File:Esketamine.webm
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Esketamine.webm (file size: 830 KB, MIME type: video/webm)
Summary
| Description |
English: A video about 3D space-filling model of Esketamine
Tiếng Việt: Video về mô hình không gian 3D của Esketamine |
| Date | |
| Source | Own work |
| Author | Geoopt1234 |
Molecular Identifier
InChI: 1S/C13H16ClNO/c1-15-13(9-5-4-8-12(13)16)10-6-2-3-7-11(10)14/h2-3,6-7,15H,4-5,8-9H2,1H3/p+1/t13-/m0/s1
InChIKey: YQEZLKZALYSWHR-ZDUSSCGKSA-O
Computational Methodology
- Geometry Optimization: GFN2-xTB [xtb 6.7.1pre (5071a88)] with triple-extreme accuracy (--acc 0.0001 --ohess extreme --input gbsa_extreme.inp)
- Solvent Model: ALPB implicit solvation of Wet Octanol
- Protonation State: Net charge = +1 at physiological pH 7.4
- Convergence: gnorm = 0.000036608599
Visualization Details
Color Scheme (CPK):
- Gray: Carbon
- White: Hydrogen
- Red: Oxygen
- Blue: Nitrogen
- Green: Chlorine
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 Esketamine.webm) - InChI Generation: IUPAC InChI Web Demo
SDF and imaginary frequency check
Command : xtb Esketamine.sdf --chrg 1 --alpb woctanol --acc 0.0001 --ohess extreme --input gbsa_extreme.inp --gfn 2 -P 1
where gbsa_extreme.inp file is
$gbsa gbsagrid=extreme $en
ImaginaryFrequencyCheckFILE
No imaginary frequency found
MOLECULEopt.sdf
energy: -47.730776942330 gnorm: 0.000036608599 xtb: 6.7.1pre (5071a88)
11092513283D
33 34 0 0 0 999 V2000
-0.7648 -2.0680 1.3697 Cl 0 0 0 0 0 0 0 0 0 0 0 0
2.2127 -1.7877 0.4867 O 0 0 0 0 0 0 0 0 0 0 0 0
0.5684 -1.4381 -1.4831 N 0 3 0 0 0 0 0 0 0 0 0 0
0.7268 -0.2527 -0.5727 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6094 0.8345 -1.2206 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9383 1.9406 -0.2147 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6620 1.3813 1.0044 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6041 -0.7478 0.5987 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8133 0.2738 1.6610 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6582 0.2091 -0.1630 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4173 -0.5677 0.7160 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2441 1.3638 -0.6736 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1070 -1.1685 -2.8554 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6908 -0.1880 1.1017 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5198 1.7477 -0.2960 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2427 0.9781 0.5978 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0979 -2.0666 -1.0084 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4770 -1.9357 -1.4718 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1207 1.2630 -2.0935 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5446 0.3716 -1.5443 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0261 2.4397 0.1111 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5725 2.6816 -0.7023 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8403 2.1702 1.7342 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6293 0.9658 0.7156 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8645 0.6948 1.9915 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3444 -0.1622 2.5065 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7122 1.9817 -1.3764 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8073 -0.5798 -2.8221 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0971 -2.1106 -3.3590 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8683 -0.6330 -3.4158 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2498 -0.8040 1.7875 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9478 2.6494 -0.7035 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.2342 1.2740 0.9006 H 0 0 0 0 0 0 0 0 0 0 0 0
1 11 1 0 0 0 0
2 8 2 0 0 0 0
3 4 1 0 0 0 0
3 13 1 0 0 0 0
4 5 1 0 0 0 0
4 8 1 0 0 0 0
4 10 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 9 1 0 0 0 0
8 9 1 0 0 0 0
10 11 1 0 0 0 0
10 12 2 0 0 0 0
11 14 2 0 0 0 0
12 15 1 0 0 0 0
14 16 1 0 0 0 0
15 16 2 0 0 0 0
3 17 1 0 0 0 0
3 18 1 0 0 0 0
5 19 1 0 0 0 0
5 20 1 0 0 0 0
6 21 1 0 0 0 0
6 22 1 0 0 0 0
7 23 1 0 0 0 0
7 24 1 0 0 0 0
9 25 1 0 0 0 0
9 26 1 0 0 0 0
12 27 1 0 0 0 0
13 28 1 0 0 0 0
13 29 1 0 0 0 0
13 30 1 0 0 0 0
14 31 1 0 0 0 0
15 32 1 0 0 0 0
16 33 1 0 0 0 0
M CHG 1 3 1
M END
$$$$
Licensing
I, the copyright holder of this work, hereby publish it under the following license:
 
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This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication. |
| The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
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File history
Click on a date/time to view the file as it appeared at that time.
| Date/Time | Dimensions | User | Comment | |
|---|---|---|---|---|
| current | 01:20, 11 November 2025 | (830 KB) | imagescommonswiki>Geoopt1234 | Uploaded own work with UploadWizard |
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