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)	RMA
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	33
Net Charge	1
Forcefield	multiple
Molecule ID	17147
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 12:55:23
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 (201-300 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
17398	None	-	-	21	0	Manual	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
17289	None	-	-	28	0	Manual	Public	N/A	Compare with
17232	None	-	-	27	0	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17231	None	-	-	27	0	Manual	Public	N/A	Compare with
17263	None	-	-	17	0	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17291	None	-	-	28	0	Manual	Public	N/A	Compare with
17264	None	-	-	17	0	Manual	Public	N/A	Compare with
17257	None	-	-	15	-1	Manual	Public	N/A	Compare with
17250	None	-	-	23	-2	Manual	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
17235	None	-	-	26	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17400	None	-	-	21	0	Manual	Public	N/A	Compare with
17391	None	-	-	18	0	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
17351	None	-	-	15	0	Manual	Public	N/A	Compare with
17333	None	-	-	30	1	Manual	Public	N/A	Compare with
17318	None	-	-	24	0	Manual	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
17240	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
17427	None	-	-	34	1	Manual	Public	N/A	Compare with
17425	None	-	-	34	1	Manual	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17421	None	-	-	21	0	Manual	Public	N/A	Compare with
17420	None	-	-	21	0	Manual	Public	N/A	Compare with
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
17417	None	-	-	21	0	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
17412	None	-	-	18	0	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
17272	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
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	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
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17255	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
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
17327	None	-	-	25	0	Manual	Public	N/A	Compare with
17323	None	-	-	18	0	Manual	Public	N/A	Compare with
17320	None	-	-	24	0	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
17312	None	-	-	25	-1	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17308	None	-	-	23	0	Manual	Public	N/A	Compare with
17303	None	-	-	25	0	Manual	Public	N/A	Compare with
17300	None	-	-	18	0	Manual	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17286	None	-	-	17	0	Manual	Public	N/A	Compare with
17283	None	-	-	23	0	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17342	None	-	-	23	-2	Manual	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17367	None	-	-	29	0	Manual	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
17359	None	-	-	30	0	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
17276	None	-	-	24	-1	Manual	Public	N/A	Compare with