| ABINIT Output Format | abinit | yes | no |
| Accelrys/MSI Biosym/Insight II CAR format | arc, car | yes | no |
| Accelrys/MSI Cerius II MSI format | msi | yes | no |
| Accelrys/MSI Quanta CSR format | csr | no | yes |
| ACES input format | acesin | no | yes |
| ACES output format | acesout | yes | no |
| ACR format | acr | yes | no |
| ADF Band output format | adfband | yes | no |
| ADF cartesian input format | adf | no | yes |
| ADF DFTB output format | adfdftb | yes | no |
| ADF output format | adfout | yes | no |
| ADF TAPE41 format | t41 | yes | no |
| Alchemy format | alc | yes | yes |
| Amber Prep format | prep | yes | no |
| ASCII format | ascii | no | yes |
| AutoDock PDBQT format | pdbqt | yes | yes |
| Ball and Stick format | bs | yes | yes |
| Cacao Cartesian format | caccrt | yes | yes |
| Cacao Internal format | cacint | no | yes |
| CAChe MolStruct format | cac, cache | no | yes |
| Canonical SMILES format | can | yes | yes |
| CASTEP format | castep | yes | no |
| CCC format | ccc | yes | no |
| Chem3D Cartesian 1 format | c3d1 | yes | yes |
| Chem3D Cartesian 2 format | c3d2 | yes | yes |
| ChemDoodle JSON | cdjson | yes | yes |
| ChemDraw binary format | cdx | yes | no |
| ChemDraw CDXML format | cdxml | yes | yes |
| ChemDraw Connection Table format | ct | yes | yes |
| Chemical JSON | cjson | yes | yes |
| Chemical Markup Language | cml, mrv | yes | yes |
| Chemical Resource Kit 3D format | crk3d | yes | yes |
| Chemical Resource Kit diagram(2D) | crk2d | yes | yes |
| ChemKin format | ck | yes | yes |
| Chemtool format | cht | no | yes |
| CML Reaction format | cmlr | yes | yes |
| Compare molecules using InChI | k | no | yes |
| Confab report format | confabreport | no | yes |
| Copy raw text | copy | no | yes |
| Crystal 09 output format | c09out | yes | no |
| Crystallographic Information File | cif | yes | yes |
| CSD CSSR format | cssr | no | yes |
| Culgi object file format | cof | yes | yes |
| DALTON input format | dalmol | yes | yes |
| DALTON output format | dallog | yes | no |
| DL-POLY CONFIG | CONFIG | yes | yes |
| DL-POLY HISTORY | HISTORY | yes | no |
| DMol3 coordinates format | dmol, outmol | yes | yes |
| Dock 3.5 Box format | box | yes | yes |
| Extended XYZ cartesian coordinates format | exyz | yes | yes |
| FASTA format | fasta, fa, fsa | yes | yes |
| Fastsearch format | fs | yes | yes |
| Feature format | feat | yes | yes |
| Fenske-Hall Z-Matrix format | fh | no | yes |
| FHIaims XYZ format | fhiaims | yes | yes |
| Fingerprint format | fpt | no | yes |
| FPS text fingerprint format (Dalke) | fps | no | yes |
| Free Form Fractional format | fract | yes | yes |
| GAMESS Input | inp, gamin | yes | yes |
| GAMESS Output | gam, gamess, gamout | yes | no |
| GAMESS-UK Input | gukin | yes | yes |
| GAMESS-UK Output | gukout | yes | yes |
| Gaussian cube format | cube, cub | yes | yes |
| Gaussian formatted checkpoint file format | fchk, fch, fck | yes | no |
| Gaussian Input | gjf, com, gau, gjc | no | yes |
| Gaussian Output | g03, g09, g16, g92, g94, g98, gal | yes | no |
| Gaussian Z-Matrix Input | gzmat | yes | yes |
| General XML format | xml | yes | no |
| Generic Output file format | log, dat, out, output | yes | no |
| Ghemical format | gpr | yes | yes |
| GRO format | gro | yes | yes |
| GROMOS96 format | gr96 | no | yes |
