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)	H31
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	24
Net Charge	-1
Forcefield	multiple
Molecule ID	17394
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:17
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 (601-633 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 >
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
565	None	-	-	9	0	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
212	None	-	-	17	0	Manual*	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
210	None	-	-	17	0	Manual*	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
207	None	-	-	20	0	Manual*	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
205	None	-	-	24	0	Manual*	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
203	None	-	-	22	0	Manual*	Public	N/A	Compare with
178	None	-	-	21	1	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
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
172	None	-	-	14	0	Manual*	Public	N/A	Compare with
171	None	-	-	14	0	Manual*	Public	N/A	Compare with
170	None	-	-	14	0	Manual*	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
163	None	-	-	13	0	Manual*	Public	N/A	Compare with