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	17294
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
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
4604	None	-	-	217	0	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
1586	None	-	-	149	0	Manual*	Public	N/A	Compare with
1552	None	-	-	149	0	Manual*	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
1564	None	-	-	143	0	Manual*	Public	N/A	Compare with
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
1540	None	-	-	143	0	Manual*	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
18675	None	-	-	140	-3	Manual	Public	N/A	Compare with
18623	None	-	-	139	-3	Manual	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
1558	None	-	-	137	0	Manual*	Public	N/A	Compare with
1563	None	-	-	137	0	Manual*	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with
1539	None	-	-	137	0	Manual*	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
1506	None	-	-	134	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	0	Manual*	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
1557	None	-	-	131	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
1566	None	-	-	129	0	Manual*	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
1588	None	-	-	125	0	Manual*	Public	N/A	Compare with
1570	None	-	-	125	0	Manual*	Public	N/A	Compare with
1562	None	-	-	125	0	Manual*	Public	N/A	Compare with
1560	None	-	-	123	0	Manual*	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
1561	None	-	-	119	0	Manual*	Public	N/A	Compare with
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
1565	None	-	-	113	0	Manual*	Public	N/A	Compare with
4603	None	-	-	113	0	Manual*	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with
6252	None	-	-	89	0	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
1736	None	-	-	80	0	Manual*	Public	N/A	Compare with
5031	None	-	-	78	0	Manual*	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
1738	None	-	-	77	0	Manual*	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
1731	None	-	-	74	0	Manual*	Public	N/A	Compare with
1732	None	-	-	73	0	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with