Nonbonded Interactions Preferences

These settings are used to set the criteria for defining hydrogen bonds, halogen bonds, salt bridges, and aromatic hydrogen bonds.

H-Bonds section

These settings control the cutoffs that define a hydrogen-bond (H-bond). Hydrogen bonds are defined by relations between four atoms: the donor hydrogen atom (H), the donor atom (D) bonded to H, the acceptor atom (A), and another neighbor atom (B) bonded to A, D–H...A–B. The following must be true for a valid hydrogen bond:

• The H...A distance must be less than a specified maximum distance.
• The D–H...A angle must be greater than a specified minimum value.
• The H...A–B angle must be greater than a specified minimum value.

NOTE: The default values used in Maestro and those used by Glide are different. Maestro uses the theoretical H-bond angle criteria that capture the expected hydrogen bonds. However, because Glide docks into a rigid receptor and to enable the recognition of H-bonds when only ligand atoms can move, Glide allows for larger H-bond angle criteria.

Maximum distance

Specify the maximum distance from the H atom to the acceptor atom for an H-bond to be identified. The Maestro default is 2.8Å; the Glide default is 2.5Å.

Donor minimum angle

Specify the minimum D–H...A angle for an H-bond to be identified. The Maestro default is 120°; the Glide default is 90°.

Acceptor minimum angle

Specify the minimum H...A–B angle for an H-bond to be identified. The Maestro default is 90°; the Glide default is 60°.

Set default criteria for buttons

Click Glide or Maestro to set the defaults for the three criteria to those for Glide or Maestro.

Halogen bonds section

These settings control the cutoffs that define a halogen bond. Halogens can act as donors or acceptors. As an acceptor it interacts with a hydrogen, so it is like a hydrogen bond but with its own characteristics. As a donor it interacts with an electronegative element in a similar way to hydrogen, but again with some differences.

Halogen bonds in which the halogen acts as donor are defined in a similar way to hydrogen bonds, by relations between four atoms: the donor halogen atom (X), the donor atom (D) bonded to it, the acceptor atom (A), and another neighbor atom (B) bonded to A, represented as D–X...A–B. The following must be true for a valid donor halogen bond:

• The X...A distance must be less than a specified maximum distance.
• The D–X...A angle must be greater than a specified minimum value.
• The X...A–B angle must be greater than a specified minimum value.

Halogen acceptor bonds likewise have relations between the donor H atom (H) and the atom bonded to it (D), the halogen acceptor (X) and the atom bonded to it (B), D–H...X–A. The following must be true for a valid acceptor halogen bond:

• The H...X distance must be less than a specified maximum distance.
• The D–H...X angle must be greater than a specified minimum value.
• The H...X–A angle must be greater than a specified minimum value.
• The H...X–A angle must be less than a specified maximum value.

Maximum distance

Specify the maximum distance from the halogen atom to the other atom for a halogen bond to be identified. This value is independent of whether the halogen atom acts as an acceptor or a donor.

Donor minimum angle

Specify the minimum D–X...A angle or D–H...X angle for a halogen bond to be identified. This angle can be set independently for halogens as donors and halogens as acceptors.

Acceptor minimum angle

Specify the minimum X...A–B or H...X–A angle for a halogen bond to be identified. This angle can be set independently for halogens as donors and halogens as acceptors.

Acceptor maximum angle

Specify the maximum H...X–A angle for a halogen bond to be identified when the halogen acts as an acceptor.

Salt bridges section

These settings control the cutoffs that define a salt bridge. Salt bridges are defined by oppositely-charged atoms that are within a specified distance and are not directly hydrogen-bonded.

Maximum distance

Specify the maximum distance between the atoms for a salt bridge to be identified. The default is 5 Å.

Aromatic H-Bonds section

These settings control the cutoffs that define an aromatic hydrogen-bond (H-bond). Aromatic hydrogen bonds are defined by relations between four atoms, just as for hydrogen bonds (see above). The criteria are different for O and N atoms as acceptors. Only sp² nitrogen atoms are considered for these types of bonds.

