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)	N3H
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	0
Forcefield	multiple
Molecule ID	17391
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
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
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
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
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
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
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
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
17158	None	-	-	20	0	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	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
2749	None	-	-	14	0	Manual*	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
1539	None	-	-	137	0	Manual*	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
1562	None	-	-	125	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	0	Manual*	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
17462	None	-	-	22	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with