Volume 1 Chapter 7 Searching with Functional Groups
Ex. 9 Consider a search for hydrogen bond dimers formed by carboxylate groups. The VDW-RAD command is used to change the tolerance to 0.0Å. Using the default van der Waals distance testing, O-H distances less than 2.72Å will now be registered as contacts. Two CONTACT commands are required to form the dimer.
VDW TOL 0.0 CONTACT INTER 1 A 5 A CONTACT INTER 4 A 8 A
An example of the results of the search is shown below.
During the search, each CONTACT is tested in turn and a hit will only be registered if all the CONTACTs succeed. Because the CONTACTs are processed in the order they are entered, it is possible to use multiple VDW-RAD commands to change the van der Waals radii of elements from one CONTACT command to another.
A typical example using multiple CONTACT commands is the search for pharmacophores.
Ex. 10 Suppose we wish to locate all molecules that contain phenyl, carbonyl, and NH groups such that :
phenyl centroid - carbonyl distance is 3.5 to 5.5Å
phenyl centroid - NH distance is 5.0 to 7.5Å
GROUP G1 1 2 3 4 5 6 CONTACT INTRA 1 999 G1 C 10 A 3.5 5.5 CONTACT INTRA 1 999 G1 C 8 A 5.0 7.5
An example of the results of the search is shown below.
Volume 1 Chapter 7 Display of Hits from Non-Bonded Searches.
