Create an input file for MM3 Molecular Mechanics Calculations
(Be patient the file downloads for the editor and 3D-viewer may take 20 seconds or more.)
Step 1: Draw your structure in the editor or type in the molecule name or Smiles string in the Search dialog box:
If you draw your structure click on the → arrow button to create a 3D-molecule in the JSmol window.
If you use Smiles or molecule name input, click on the Search button:
- ..the 2D molecule should be converted to 3D with automatically added hydrogens.
- ..If the molecule in the JSmol window isn't 3D (i.e. it is flat), click right in the JSmol window,
slide right on Computation and choose Optimize Structure.
- You can input your structure by drawing in the 2D-Structure editor or using Smiles notation.
- Smiles notation is useful for finding 3D structures for hits from chemical structure databases.
- Examples of Smiles strings:
- 2-Butene: CC=CC
- Ethanol: CCO
- tert-butyl alcohol: CC(C)(C)O
- Cyclohexanol: C1CCCCC1O
- Toluene: c1ccccc1C or C1=CC=CC=C1C
- Acetic acid: CC(=O)O
- Acetamide: CC(=O)N
- Methyl-tert-butyl ether: CC(C)(C)OC
- Benzoic acid (the default input string, above): c1ccccc1C(=O)O
- Guanine: Nc2nc1[nH]cnc1c(=O)[nH]2
- Progesterone: CC(=O)C3CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C
- If "Using Delocalized-pi calculation" is checked, MM3 uses a molecular orbital calculation to
find the partial bond order for conjugated bonds. For calculations with non-conjugated substituents on
benzene rings, this option is not necessary.
- MM3 normally assigns atom types automatically. This applet can also assign atoms types. The atom types
will be listed in the MM3 input file for you to check if you clear the "Using Automatic Type Assignments in MM3"
option. Checking the assigned atom types is useful as you learn how molecular mechanics works.