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
Residue Name (RNME)	SDH
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	12
Net Charge	0
Forcefield	multiple
Molecule ID	17361
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 (1-100 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
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
17255	None	-	-	27	0	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17357	None	-	-	30	0	Manual	Public	N/A	Compare with
17389	None	-	-	18	0	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
17289	None	-	-	28	0	Manual	Public	N/A	Compare with
17321	None	-	-	18	0	Manual	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
17238	None	-	-	16	-1	Manual	Public	N/A	Compare with
17270	None	-	-	18	0	Manual	Public	N/A	Compare with
17423	None	-	-	21	0	Manual	Public	N/A	Compare with
17455	None	-	-	28	0	Manual	Public	N/A	Compare with
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
17187	None	-	-	15	0	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
17513	None	-	-	26	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
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
17170	None	-	-	28	0	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	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
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
17287	None	-	-	17	0	Manual	Public	N/A	Compare with
17319	None	-	-	24	0	Manual	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
17236	None	-	-	26	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
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
17185	None	-	-	15	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
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
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
17168	None	-	-	27	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
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17302	None	-	-	25	0	Manual	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
2172	None	-	-	26	-1	Manual*	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	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