nextuppreviouscontentsindex
Next:Geometry LibrariesUp:Standard Geometry DefinitionPrevious:Standard Geometry Definition

The Geometry Statement

GEOMETRY <Name> {BOND | ANGLE | TORSION | PSEUDO |
                 TRIGONAL | PLANE | BCORREL | CHIRAL} -
         <Value>  <Sigma>   N(<Atom name>)
The GEOMETRY statement is used to supply an ideal value for some type of restraint. The restraint is identified by the residue type and the names of the involved atoms. The order of the atom names is usually significant.

The syntax of the GEOMETRY statement is the same regardless of which type of restraint is being defined. First is the word GEOMETRY. This is followed by the name of the object being defined (e.g. ALA, GLU, PEPTIDE). This object can be either a residue type or a linkage type. (ALA and GLU are both residue types where PEPTIDE is a linkage type.) Next is the name of the type of restraint being defined (either BOND, ANGLE, TORSION, PSEUDO, TRIGONAL, PLANE, BCORREL, CHIRAL). The next number given is, in all cases except that of a PLANE, the standard value for this restraint. (With a PLANE restraint this number is the number of atoms in the plane and the standard value is assumed zero.) The second number is the standard deviation from ideality as seen in small molecule structures. Last is the list of the names of the atoms involved in this restraint.

When defining a geometry restraint in a link there is always the question of which residue each atom belongs to. When the bond between the atom C and atom N in the PEPTIDE link is defined there is a problem in that there is an atom named C in both residues, as well as two atoms named N. To remove this ambiguity we recognize that each link has a source residue and a target. In a PEPTIDE link between residues 10 and 11 the source of the link is 10 while the target is 11.

In the geometry restraint an atom from the source residue has the prefix `-' added to its name, and an atom from the target residue has a `+' added. The default is `-', therefore generally one refers to the source residue by typing the atom names directly, and to the target residue by placing a `+' before the atom name.

Here are some examples of geometry declarations broken down by restraint type.

  BOND

GEOMETRY PEPTIDE    BOND    1.45    0.02    N, CA
GEOMETRY PEPTIDE    BOND    1.52    0.02    CA, C
GEOMETRY PEPTIDE    BOND    1.33    0.02    C, +N
GEOMETRY CTERM      BOND    1.25    0.02    C, +OH
GEOMETRY SS         BOND    2.036   0.03    SG, +SG
GEOMETRY CYS        BOND    1.54    0.02    CA, CB
GEOMETRY CYS        BOND    1.43    0.02    CB, SG
The first word after ``GEOMETRY'' is the name of the standard group being defined. The first number is the ideal bond length, and the second number is the standard deviation from ideality seen in small molecule structures. Last come the names of the two bonded atoms.

Note that PEPTIDE, CTERM, and SS are kinds of links while CYS is a part of the declaration of a cystine. In the PEPTIDE group the N, CA, and C refer to atoms in the preceding residue, and the +N refers to the N atom of the next residue.

  ANGLE

GEOMETRY PEPTIDE    ANGLE    112      3    N, CA, C
GEOMETRY PEPTIDE    ANGLE    121.2    3    CA, C, O
GEOMETRY PEPTIDE    ANGLE    115.6    3    CA, C, +N
GEOMETRY CTERM      ANGLE    118      3    CA, C, O
GEOMETRY CTERM      ANGLE    118      3    CA, C, +OH
GEOMETRY SS    ANGLE    104.5  3    +CB, +SG, SG
GEOMETRY ALA   ANGLE    112    3    N, CA, CB
GEOMETRY ALA   ANGLE    111    3    C, CA, CB
Bond angles are defined in the same way as bond lengths. The ideal bond angle and standard deviation are both in degrees. The three atoms involved are listed in the order in which they are bonded to each other (i.e. the middle atom in the list is the atom at the vertex of the angle).

