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)	P5H
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	17322
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:16
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
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-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
17176	None	-	-	25	0	Manual	Public	N/A	Compare with
2172	None	-	-	26	-1	Manual*	Public	N/A	Compare with
17208	None	-	-	18	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
17361	None	-	-	12	0	Manual	Public	N/A	Compare with
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
17546	None	-	-	26	1	Manual	Public	N/A	Compare with
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
17310	None	-	-	25	-1	Manual	Public	N/A	Compare with
17191	None	-	-	44	0	Manual	Public	N/A	Compare with
3409	None	-	-	27	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
17529	None	-	-	18	0	Manual	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
1552	None	-	-	149	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	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
205	None	-	-	24	0	Manual*	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	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
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
567	None	-	-	10	0	Manual*	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
17257	None	-	-	15	-1	Manual	Public	N/A	Compare with
17147	None	-	-	33	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
17174	None	-	-	25	0	Manual	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
17206	None	-	-	18	0	Manual	Public	N/A	Compare with
3923	None	-	-	4	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
17544	None	-	-	29	0	Manual	Public	N/A	Compare with
1570	None	-	-	125	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	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
17221	None	-	-	22	0	Manual	Public	N/A	Compare with
17342	None	-	-	23	-2	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
18675	None	-	-	140	-3	Manual	Public	N/A	Compare with
1550	None	-	-	24	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	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
17508	None	-	-	29	0	Manual	Public	N/A	Compare with
203	None	-	-	22	0	Manual*	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
17272	None	-	-	18	0	Manual	Public	N/A	Compare with
17162	None	-	-	23	0	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
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
565	None	-	-	9	0	Manual*	Public	N/A	Compare with
5011	None	-	-	40	-4	Manual*	Public	N/A	Compare with
17255	None	-	-	27	0	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	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
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
2002	None	-	-	24	0	Manual*	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
3505	None	-	-	18	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
17542	None	-	-	29	0	Manual	Public	N/A	Compare with
1566	None	-	-	129	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with