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)	TDH
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	15
Net Charge	0
Forcefield	multiple
Molecule ID	17352
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:16
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 (1-100 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
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
17548	None	-	-	26	1	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
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
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
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
1540	None	-	-	143	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
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
176	None	-	-	20	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
17429	None	-	-	15	0	Manual	Public	N/A	Compare with
1563	None	-	-	137	0	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
17346	None	-	-	20	-2	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
17531	None	-	-	18	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
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17327	None	-	-	25	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
1736	None	-	-	80	0	Manual*	Public	N/A	Compare with
3501	None	-	-	21	0	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17310	None	-	-	25	-1	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
2747	None	-	-	20	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
17412	None	-	-	18	0	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
17176	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
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
577	None	-	-	37	0	Manual*	Public	N/A	Compare with
17546	None	-	-	26	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
1561	None	-	-	119	0	Manual*	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
17191	None	-	-	44	0	Manual	Public	N/A	Compare with
17223	None	-	-	22	0	Manual	Public	N/A	Compare with
17344	None	-	-	23	-2	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
17529	None	-	-	18	0	Manual	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17325	None	-	-	25	0	Manual	Public	N/A	Compare with
17478	None	-	-	27	-1	Manual	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
1732	None	-	-	73	0	Manual*	Public	N/A	Compare with
3496	None	-	-	15	0	Manual*	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17155	None	-	-	17	0	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
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
17257	None	-	-	15	-1	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
17174	None	-	-	25	0	Manual	Public	N/A	Compare with
17206	None	-	-	18	0	Manual	Public	N/A	Compare with
17359	None	-	-	30	0	Manual	Public	N/A	Compare with
172	None	-	-	14	0	Manual*	Public	N/A	Compare with
17391	None	-	-	18	0	Manual	Public	N/A	Compare with
575	None	-	-	20	0	Manual*	Public	N/A	Compare with
17544	None	-	-	29	0	Manual	Public	N/A	Compare with
17457	None	-	-	28	0	Manual	Public	N/A	Compare with