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
Residue Name (RNME)YCH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID17533
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:19
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 (401-500 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 >
17161 None - 23 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
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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)