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)	RSM
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	32
Net Charge	0
Forcefield	multiple
Molecule ID	17313
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:16
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 (101-200 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
17374	None	-	-	30	-1	Manual	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17312	None	-	-	25	-1	Manual	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17552	None	-	-	15	-1	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17477	None	-	-	27	-1	Manual	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
17434	None	-	-	21	-1	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
17480	None	-	-	27	-1	Manual	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17551	None	-	-	15	-1	Manual	Public	N/A	Compare with
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
6252	None	-	-	89	0	Manual*	Public	N/A	Compare with
6451	None	-	-	27	0	Manual	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
1506	None	-	-	134	0	Manual*	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with