Chemistry File Types

Select a format below. We'll wire each to an editor page next.

Molecular structures (2D/3D)

• MOL (.mol), MOL2 (.mol2)
• SDF (.sdf)
• PDB (.pdb), PQR (.pqr)
• XYZ (.xyz)
• CML (.cml)
• ChemDraw: CDX (.cdx), CDXML (.cdxml)
• Marvin: MRV (.mrv)
• Crystallographic: CIF (.cif), mmCIF (.cif/.mmcif)

Line notations / identifiers

• SMILES (.smi)
• SMARTS
• InChI, InChIKey
• RInChI (reactions)

Reactions

• RXN (.rxn)
• RDF (Reaction Data File)
• SMIRKS

Quantum chemistry (inputs/outputs)

• Gaussian: .gjf/.com, .log, .chk/.fchk, .cube
• ORCA: .inp, .out
• Q-Chem: .inp, .out
• NWChem: .nw, .out
• GAMESS/Firefly: .inp, .out
• MOPAC: .mop, .out/.arc
• Molden: .molden
• CP2K: .inp
• VASP: POSCAR/CONTCAR, POTCAR, OUTCAR
• Quantum ESPRESSO: .pw.in, .pwo

Volumetric/grids and maps

• Gaussian Cube (.cube)
• DX/OpenDX (.dx)
• CCP4/MRC, DSN6 (electron density)

Crystallography/materials

• CIF (.cif), mmCIF
• SHELX: .ins, .res
• Reflection/data: .hkl, .mtz
• XSF (.xsf), CFG (.cfg)

Molecular mechanics / MD

• Coordinates/topologies: PDB, GRO (.gro), PSF (.psf), PRMTOP (.top/.prmtop), TPR (.tpr), TOP/ITP, MOL2
• Trajectories: DCD (.dcd), XTC (.xtc), TRR (.trr), NetCDF (.nc), LAMMPS dump (.dump) / data (.data)
• GROMACS: .gro, .top, .mdp, .tpr
• AMBER: .prmtop, .inpcrd, .rst/.rst7, .mdcrd
• NAMD/CHARMM: .psf, .dcd
• AutoDock: PDBQT (.pdbqt)

Spectroscopy / MS / Chromatography

• JCAMP-DX (.jdx/.dx) for IR/NMR/MS
• mzML (.mzML), mzXML (.mzXML), imzML (.imzML)
• ANDI/NetCDF (.cdf) for GC/LC/MS
• nmrML (.nmrML)

Data exchange / markup

• CML (Chemical Markup Language)
• AnIML (Analytical Information Markup Language)
• SBML, CellML (systems biology related)

Note: some vendor formats (e.g., Thermo/Waters/Bruker proprietary) are not listed due to limited web editability.