Chem3D Users Manual - CambridgeSoft

Appendix C: Substructures
Overview
You can define substructures and add them to a
substructures table. When you define a
substructure, the attachment points (where
unselected atoms are bonded to selected atoms) are
stored with the substructure.
If a substructure contains more than one
attachment point (such as Ala), the atom with the
lowest serial number normally becomes the first
attachment point. The atom with the second lowest
serial number becomes the second attachment
point, and so on. However, there are situations
where this general rule is not valid.
Attachment point rules
The following rules cover all possible situations for
multiple attachment points in substructures; Rule 3
is the normal situation described above:
Angles and measurements
In addition to the attachment points, the
measurements between the selected atoms and
nearby unselected atoms are saved with the
substructure to position the substructure relative to
other atoms when the substructure is used to
convert labels into atoms and bonds.
For example, Chem3D stores with the substructure
a dihedral angle formed by two atoms in the
substructure and two unselected atoms. If more
than one dihedral angle can be composed from
selected (substructure) and unselected
(non-substructure) atoms, the dihedral angle that is
saved with the substructure consists of the atoms
with the lowest serial numbers.
Consider the following model to define a
substructure for alanine:
1. If an atom has an open valence and is not
attached to an atom that is unselected, it goes
after any atom that is attached to an unselected
atom.
2. If an atom is attached only to rectification
atoms, it goes after any atom that is attached to
non-rectification atoms.
3. If two atoms are the same according to the
above criteria, the atom with the lowest serial
number goes first.
4. If two atoms are the same according to the
above criteria, then the one which is attached
to the atom with the lowest serial number goes
first.
Since polypeptides are specified beginning with the
N-terminal amino acid, N(4) should have a lower
serial number than the Carboxyl C(6). To ensure
that a chain of alanine substructures is formed
correctly, C(1) should have a lower serial number
than O(3) so that the C-C-N-C dihedral angle is
used to position adjacent substructures within a
label.
Appendices
ChemOffice 2005/Appendix Substructures • 231
Overview