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)	WBR
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	27
Net Charge	0
Forcefield	multiple
Molecule ID	17256
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:15
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 (401-500 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
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17166	None	-	-	27	0	Manual	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17163	None	-	-	23	0	Manual	Public	N/A	Compare with
17162	None	-	-	23	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
17159	None	-	-	20	0	Manual	Public	N/A	Compare with
17158	None	-	-	20	0	Manual	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17155	None	-	-	17	0	Manual	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
17257	None	-	-	15	-1	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17255	None	-	-	27	0	Manual	Public	N/A	Compare with
17254	None	-	-	27	0	Manual	Public	N/A	Compare with
17253	None	-	-	27	0	Manual	Public	N/A	Compare with
17252	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
17249	None	-	-	23	-2	Manual	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17246	None	-	-	27	-2	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17261	None	-	-	17	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
17263	None	-	-	17	0	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
17277	None	-	-	24	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
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17272	None	-	-	18	0	Manual	Public	N/A	Compare with
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
17270	None	-	-	18	0	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17268	None	-	-	19	0	Manual	Public	N/A	Compare with
17267	None	-	-	19	0	Manual	Public	N/A	Compare with
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
17265	None	-	-	19	0	Manual	Public	N/A	Compare with
17264	None	-	-	17	0	Manual	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17223	None	-	-	22	0	Manual	Public	N/A	Compare with
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17221	None	-	-	22	0	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
17214	None	-	-	29	0	Manual	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
17212	None	-	-	27	-2	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
17210	None	-	-	27	-2	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17208	None	-	-	18	0	Manual	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17238	None	-	-	16	-1	Manual	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17236	None	-	-	26	0	Manual	Public	N/A	Compare with
17235	None	-	-	26	0	Manual	Public	N/A	Compare with
17234	None	-	-	26	0	Manual	Public	N/A	Compare with
17233	None	-	-	26	0	Manual	Public	N/A	Compare with
17232	None	-	-	27	0	Manual	Public	N/A	Compare with
17231	None	-	-	27	0	Manual	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
17229	None	-	-	27	0	Manual	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with