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590. DGEOM: Distance Geometry Program
by Jeffrey M. Blaney, Gordon M. Crippen, Andrew Dearing
and J. Scott Dixon
COPYRIGHT 1990 E. I. du Pont de Nemours and Co.
All Rights Reserved
This software is proprietary and confidential to the Du
Pont Company and is furnished under a license
agreement. This software may be used and disclosed
only in accordance with the terms of such license.
DGEOM is a distance geometry program for molecular
model building, receptor modeling, conformational
analysis, and solution structure determination from 2D-
NMR data using the algorithms developed by Crippen,
Havel and Kuntz1-3. Distance geometry is a general
method for converting a set of (NxN) -N distance bounds
into a set of 3xN Cartesian coordinates consistent with
these bounds. Molecular structures can be described by
the set of all pairs of interatomic distances. For
example, the distance matrix for cyclohexane is:
1 2 3 4 5 6
10.0 1.5 2.5 3.8 2.5 1.5
21.5 0.0 1.5 2.5 3.8 2.5
32.5 1.5 0.0 1.5 2.5 3.8
42.6 2.5 1.5 0.0 1.5 2.5
52.5 2.6 2.5 1.5 0.0 1.5
61.5 2.5 2.6 2.5 1.5 0.0
The upper triangular matrix contains the upper bounds
(maximum distance) and the lower triangular matrix
contains the lower bounds (minimum distance) allowed
between each pair of atoms. For this example, the
upper and lower bounds are equal (except for 1-4, 2-5
and 3-6) since all other pairs involve atoms which are
covalently bonded to each other or form a bond angle
(bond lengths and angles are fixed). The lower and
upper bounds for 1-4, 2-5 and 3-6 are set to values
corresponding to a cis- or trans-conformation,
respectively.
Upper and lower bounds are generated from the input
structure, which is assumed to contain an accurate set
of starting coordinates (e.g., from molecular mechanics
energy and geometry refinement or crystallographic
data) in Protein Data Bank format with explicit
connectivity for double and triple bonds. The standard
Protein Data Bank CONECT records are modified to
explicitly show double or triple bonds simply by
repeating the atom which is multiply bonded; e.g., if
atom 3 and 5 are connected by a double bond, the CONECT
record is: CONECT 3 5 5. For peptides and nucleotides,
program DBOND is provided to generate automatically
explicit double bond connectivity from the original
CONECT records. Aromatic systems should be represented
with alternating single and double bonds.
Note that the starting conformation is irrelevant in
most cases, since DGEOM extracts only bond length and
angles from the coordinate file. Bond length and bond
angle distance constraints are set equal to the values
found in the input structure. The explicit
connectivity from the input structure is used to locate
non-rotatable bonds (double and triple bonds, amide and
ester bonds, and bonds within aromatic rings) and set
their distance constraints to the values found in the
input structure. Remaining torsion lower bounds are
assigned a distance corresponding to gauche (60
degrees) for acyclic bonds and eclipsed (0 degrees) for
cyclic bonds or bonds alpha to a double bond or
aromatic ring. Torsion upper bound distances are set
to anti (180 degrees). Torsion angle lower bounds can
be set to 0 degrees with the ECLIPSED option. Distance
constraints for all other atom pairs are derived by
setting the lower bound to the sum of the Van der Waals
radii (or hydrogen-bonding distance for polar
interactions), while the upper bound is determined by
the triangle inequality (equivalent to the length of a
fully extended chain connecting the two atoms).
Intermolecular distance lower bounds are set by default
to 0.0 (allowing molecules to pass through each other
and superimpose) and upper bounds to 999.0, but
explicit values may be assigned by reading in a
*CONSTRAINTS* file.
Constraints for chiral centers and planar groups (e.g.
double bonds, aromatic rings, amide and esters) are
generated automatically.
DGEOM is written in standard FORTRAN-77. It has been
tested on VAX/VMS 5.1, Silicon Graphics IRIS 4D/240 and
4D70/GT running IRIX 3.2, CRAY/COS 1.17 with CFT77, and
SUN-4/60 4.0.3 (Sparcstation).
This package contains a VAX (VMS) version or UNIX
version of the program as well as a complete CRAY
version. Because the directory structure of the system
is essential for its ease of use and understandng, QCPE
will be distributing DGEOM on VAX BACKUP format
magnetic tapes ONLY. DGEOM can easily be ported to
other systems, but you must have access to a VAX/VMS
magnetic tape drive to read this release of DGEOM.
IMPORTANT:A COPY OF THE DGEOM USE AGREEMENT
CONSTITUTES THE LAST PAGE OF THIS CATALOGUE.
ANY ORDER FOR THIS SYSTEM MUST BE ACCOMPANIED
BY THIS AGREEMENT, DULY SIGNED.
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References:
1. G. M. Crippen, Distance Geometry and
Conformational Calculations, Ed. D.Bawden
(Research Studies Press (Wiley): New York), 1981.
2. T. F. Havel, I. D. Kuntz and G. M. Crippen, Bull.
Math. Biol., 45, 665 (1983).
3. G. M. Crippen and T. F. Havel, Distance Geometry
and Molecular Conformation, Ed. D. Bawden (Research
Studies Press (Wiley): New York), 1988.
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FORTRAN 77 (VAX)
Lines of Code: 12,000
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