Uppsala Software Factory - Hetero compounds

Uppsala Software Factory - Hetero compounds

Here are some suggestions if you are looking for information about or dictionaries for hetero-compounds:

Check the (public domain) collection of X-PLOR topology and parameter files for hetero entities, available from Yale and Uppsala
Check the collection of O dictionary files for hetero entities (public domain)
Use the ODICT WWW server for generating O dictionaries for your own compounds in a jiffy. This service is provided free of charge to all licensed O users
Use the XDICT WWW server for generating X-PLOR topology and parameter files for your own compounds in a jiffy. This service is provided free of charge to all licensed X-PLOR users
Use the HETZE WWW server to check the quality of your hetero compound. This service is provided free of charge to all users
Pick up a copy of the hetero.pdb collection of hetero-compounds (public domain). This file is now also used by the BioMagResBank in their electronic data-deposition process.
If you are an academic user, or a commercial user with a license for the X-UTIL package, you may also want to download MOLEMAN (to generate O dictionaries from a PDB file), XPLO2D (to generate X-PLOR topology and parameter files from a PDB file), and CT2HET (to query the collection using a simple connectivity-table file); all these programs are part of the X-UTIL package
For more information, read "Dictionaries for Heteros", a short article that appeared in the CCP4 Newsletter
For infrequent academic users of the Cambridge Database, there is a free service, offered by the CAOS/CAMM Centre in the Netherlands (under "Free Services", click on "Modeling", and then on "CSDS" or "user registration")
Ftp the PDB dictionary of hetero compounds
RELIBase, an archive for structural data about receptor/ligand complexes. You can use their Java-based program to draw and search for the ligand you are interested in (or a substructure) !
The Klotho alphabetical list of small molecules found in PDB files
The MathMol Library of small molecule structures, and their page with links to other 3D databases
The Virtual Molecular Studio
Several useful services are provided by the Computer Chemistry Center at the University of Erlangen-Nürnberg

Some typical bond lengths

A more extensive table, derived using information from the Handbook of Chemistry and Physics, is also available.

Type Bond length(Å)

C-C single 1.54

C-C aromatic 1.40

C-C double 1.34

C-C triple 1.20

C-N single 1.48

C-N double 1.35

C-N triple 1.16

C-O single 1.45

C-O double 1.23

C-S single 1.82

C-S double 1.72

Type	Bond length(Å)
C-C single	1.54
C-C aromatic	1.40
C-C double	1.34
C-C triple	1.20
C-N single	1.48
C-N double	1.35
C-N triple	1.16
C-O single	1.45
C-O double	1.23
C-S single	1.82
C-S double	1.72

Latest update at 15 July, 1997.