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
