According to your example of Predicting Covalently Modified Proteins you specify the chirality for ND2 nitrogen of asparagine residue which is expected to be planar based on the structure.
Could you elaborate on why this parameter needs explicit definition for nitrogen and how the value was chosen? Does "CW" and "CCW" correspond to E–Z notation for the new bond rather than the nitrogen atom? If not how is chirality defined when all atoms are in the same plane?
For the classification of atoms order for chirality, do you adhere to the standard Kan-Ingold-Prelog classification, or is another method employed? Specifically, does the “R” stereoisomer correspond to “CW” - clockwise and “S” correspond to “CCW” - counterclockwise?
According to your example of Predicting Covalently Modified Proteins you specify the chirality for
ND2nitrogen of asparagine residue which is expected to be planar based on the structure.Could you elaborate on why this parameter needs explicit definition for nitrogen and how the value was chosen? Does "CW" and "CCW" correspond to E–Z notation for the new bond rather than the nitrogen atom? If not how is chirality defined when all atoms are in the same plane?
For the classification of atoms order for chirality, do you adhere to the standard Kan-Ingold-Prelog classification, or is another method employed? Specifically, does the “R” stereoisomer correspond to “CW” - clockwise and “S” correspond to “CCW” - counterclockwise?