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)	L5H
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	17162
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:14
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 >
6451	None	-	-	27	0	Manual	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
6461	None	-	-	15	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
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
9411	None	-	-	17	-2	Manual*	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17155	None	-	-	17	0	Manual	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17158	None	-	-	20	0	Manual	Public	N/A	Compare with
17159	None	-	-	20	0	Manual	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17162	None	-	-	23	0	Manual	Public	N/A	Compare with
17163	None	-	-	23	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17166	None	-	-	27	0	Manual	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
17168	None	-	-	27	0	Manual	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
17170	None	-	-	28	0	Manual	Public	N/A	Compare with
17171	None	-	-	28	0	Manual	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17174	None	-	-	25	0	Manual	Public	N/A	Compare with
17175	None	-	-	25	0	Manual	Public	N/A	Compare with
17176	None	-	-	25	0	Manual	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17178	None	-	-	20	-1	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17180	None	-	-	20	-1	Manual	Public	N/A	Compare with
17181	None	-	-	23	0	Manual	Public	N/A	Compare with
17182	None	-	-	23	0	Manual	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
17185	None	-	-	15	0	Manual	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
17187	None	-	-	15	0	Manual	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
17191	None	-	-	44	0	Manual	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17193	None	-	-	28	0	Manual	Public	N/A	Compare with
17194	None	-	-	28	0	Manual	Public	N/A	Compare with
17195	None	-	-	28	0	Manual	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17205	None	-	-	18	0	Manual	Public	N/A	Compare with
17206	None	-	-	18	0	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
17208	None	-	-	18	0	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17210	None	-	-	27	-2	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
17212	None	-	-	27	-2	Manual	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
17214	None	-	-	29	0	Manual	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17221	None	-	-	22	0	Manual	Public	N/A	Compare with
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17223	None	-	-	22	0	Manual	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17225	None	-	-	20	0	Manual	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with