2.5 Output File(s) Format

The format of the main output file, the hydrogen bond list, is given in
Table I below.

============================================================================
                         Table I: *.hb2 format

01-13 Donor Atom, including . . .

01    Chain ID (defaults to '-')
02-05 Residue Number 
06    Insertion Code (defaults to '-')
07-09 Amino Acid Three Letter Code
10-13 Atom Type Four Letter Code

15-27 Acceptor Atom, same format as Donor atom
28-32 Donor - Acceptor distance, in Angstroms
34-35 Atom Categories - M(ain-chain), S(ide-chain) or H(etatm) - of D & A
37-39 Gap between donor and acceptor groups, in amino acids
      (-1 if not applicable)
41-45 Distance between the CA atoms of the donor and acceptor residues
      (-1 if one of the two atoms is in a hetatm)
47-51 Angle formed by the Donor and Acceptor at the hydrogen, in degrees.
      (-1 if the hydrogen is not defined)
53-57 Distance between the hydrogen and the Acceptor, in Angstroms
      (-1 if the hydrogen is not defined)
59-63 The smaller angle at the Acceptor formed by the hydrogen and an
      acceptor antecedent (-1 if the hydrogen, or the acceptor antecedent,
      is not defined)
65-69 The smaller angle at the Acceptor formed by the donor and an acceptor
      antecedent (-1 if not applicable)
71-75 Count of hydrogen bonds

For example:

HBPLUS Hydrogen Bond Calculator v 2.06            Jul 30 13:24:14 BST 1993
(c) I McDonald, D Naylor, D Jones and J Thornton 1993 All Rights Reserved.
1MBD <- Brookhaven Code "/idata/new/p1mbd.new" <- PDB file
<---DONOR---> <-ACCEPTOR-->    atom                        ^
c    i                          cat <-CA-CA->   ^        H-A-AA   ^      H-
h    n   atom  resd res      DA  || num        DHA   H-A  angle D-A-AA Bond
n    s   type  num  typ     dist DA aas  dist angle  dist       angle   num
-0002-LEU N   -0153-HOH O   2.94 MH  -1 -1.00 151.8  2.02  -1.0  -1.0     1
-0146-HOH O   -0002-LEU O   2.78 HM  -1 -1.00  -1.0 -1.00  -1.0 128.7     2
-0289-HOH O   -0002-LEU O   3.45 HM  -1 -1.00  -1.0 -1.00  -1.0 136.5     3
============================================================================

In addition, the *.h file is used for the optional output file - the
structure of the protein, with added hydrogens.  The format is based on the
Brookhaven PDB file.  There is no temperature factor or occupancy in the
ATOM or HETATM records.  The only records included are HEADER, some
REMARKs and the ATOM and HETATM records.

HEADER    PDB FORMAT FILE                         30-JUL-93   1MBD
REMARK   1 REFERENCE 1
REMARK   1  AUTH   I.K.MCDONALD,D.NAYLOR,D.T.JONES,J.M.THORNTON
...
...
REMARK   4 CONTACT I.K.MCDONALD AT ABOVE ADDRESS OR ON ELECTRONIC
REMARK   4 MAIL AT \MCDONALD@UK.AC.UCL.BSM$ FOR INFORMATION
ATOM      1  N   VAL     1      -0.594  14.769  15.940  7.00 44.29
ATOM      2 1H   VAL     1      -0.641  14.029  15.248  7.00 44.29
ATOM      3 2H   VAL     1      -0.737  14.334  16.845  7.00 44.29