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.
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, SGThe 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.
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, CBBond 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).
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, CEWhile 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.
GEOMETRY PRO PSEUDO 2000 20 CA, CB, CG, CD, NThe 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.
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, ND2This 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.
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,NE2The 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.
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 CGThe 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.
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, CG1The 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: