Cambridge Structural Database

• Introduction
• Performing a CSD search
• General outline of ConQuest
  • Build queries
  • Combine queries
  • View results
• Output file format of ConQuest
• Options that are not yet in ConQuest 1.4
• Tutorial (for C637 Spring 2001)

The Cambridge Structural Database (CSD) contains over 355,000 (Version 5.27) organic and metal organic structures determined by X-ray and neutron diffraction studies. The database is fully retrospective with the earliest entry dating to 1923. The primary source of coordinate data is the literature and the CSD acts as a depository for many major journals. Each CSD entry contains bibliographic information as well as 2-D and 3-D representations of structures. The database can be searched by molecules or fragments of molecules drawn in the search program; or searches can be conducted on textual items such as authors, publication year, journal, compound name, etc.

This guide is intended to be reference for first-time CSD users (some contents in this page came from the CCDC's CSD documents). This guide is NOT necessarily updated or complete. Consult the online CSD manuals on the CCDC web site for a more detailed description.

For more information, see the Cambridge Crystallographic Data Centre (CCDC) web site.

• bibliographic items compound name, journal reference, etc.
• chemical text strings molecular formula, amino acid sequences.
• simple numerical items unit-cell parameters, R-factor, etc.
• text comment describing e.g., disorder, errors, etc.

2D information

• bond properties pair of atom sequence numbers and formal chemical bond type.
• atom properties atom sequence number, element symbol, number of connected non-H atoms, number of terminal H atoms, net charge, 2D display coordinates.

3D information

• space-group and symmetry operators.
• 3D atomic coordinates (fractional).
• crystallographic connectivity.

Two programs distributed with the CSD are used for searching and retrieving information from the CSD. QUEST is the basic search engine for the CSD. ConQuest is a new program, which contains almost all of the functionality of QUEST and is being onwardly developed by CCDC. We highly recommend ConQuest because of its better graphic interface and many new features. The following brief instructions are written for the use of ConQuest. You are encouraged to go through the online ConQuest tutorials on the CCDC web site. If you perfer QUEST, please see the instructions for QUEST.

1. Open a UNIX shell: Click the left mouse button on Desktop (in the toolbox in the upper left corner), then click on UNIX shell in the new pop-up menu.
2. With the mouse cursor positioned in the new UNIX shell, type cq to start the ConQuest program.
3. Start search:
   • Use the Build Queries screen to build queries i.e., to specify what you are searching for.
   • If necessary, use the Combine Queries screen to combine the queries using logical operations.
   • Click the Search button to start the search.
   • Use the View Results screen to look at the structures found by the search.
   • Keep or reject structures that have met your search requirements.
   • Save the search results (in various file format).

Crystal structures found by the search could be visualized within ConQuest and QUEST programs, or by other more powerful crystal structure visualization software, such as Cerius² or Mercury -- a crystal structure visualizer developed by CCDC (see http://www.ccdc.cam.ac.uk/prods/mercury). Mercury is also able to download hit lists from ConQuest and browse the entire CSD database.

• To start Mercury program, type mercury in a UNIX shell.

Draw

Draw a molecular structure or fragment (substructure), which is then used for a structure / substructure (2D or 3D) search e.g., find structures containing a benzene ring.

Author/Journal

Find structures mentioned in particular papers, or publications by specific author(s). You can search for the author name, journal name, volume, page number, and year of publication.

Compound Name

Use compound names to search for structures, or use partial names to find certain types of compounds or structures.

Elements

Find structures containing particular chemical elements or structures containing one of a group of element e.g., find structures containing Au and O.

Formula

Find structures with a particular molecular formula e.g., Fe₁C₃₀H₂₈N₂O₂Cl₁.

Space Group

Find all entries for a particular crystal system (e.g., tetragonal) or for a particular space group (e.g., C2/c).

Unit Cell

Search for structures with specific unit cell parameters (or reduced cell parameters) to find out whether a crystal structure with those particular cell dimensions was already determined.

Z/Density

Find crystals with densities in a particular range, or with a specific Z (number of molecules per unit cell) or Z' (number of molecules per asymmetric unit) values.

Experimental

Search structures by experimental details e.g., find structure determinations carried out at high or low temperatures, structures determined by neutron diffraction.

All Text

General text search e.g., find crystals of a specific colour, with specific morphology; find structures whose absolute configuration was determined by X-ray methods; find pharmaceutically or agrochemically active molecules by looking for the words drug, activity, agent etc.; search for particular experimental conditions; find polymorphs by searching for the words form phase or polymorph.

Refcode (entry ID)

Find an entry whose CSD Refcode (i.e., CSD entry identifier) is known.

The Combine Queries screen can be used to find structures that satisfy a logical combination of queries e.g., structures which contain magnesium or a benzene ring, do not crystallize in space group P2₁/c, and were determined at a temperature below 273K.

Author/Journal

Bibliographic information.

Chemical

Compound name, formula, colour, melting point, etc.

Crystal

Unit cell and space group information.

Experimental

Information about experimental conditions, accuracy and precision.

Diagram

Chemical structural diagram. If the search was carried out for a substructure, the substructure will be highlighted in the diagram.

3D Visualiser

3D view of the molecule, which allows you to: rotate, translate and scale molecules; select from a variety of display styles; measure molecular geometry (distances, angles and torsions); label atoms; display crystallographic unit-cell contents.

CSD Internals

CSD internal information.

Search Overview

Summary of the query (or queries), filter(s), etc.

CIF (default file extension .cif)

Crystallographic Information File (CIF) format -- International Union of Crystallography format for crystal structure data (meet the IUCr format rules exactly).

CIFMIF (.cif)

Format which combines CIF crystallographic data names with chemical data names from the Molecular Information File, and additional non-standard fields containing CSD-specific information (e.g., information about whether the structure has unresolved errors).

COORD (.cor)

Simple ASCII listing of 3D coordinates and, where appropriate, cell data.

FDAT (.dat)

CCDC format for crystal structures, necessary for transferring structures into Pluto.

MOL2 (.mol2)

Tripos Inc. format for 3D molecules and crystal structures.

PDB (.pdb)

Protein Data Bank format for 3D molecules.

REFCODE (.gcd)

Simple ASCII listing of CSD refcodes.

SD (.sd)

SDfile (Structure-Data file) format for 3D molecules produced by MDL Information Systems Inc.

SHELX (.res)

Simulated SHEL-X .res file.

TXT (.txt)

Plain text format. Selected text items (Bibliography, Chemical, etc.) may be included.

TAB (.tsv)

Tab separated list of text items. Selected text items may be included.