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)	P3H
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	17207
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (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
178	None	-	-	21	1	Manual*	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
17550	None	-	-	15	-1	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
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
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
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17448	None	-	-	28	0	Manual	Public	N/A	Compare with
1548	None	-	-	24	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
17365	None	-	-	29	0	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
1565	None	-	-	113	0	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
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
17533	None	-	-	24	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
17297	None	-	-	18	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
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
3504	None	-	-	15	0	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
17395	None	-	-	24	-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
17244	None	-	-	26	-1	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