FindHBond

FindHBond uses atom types and geometric criteria to identify possible hydrogen bonds (H-bonds). It is not necessary for hydrogen atoms to be present. All potential H-bonding interactions fulfilling the criteria are shown. For example, even if it is not possible for a particular hydroxyl group to donate a hydrogen bond to two particular acceptors simultaneously, both possibilities will be displayed if the hydroxyl lacks an explicit hydrogen atom. If the hydroxyl group has an explicit hydrogen atom, however, only H-bonds compatible with the position of the hydrogen will be found. See also: AddH, Distances, Find Clashes/Contacts, Intersurf, Rotamers, Metal Geometry

There are several ways to start FindHBond, a tool in the Structure Analysis and Surface/Binding Analysis categories. FindHBond is also implemented as the command hbonds (or findhbond).

The H-bonds will be shown as lines (a group of pseudobonds named hydrogen bonds) between the donor and acceptor atoms, or if hydrogens are present, between the hydrogens and acceptor atoms. Appearance options:

• H-bond color (a color well)
• Line width
• Label H-bond with distance - if active, there will be a button to Show distance formatting options, namely the Distances panel for setting the number of decimal points and whether the Å symbol is displayed (other settings in that tool will not affect hydrogen bonds pseudobonds)

Relax H-bond constraints indicates that tolerances to Relax constraints by should be applied to the precise geometric criteria. These criteria come from a survey of high-resolution structures; empirically, tolerances of 0.4 angstroms and 20.0 degrees work well for most macromolecular structures. H-bonds within the tolerances but that do not meet the precise criteria can be colored differently than the H-bonds that meet the precise criteria.

The scope of the calculation is controlled under Find these bonds:

• inter-model - between models only
• intra-model - within models only
• both (default)

• Restrict to models... show a list of molecule models from which one or more can be chosen. Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.
• Only find H-bonds
  • with at least one end selected
  • with exactly one end selected
  • with both ends selected
  • between selection and atom spec... [ atom-spec ]
  Whether to limit H-bond detection based on the current selection. In the last option, the selection and the atom-spec may overlap, but the specification will not overrule other restrictions (for example, if the specified atoms are in a different model than the selected atoms but inter-model detection is turned off, no H-bonds will be found).
• Include intra-molecule H-bonds - whether to include intramolecular H-bonds, where a molecule is defined as a covalently bonded set of atoms
• Include intra-residue H-bonds - whether to include H-bonds between atoms in the same residue

• If endpoint atom hidden, show endpoint residue - turn on the display of residues containing an H-bonding atom if that atom is not displayed initially (By default, if the atom on either end of a pseudobond representing an H-bond is not shown, the pseudobond itself is not shown, although it still exists; displaying the atom allows the H-bond to be shown.)
• Retain currently displayed H-bonds - retain a previously determined set of H-bonds through a subsequent round of H-bond detection
• Write information to file - write H-bond information (atom specifications and distances) to a file. The dialog for saving the file includes a Naming style option to control how atoms will be listed:
  • simple (for example, HIS 16.A ND1)
  • command-line specifier (for example, :16.A@ND1)
  • serial number (for example, 126)
• Write information to reply log - write H-bond information (atom specifications and distances) to the Reply Log. The Atomspec display style setting in the Labels preferences controls how atoms will be listed.

The geometric criteria are based on a survey of small-molecule crystal structures, as described in

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.

Chimera uses atom and residue names, or if these are not “standard,” the coordinates of atoms, to determine connectivity and atom types, which in turn determine which geometric criteria are appropriate for detecting a hydrogen bond between specific atoms. Possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair. H-bonds involving other types of atoms are not considered. Not all of the possible donor-acceptor combinations were listed in the Mills and Dean parameter tables; some categories of sulfur were not surveyed, and several combinations of the surveyed types were not observed frequently enough to collect good statistics on their geometries. In such cases, FindHbond applies estimated H-bond criteria.

When there are no explicit hydrogens on a potential donor atom, FindHBond will use the donor atom type to infer their presence. For functional groups where the hydrogen positions are well-determined by the positions of the nonhydrogen atoms, the H-bonds detected in the presence and absence of explicit hydrogen atoms should be virtually identical. For functional groups where the hydrogen position is not well-determined (such as rotatable hydroxyls), the presence of an explicit hydrogen atom will limit the detected H-bonds to those appropriate for the observed position, instead of all of its possible positions.