Maximum distance (O Acc.)

Specify the maximum distance from the H atom to an O acceptor atom for an aromatic H-bond to be identified. The default is 2.8Å.

Maximum distance (N= Acc.)

Specify the maximum distance from the H atom to an sp² N acceptor atom for an aromatic H-bond to be identified. The default is 2.5Å.

Donor minimum angle (O Acc.)

Specify the minimum D–H...A angle for an aromatic H-bond to O to be identified. The default is 90°.

Donor minimum angle (N= Acc.)

Specify the minimum D–H...A angle for an aromatic H-bond to an sp² N to be identified. The default is 108°.

Donor maximum angle (N= Acc.)

Specify the minimum D–H...A angle for an aromatic H-bond to an sp² N to be identified. The default is 130°.

Acceptor minimum angle

Specify the minimum H...A–B angle for an aromatic H-bond to be identified. The default is 90°.

These settings define the criteria for pi-pi stacking interactions and contacts.

Contacts section

These settings define the distance ratios for contacts and allow the exclusion of certain types of contacts from consideration as contacts.

Contacts are classified into three types: good, bad, and ugly. The criteria are based on the following formula:

C = D₁₂ / ( R₁ + R₂)

where D₁₂ is the distance between atomic centers 1 and 2, and R₁ and R₂ are the van der Waals radii of atomic centers 1 and 2. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). The default values are:

good	1.30
bad	0.89
ugly	0.75

A contact is considered to belong to a particular type if the value of C is less than the cutoff value (but greater than any smaller cutoff value). Any distance ratio larger than the Good cutoff is not considered a contact.

Cutoff ratios text boxes

Specify the ratios C that define Good, Bad, and Ugly contacts.

Exclude options

These options control whether certain atoms are considered to be in contact or not.

H-bonds—Do not consider the hydrogen and the acceptor atom in a hydrogen bond to be in contact. This option is on by default.

Salt bridges—Do not consider atoms involved in a salt bridge to be in contact. This option is on by default.

1,4 interactions—Do not consider pairs of atoms that are connected by a sequence of 3 bonds to be in contact. Intra-ring contacts are always excluded. This option is on by default.

Pi interactions section

These settings control the cutoffs that define pi-pi and pi-cation interactions. For each of the three types of interaction, a maximum distance and an angle is specified. The default values are based on the work by Marcou, G. and Rognan, D. "Optimizing fragment and scaffold docking by use of molecular interaction fingerprints", J. Chem. Inf. Model., 2007, 47, 195-207; the maximum distances used here are somewhat larger.

Pi-pi, face to face text boxes

Maximum distance

Specify the maximum distance between the centroids of the rings. The default is 4.4Å.

Maximum angle

Specify the maximum angle between the ring planes. The default is 30°.

Pi-pi, edge to face text boxes

Maximum distance

Specify the maximum distance between the centroids of the rings. The default is 5.5Å.

Maximum angle

Specify the minimum angle between the ring planes. The default is 30°.

Pi-cation text boxes

Maximum distance

Specify the maximum distance between the cation center and the ring center. The default is 6.6Å.

Maximum angle

Specify the maximum angle between the normal to the ring plane and the line between the cation center and the ring center. The default is 30°.

These settings control the color and line width of the non-bonded interaction markers, whether any interactions are displayed while adjusting or transforming structures, and if so, which interactions are displayed.

Colors buttons

These buttons opens a color selector, in which you can choose a color for the markers. There is one button for each marker type.

Line width slider and text box

Set the width of the lines drawn to represent the markers, in pixels.

Display interactions while adjusting or transforming structures option

Select this option to display selected interactions while adjusting structures or transforming structures. The interactions are updated dynamically as you perform the adjustment or transformation. The interactions to display can be selected from the options given below this option.