This directory contains individually crystallized receptor and ligand
PDBs (unbound/unbound or unbound/bound), after they have been superposed
onto the corresponding molecules in a co-crystallized protein complex.  
For convenience, files are named using the PDB ID of the co_crystallized
protein complex.  ????_r.pdb denotes a receptor; ????_l.pdb denotes
a ligand.  Their actual PDB IDs can be found in
http://zlab.bu.edu/~rong/dock/benchmark.shtml

These files largely conform to the PDB format, except for some
columns, which we have inserted for the convenience of our docking algorithm
ZDOCK.  They are explained as follows (column counts starts from 0):

Columns 55-56 store the Atomic Contact Energy atom type. The definition
was described in "Zhang C, Vasmatzis G, Cornette JL, and DeLisi C,
Determination of atomic desolvation energies from the structures of
crystallized proteins. J Mol Biol 1997;267:707-26". For antibodies
in antibody-antigen complexes, constant domains have been deleted.
All non-CDR residues are labeled as type 19 in Column 55-56. The method
used to determine CDR residues from the sequence and secondary structure
information is described in
http://zlab.bu.edu/~rong/dock/cdrlist.html.

Column 62 specifies surface or core atom.  If an atom has more than 1
angstrom-square solvent accessible area, it is designated as a surface
atom (indicated by "1").  Otherwise, it is a core atom (indicated by "0").

Columns 64-67 store the van der Waals radius of an atom according to the
CHARMM 19 parameter set.

Columns 77-81 store the partial charge of an atom according to the CHARMM 19
potential. The charges of some terminal atoms may need to be corrected.


