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)	NME
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	20
Net Charge	0
Forcefield	multiple
Molecule ID	17227
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:15
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
17434	None	-	-	21	-1	Manual	Public	N/A	Compare with
1570	None	-	-	125	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	0	Manual*	Public	N/A	Compare with
17166	None	-	-	27	0	Manual	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
17351	None	-	-	15	0	Manual	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
17383	None	-	-	23	0	Manual	Public	N/A	Compare with
567	None	-	-	10	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
17300	None	-	-	18	0	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
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
3923	None	-	-	4	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
17162	None	-	-	23	0	Manual	Public	N/A	Compare with
17283	None	-	-	23	0	Manual	Public	N/A	Compare with
17315	None	-	-	32	0	Manual	Public	N/A	Compare with
17468	None	-	-	31	0	Manual	Public	N/A	Compare with
17500	None	-	-	25	0	Manual	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
17232	None	-	-	27	0	Manual	Public	N/A	Compare with
17264	None	-	-	17	0	Manual	Public	N/A	Compare with
17417	None	-	-	21	0	Manual	Public	N/A	Compare with
17449	None	-	-	23	0	Manual	Public	N/A	Compare with
1550	None	-	-	24	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	0	Manual*	Public	N/A	Compare with
17181	None	-	-	23	0	Manual	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
17366	None	-	-	29	0	Manual	Public	N/A	Compare with
203	None	-	-	22	0	Manual*	Public	N/A	Compare with
17398	None	-	-	21	0	Manual	Public	N/A	Compare with
17519	None	-	-	28	0	Manual	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
17551	None	-	-	15	-1	Manual	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
1566	None	-	-	129	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
565	None	-	-	9	0	Manual*	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
5011	None	-	-	40	-4	Manual*	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
17298	None	-	-	18	0	Manual	Public	N/A	Compare with
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
2002	None	-	-	24	0	Manual*	Public	N/A	Compare with
3505	None	-	-	18	0	Manual*	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
1547	None	-	-	24	0	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
581	None	-	-	16	0	Manual*	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
6252	None	-	-	89	0	Manual*	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with
17194	None	-	-	28	0	Manual	Public	N/A	Compare with
17347	None	-	-	20	-2	Manual	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
4604	None	-	-	217	0	Manual*	Public	N/A	Compare with
9411	None	-	-	17	-2	Manual*	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
17328	None	-	-	25	0	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
1738	None	-	-	77	0	Manual*	Public	N/A	Compare with
3502	None	-	-	19	0	Manual*	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
1564	None	-	-	143	0	Manual*	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with