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 building block
Residue Name (RNME)	L3H
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	17384
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
17168	None	-	-	27	0	Manual	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
1557	None	-	-	131	0	Manual*	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17538	None	-	-	19	-2	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
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
17487	None	-	-	21	0	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17400	None	-	-	21	0	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
17285	None	-	-	17	0	Manual	Public	N/A	Compare with
17317	None	-	-	24	0	Manual	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
17470	None	-	-	24	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
17234	None	-	-	26	0	Manual	Public	N/A	Compare with
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
17419	None	-	-	21	0	Manual	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17451	None	-	-	23	0	Manual	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
17249	None	-	-	23	-2	Manual	Public	N/A	Compare with
1677	None	-	-	34	0	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
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17434	None	-	-	21	-1	Manual	Public	N/A	Compare with
17166	None	-	-	27	0	Manual	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
577	None	-	-	37	0	Manual*	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
17351	None	-	-	15	0	Manual	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
17383	None	-	-	23	0	Manual	Public	N/A	Compare with
17536	None	-	-	24	0	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
6871	None	-	-	108	0	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
17398	None	-	-	21	0	Manual	Public	N/A	Compare with
17519	None	-	-	28	0	Manual	Public	N/A	Compare with
17551	None	-	-	15	-1	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
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
17468	None	-	-	31	0	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17500	None	-	-	25	0	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
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
17417	None	-	-	21	0	Manual	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17449	None	-	-	23	0	Manual	Public	N/A	Compare with
17181	None	-	-	23	0	Manual	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
17366	None	-	-	29	0	Manual	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
172	None	-	-	14	0	Manual*	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
575	None	-	-	20	0	Manual*	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17534	None	-	-	24	0	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
6461	None	-	-	15	0	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
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with