  TORSION

GEOMETRY PEPTIDE    TORSION   2160   30    N, CA, C, +N
GEOMETRY PEPTIDE    TORSION   3060   20    C, +N, +CA, +C
GEOMETRY PEPTIDE    TORSION   2180   10    CA, C, +N, +CA
GEOMETRY SS     TORSION    2090    10    CB, SG, +SG, +CB
GEOMETRY CYS    TORSION    3060    15    N, CA, CB, SG
GEOMETRY MET    TORSION    3060    15    N, CA, CB, CG
GEOMETRY MET    TORSION    3060    15    CA, CB, CG, SD
GEOMETRY MET    TORSION    3060    15    CB, CG, SD, CE
While most aspects of these statements should be clear by now, the first four-digit number is special in that it actually contains two pieces of information. The thousands digit gives the number of evenly spaced minima in the 360 degree range of possible values. The three digits following this digit (but including the sign of the number) is the value of one of the minima measured in degrees.

For example, the first torsion angle defined uses the number 2160. This means that there are 2 minima and one of them is at 160 degrees. The next number on the line is the standard deviation in degrees. It is followed by a list, in bonding order, of the four atoms involved.

  PSEUDOROTATION

GEOMETRY PRO    PSEUDO    2000    20    CA, CB, CG, CD, N
The pucker of a 5 membered ring is described by a pseudorotation angle (Altona, C., Sundaralingam, M., JACS (1972). 94, 8205-8212). Its standard value is encoded just like that of a torsion angle. There is a multiplicity and a particular value. The line ends with a list of the five atoms of the ring, listed as they occur in the ring. The first atom in the list determines the origin against which the phase shift of the pseudorotation angle is measured.

  TRIGONAL

GEOMETRY CTERM    TRIGONAL  0  0.02    C, CA, O, +OH
GEOMETRY ASP      TRIGONAL  0  0.02    CG, CB, OD1, OD2
GEOMETRY ASN      TRIGONAL  0  0.02    CG, CB, OD1, ND2
This type of restraint is just a subset of the planarity restraint, and is designed to be used for planarity around a trigonal carbon. The first number in the list is the standard value for the r.m.s. deviation from the plane, which should always be zero.

  PLANE

GEOMETRY PEPTIDE  PLANE   5  0.02    C, CA, O, +N, +CA
GEOMETRY ARG      PLANE   5  0.02    CD, NE, CZ, NH1, NH2
GEOMETRY HIS      PLANE   6  0.02    CB,CG,ND1,CE1,CD2,NE2
The first number is the number of coplanar atoms. The next number is the standard deviation of the r.m.s. deviation from the plane in Ångstroms, followed by a list of the coplanar atoms. The order of the names is unimportant.

  BCORREL

GEOMETRY PEPTIDE  BCORREL    3.70   7.44     CA   C   
GEOMETRY ARG      BCORREL   10.59  16.52     CB   CG  
GEOMETRY HIS      BCORREL    3.37   3.82     CB   CG
The first number is the average increase in temperature factor the second atom shows relative to the first. The second number is the standard deviation for this observation.

  CHIRAL

GEOMETRY CYS    CHIRAL    1    1    CA, N, CB, C
GEOMETRY THR    CHIRAL    1    1    CB, CA, CG2, OG1
GEOMETRY ILE    CHIRAL    1    1    CB, CA, CG2, CG1
The chiral atom is named first in the list, followed by the names of three of the atoms bound to it. The order of the final three names specifies the chirality of the first. The rule is: If the priority of the three atoms as listed on the GEOMETRY statement is (1,2,3) or a permutation the central atom has an R configuration. If the order is (3,2,1) then the configuration is S.


nextuppreviouscontentsindex
Next:Geometry LibrariesUp:Standard Geometry DefinitionPrevious:Standard Geometry Definition
Dale Edwin Tronrud

Wed Jul 5 13:21:03 PDT 2000