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	17396
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (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
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
17191	None	-	-	44	0	Manual	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
5838	None	-	-	43	-1	Manual*	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
5011	None	-	-	40	-4	Manual*	Public	N/A	Compare with
4908	None	-	-	40	-4	Manual*	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
577	None	-	-	37	0	Manual*	Public	N/A	Compare with
1678	None	-	-	35	0	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
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
17315	None	-	-	32	0	Manual	Public	N/A	Compare with
17316	None	-	-	32	0	Manual	Public	N/A	Compare with
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
17504	None	-	-	32	0	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17465	None	-	-	31	0	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
17468	None	-	-	31	0	Manual	Public	N/A	Compare with
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17374	None	-	-	30	-1	Manual	Public	N/A	Compare with
17336	None	-	-	30	1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
17333	None	-	-	30	1	Manual	Public	N/A	Compare with
17358	None	-	-	30	0	Manual	Public	N/A	Compare with
1680	None	-	-	30	0	Manual*	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
17357	None	-	-	30	0	Manual	Public	N/A	Compare with
17359	None	-	-	30	0	Manual	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
17507	None	-	-	29	0	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	Manual	Public	N/A	Compare with
17543	None	-	-	29	0	Manual	Public	N/A	Compare with
17544	None	-	-	29	0	Manual	Public	N/A	Compare with
17542	None	-	-	29	0	Manual	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
17366	None	-	-	29	0	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17541	None	-	-	29	0	Manual	Public	N/A	Compare with
17508	None	-	-	29	0	Manual	Public	N/A	Compare with
17367	None	-	-	29	0	Manual	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17214	None	-	-	29	0	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17291	None	-	-	28	0	Manual	Public	N/A	Compare with
17195	None	-	-	28	0	Manual	Public	N/A	Compare with
17290	None	-	-	28	0	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17193	None	-	-	28	0	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
17171	None	-	-	28	0	Manual	Public	N/A	Compare with
17518	None	-	-	28	0	Manual	Public	N/A	Compare with
17517	None	-	-	28	0	Manual	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
17170	None	-	-	28	0	Manual	Public	N/A	Compare with
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
17194	None	-	-	28	0	Manual	Public	N/A	Compare with
17460	None	-	-	28	0	Manual	Public	N/A	Compare with
17289	None	-	-	28	0	Manual	Public	N/A	Compare with