Dear all
I ran into a problem with monomer sketcher. One of my compounds has a
benzimidazole group.
C12=CC=CC=C1N=CN2
When I used monomer sketcher regularizing with refmac, the C-C bond
that connect the benzene ring and the imidazole has a length of 1.49
A. I defined them as delocalized bond.
When I used PRODRG server, it refined to 1.39A and defined as aromatic bond
Then I checked PDB entry with similar group 1D0S. 1JHM, 1KXM, L5F,
1RYC. They all have 1.38-1.39A.
Then I though about load the monomer directly into coot with code name
BZI, the bond length is 1.48.
Is there a clear definition of delocalized bond or armatic bond? I
tried to look for the manual of monomer sketcher. Thanks for your
suggestion in advance.
Best,
Joe
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