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 (601-633 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
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17454	None	-	-	28	0	Manual	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
17437	None	-	-	25	0	Manual	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17354	None	-	-	23	0	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
17386	None	-	-	20	-2	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17303	None	-	-	25	0	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17252	None	-	-	23	-2	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with