MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

Click table to toggle details.

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)	L5H
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	23
Net Charge	0
Forcefield	multiple
Molecule ID	17162
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 (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 >
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
18675	None	-	-	140	-3	Manual	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18623	None	-	-	139	-3	Manual	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18620	None	-	-	49	-3	Manual	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
17552	None	-	-	15	-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
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
17548	None	-	-	26	1	Manual	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
17546	None	-	-	26	1	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with
17544	None	-	-	29	0	Manual	Public	N/A	Compare with
17543	None	-	-	29	0	Manual	Public	N/A	Compare with
17542	None	-	-	29	0	Manual	Public	N/A	Compare with
17541	None	-	-	29	0	Manual	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
17537	None	-	-	19	-2	Manual	Public	N/A	Compare with
17536	None	-	-	24	0	Manual	Public	N/A	Compare with
17535	None	-	-	24	0	Manual	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
17533	None	-	-	24	0	Manual	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
17531	None	-	-	18	0	Manual	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
17529	None	-	-	18	0	Manual	Public	N/A	Compare with
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
17527	None	-	-	18	0	Manual	Public	N/A	Compare with
17526	None	-	-	18	0	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
17519	None	-	-	28	0	Manual	Public	N/A	Compare with
17518	None	-	-	28	0	Manual	Public	N/A	Compare with
17517	None	-	-	28	0	Manual	Public	N/A	Compare with
17516	None	-	-	26	0	Manual	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
17514	None	-	-	26	0	Manual	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
17512	None	-	-	27	0	Manual	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
17509	None	-	-	27	0	Manual	Public	N/A	Compare with
17508	None	-	-	29	0	Manual	Public	N/A	Compare with
17507	None	-	-	29	0	Manual	Public	N/A	Compare with
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	Manual	Public	N/A	Compare with
17504	None	-	-	32	0	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
17500	None	-	-	25	0	Manual	Public	N/A	Compare with
17499	None	-	-	25	0	Manual	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
17497	None	-	-	25	0	Manual	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
17492	None	-	-	22	0	Manual	Public	N/A	Compare with
17491	None	-	-	22	0	Manual	Public	N/A	Compare with
17490	None	-	-	22	0	Manual	Public	N/A	Compare with
17489	None	-	-	22	0	Manual	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
17487	None	-	-	21	0	Manual	Public	N/A	Compare with
17486	None	-	-	21	0	Manual	Public	N/A	Compare with
17485	None	-	-	21	0	Manual	Public	N/A	Compare with
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
17482	None	-	-	15	0	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17480	None	-	-	27	-1	Manual	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
17478	None	-	-	27	-1	Manual	Public	N/A	Compare with
17477	None	-	-	27	-1	Manual	Public	N/A	Compare with
17476	None	-	-	23	0	Manual	Public	N/A	Compare with
17475	None	-	-	23	0	Manual	Public	N/A	Compare with
17474	None	-	-	23	0	Manual	Public	N/A	Compare with
17473	None	-	-	23	0	Manual	Public	N/A	Compare with
17472	None	-	-	24	0	Manual	Public	N/A	Compare with
17471	None	-	-	24	0	Manual	Public	N/A	Compare with
17470	None	-	-	24	0	Manual	Public	N/A	Compare with
17469	None	-	-	24	0	Manual	Public	N/A	Compare with
17468	None	-	-	31	0	Manual	Public	N/A	Compare with
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
17465	None	-	-	31	0	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17462	None	-	-	22	0	Manual	Public	N/A	Compare with