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)	DMA
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	19
Net Charge	0
Forcefield	multiple
Molecule ID	17494
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:18
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 (101-200 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
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
212	None	-	-	17	0	Manual*	Public	N/A	Compare with
572	None	-	-	17	0	Manual*	Public	N/A	Compare with
210	None	-	-	17	0	Manual*	Public	N/A	Compare with
17329	None	-	-	17	-2	Manual	Public	N/A	Compare with
574	None	-	-	17	0	Manual*	Public	N/A	Compare with
17332	None	-	-	17	-2	Manual	Public	N/A	Compare with
17261	None	-	-	17	0	Manual	Public	N/A	Compare with
17285	None	-	-	17	0	Manual	Public	N/A	Compare with
17263	None	-	-	17	0	Manual	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17288	None	-	-	17	0	Manual	Public	N/A	Compare with
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
17155	None	-	-	17	0	Manual	Public	N/A	Compare with
17286	None	-	-	17	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
17331	None	-	-	17	-2	Manual	Public	N/A	Compare with
17287	None	-	-	17	0	Manual	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
17264	None	-	-	17	0	Manual	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17526	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
17272	None	-	-	18	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	0	Manual*	Public	N/A	Compare with
3505	None	-	-	18	0	Manual*	Public	N/A	Compare with
17206	None	-	-	18	0	Manual	Public	N/A	Compare with
17323	None	-	-	18	0	Manual	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17531	None	-	-	18	0	Manual	Public	N/A	Compare with
17270	None	-	-	18	0	Manual	Public	N/A	Compare with
17297	None	-	-	18	0	Manual	Public	N/A	Compare with
17412	None	-	-	18	0	Manual	Public	N/A	Compare with
17340	None	-	-	18	0	Manual	Public	N/A	Compare with
17339	None	-	-	18	0	Manual	Public	N/A	Compare with
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
17389	None	-	-	18	0	Manual	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17299	None	-	-	18	0	Manual	Public	N/A	Compare with
17390	None	-	-	18	0	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17208	None	-	-	18	0	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17391	None	-	-	18	0	Manual	Public	N/A	Compare with
17324	None	-	-	18	0	Manual	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
17298	None	-	-	18	0	Manual	Public	N/A	Compare with
17322	None	-	-	18	0	Manual	Public	N/A	Compare with
17321	None	-	-	18	0	Manual	Public	N/A	Compare with
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
17527	None	-	-	18	0	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
17337	None	-	-	18	0	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
17300	None	-	-	18	0	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
17205	None	-	-	18	0	Manual	Public	N/A	Compare with
17370	None	-	-	18	-1	Manual	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
17537	None	-	-	19	-2	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
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
5796	None	-	-	19	0	Manual*	Public	N/A	Compare with
17267	None	-	-	19	0	Manual	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
17265	None	-	-	19	0	Manual	Public	N/A	Compare with
3502	None	-	-	19	0	Manual*	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
2752	None	-	-	19	0	Manual*	Public	N/A	Compare with
17268	None	-	-	19	0	Manual	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17178	None	-	-	20	-1	Manual	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with