generate 3D coordinates for small molecules
This tool generates 3D conformations for small molecules and adds hydrogens to them.
As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.