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*LP2

*LP2 is used to define the angular relationship of a vector to an sp2-plane.

Remarks

In practice this command is most often used in studying the approach of a hydrogen atom to a carbonyl group and the consequent potential for hydrogen bonding.

Consider the following:

The format of the *LP2 command is:

DEFINE *LP2  <parnam1>  <parnam2>  i  j  k  n

<parnam1> : 

The angle between the probe atom vector (k->n) and the sp2 plane, as illustrated in the Figure above. The range of values is -90.0° <= parnam1 <= +90.0. The sp2 plane generates two hemispheres of parnam1 values. The hemisphere of positive parnam1 values is identified by the cross product of j->i and j->k (the upward arrow in Figure above).

It should be noted that the definition of parnam1 is different from the polar angle usually found in the spherical polar coordinate system. Parnam1 starts from the sp2 plane instead of the normal to the plane as in the standard spherical polar coordinate system. This modification was made so that the angular parameters have more intuitive chemical meaning. A parnam1 value of 0.0 means the probe atom lies in the plane of the sp2 atom.

<parnam2> : 

The angle between the vector k-> j and the projection of the probe atom vector (k->n) on to the sp2 plane defined by atoms i j k. The range of values is -180.0 <= parnam2 <= +180.0°. Two hemispheres are generated by a plane containing j k and perpendicular to the sp2 plane. Positive values of parnam2 are in the hemisphere that contains the vector j->i, i.e. atom X. Parnam2 is the same as the azimuth angle in the standard spherical polar coordinate system. A value of +/- 180.0 means that the probe atom is collinear with j k.

i  j  k  n :

Atoms, centroids, and/or dummy points.

i j k specify an sp2 plane with origin k, and n is the probe atom for calculating angular parameters. i and j define the positive hemispheres for parnam1 and parnam2. The order in which i j k n are given is CRITICAL to obtain the correct results.

Example

• Select *LP2

• Select or type items for *LP2. If necessary reselect *LP2 to end
  input.
  Select CANCEL to cancel command.

• Select atom number 1

• 1 appears in the dialogue area

  A red + appears at atom 1 in the fragment.

• Select in turn atoms 2 4 5

  As each atom is selected a red + appears at the atom in the fragment.

  After the selection of the fourth atom these red crosses disappear.

• In the dialogue area we now have:

  DEFINE, *LP2,
  Input *LP2 parameter name no.  1

• Type THETA <RETURN>

• In the dialogue area we now have:

  DEFINE, *LP2, THETA,
  Input *LP2 parameter name no.  2

• Type PHI <RETURN>

• In the summary area we now have:

  *LP2  THETA  PHI  1  2  4  5

  This line is displayed in green to indicate that it is a DEFINE command.

  In the dialogue area we now have the "home" prompt:

  Search for ALL crystal fragments
  OVERLAP of crystal fragments permitted
  Select a menu command or TO-BUILD to return to the BUILD menu.

  The resultant command in the instruction document is:

  DEFINE  *LP2  THETA  PHI  1  2  4  5

The order in which the four atoms, centroids and/or dummy points i j k n are specified is important.

Either of the two possible atoms, centroids and/or dummy points, i can be specified, but only one of them.

The sp2=sp2 double bond must be between atoms j and k.

The non-bonded vector must be between atoms k and n.

In a single search test there can be a maximum of 10 *LP2 instructions.

Related Command

DEFINE *LP3

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Volume 2 Chapter 3 3D-Constrain Sub-menu *LP3.