General Molecule Tools

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Stereochemistry, Chirality, Parity
Where to find FAQ (Frequently Asked Questions) in understanding how stereochemistry is supported in SDF/Mol file format? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding how stereochemistry is supported in SDF/Mol file format. What... 2021-04-04, 148👍, 0💬

Tools for SDF/Mol V3000 File Format
What are tools that support the SDF/Mol V3000 file format? There are a number of online or standalone tools that support the SDF/Mol V3000 file format. Open Babel - Can read and write molecules in SDF/Mol V3000 file format. (Convert SDF to SDF V3) fyicenter$ obabel FYI-001.sdf -o sdf -O test.sd3 -x3... 2021-04-04, 140👍, 0💬

Molecule FYI-1000267
Molecule Summary: ID: FYI-1000267 SMILES: N[17C@@](F)([18C])C(=[19O])O Received at FYIcenter.com on: 2021-02-24 2021-04-04, 116👍, 0💬

Molecule FYI-1000264
Molecule Summary: ID: FYI-1000264 SMILES: COc1cc2c(CC3C4CCCCC24CCN3CCc2c cccc2)cc1Received at FYIcenter.com on: 2021-02-24 2021-04-04, 113👍, 0💬

Molecule FYI-1000268
Molecule Summary: ID: FYI-1000268 SMILES: N[17C@@](F)([18C])C(=[19O])[20 O]Received at FYIcenter.com on: 2021-02-24 2021-04-04, 106👍, 0💬

Molecule FYI-1000269
Molecule Summary: ID: FYI-1000269 SMILES: N[17C@@](F)([18C])C(=[1912O])[ 20O]Received at FYIcenter.com on: 2021-02-24 2021-04-04, 105👍, 0💬

Molecule FYI-1000266
Molecule Summary: ID: FYI-1000266 SMILES: N[17C@@](F)([18C])C(=O)O Received at FYIcenter.com on: 2021-02-24 2021-04-04, 104👍, 0💬

Molecule FYI-1000265
Molecule Summary: ID: FYI-1000265 SMILES: N[17C@@](F)(C)C(=O)O Received at FYIcenter.com on: 2021-02-24 2021-04-04, 104👍, 0💬

Stereoinformation Presentation in SDF/Mol File
How Stereoinformation Is Presented in SDF/Mol and SDF/Mol V3000 Files? Ideally stereoinformation should be stored in atom's coordinates, since SDF/Mol files support x, y, and z, 3-dimensional coordinates. However, not all software supports 3-dimensional coordinates. So SDF/Mol file uses 3 types of p... 2021-03-21, 146👍, 0💬

What Is Stereochemistry
What Is Stereochemistry? Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements. Here are some stereoisomers listed in the picture below: Example of Stereoisomers   ⇒ Stereoinformation Presentation in SDF/... 2021-03-21, 134👍, 0💬

Molecule FYI-1000262
Molecule Summary: ID: FYI-1000262 SMILES: [CH+]=C1CC=C(N2N=CC=N2)C=N1 Received at FYIcenter.com on: 2021-02-12 2021-03-21, 129👍, 0💬

Molecule FYI-1000263
Molecule Summary: ID: FYI-1000263 SMILES: Cc4ccc2c(ccc3c1ccccc1ccc23)c4 Received at FYIcenter.com on: 2021-02-20 2021-03-21, 119👍, 0💬

Run Open Babel GUI on Windows
How to run OpenBabelGUI on Windows computers? Open Babel GUI is the graphical user interface for Open Babel. You can use Open Babel GUI to open a molecule file in any supported format and convert it to any other format. Here is how to Open Babel GUI on Windows. 1. Search for "Open Babel GUI" in "Sta... 2021-03-07, 344👍, 0💬

Molecule FYI-1000233
Molecule Summary: ID: FYI-1000233 SMILES: [Zn]=O Received at FYIcenter.com on: 2021-01-22 2021-03-07, 131👍, 0💬

Open Babel Options on SDF/Mol Files
What options are offerred in Parity Code to support stereoinformation in SDF/Mol V2000 and V3000 files generated by Open Babel? Here is the documentation of Open Babel 2.4.1 with options listed to support stereoinformation in SDF/Mol V2000 and V3000 files: fyicenter$ obabel -V Open Babel 2.4.1 -- Ma... 2021-03-07, 148👍, 0💬

Parity and Stereo with Open Babel
Cam Open Babel support stereoinformation represented by the Parity Code and Stereo Code in SDF/Mol files? Yes. Open Babel can support stereoinformation represented by the Parity Code and Stereo Code in SDF/Mol files. But you should use Open Babel 2.4.1 and newer versions. Open Babel 2.3.1 seems to h... 2021-03-07, 145👍, 0💬

Molecule FYI-1000260
Molecule Summary: ID: FYI-1000260 SMILES: C=C(C=NC1=NC=C(C(F)(F)F)N=C1)[ NH+](C)CC1=NC(=C)CC=C1N1N=CC=N 1Received at FYIcenter.com on: 2021-02-12 2021-03-07, 131👍, 0💬

Molecule FYI-1000259
Molecule Summary: ID: FYI-1000259 SMILES: CC1=CC2=C(C=C1C3=CC=CC(=C3)C[N +]#[C-])N=C(N=C2N)NReceived at FYIcenter.com on: 2021-02-07 2021-03-07, 129👍, 0💬

Molecule FYI-1000261
Molecule Summary: ID: FYI-1000261 SMILES: C=C(C)[NH+](C)C(=O)C1=NC(=C)CC =C1N1N=CC=N1Received at FYIcenter.com on: 2021-02-12 2021-03-07, 124👍, 0💬

Running Open Babel on Windows
Where to find FAQ (Frequently Asked Questions) on running Open Babel on Windows? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on Windows. Install Open Babel Binary Package on Windows Run Open Babel GUI on Windows Structure... 2021-02-17, 325👍, 0💬

Install Open Babel Binary Package on Windows
How to Install Open Babel binary package on Windows computers? The easiest option to install Open Babel on Windows computers is to install the Open Babel pre-compiled binary package as shown in this tutorial.: 1. Go to GitHub Website for Open Babel 3.0.0. 2. Click to download "OpenBabel-3.0.0.exe" f... 2021-02-17, 320👍, 0💬

Molecule FYI-1000237
Molecule Summary: ID: FYI-1000237 SMILES: CCCCC Received at FYIcenter.com on: 2021-02-04 2021-02-17, 143👍, 0💬

Molecule FYI-1000235
Molecule Summary: ID: FYI-1000235 SMILES: COC1=CC=C(C=C1)C=O Received at FYIcenter.com on: 2021-01-29 2021-02-17, 141👍, 0💬

Molecule FYI-1000234
Molecule Summary: ID: FYI-1000234 SMILES: O=Cc1ccc(cc1)C(=O)OC Received at FYIcenter.com on: 2021-01-25 2021-02-17, 141👍, 0💬

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General Molecule Tools