MD Topology | NMR | X-Ray

Visualize with JSmol

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
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	17379
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (401-500 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
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17162	None	-	-	23	0	Manual	Public	N/A	Compare with
17178	None	-	-	20	-1	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
17504	None	-	-	32	0	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	Manual	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
17516	None	-	-	26	0	Manual	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
17487	None	-	-	21	0	Manual	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
17485	None	-	-	21	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
17497	None	-	-	25	0	Manual	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17480	None	-	-	27	-1	Manual	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
1680	None	-	-	30	0	Manual*	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
9411	None	-	-	17	-2	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
6252	None	-	-	89	0	Manual*	Public	N/A	Compare with
212	None	-	-	17	0	Manual*	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
5838	None	-	-	43	-1	Manual*	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
1588	None	-	-	125	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	0	Manual*	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	0	Manual*	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
1506	None	-	-	134	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with