Volume 1 Chapter 2 Coverage

The Cambridge Structural Database (CSD) covers the crystal structures, determined by X-ray or neutron diffraction, of organic compounds and metal-organic compounds. High polymers and oligomers having more than 25 residues are not included.

The database is fully retrospective and is updated regularly with ca. 750 new entries per month.

The principal source of the data is the primary journal literature, together with any associated deposited data.

Until the early-1980's conference abstracts were also included but this practice was then discontinued.

2.2 Information Content

The information recorded for a particular crystal structure determination may be divided as follows:

2.2.1 1D Textual and Simple Numeric Information

bibliographic items
- compound name, journal reference, etc.
chemical text strings
- molecular formula
numeric items
- unit cell parameters, crystal density, R-factor, etc.
comment text strings
- details of published errors which have been corrected, nature of disorder present in the crystal, etc.

2.2.2 2D Chemical Connection Table

The 2D chemical connection table is encoded in terms of atom and bond properties.

Atom properties are:
- atom sequence number
- element symbol
- number of connected non-H atoms
- number of attached terminal H atoms
- net charge
- coordinates (x,y) for the display of the 2D chemical structural diagram.
Bond properties are:
- pair of atom numbers (i and j) connected by a bond
- bond type of the bond i-j

2.2.3 3D Crystallographic Data

space group symmetry operators
atomic coordinates, in fractional units, for the crystal chemical unit
the crystallographic connectivity established with the use of standard covalent radii
information specifying which crystal atom matches which atom in the 2D chemical connection table.

2.2.4. "Database Use" - Introduction

Version 5.09 of the Cambridge Structural Database System incorporates for the first time a facility to perform QUEST searches of those papers in the literature which use the Cambridge Structural Database as the major input to a structural review or other study. These literature references have been abstracted and compiled into a separate bibliographic database, known as DBUSE (database use), which currently contains 462 entries.

An appropriately customised QUEST interface is available for searching the DBUSE database. The commands that are relevant for searching the DBUSE file are present in their standard QUEST format, but those commands which are not relevant for a search of this database are greyed-out.

2.2.5. "Database Use" - Initialisation

To initialise the customised version of QUEST and search the DBUSE file the following commands must be used.

Under UNIX, the command to start QUEST on the DBUSE file is:

$ quest -j [problem_name] -db DBUSE	(interactive)
$ quest -j [problem_name] -if dbuse.que -db DBUSE	(non-interactive)

Under VMS, the command to start QUEST on the DBUSE file is:

$ QUEST [problem_name] TT: DBUSE	(interactive)
$ QUEST [problem_name] dbuse.que DBUSE	(non-interactive)

2.2.6. "Database Use" - Information Content

The database can be searched using questions based on the textual content of any of the information fields stored for these entries. The relevant information is categorised as:

ASER Field               Information                                               

COMP                     title of the paper                                        

QUAL                     classification of the paper's content (see later)         

AUTH                     full list of authors                                      

JRNL                     journal in which the paper was published                  

CODE                     journal coden number                                      

VOLU/PAGE/YEAR           bibliographic reference information                       

REMA                     an abstract of the paper's content and its relevance to   
                         CSD use.

The QUALifier field contains classifications of the paper's content in terms of the subject classifications given below. Multiple QUALifiers may be present for some entries where the paper content has been determined to span several topics.

(This list is reproduced in the help files of QUEST, and can be accessed by typing "help bibliography" at the prompt after initialisation of QUEST)

  QUALifier   Subject                                                            

      A       Database description                                               

      B       Review articles                                                    

      C       Numerical and statistical methods                                  

      D       Mean molecular dimensions                                          

      E       Intramolecular geometry, substitution effects, bonding (organic)   

      F       Conformational analysis and stereochemistry                        

      G       Hydrogen bonding                                                   

      H       Intermolecular interactions, reaction pathways, molecular          
              dynamics                                                           

      I       Crystallographic applications and properties                       

      J       Drug design and modelling                                          

      K       Applications in chemical information science                       

      L       Relevant but do not use the CSD                                    

      M       Peptide/protein crystal structures                                 

      N       Molecular geometry and bonding in metal complexes                  

      P       Pharmacophore models                                               

      Q       Determination of 3D coordinates/structure                          

      R       Molecular recognition                                              

      S       QSAR                                                               

      T       Neural networks                                                    

      U       2D / 3D similarity searching                                       

      V       Artificial intelligence                                            

      W       Screens                                                            

      X       2D searching                                                       

      Y       3D searching                                                       

      Z       Crystal engineering

2.2.7. "Database Use" - Searching the DBUSE file

The DBUSE file is searched in a similar fashion to the general CSD, by constructing a query from a variety of arguments and tests. Searching on the *QUALIFIER field may be the most useful way to get information from this database, but it is also possible to search for text items in the paper title (*COMPOUND), the author names (*AUTHOR), journal (*JRNL) or abstract (*REMARKS). If a text item is specified under miscellaneous *TEXT then a hit will be registered if the item is present in any of the above information fields.

A typical example of a DBUSE entry:

?DEJPUD
#JRNL 622,49,910-928,1993
#AUTHOR F.H.Allen,J.A.K.Howard,N.A.Pitchford
#QUAL F, C, X
#SYSCAT cat 5
#RMARKS Symmetry-modified conformational mapping and classification of 
cycloheptane fragments is presented. 101 non-bridged, and 310 bridged 
structures were retrieved from the CSD and analysed using symmetry-adapted 
deformation coordinates, PCA, and symmetry-modified cluster analysis. 
Two independent pseudorotation itineraries are identified and observed to 
follow helical tracks on mutually orthogonal surfaces in 4-D space. 
Environmental and structural effects are discussed in relation to 
conformational variety.
#COMPND Symmetry-Modified Conformational Mapping and Classification of 
the Medium Rings from Crystallographic Data.I.Cycloheptane
#END

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Volume 1 Chapter 2 Fundimental Concepts .