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363. CYCORD: Program for Calculating the Coordinates
of Atoms in Mono- and Polycyclic Molecules When the
Dihedral Angles Are Not Known
by D.V.S. Jain, S. Singh and V. K. Gombar, Department
of Chemistry, Punjab University, Chandigargh, India
The underlying method fixes the reference axes-frame
with atom 1 (I-1) at the origin, atom 2 (I) on the x-
axis, and atom 3 (I+1) in the X-Y plane. Then the
coordinates of the atom I+2 in a new frame of axes in
which origin has been shifted to atom I+1 followed by
the rotations
around z-axis to make y(I) = 0 and x(I)
+ve
around y-axis to make z(I) = 0 and x(I)
+ve
around z-axis to make z(I-1) = 0 and Y(I-1)
+ve
are given by
x(I+2) = D(I+1) cos A(I+1)
y(I+2) = D(I+1) sin A(I+1) cos TILT(I)
z(I+2) = D(I+1) A(I+1) sin TILT(I)
whereD(I+1) is the distance between atoms I+1 and
I+2
A(I+1) is the angle at atom I+1 subtended by the
atoms I and I+2,
TILT(I) is the approximate dihedral angle of the
lines between I-1, I and atoms I+1, I+2.
This set of coordinates is then transferred back to the
reference frame of axes.
These calculations are carried out for the values of I
varying from 2 to N, so that coordinates of atoms 4 to
N and 1 and 2 (now named 1' and 2') are known afresh.
The present iterative method modifies the dihedral
angles in a way that the sum of squares of distances
between 1,1' and 2,2' (DIST) minimizes.
For a given conformation, the dihedral angles of the
substituents are exactly known, hence the calculations
of their coordinates are trivial.
In the case more than one ring are present, the atoms
of the second ring which are directly attached to the
first ring are considered as the substituent to the
first ring. The rest of the atoms of the second ring
are treated like those of the first ring.
FORTRAN
Lines of Code: 463
Recommended Citation: D.V.S. Jain et al., QCPE 11, 363
(1978).
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