MD Topology | NMR | X-Ray

Visualize with JSmol

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
Residue Name (RNME)	QME
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	17283
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:16
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
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4908	None	-	-	40	-4	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
5011	None	-	-	40	-4	Manual*	Public	N/A	Compare with
18675	None	-	-	140	-3	Manual	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18623	None	-	-	139	-3	Manual	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18620	None	-	-	49	-3	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17331	None	-	-	17	-2	Manual	Public	N/A	Compare with
17332	None	-	-	17	-2	Manual	Public	N/A	Compare with
17252	None	-	-	23	-2	Manual	Public	N/A	Compare with
17342	None	-	-	23	-2	Manual	Public	N/A	Compare with
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
17250	None	-	-	23	-2	Manual	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17343	None	-	-	23	-2	Manual	Public	N/A	Compare with
17246	None	-	-	27	-2	Manual	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
9411	None	-	-	17	-2	Manual*	Public	N/A	Compare with
17386	None	-	-	20	-2	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17347	None	-	-	20	-2	Manual	Public	N/A	Compare with
17212	None	-	-	27	-2	Manual	Public	N/A	Compare with
17249	None	-	-	23	-2	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17537	None	-	-	19	-2	Manual	Public	N/A	Compare with
17344	None	-	-	23	-2	Manual	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
17346	None	-	-	20	-2	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
17329	None	-	-	17	-2	Manual	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
17210	None	-	-	27	-2	Manual	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
17180	None	-	-	20	-1	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17238	None	-	-	16	-1	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
17310	None	-	-	25	-1	Manual	Public	N/A	Compare with
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17276	None	-	-	24	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
17370	None	-	-	18	-1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17374	None	-	-	30	-1	Manual	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17178	None	-	-	20	-1	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17312	None	-	-	25	-1	Manual	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with