MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 2000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid
Residue Name (RNME)KCN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17231
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:15
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1) >
Compare 
1590 None - 147 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
Previous Page Next Page

ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)