| GULP format | got | yes | no |
| HyperChem HIN format | hin | yes | yes |
| InChI format | inchi | yes | yes |
| InChIKey | inchikey | no | yes |
| Jaguar input format | jin | yes | yes |
| Jaguar output format | jout | yes | no |
| Ketcher KET JSON format | ket | yes | yes |
| LPMD format | lpmd | yes | yes |
| M.F. Sanner's MSMS input format | msms | no | yes |
| MacroModel format | mmd, mmod | yes | yes |
| Macromolecular Crystallographic Info | mmcif, mcif | yes | yes |
| Maestro format | mae, maegz | yes | yes |
| MCDL format | mcdl | yes | yes |
| MDFF format | CONTFF, MDFF, POSFF | yes | yes |
| MDL MOL format | mol, mdl, sd, sdf | yes | yes |
| MDL RXN format | rxn | yes | yes |
| Molden format | molden, mold, molf | yes | yes |
| MolPrint2D format | mpd | no | yes |
| Molpro input format | mp | no | yes |
| Molpro output format | mpo | yes | no |
| MOPAC Cartesian format | mop, mopcrt, mpc | yes | yes |
| MOPAC Internal | mopin | yes | yes |
| MOPAC Output format | moo, mopout | yes | no |
| MPQC output format | mpqc | yes | no |
| MPQC simplified input format | mpqcin | no | yes |
| MSI BGF format | bgf | yes | yes |
| Multilevel Neighborhoods of Atoms (MNA) | mna | no | yes |
| NWChem input format | nw | no | yes |
| NWChem output format | nwo | yes | no |
| Open Babel molecule report | molreport | no | yes |
| Open Babel report format | report | no | yes |
| OpenDX cube format for APBS | dx | yes | yes |
| ORCA input format | orcainp | no | yes |
| ORCA output format | orca | yes | no |
| Outputs nothing | nul | no | yes |
| Painter format | paint | no | yes |
| Parallel Quantum Solutions format | pqs | yes | yes |
| PCModel Format | pcm | yes | yes |
| PNG 2D depiction | png | yes | yes |
| Point cloud on VDW surface | pointcloud | no | yes |
| POS cartesian coordinates format | pos | yes | no |
| POV-Ray input format | pov | no | yes |
| PQR format | pqr | yes | yes |
| Protein Data Bank format | pdb, ent | yes | yes |
| PubChem format | pc | yes | no |
| PubChem JSON | pcjson | yes | yes |
| PWscf format | pwscf | yes | no |
| Q-Chem input format | qcin | no | yes |
| Q-Chem output format | qcout | yes | no |
| Reaction SMILES format | rsmi | yes | yes |
| Read and write raw text | text | yes | yes |
| RInChI | rinchi | no | yes |
| ShelX format | ins, res | yes | no |
| SIESTA format | siesta | yes | no |
| SMILES FIX format | fix | no | yes |
| SMILES format | smi, smiles | yes | yes |
| SMILES format using Smiley parser | smy | yes | no |
| STL 3D-printing format | stl | no | yes |
| SVG 2D depiction | svg | no | yes |
| Sybyl Mol2 format | mol2, ml2, sy2 | yes | yes |
| The LAMMPS data format | lmpdat | no | yes |
| Thermo format | tdd, therm | yes | yes |
| Tinker XYZ format | txyz | yes | yes |
| Title format | txt | yes | yes |
| Turbomole AOFORCE output format | aoforce | yes | no |
| TurboMole Coordinate format | tmol | yes | yes |
| UniChem XYZ format | unixyz | yes | yes |
| VASP format | POSCAR, CONTCAR, VASP | yes | yes |
| ViewMol format | vmol | yes | yes |
| Wiswesser Line Notation | wln | yes | no |
| XCrySDen Structure Format | axsf, xsf | yes | no |
| XED format | xed | no | yes |
| XYZ cartesian coordinates format | xyz | yes | yes |
| YASARA.org YOB format | yob | yes | yes |
| ZINDO input format | zin | no | yes |