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)	PH5
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	0
Forcefield	multiple
Molecule ID	17272
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:15
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 (101-200 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 >
17461	None	-	-	22	0	Manual	Public	N/A	Compare with
17460	None	-	-	28	0	Manual	Public	N/A	Compare with
17459	None	-	-	28	0	Manual	Public	N/A	Compare with
17458	None	-	-	28	0	Manual	Public	N/A	Compare with
17457	None	-	-	28	0	Manual	Public	N/A	Compare with
17456	None	-	-	28	0	Manual	Public	N/A	Compare with
17455	None	-	-	28	0	Manual	Public	N/A	Compare with
17454	None	-	-	28	0	Manual	Public	N/A	Compare with
17453	None	-	-	28	0	Manual	Public	N/A	Compare with
17452	None	-	-	23	0	Manual	Public	N/A	Compare with
17451	None	-	-	23	0	Manual	Public	N/A	Compare with
17450	None	-	-	23	0	Manual	Public	N/A	Compare with
17449	None	-	-	23	0	Manual	Public	N/A	Compare with
17448	None	-	-	28	0	Manual	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
17439	None	-	-	25	0	Manual	Public	N/A	Compare with
17438	None	-	-	25	0	Manual	Public	N/A	Compare with
17437	None	-	-	25	0	Manual	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
17434	None	-	-	21	-1	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
17431	None	-	-	15	0	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
17429	None	-	-	15	0	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17427	None	-	-	34	1	Manual	Public	N/A	Compare with
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
17425	None	-	-	34	1	Manual	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17423	None	-	-	21	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17421	None	-	-	21	0	Manual	Public	N/A	Compare with
17420	None	-	-	21	0	Manual	Public	N/A	Compare with
17419	None	-	-	21	0	Manual	Public	N/A	Compare with
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
17417	None	-	-	21	0	Manual	Public	N/A	Compare with
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
17412	None	-	-	18	0	Manual	Public	N/A	Compare with
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17400	None	-	-	21	0	Manual	Public	N/A	Compare with
17399	None	-	-	21	0	Manual	Public	N/A	Compare with
17398	None	-	-	21	0	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
17391	None	-	-	18	0	Manual	Public	N/A	Compare with
17390	None	-	-	18	0	Manual	Public	N/A	Compare with
17389	None	-	-	18	0	Manual	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
17386	None	-	-	20	-2	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17384	None	-	-	23	0	Manual	Public	N/A	Compare with
17383	None	-	-	23	0	Manual	Public	N/A	Compare with
17382	None	-	-	23	0	Manual	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17376	None	-	-	30	-1	Manual	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
17374	None	-	-	30	-1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
17370	None	-	-	18	-1	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17367	None	-	-	29	0	Manual	Public	N/A	Compare with
17366	None	-	-	29	0	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with