MD Topology | NMR | X-Ray

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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)	P5H
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	17321
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:16
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
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
6461	None	-	-	15	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
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
17345	None	-	-	20	-2	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
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	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
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
17360	None	-	-	30	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
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	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
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17163	None	-	-	23	0	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	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
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
3408	None	-	-	24	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
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
17182	None	-	-	23	0	Manual	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17214	None	-	-	29	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
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
17509	None	-	-	27	0	Manual	Public	N/A	Compare with
584	None	-	-	15	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
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	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
163	None	-	-	13	0	Manual*	Public	N/A	Compare with
17492	None	-	-	22	0	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
5031	None	-	-	78	0	Manual*	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17409	None	-	-	18	0	Manual	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with