DrawMol

Features

With DrawMol, you can:

Build a structure by clicking and dragging to add atoms and bonds. You can then refine your structure with a single click using UFF force field optimization. When building a structure, DrawMol can guess for you the type of bonds (single, double, triple or aromatic), or you can force it by clicking on a bond. What's more, hydrogen atoms can be added automatically
Save your structure in xyz format or create a Gaussian or Gamess input file directly. For Gamess, if the program is installed locally, you can even run the job from DrawMol (in the background) and monitor progress.
Paste a structure directly into DrawMol's Cartesian editor. It can recognize XYZ, Gaussian, Gamess, Turbomole and Z-matrix formats. The Cartesian editor can also be used to output the structure in any of these formats, as well as to modify a given structure by adding/removing certain atoms or changing a given atomic element.
Import a structure from the ChemSpider database

Open XYZ, MDL molfile, Gaussian log, Gaussian fchk, Gamess log, Dalton out, Molpro out file formats.
In addition to molecular structure, DrawMol can read various molecular properties (currently only available for the Gaussian fchk file format) :
- Mulliken charges
- Dipolar moment
- Polarizability and first hyperpolarizability
- Vibrational normal modes
- Magnetic shields (NMR)
- Molecular orbits from basis set and LCAO coefficients
Visualization of molecular properties:
- Atom labels
- Mulliken charges
- Chemical displacements in NMR
- Dipole moment vector
- Beta vector
- Unit sphere representation of polarizability and hyperpolarizability
- Atomic displacements of the normal modes of a vibration via vectors, spheres or even animations
- Isosurfaces of molecular orbitals
Open Gaussian cube files and visualize stored date isosurfaces.

To match two molecules or fragments with each other using a matching procedure (least-squares approach).
To orient the Z axis of a molecule so that it is perpendicular to a plane formed by three or more atoms, or passes through two or more atoms, using a least-squares approach.

As an image either in png, tiff, jpeg or dae (Collada)
As a movie for normal mode animation
As an XYZ, CIF, PDB file
As an h5mol file. This format is essentially an HDF5 container that stores all molecular properties as well as visualization preferences. This file can be read by DrawMol but can also be easily analyzed using C, Fortran, Python, ... and even unloaded (with the h5dump utility) into an ascii file (see https://www.hdfgroup.org for details).