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)	KMN
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	27
Net Charge	0
Forcefield	multiple
Molecule ID	17166
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:14
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 (201-300 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
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
2747	None	-	-	20	0	Manual*	Public	N/A	Compare with
17304	None	-	-	25	0	Manual	Public	N/A	Compare with
17336	None	-	-	30	1	Manual	Public	N/A	Compare with
17489	None	-	-	22	0	Manual	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
17253	None	-	-	27	0	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17438	None	-	-	25	0	Manual	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
17472	None	-	-	24	0	Manual	Public	N/A	Compare with
17504	None	-	-	32	0	Manual	Public	N/A	Compare with
1561	None	-	-	119	0	Manual*	Public	N/A	Compare with
17236	None	-	-	26	0	Manual	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
17268	None	-	-	19	0	Manual	Public	N/A	Compare with
17421	None	-	-	21	0	Manual	Public	N/A	Compare with
17453	None	-	-	28	0	Manual	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
17185	None	-	-	15	0	Manual	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17370	None	-	-	18	-1	Manual	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
1732	None	-	-	73	0	Manual*	Public	N/A	Compare with
17287	None	-	-	17	0	Manual	Public	N/A	Compare with
3496	None	-	-	15	0	Manual*	Public	N/A	Compare with
17319	None	-	-	24	0	Manual	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
17302	None	-	-	25	0	Manual	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
17487	None	-	-	21	0	Manual	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
172	None	-	-	14	0	Manual*	Public	N/A	Compare with
17168	None	-	-	27	0	Manual	Public	N/A	Compare with
575	None	-	-	20	0	Manual*	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
1558	None	-	-	137	0	Manual*	Public	N/A	Compare with
17234	None	-	-	26	0	Manual	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
17419	None	-	-	21	0	Manual	Public	N/A	Compare with
17451	None	-	-	23	0	Manual	Public	N/A	Compare with
212	None	-	-	17	0	Manual*	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17400	None	-	-	21	0	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
1680	None	-	-	30	0	Manual*	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17285	None	-	-	17	0	Manual	Public	N/A	Compare with
3487	None	-	-	12	0	Manual*	Public	N/A	Compare with
17317	None	-	-	24	0	Manual	Public	N/A	Compare with
17470	None	-	-	24	0	Manual	Public	N/A	Compare with
17351	None	-	-	15	0	Manual	Public	N/A	Compare with
17383	None	-	-	23	0	Manual	Public	N/A	Compare with
17536	None	-	-	24	0	Manual	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
17300	None	-	-	18	0	Manual	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17332	None	-	-	17	-2	Manual	Public	N/A	Compare with
17485	None	-	-	21	0	Manual	Public	N/A	Compare with
17517	None	-	-	28	0	Manual	Public	N/A	Compare with
1578	None	-	-	144	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
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
17434	None	-	-	21	-1	Manual	Public	N/A	Compare with
170	None	-	-	14	0	Manual*	Public	N/A	Compare with
17166	None	-	-	27	0	Manual	Public	N/A	Compare with
573	None	-	-	20	0	Manual*	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
17232	None	-	-	27	0	Manual	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
17264	None	-	-	17	0	Manual	Public	N/A	Compare with