MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

Click table to toggle details.

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)	PYA
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	9
Net Charge	-1
Forcefield	multiple
Molecule ID	17296
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 (201-300 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
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17343	None	-	-	23	-2	Manual	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17324	None	-	-	18	0	Manual	Public	N/A	Compare with
17477	None	-	-	27	-1	Manual	Public	N/A	Compare with
17509	None	-	-	27	0	Manual	Public	N/A	Compare with
1731	None	-	-	74	0	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
17307	None	-	-	23	0	Manual	Public	N/A	Compare with
17339	None	-	-	18	0	Manual	Public	N/A	Compare with
17460	None	-	-	28	0	Manual	Public	N/A	Compare with
17492	None	-	-	22	0	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17205	None	-	-	18	0	Manual	Public	N/A	Compare with
17358	None	-	-	30	0	Manual	Public	N/A	Compare with
171	None	-	-	14	0	Manual*	Public	N/A	Compare with
17390	None	-	-	18	0	Manual	Public	N/A	Compare with
574	None	-	-	17	0	Manual*	Public	N/A	Compare with
17543	None	-	-	29	0	Manual	Public	N/A	Compare with
5796	None	-	-	19	0	Manual*	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
17526	None	-	-	18	0	Manual	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
17290	None	-	-	28	0	Manual	Public	N/A	Compare with
17322	None	-	-	18	0	Manual	Public	N/A	Compare with
17475	None	-	-	23	0	Manual	Public	N/A	Compare with
17507	None	-	-	29	0	Manual	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17456	None	-	-	28	0	Manual	Public	N/A	Compare with
1557	None	-	-	131	0	Manual*	Public	N/A	Compare with
17337	None	-	-	18	0	Manual	Public	N/A	Compare with
17490	None	-	-	22	0	Manual	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17254	None	-	-	27	0	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17439	None	-	-	25	0	Manual	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
17171	None	-	-	28	0	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17356	None	-	-	23	0	Manual	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
572	None	-	-	17	0	Manual*	Public	N/A	Compare with
17541	None	-	-	29	0	Manual	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17305	None	-	-	23	0	Manual	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
17288	None	-	-	17	0	Manual	Public	N/A	Compare with
17320	None	-	-	24	0	Manual	Public	N/A	Compare with
17473	None	-	-	23	0	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	Manual	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17454	None	-	-	28	0	Manual	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with