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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

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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)

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– 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

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–Result:

Current method in a nutshell

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Comparison with Corina

Corina Marvin/Clean3D

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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 butlets the user select theresulting structure

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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 <Energy> SDF property flag

- c01 : do not build structure for already 3D molecules

- o113 : do Dreiding optimization & print final energy &

use tight optimization criteria

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Some more info about Clean/3D

•NCI’s 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

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