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)	PH5
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	0
Forcefield	multiple
Molecule ID	17270
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:15
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
17478	None	-	-	27	-1	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
5031	None	-	-	78	0	Manual*	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17427	None	-	-	34	1	Manual	Public	N/A	Compare with
17459	None	-	-	28	0	Manual	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17344	None	-	-	23	-2	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17529	None	-	-	18	0	Manual	Public	N/A	Compare with
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	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
17359	None	-	-	30	0	Manual	Public	N/A	Compare with
17391	None	-	-	18	0	Manual	Public	N/A	Compare with
1548	None	-	-	24	0	Manual*	Public	N/A	Compare with
17544	None	-	-	29	0	Manual	Public	N/A	Compare with
1588	None	-	-	125	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
17308	None	-	-	23	0	Manual	Public	N/A	Compare with
17340	None	-	-	18	0	Manual	Public	N/A	Compare with
17461	None	-	-	22	0	Manual	Public	N/A	Compare with
178	None	-	-	21	1	Manual*	Public	N/A	Compare with
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
6451	None	-	-	27	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17291	None	-	-	28	0	Manual	Public	N/A	Compare with
17323	None	-	-	18	0	Manual	Public	N/A	Compare with
17476	None	-	-	23	0	Manual	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
17508	None	-	-	29	0	Manual	Public	N/A	Compare with
4908	None	-	-	40	-4	Manual*	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17425	None	-	-	34	1	Manual	Public	N/A	Compare with
17457	None	-	-	28	0	Manual	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
3504	None	-	-	15	0	Manual*	Public	N/A	Compare with
17246	None	-	-	27	-2	Manual	Public	N/A	Compare with
17342	None	-	-	23	-2	Manual	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
17374	None	-	-	30	-1	Manual	Public	N/A	Compare with
17527	None	-	-	18	0	Manual	Public	N/A	Compare with
1565	None	-	-	113	0	Manual*	Public	N/A	Compare with
18675	None	-	-	140	-3	Manual	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
17195	None	-	-	28	0	Manual	Public	N/A	Compare with
2752	None	-	-	19	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
17357	None	-	-	30	0	Manual	Public	N/A	Compare with
17389	None	-	-	18	0	Manual	Public	N/A	Compare with
1540	None	-	-	143	0	Manual*	Public	N/A	Compare with
17542	None	-	-	29	0	Manual	Public	N/A	Compare with
1586	None	-	-	149	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
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
17491	None	-	-	22	0	Manual	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
5838	None	-	-	43	-1	Manual*	Public	N/A	Compare with
17159	None	-	-	20	0	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
17321	None	-	-	18	0	Manual	Public	N/A	Compare with
17474	None	-	-	23	0	Manual	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
4603	None	-	-	113	0	Manual*	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
17423	None	-	-	21	0	Manual	Public	N/A	Compare with
17455	None	-	-	28	0	Manual	Public	N/A	Compare with
1736	None	-	-	80	0	Manual*	Public	N/A	Compare with
3501	None	-	-	21	0	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
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
1563	None	-	-	137	0	Manual*	Public	N/A	Compare with
18623	None	-	-	139	-3	Manual	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
17193	None	-	-	28	0	Manual	Public	N/A	Compare with
17289	None	-	-	28	0	Manual	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with