RDKit Two Component Reaction, chirality of building block not retained.

Hello all,

I am trying to enumerate a virtual library using the RDKit Two Component Reaction node in Knime.

The enumeration is based on an amide coupling of a chiral amine and different acidic building blocks.

Although the chirality of some building blocks is defined, I am unable to retain this information in the enumerated products. Interestingly, the chirality of the amine is retained.

I am using Knime 5.3.3 installed automatically with the Maestro (Schrodinger).

Can you please advise?

Many thanks in advance,

Kind regards,

Silvia

Example of workflow

Enumeration_WF.knwf

Example of acidic BBs

CC(C)(C)OC(=O)N1CC@HC(=O)O

CC(=O)NC@@HC(=O)O

Amine: NC@HC1=CC=CC=C1