different molecules are also rejected.

A particular advantage of ChemBrain is the possibility to not only add new molecules to the structure database, but to also edit any of the already present set of records, e. g. to add further molecular properties. Beyond this, you can add any free text in a notes sheet attached to a stored molecule (see last screenshot), enabling you to use the database as a lab journal.