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 StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information
Molecule Typeamino acid building block
Residue Name (RNME)H11
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge-1
Forcefieldmultiple
Molecule ID17274
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:15
Literature ReferenceDrazen 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 (301-400 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  Atoms  Charge > Curation  Δ Qm Optimized Energy
(kJ.mol-1)  		Compare 
580 None - 12 0 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
576 None - 26 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
6458 None - 13 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
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Conditions of Use

ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)

Solvent > Experimental Value
(kJ.mol-1)  		Experimental Uncertainty
(kJ.mol-1)  		Doi 
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