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)	H12
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	23
Net Charge	-2
Forcefield	multiple
Molecule ID	17252
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 (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
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
18620	None	-	-	49	-3	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	0	Manual*	Public	N/A	Compare with
17471	None	-	-	24	0	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17537	None	-	-	19	-2	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17486	None	-	-	21	0	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
17518	None	-	-	28	0	Manual	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
17175	None	-	-	25	0	Manual	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
576	None	-	-	26	0	Manual*	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
1560	None	-	-	123	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
17450	None	-	-	23	0	Manual	Public	N/A	Compare with
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
1511	None	-	-	131	0	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
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17552	None	-	-	15	-1	Manual	Public	N/A	Compare with
17324	None	-	-	18	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
17469	None	-	-	24	0	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17535	None	-	-	24	0	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
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
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17516	None	-	-	26	0	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
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	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
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
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
17448	None	-	-	28	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
1507	None	-	-	138	0	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
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
17322	None	-	-	18	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
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17499	None	-	-	25	0	Manual	Public	N/A	Compare with
17271	None	-	-	18	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
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with