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)	KPH
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	26
Net Charge	1
Forcefield	multiple
Molecule ID	17547
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:19
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
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
17299	None	-	-	18	0	Manual	Public	N/A	Compare with
17331	None	-	-	17	-2	Manual	Public	N/A	Compare with
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
17516	None	-	-	26	0	Manual	Public	N/A	Compare with
2749	None	-	-	14	0	Manual*	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
1539	None	-	-	137	0	Manual*	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
17350	None	-	-	15	0	Manual	Public	N/A	Compare with
17382	None	-	-	23	0	Manual	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
17535	None	-	-	24	0	Manual	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
17158	None	-	-	20	0	Manual	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
17180	None	-	-	20	-1	Manual	Public	N/A	Compare with
17212	None	-	-	27	-2	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17499	None	-	-	25	0	Manual	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	0	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
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17448	None	-	-	28	0	Manual	Public	N/A	Compare with
1562	None	-	-	125	0	Manual*	Public	N/A	Compare with
17329	None	-	-	17	-2	Manual	Public	N/A	Compare with
17482	None	-	-	15	0	Manual	Public	N/A	Compare with
17514	None	-	-	26	0	Manual	Public	N/A	Compare with
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17246	None	-	-	27	-2	Manual	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
17431	None	-	-	15	0	Manual	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
17195	None	-	-	28	0	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
17533	None	-	-	24	0	Manual	Public	N/A	Compare with
576	None	-	-	26	0	Manual*	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17297	None	-	-	18	0	Manual	Public	N/A	Compare with
17178	None	-	-	20	-1	Manual	Public	N/A	Compare with
17210	None	-	-	27	-2	Manual	Public	N/A	Compare with
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
17548	None	-	-	26	1	Manual	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
17312	None	-	-	25	-1	Manual	Public	N/A	Compare with
17465	None	-	-	31	0	Manual	Public	N/A	Compare with
17497	None	-	-	25	0	Manual	Public	N/A	Compare with
1731	None	-	-	74	0	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
17229	None	-	-	27	0	Manual	Public	N/A	Compare with
17261	None	-	-	17	0	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
1560	None	-	-	123	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
17480	None	-	-	27	-1	Manual	Public	N/A	Compare with
17512	None	-	-	27	0	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17276	None	-	-	24	-1	Manual	Public	N/A	Compare with
17429	None	-	-	15	0	Manual	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
17193	None	-	-	28	0	Manual	Public	N/A	Compare with
17346	None	-	-	20	-2	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
171	None	-	-	14	0	Manual*	Public	N/A	Compare with
17531	None	-	-	18	0	Manual	Public	N/A	Compare with
574	None	-	-	17	0	Manual*	Public	N/A	Compare with
5796	None	-	-	19	0	Manual*	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17327	None	-	-	25	0	Manual	Public	N/A	Compare with
17208	None	-	-	18	0	Manual	Public	N/A	Compare with
17361	None	-	-	12	0	Manual	Public	N/A	Compare with