2.2 Glossary of terms used in this guide, and in the program.

Atoms are described by their position relative to the hydrogen bonds.

Fig 1:  abbreviations used for atoms round H-bonds

     DD1         AA1         DDD    D                                       
        \       /               \  / \                                  
         D--H::A                 DD   H::A                                  
        /       \                         \                               
     DD2         AA2                       AA                               

Legend

-- Covalent Bond	H  Hydrogen	DD1,DD2 Donor Antecedents
:: Hydrogen Bond	D  Donor	AA1,AA2 Acceptor Antecednets
			A  Acceptor

Atom Names

Througout this document, and in the output files, atoms are named with the
four-letter atom codes used in the Brookhaven database.  The first two
letters specify the element name, eg C, N, O, CU etc.  The third digit is
the greek letter remoteness code translated as A, B, G, D, E, Z, H instead
of alpha, beta, gamma, delta, epsilon, zeta, eta.  The fourth digit is a
numeric branch designator.  For instance the two side-chain oxygens of
glutamate are labelled "GLU OE1" and "GLU OE2".

A hydrogen atom is specified slightly differently.  The third and fourth
digits are the same as for the atom it is attached to, the second digit is
the chemical symbol and the first digit is an additional branch
designator.  For instance, the hydrogens on the side-chain nitrogen of a
glutamine are labelled "GLN1HE2" and "GLN2HE2".