1. 1/10

2. 2/10 G. Imre, G. Veress, A. Volford, Ö. Farkas Molecules from the Minkowski space: an approach to building 3D molecular structures J. Mol. Struct. (Theochem) 666-667, 51 (2003) Clean3D project at ELTE Goal: -Generate useful 3D molecular structures from topology -First priority is to generate structure for any valid topology -Second priority fast process History: -Atomic coordinates can fulfill any set of inter-atomic distances in a multidimensional space with Minkowski metric -Extremely powerful for rigid, fused ring systems -In general too slow due to the quadratic scaling

3. 3/10 Clean3D project at ELTE History: G. Imre, G. Veress, A. Volford, Ö. Farkas Molecules from the Minkowski space: an approach to building 3D molecular structures J. Mol. Struct. (Theochem) 666-667, 51 (2003)

4. 4/10 –Find the most complex substructures, set priorities –Set up the order of atoms –Iterative and multiple fragment- atom fuse steps Set the whish list, choices and place atom via triangulation Modify Cartesian coordinates if necessary to fulfill the wishes via redundant internal coordinate transformation Optimize the fragment Check for equivalent structures Check stereo criteria Select surviving conformers –Final optimization Current method in a nutshell

5. 5/10 –Result: Current method in a nutshell

6. 6/10 Comparison with Corina CorinaMarvin/Clean3D

7. 7/10 Using Clean/3D from the GUI from the GUI (MSketch/MView) Draw or read a structure Adding hydrogens is recommended Clean/3D options in the GUI Default 3D clean (Ctrl-3) Change default to Fast Usually faster but may lead to incorrect stereo Find conformers (Ctrl-F) Same process but lets the user select the resulting structure

8. 8/10 Using Clean/3D from molconvert Detailed help for Clean/3D options $molconvert –H3D Use fixed number of conformers and store them $molconvert -3:S0[fm]{500}{500}{500}[ca][writeconfs]{cnfs} -S0: Resets default settings -[fm]{n}{n}{n}: Set the size of the fragment storage to n -[ca]: Perform conformational analysis -[writeconfs]{cnfs}: Write the conformers to the file cnfs.0.mol Perform geometry optimization of a structure already in 3D $molconvert -3:Ec01o113 sdf bad_3D.mol -E: put the final energy to the SDF property flag -c01: do not build structure for already 3D molecules -o113: do Dreiding optimization & print final energy & use tight optimization criteria

9. 9/10 Some more info about Clean/3D NCIs database of August 2000 (~250000 molecules) Released Clean/3D can clean more than 99.8% At the next release of Marvin we expect more than 99.9% default and optional time limit adding hydrogens optionally before processing The next major release of Clean/3D this summer Fragment-fragment fusion Fragment database Internal coordinate based Newton optimization

10. 10/10