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)	Y1P
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	28
Net Charge	-1
Forcefield	multiple
Molecule ID	17378
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:17
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 (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
17298	None	-	-	18	0	Manual	Public	N/A	Compare with
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
571	None	-	-	14	0	Manual*	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
207	None	-	-	20	0	Manual*	Public	N/A	Compare with
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
17328	None	-	-	25	0	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
2172	None	-	-	26	-1	Manual*	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
17194	None	-	-	28	0	Manual	Public	N/A	Compare with
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
17347	None	-	-	20	-2	Manual	Public	N/A	Compare with
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
205	None	-	-	24	0	Manual*	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
3409	None	-	-	27	0	Manual*	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
1552	None	-	-	149	0	Manual*	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	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
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
567	None	-	-	10	0	Manual*	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
203	None	-	-	22	0	Manual*	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with