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
Residue Name (RNME)	T1P
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	21
Net Charge	-1
Forcefield	multiple
Molecule ID	17521
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:18
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
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
1548	None	-	-	24	0	Manual*	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
1588	None	-	-	125	0	Manual*	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17530	None	-	-	18	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
178	None	-	-	21	1	Manual*	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
3504	None	-	-	15	0	Manual*	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17175	None	-	-	25	0	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
1565	None	-	-	113	0	Manual*	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
564	None	-	-	6	0	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
17462	None	-	-	22	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
1586	None	-	-	149	0	Manual*	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
21025	None	-	-	209	-4	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
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17324	None	-	-	18	0	Manual	Public	N/A	Compare with
17477	None	-	-	27	-1	Manual	Public	N/A	Compare with
17509	None	-	-	27	0	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
2752	None	-	-	19	0	Manual*	Public	N/A	Compare with
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
17458	None	-	-	28	0	Manual	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
1540	None	-	-	143	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
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
1736	None	-	-	80	0	Manual*	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
3501	None	-	-	21	0	Manual*	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17205	None	-	-	18	0	Manual	Public	N/A	Compare with
1563	None	-	-	137	0	Manual*	Public	N/A	Compare with
17358	None	-	-	30	0	Manual	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
17390	None	-	-	18	0	Manual	Public	N/A	Compare with
17543	None	-	-	29	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
216	None	-	-	13	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
17460	None	-	-	28	0	Manual	Public	N/A	Compare with
17492	None	-	-	22	0	Manual	Public	N/A	Compare with
17526	None	-	-	18	0	Manual	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
174	None	-	-	19	-1	Manual*	Public	N/A	Compare with
577	None	-	-	37	0	Manual*	Public	N/A	Compare with
17290	None	-	-	28	0	Manual	Public	N/A	Compare with
17322	None	-	-	18	0	Manual	Public	N/A	Compare with
17475	None	-	-	23	0	Manual	Public	N/A	Compare with
17507	None	-	-	29	0	Manual	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
2747	None	-	-	20	0	Manual*	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17456	None	-	-	28	0	Manual	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
17254	None	-	-	27	0	Manual	Public	N/A	Compare with
1732	None	-	-	73	0	Manual*	Public	N/A	Compare with