Cambridge Structural Database

Cambridge Structural Database (CSD) is a worldwide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The latest release is 2023.2 (Sept 2023). This update adds 13,367 new experimentally determined structures and brings the total number of structures in the CSD to just over 1.25 million.

To stay up-to-date with the latest releases, check the CCDC page What's New 

The University of Michigan has an unlimited site license to access CSD. You may access the database via either of the following two means.

1. WebCSD - the online portal to the CSD (Read more about WebCSD)

                                                OR
2. Install Cambridge Structural Database (CSD) on your own computer. 

Note, that you no longer need to completely re-install the software or data to allow new update installation! 

The installation takes 3 steps: files download, installation, and entering the license information.

Step 1. File Download

Request the software download links directly from CCDC: http://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/. You will need our site number and confirmation code, and your uniquename@umich.edu email address. Once you submit the request successfully, an email with the download links will be sent to you. (Be sure to check your Spam folder. It may take some time for the email to be sent, it is not immediate.  Please allow for up to an hour.) Follow the links and instructions in the email to download and install the software appropriate to your operating system. Please contact the Chemistry Librarian if you encounter an error message.

Step 2. Run the Installer

Optional, if prefer using the command line: https://www.ccdc.cam.ac.uk/support-and-resources/support/case/?caseid=18f1ab86-2a9a-e711-850b-005056975d8a

Step 3. Enter License Information

Since we recently installed the license server, two options to configure the new install are available to you:

• Using node-locked activation key on individual machines: You will need our site number and confirmation code to register for the system after it is installed. Use the software activation tool instead of registering through Mercury.
• Using the license server: Refer to this page that shows the boxes used for entering license information (section What does it mean for me?). Ignore the box on the right.  The box on the left – the one with multiple Tabs along the top -- is the one you want to see. Click on the tab that says "Configure local server". That should bring up a box into which you shall enter the server name and the port number - you will need License Server-assisted activation (Note, that UMich VPN must be running to use the license server).

Different operating systems:

If you are running on Windows or Linux, you should be able to install the latest updates seamlessly by simply clicking on Help > Check for Updates in either Mercury or Hermes. If you experience any problems, or you are running on Mac OSX, you will need to download and install the updates manually from the CCDC website: https://www.ccdc.cam.ac.uk/support-and-resources/downloads/​

Troubleshooting:

• Unit IT support that belong to UmichITAM can access installer location & licensing details from SharePoint
• Find more troubleshooting tips on the CCDC Support page
•  Contact the Chemistry Librarian 

ConQuest: Advanced Searching of Structures in the Cambridge Structural Database

You have access to ConQuest, the primary program for searching and retrieving information from the CSD. Search options include:

• A full range of text and numeric database search options allowing you to locate structures based on compound name, formula, elemental composition, literature reference and experimental details.
• Chemical substructure searching including the ability to define chemical constrains such as charge, hybridization state and cyclicity.  
• 3D geometric searching enabling you to quickly analyze molecular dimensions and determine conformational preferences.  
• Intermolecular and non-bonded contact searching allowing you to explore interactions of all types and to locate pharmacophoric patterns.

Mercury: Crystal Structure Visualization, Exploration and Analysis Made Easy

You have access to Mercury, a visualization software that offers a comprehensive range of tools for 3D structure visualization, the exploration of crystal packing and the statistical analysis of CSD search data. Mercury allows to:

• Generate packing diagrams, define and visualize Miller planes, and take slices through a crystal in any direction
• Build and explore networks of intermolecular contacts to gain an understanding of the strengths and weaknesses of structures and identify the key interactions that drive crystal packing.
• Display space-group symmetry elements 
• Calculate and display voids (free space in crystal structures) based either on contact surface or solvent accessible surface
• Perform molecule-based gas phase calculations via an interface to MOPAC
• Calculate intermolecular potentials and display e.g. the strongest user-defined interactions in the crystal structure
• View Bravais, Friedel, Donnay and Harker (BFDH) theoretical crystal morphologies
• Select Polyhedral display option for any metal-organic coordination centers based on the local environment, with settings to tune the behavior.

EnCIFer: Safely Check and Edit Crystallographic Information Files (CIFs) 

You have access to EnCIFer that enables validation of CIFs and ensures that files are format-compliant for deposition with journals and databases or for storage in laboratory archives. EnCIFer allows to:

• Identify and correct syntax/format violations;
• Safely edit information to your CIF without corrupting the strict syntax, for both single data items and data loops;
• Supplement the data in your CIF via two data entry wizards, one for publication details and the other for chemical, physical and crystallographic properties;
• Select from a choice of CIF dictionaries and check against a user-customizable list of mandatory data items;
• Visualize structure(s) in a CIF, including displacement ellipsoids.

Mogul: Knowledge Base

You have access to Mogul that you can use to validate your experimental or predicted structures using experimentally-derived, peer-reviewed data. It can display distributions of important geometries based on the bond lengths, angles, ring geometries, and torsions of the expertly curated structures in the CSD. 

IsoStar: Knowledge-based Library of Intermolecular Interactions

You have access to IsoStar, is a web application that allows displaying the probability of occurrence and spatial characteristics of interactions between pairs of chemical functional groups.These scatterplots facilitate the rapid exploration and assessment of intermolecular interactions without the need to construct complex search queries, or carry out detailed data analyses. IsoStar contains information on intermolecular interactions derived from both small-molecule crystal structures in the CSD and from protein-ligand interactions observed in the Protein Data Bank (PDB). Interaction energies, computed using intermolecular perturbation theory (IMPT), are also included for many important systems.

SuperStar: Knowledge-based Pharmacophore Generation and Prediction of Intermolecular Interactions

You have access to SuperStar that uses crystallographic information about non-bonded interactions to generate interaction maps within protein binding sites or around small molecules, i.e. it predicts ‘hot-spots’ where a chosen interaction type is particularly favorable.

CSD-CrossMiner: Versatile Pharmacophore Query Tool for Successful Drug Discovery

You have access to CSD-CrossMiner, a tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries. Intuitive pharmacophore queries describing, among others, protein−ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the pharmacophore query and visualized as soon as they are available, enabling the user to quickly modify a hypothesis on the fly. This delivers an overall interactive search experience with application in the areas of interaction searching, scaffold hopping or the identification of novel fragments for specific protein environments.
For example use cases, read: Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C & Stahl M “Interactive and Versatile Navigation of Structural Databases” J Med Chem, 2016, 59(9):4257, DOI: 10.1021/acs.jmedchem.5b01756.

Hermes: 3D Visualization Package for Macromolecules

You have access to Hermes that allows displaying protein and other macromolecular structures in 3D from the most common file types including PDB files, Mol2 files, Mol files and contoured surface files (.acnt format). The flexible and comprehensive controls let you navigate around the structure and modify the appearance to display ribbons, wireframe or spacefill to suit your needs. Hermes also hosts interfaces to GOLD, Mogul, SuperStar, and descriptors for GOLD docking poses.

GOLD: Protein-Ligand Docking Software

You have access to GOLD that allows structure-based docking screens of large compound libraries.

CSD Python API

You have access to the CSD Python API (Application Programming Interface) that enables you to create, or download from the CSD Python API user forum CSD-driven analyses and workflows, tailor them to your needs and then publish them to your own menu in Mercury for specialist visualization and easier communication.