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)	L3H
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	23
Net Charge	0
Forcefield	multiple
Molecule ID	17381
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
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
17176	None	-	-	25	0	Manual	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17208	None	-	-	18	0	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
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17310	None	-	-	25	-1	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17412	None	-	-	18	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
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
17242	None	-	-	26	-1	Manual	Public	N/A	Compare with
17274	None	-	-	24	-1	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
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
17191	None	-	-	44	0	Manual	Public	N/A	Compare with
4013	None	-	-	176	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
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
17174	None	-	-	25	0	Manual	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
17206	None	-	-	18	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
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
17155	None	-	-	17	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
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
17257	None	-	-	15	-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
17323	None	-	-	18	0	Manual	Public	N/A	Compare with
17476	None	-	-	23	0	Manual	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
17508	None	-	-	29	0	Manual	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
17272	None	-	-	18	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
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
3924	None	-	-	176	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
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
17291	None	-	-	28	0	Manual	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
17204	None	-	-	33	1	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
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
17491	None	-	-	22	0	Manual	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with