Subject: rotatable bonds question, using autodock

From: Susan Heffron <[email-masked]>
Date: Mon, 13 May 2002 13:25:50 -0700

Hi.

Forgive my basic chemistry questions...  I am planning to dock various
small molecules to a protein using Autodock.  Some of my small molecules
have structures such that I am not sure how to assign certain bonds...
rotatable or not (e.g., partial double-bond character or not). 
Specifically, my questions are:

1.  In a structure with -N-C-N-  would there be partial double-bond 
                           "
                           O

character to both C-N bonds, or only one (like a peptide bond)?

2.  In a structure with -N-C-N- would there be a partial double-bond
                           "
                           S

character to the N-C and C=S bonds, or not?

Thanks in advance for your help.

                     Susan

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        Susan Heffron
Dept. of Physiology and Biophysics                               
University of California, Irvine                
 Irvine, CA  92697-4560   U.S.A.                         
    phone:  (949) 824-4625
    FAX:    (949) 824-8540
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