| alc | Alchemy file |
| prep | Amber PREP file |
| bs | Ball & Stick file |
| caccrt | Cacao Cartesian file |
| ccc | CCC file |
| box | Dock 3.5 Box file |
| dmol | DMol3 Coordinates file |
| feat | Feature file |
| gam | GAMESS Output file |
| gamout | GAMESS Output file |
| mm1gp | Ghemical MM file |
| qm1gp | Ghemical QM file |
| hin | HyperChem HIN file |
| jout | Jaguar Output file |
| bin | OpenEye Binary file |
| mmd | MacroModel file |
| mmod | MacroModel file |
| out | MacroModel file |
| dat | MacroModel file |
| car | MSI Biosym/Insight II CAR file |
| sdf | MDL Isis SDF file |
| sd | MDL Isis SDF file |
| mdl | MDL Molfile file |
| mol | MDL Molfile file |
| mopcrt | MOPAC Cartesian file |
| mopout | MOPAC Output file |
| mpqc | MPQC file |
| bgf | MSI BGF file |
| nwo | NWChem Output file |
| pdb | PDB file |
| qcout | QChem Output file |
| smi | SMILES file |
| mol2 | Sybyl Mol2 file |
| unixyz | UniChem XYZ file |
| xyz | XYZ file |