Z-Matrix

A Z-Matrix defines molecular geometry using internal coordinates: bond lengths, bond angles, and dihedral angles relative to previously-defined atoms.

Syntax

zmatrix{
  atom
  atom  ref1  distance
  atom  ref1  distance  ref2  angle
  atom  ref1  distance  ref2  angle  ref3  dihedral
}

Each row defines one atom. The first row is the origin (no references). The second references one prior atom (distance only). The third references two (distance + angle). Subsequent rows reference three (distance + angle + dihedral).

Example: methane

Source Rendered

zmatrix{ C1 H2 C1 1.09 H3 C1 1.09 H2 109.5 H4 C1 1.09 H2 109.5 H3 120.0 }

$\mathrm{zmatrix}\begin{array}{c}\mathrm{C1}\\ \mathrm{H2}& \mathrm{C1}& 1.09\\ \mathrm{H3}& \mathrm{C1}& 1.09& \mathrm{H2}& 109.5\\ \mathrm{H4}& \mathrm{C1}& 1.09& \mathrm{H2}& 109.5& \mathrm{H3}& 120.0\end{array}$

• C1 is the origin
• H2 is 1.09 Å from C1
• H3 is 1.09 Å from C1, with angle H2-C1-H3 = 109.5°
• H4 is 1.09 Å from C1, angle 109.5°, dihedral 120.0°

Units

• Distances: Angstroms (Å)
• Angles: degrees

CML wire (v0.11+)

Emits as <zMatrix> inside a <molecule>:

<molecule>
  <zMatrix>zmatrix{...}</zMatrix>
</molecule>

Future enhancement: structural <length>, <angle>, <torsion> child elements per row.