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Clean3D project at ELTE Goal: Generate useful 3D molecular structures from topology

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:

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Clean3D project at ELTE Goal: Generate useful 3D molecular structures from topology

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  1. 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 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)

  2. 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)

  3. Current method in a nutshell • 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

  4. Current method in a nutshell • Result:

  5. Corina Marvin/Clean3D Comparison with Corina

  6. 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

  7. 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

  8. 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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