MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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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 State	Completed
Total Processing Time	NA (hh:mm:ss)

Molecule Information
Molecular Dynamics (MD) Files

Molecule Information


Molecule Type	amino acid building block
Residue Name (RNME)	KH5
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	25
Net Charge	0
Forcefield	multiple
Molecule ID	17438
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:17
Literature Reference	Drazen 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 (301-400 of 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol^-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol^-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid	Formula	Iupac	Common Name	Atoms >	Charge	Curation	Visibility	Δ Qm Optimized Energy (kJ.mol^-1)	Compare
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
1548	None	-	-	24	0	Manual*	Public	N/A	Compare with
17320	None	-	-	24	0	Manual	Public	N/A	Compare with
17319	None	-	-	24	0	Manual	Public	N/A	Compare with
205	None	-	-	24	0	Manual*	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
17276	None	-	-	24	-1	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17317	None	-	-	24	0	Manual	Public	N/A	Compare with
17318	None	-	-	24	0	Manual	Public	N/A	Compare with
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17536	None	-	-	24	0	Manual	Public	N/A	Compare with
1550	None	-	-	24	0	Manual*	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
2002	None	-	-	24	0	Manual*	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
17472	None	-	-	24	0	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
17535	None	-	-	24	0	Manual	Public	N/A	Compare with
17533	None	-	-	24	0	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17449	None	-	-	23	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17344	None	-	-	23	-2	Manual	Public	N/A	Compare with
17476	None	-	-	23	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17162	None	-	-	23	0	Manual	Public	N/A	Compare with
17163	None	-	-	23	0	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
17451	None	-	-	23	0	Manual	Public	N/A	Compare with
17181	None	-	-	23	0	Manual	Public	N/A	Compare with
17305	None	-	-	23	0	Manual	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17182	None	-	-	23	0	Manual	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
17382	None	-	-	23	0	Manual	Public	N/A	Compare with
17474	None	-	-	23	0	Manual	Public	N/A	Compare with
17383	None	-	-	23	0	Manual	Public	N/A	Compare with
17384	None	-	-	23	0	Manual	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17308	None	-	-	23	0	Manual	Public	N/A	Compare with
17307	None	-	-	23	0	Manual	Public	N/A	Compare with
17450	None	-	-	23	0	Manual	Public	N/A	Compare with
17284	None	-	-	23	0	Manual	Public	N/A	Compare with
17283	None	-	-	23	0	Manual	Public	N/A	Compare with
17343	None	-	-	23	-2	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
17356	None	-	-	23	0	Manual	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
17473	None	-	-	23	0	Manual	Public	N/A	Compare with
17475	None	-	-	23	0	Manual	Public	N/A	Compare with
17452	None	-	-	23	0	Manual	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
17354	None	-	-	23	0	Manual	Public	N/A	Compare with
17252	None	-	-	23	-2	Manual	Public	N/A	Compare with
17282	None	-	-	23	0	Manual	Public	N/A	Compare with
17249	None	-	-	23	-2	Manual	Public	N/A	Compare with
17281	None	-	-	23	0	Manual	Public	N/A	Compare with
17342	None	-	-	23	-2	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17250	None	-	-	23	-2	Manual	Public	N/A	Compare with
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
17461	None	-	-	22	0	Manual	Public	N/A	Compare with
17490	None	-	-	22	0	Manual	Public	N/A	Compare with
17491	None	-	-	22	0	Manual	Public	N/A	Compare with
17492	None	-	-	22	0	Manual	Public	N/A	Compare with
17223	None	-	-	22	0	Manual	Public	N/A	Compare with
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
17489	None	-	-	22	0	Manual	Public	N/A	Compare with
17462	None	-	-	22	0	Manual	Public	N/A	Compare with
203	None	-	-	22	0	Manual*	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17221	None	-	-	22	0	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
17485	None	-	-	21	0	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
17486	None	-	-	21	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
17423	None	-	-	21	0	Manual	Public	N/A	Compare with