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)	KAL
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	21
Net Charge	0
Forcefield	multiple
Molecule ID	17424
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 (301-400 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
17437	None	-	-	25	0	Manual	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
581	None	-	-	16	0	Manual*	Public	N/A	Compare with
1558	None	-	-	137	0	Manual*	Public	N/A	Compare with
17354	None	-	-	23	0	Manual	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
17386	None	-	-	20	-2	Manual	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
17303	None	-	-	25	0	Manual	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
18620	None	-	-	49	-3	Manual	Public	N/A	Compare with
17286	None	-	-	17	0	Manual	Public	N/A	Compare with
17318	None	-	-	24	0	Manual	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17471	None	-	-	24	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
17235	None	-	-	26	0	Manual	Public	N/A	Compare with
17267	None	-	-	19	0	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
17420	None	-	-	21	0	Manual	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17452	None	-	-	23	0	Manual	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17250	None	-	-	23	-2	Manual	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
17282	None	-	-	23	0	Manual	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
17352	None	-	-	15	0	Manual	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
17384	None	-	-	23	0	Manual	Public	N/A	Compare with
17537	None	-	-	19	-2	Manual	Public	N/A	Compare with
17301	None	-	-	25	0	Manual	Public	N/A	Compare with
17333	None	-	-	30	1	Manual	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
17486	None	-	-	21	0	Manual	Public	N/A	Compare with
17518	None	-	-	28	0	Manual	Public	N/A	Compare with
17399	None	-	-	21	0	Manual	Public	N/A	Compare with
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
17552	None	-	-	15	-1	Manual	Public	N/A	Compare with
17284	None	-	-	23	0	Manual	Public	N/A	Compare with
17316	None	-	-	32	0	Manual	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
17469	None	-	-	24	0	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
17233	None	-	-	26	0	Manual	Public	N/A	Compare with
17265	None	-	-	19	0	Manual	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
17450	None	-	-	23	0	Manual	Public	N/A	Compare with
17182	None	-	-	23	0	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
17214	None	-	-	29	0	Manual	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
17367	None	-	-	29	0	Manual	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
1668	None	-	-	27	0	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
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
576	None	-	-	26	0	Manual*	Public	N/A	Compare with
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
17350	None	-	-	15	0	Manual	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
17382	None	-	-	23	0	Manual	Public	N/A	Compare with
17535	None	-	-	24	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
6870	None	-	-	24	0	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
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17499	None	-	-	25	0	Manual	Public	N/A	Compare with