File:Prednisolone woctanol.webm
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Prednisolone_woctanol.webm (file size: 1.88 MB, MIME type: video/webm)
Summary
| Description |
English: 3D space-filling model of Prednisolone under physiological conditions (pH 7.4) and in ALPB solvent Wetoctanol.
Tiếng Việt: Mô hình không gian 3D của Prednisolone trong điều kiện sinh lý (pH 7.4) và được mô phỏng trong môi trường tham số hóa ALPB wetoctanol. |
| Date | |
| Source | Own work |
| Author | Geoopt1234 |
Molecular Identifier
InChI: InChI=1S/C21H28O5/c1-19-7-5-13(23)9-12(19)3-4-14-15-6-8-21(26,17(25)11-22)20(15,2)10-16(24)18(14)19/h5,7,9,14-16,18,22,24,26H,3-4,6,8,10-11H2,1-2H3/t14-,15-,16-,18+,19-,20-,21-/m0/s1
InChIKey: OIGNJSKKLXVSLS-VWUMJDOOSA-N
Computational Methodology
- Geometry Optimization: GFN2-xTB with triple-extreme accuracy (
--acc 0.0001 --ohess extreme --input gbsa_extreme.inp) - Solvent Model: ALPB implicit solvation of
woctanol - Protonation State: Net charge = 0 at physiological pH 7.4
- Convergence: gnorm = 0.000039044641
Visualization Details
Color Scheme (CPK):
- Gray: Carbon
- White: Hydrogen
- Red: Oxygen
Software & Sources
- Structure Source: PubChem CID
- Geometry Optimization: xtb 6.7.1pre (5071a88)
- Molecular Editor: Avogadro 2 (1.102.1)
- Visualization: Jmol-16.3.33
- Animation: FFmpeg (
ffmpeg -y -framerate 20 -i frame_%03d.png -c:v libvpx-vp9 -pix_fmt yuva420p -b:v 0 -crf 18 -loop 0 Prednisolone.webm) - InChI Generation: IUPAC InChI Web Demo
SDF and xtb command
Command : xtb Prednisolone.sdf --alpb woctanol --acc 0.0001 --ohess extreme --input gbsa_extreme.inp
where gbsa_extreme.inp file is
$gbsa gbsagrid=extreme $end
Prednisolone_opt.sdf
energy: -79.619949309254 gnorm: 0.000039044641 xtb: 6.7.1pre (5071a88)
11142514503D
54 57 0 0 0 999 V2000
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-5.8376 -0.6709 1.8590 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.1362 -1.2246 1.4162 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8345 -2.1135 0.0594 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4074 3.2941 0.5495 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7327 2.7427 -1.0938 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6498 -2.2852 0.3163 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9017 2.1955 -0.4116 H 0 0 0 0 0 0 0 0 0 0 0 0
3.5090 2.5562 1.2653 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8971 3.2060 -0.4632 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3435 2.3299 1.0046 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3058 -0.2130 -2.2244 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6971 0.8534 -1.9936 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8796 -0.8815 -1.8186 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7781 2.2379 -1.6792 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3778 2.9385 -0.1743 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0402 -1.2854 -2.5966 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5882 -0.4255 -2.5661 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0688 0.4706 -2.6521 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.6819 -2.5627 -0.6452 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3044 0.8625 2.5968 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4151 -2.6183 -1.7166 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.8820 1.5683 0.9852 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9317 -2.0943 1.1562 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0647 -1.0771 2.0510 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.6035 -2.7236 0.8520 H 0 0 0 0 0 0 0 0 0 0 0 0
6.1773 -1.5461 -0.2816 H 0 0 0 0 0 0 0 0 0 0 0 0
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M END
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| Date/Time | Dimensions | User | Comment | |
|---|---|---|---|---|
| current | 15:33, 14 November 2025 | (1.88 MB) | wikimediacommons>Geoopt1234 | Uploaded own work with UploadWizard |
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