Volume 1 Chapter 7 The Connectivity Basis of 3D Searching

In the CSD two representations of molecular connectivity are stored:

a chemical representation, fully described in chapter 6
a crystallographic representation, fully described in chapter 5 of Vol.4.

The crystallographic representation is established in distance terms using a set of covalent radii values and a tolerance value.

Examples of both representations are illustrated below and the atom and bond properties which are available are listed in each case.

       Chemical                 Crystallographic

................................

    Atom Properties             Atom Properties
           n                           N
          el                          el
         nca                        ncah
          nh                          --
          ch                          --
           u                          --
           v                          --
          --                           x
          --                           y
          --                           z
 
    Bond Properties             Bond properties
          n1                          N1
          n2                          N2
          bt                    distance
         A/C                         A/C

The points of difference in the atom properties are:

treatment of terminal H atoms; implicit in chemical connectivity, explicit in crystallographic connectivity
hydrogen atoms may be absent or incomplete in crystallographic connectivity
different enumeration of atoms in the two representations
no indication of formal charge in crystallographic connectivity
no association between chemical atoms and the crystallographic x,y,z-coordinates.

The point of difference in the bond properties is:

no indication of formal chemical bond type in crystallographic connectivity; bond types may sometimes be deduced from local geometry.

These differences have implications for the Basic CSD Software System:

QUEST:

Can locate fragments very precisely in chemical terms but cannot then apply 3D constraints

GSTAT:

Can apply 3D constraints very precisely but cannot ensure chemical precision of fragment location; extra 3D constraints can often circumvent this problem, eg. the use of distance constraints to imitate bond types.

For the latest Graphical CSD Software System the two separate connectivity representations have been mapped on to each other. This means that the crystallographic connectivity is now embellished with the chemical properties of the atoms and bonds; in this way 2D and 3D searching is now integrated in QUEST3D.

The complete connectivity representation now effectively includes both the 2D display coordinates (u,v) and the 3D crystallographic coordinates (x,y,z) as atom properties. The integrated connectivity table now represents both 2D and 3D structures.

It is this mapping, as stored in the Version 5 database, which underpins all of the search extensions reported in this chapter.

These extensions are available only in Graphics QUEST3D.

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Volume 1 Chapter 7 The Geometric Basis of 3D Searching .

7.2 The Connectivity Basis of 3D Searching