Hydrogen atom positions

Distance normalisation

The command HNORM n1 n2 n3 re-normalises X-H distances, along the current X-H vectors, for X = C, N, O, to values derived from neutron diffraction data (C-H 1.083, N-H 1.009, O-H 0.983; J. Chem. Soc. Perkin II, 1987, S1-S19) or to distances n1 n2 n3 given explicitly in the command line.

The original hydrogen atom coordinates are replaced and the process is irreversible, such that the entry must be read again to restore the former values. This feature may be applied prior to H-bond geometry calculations and hydrogen-bond searches.

Calculation of hydrogen postions

The command HCALcalculates idealised hydrogen atom positions for C, N, and O atoms on the basis of intramolecular geometry. The same default distances are used as for the HNORM command. Various options are available to supplement default assignments, which rely on bond types assigned on the basis of bond distances atomic connectivity. This feature is particularly useful where some or all H atoms are absent or have poor geometry as well as X-H distances. As with the HNORM command any original H-atom positions are lost.

HCAL (blank) will delete any existing hydrogens and insert new, default, positions.

HCAL SP1 at1 gives one hydrogen with sp1 (linear) geometry at named atom at1.

HCAL SP2 at2 gives two hydrogens with sp2 (trigonal planar) geometry at named atom at2.

HCAL SP3 at3 gives 1,2, or 3 hydrogens with sp3 (tetrahedral) geometry at named atom at3.

HCAL DEL removes all hydrogens from the atom and bond lists.

This feature is currently under development and subject to number of limitations:

Calculation of hydrogen positions is not handled correctly when the molecule has internal crystallographic symmetry and the hydrogen atoms are all considered as being in the asymmetric unit. However, the coordinates themselves may still be correct. This affects any FDAT output saved after HCAL; in particular, the symmetry of the non-H atoms in a FDAT file saved after HCAL may be incorrect although the file should be readable.

Intermolecular contacts and hydrogen bonds

Intermolecular contacts

Intermolecular contact atoms are added as link atoms. These are regarded are being a property of the base residue to which they are in contact.

Menu buttons

Sphr calculates all intermolecular contacts in a sphere of specified radius about a named atom, by clicking on the atom required and typing the required radius. Contacts to several atoms may be added in this way by repeated application of Sphr. Symmetry-related contacts are not added automatically, which has implications for the expansion of networks with the Expand feature and graph set analysis.

Inter calculates all intermolecular contacts less than or equal to the sum of the Van der Waals radii of the respective elements.

Typed commands

CALC INTER (VDW) (el1 n1 el2 n2) ... (TOL t) calculates the intermolecular connectivity for the element types and radii specified in the command line. Alternatively, the sub-keyword VDW defines a search including all elements using their default van der Waals radii and is equivalent to the menu button Inter. The TOL sub-keyword permits the radius sum tolerance to be changed from the default value of 0.0 Angstrom.

Hydrogen bonds

Hbond now calculates intra- and/or inter-molecular hydrogen bond D-H...A contacts on the basis of default or user-defined geometrical criteria which are dependent on H-atom coordinates being present. Donor and acceptor types may be defined or defaults (D=A = N or O) employed. The search algorithm is the same as that used in QUEST and similar options are available. This replaces the previous button Hbnd which performed only a CALC INTER N 1.6 O 1.6 S 1.6 F 1.47 CL 1.6 BR 1.6 contact search, regardless of H atoms being present.

The atom types for the contact definitions may be element types or Sybyl-style (Mol2) atom types. The atom typing is performed by the same routines as used by the program QUEST for Mol2 output and is based on bond types derived by the same routine as used by the program PREQUEST for automatic chemical diagram generation. An atom is taken as matching a donor or acceptor string in the contact definition if the characters typed for the atom definition match the corresponding characters in the assigned Sybyl-style atom type. This is not case-sensitive and a period (.) is implied after a single-character element type. Thus N.a would match both the atom types N.ar and N.am, and O would match any oxygen but not Os etc. The provides the ability to search for specific chemical interactions, e.g. aromatic C-H...O=C contacts (D = C.ar, A = O.2) No check is made to ensure that the defined string is meaningful, beyond checking that it is not blank or H.

The H-bond search is constructed by following a series of prompts. The current settings may be retained, augmented or discarded; in the latter case the default values may be used instead. The control options available apply individually to each contact definition and include:

Crystallographically-equivalent H-bonds or other non-bonded contacts may be colour coded using the command COL HBOND.

Graph Sets

A new experimental command GSET ACC acceptor elements DON donor elements allows graph sets to be determined for non-bonded networks up to second level on basis of intermolecular contacts found previously. (Acc. Chem. Res., 1990, 23, 120-126; Angew. Chem., Int. Ed. Engl., 1995, 34, 1555-1573). If the sub-keywords ACC and DON are omitted, the donor atoms are assumed to be H and the acceptor atoms all non-hydrogen atoms.

Graph sets are assigned on the basis of non-bonded contacts as defined by the Hbond, Inter or Sphr functions, and one of these should be performed first (care should be taken to ensure that symmetry-related contacts are present if Sphr is used). In order to remove an unwanted contact from the intermolecular bond list it may be deleted with DelB. This operation should be performed on the base residues. It is not sufficient to hide the respective link atoms with HideA. In order to delete intermolecular contacts between base residues it is necessary to select each residue individually with Resi.

The graph sets are displayed on screen with colour-key coding in the style:

G a,d(n) m [note the order of a and d]

where G is the pattern descriptor:

ring (intermolecular)
(infinite) chain
discrete (finite)
self (intramolecular ring)


is the number of acceptors,
the number of donors,
the degree of the pattern (path length), and
identifies which crystallographically-independent H-bonds comprise the pattern
and the atoms are highlighted by colour in the diagram. The key lists the motifs for each crystallographically-independent H-bond with a number m following, which is the first level motif number. It then lists systematically the second level motif patterns formed by pairs of these independent H-bonds, e.g. if we have three independent H-bonds we have first level motifs m=1,2,3 and second level motifs labelled >1>2, >1>3, >2>3 (for patterns in which the direction D-A or A-D is the same for the independent non-bonds), and/or >1<2, >1<3, >2<3 (for patterns in which the direction D-A or A-D is opposed for the independent non-bonds) and/or 1&2, 1&3, 2&3 (for composite discrete motifs of the form >1>2<1 and >2>1<2). The conventional graph set matrix is also written to the command window in 120-column format.

These motifs can be explored by expansion with the Exp button in the usual way. Where two or contacts are formed to the same adjacent molecule, the atoms comprising intramolecular shortest paths in this molecule are also added as link atoms.

This feature is currently under development and has a number of limitations: