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Merge pull request #1 from samplchallenges/input_files
SAMPL2 challenge input files and README
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‎.gitignore‎

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# Pyre type checker
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.pyre/
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# MacOS related
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*.DS_Store
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‎LICENSE_other‎

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‎README.md‎

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# SAMPL2
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Archived information/files for the SAMPL2 challenge
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## Challenge overview
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The SAMPL2 evaluation was carried out in the spring of 2009, organized by OpenEye, and discussed at a workshop help at McGill University in Montreal in June of 2009.
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The participants were required to predict **solvation energies** and **tautomer ratios**.
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## SAMPL2 special issue
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The papers covering the results of the challenge were published in a [special issue](https://link.springer.com/journal/10822/volumes-and-issues/24-4) of Journal of Computer-Aided Molecular Design.
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Editorial: [DOI](https://doi.org/10.1007/s10822-010-9358-0) • [Full-text](https://rdcu.be/cim29)
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Overview paper: [DOI](https://doi.org/10.1007/s10822-010-9350-8) • [Full-text](https://rdcu.be/cim4G)
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## Files
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Input files provided to participants:
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* [solvation energy](solvation_energy)
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* [tautomer ratios](tautomer_ratios)
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## LICENSE
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This material here is made available under CC-BY and MIT licenses, as appropriate:
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* MIT for all software/code
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* CC-BY 4.0 for all other materials

‎solvation_energy/xfer.09.tar.gz‎

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‎solvation_energy/xfer.09/2009 SAMPL Transfer energies.pdf‎

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‎solvation_energy/xfer.09/SAMPL09_Guidelines.txt‎

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Thank you for downloading data from SAMPL 09. In the data packet you should find several varieties of files:
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.pdf files contain an overview of the compounds as well as some background information.
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.ism files contain isomeric SMILES strings for each of the molecules in the data set.
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.sdf files contain 3D coordinates for each molecule in SD format.
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.data files are example plain text files for submission of your data. Please read the information at the head of the file which describes the required format for data submission. Ideally, you can modify this file and turn it in when you submit predictions.
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Each data set is split into three groups: obscure, explanatory, and investigatory compounds. Quantitative data is known for obscure compounds, but is not widely available. Quantitative data is provided for explanatory data: we ask participants to attempt to reproduce and explain the unusual or surprising physical properties of these compounds. Lastly, qualitative data is lacking for investigatory compounds, providing a purely blind opportunity for prediction.
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The deadline for submission of predictions is May 18, 2009. A complete submission will include the data file referenced above, as well as another plaintext file with a detailed description of the prediction method as well as insights and comments on the explanatory compounds.
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Thank you for taking part in SAMPL, and we hope this experience will spark insight and spur discussions regarding the prediction of these physical properties. We hope you can join us for the SAMPL workshop, which will take place in Montreal during June, 2009.

‎solvation_energy/xfer.09/explain.ism‎

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Clc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl hexachlorobenzene
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ClC(Cl)(Cl)C(Cl)(Cl)Cl hexachloroethane
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FC1(F)C(F)(F)C(F)(F)C1(F)F octafluorocyclobutane
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FC(F)(F)C(OC)(OC)OC trimethyl orthotrifluoroacetate
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COP(=O)(OC)OC trimethyl phosphate
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Nc(cc1)ccc1[N+]([O-])=O 4-nitroaniline
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OCC(O)CO glycerol
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Clc1c(Cl)c(Cl)c(Cl)c(Cl)c1[N+]([O-])=O pentachloronitrobenzene

‎solvation_energy/xfer.09/explain.sdf‎

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hexachlorobenzene
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-OEChem-01020923443D
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12 12 0 0 0 0 0 0 0999 V2000
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1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.9380 -1.0112 -1.8554 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4881 0.2811 -0.3402 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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4.2690 -2.3475 -0.2335 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5844 0.2329 2.7968 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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4.1730 -2.3956 2.9032 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1.7465 -1.1054 4.4182 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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1 3 1 0 0 0 0
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1 7 1 0 0 0 0
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2 4 1 0 0 0 0
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2 8 1 0 0 0 0
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3 5 2 0 0 0 0
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3 9 1 0 0 0 0
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4 6 2 0 0 0 0
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4 10 1 0 0 0 0
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5 6 1 0 0 0 0
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5 11 1 0 0 0 0
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6 12 1 0 0 0 0
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M END
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$$$$
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hexachloroethane
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-OEChem-01020923443D
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8 7 0 0 0 0 0 0 0999 V2000
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-0.4112 0.7268 1.3109 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3724 -0.3458 2.3995 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1.0271 1.2813 2.2506 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4213 2.1863 0.9806 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4385 -0.5542 -0.9395 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1.0101 -1.4593 0.3306 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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0.9612 1.0726 -1.0886 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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1 3 1 0 0 0 0
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1 4 1 0 0 0 0
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1 5 1 0 0 0 0
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2 6 1 0 0 0 0
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2 7 1 0 0 0 0
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2 8 1 0 0 0 0
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M END
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$$$$
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octafluorocyclobutane
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-OEChem-01020923443D
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12 12 0 0 0 0 0 0 0999 V2000
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0.7739 -0.6328 -0.4493 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7841 -2.0794 0.0876 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.3765 -1.2249 -1.8175 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.2080 -2.4242 -1.0427 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1416 0.1882 0.1151 F 0 0 0 0 0 0 0 0 0 0 0 0
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1.9582 0.0159 -0.4118 F 0 0 0 0 0 0 0 0 0 0 0 0
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1.9779 -2.7127 0.0247 F 0 0 0 0 0 0 0 0 0 0 0 0
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0.3204 -2.2421 1.3459 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5099 -0.5013 -2.5355 F 0 0 0 0 0 0 0 0 0 0 0 0
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1.4069 -1.5160 -2.6445 F 0 0 0 0 0 0 0 0 0 0 0 0
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-1.5173 -2.3351 -0.7226 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0273 -3.6329 -1.6237 F 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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1 3 1 0 0 0 0
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1 5 1 0 0 0 0
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1 6 1 0 0 0 0
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2 4 1 0 0 0 0
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2 7 1 0 0 0 0
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2 8 1 0 0 0 0
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3 4 1 0 0 0 0
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3 9 1 0 0 0 0
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3 10 1 0 0 0 0
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4 11 1 0 0 0 0
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4 12 1 0 0 0 0
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M END
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$$$$
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trimethyl orthotrifluoroacetate
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-OEChem-01020923443D
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20 19 0 0 0 0 0 0 0999 V2000
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-0.0479 -0.9854 -0.3145 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.7161 0.3589 1.3307 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.5539 -3.7028 1.4934 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3547 -1.5982 1.6332 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1309 -2.0156 2.4573 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.1216 -1.7449 0.2209 O 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6023 -0.2208 1.9984 O 0 0 0 0 0 0 0 0 0 0 0 0
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-2.4889 -2.3943 2.0416 O 0 0 0 0 0 0 0 0 0 0 0 0
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0.9459 -1.2598 2.1411 F 0 0 0 0 0 0 0 0 0 0 0 0
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0.2101 -3.3043 2.2281 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.3477 -1.8862 3.7840 F 0 0 0 0 0 0 0 0 0 0 0 0
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0.0343 -1.1754 -1.3875 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.8821 -1.2631 0.1878 H 0 0 0 0 0 0 0 0 0 0 0 0
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-0.2462 0.0762 -0.1490 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.8388 1.3946 1.6569 H 0 0 0 0 0 0 0 0 0 0 0 0
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-3.6177 -0.2152 1.5582 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.5351 0.3377 0.2534 H 0 0 0 0 0 0 0 0 0 0 0 0
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-3.4457 -4.2115 1.8677 H 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6577 -4.2616 1.7746 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.6088 -3.6298 0.4047 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 6 1 0 0 0 0
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2 7 1 0 0 0 0
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3 8 1 0 0 0 0
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4 5 1 0 0 0 0
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4 6 1 0 0 0 0
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4 7 1 0 0 0 0
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4 8 1 0 0 0 0
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5 9 1 0 0 0 0
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5 10 1 0 0 0 0
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5 11 1 0 0 0 0
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1 12 1 0 0 0 0
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1 13 1 0 0 0 0
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1 14 1 0 0 0 0
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2 15 1 0 0 0 0
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2 16 1 0 0 0 0
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2 17 1 0 0 0 0
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3 18 1 0 0 0 0
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3 19 1 0 0 0 0
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3 20 1 0 0 0 0
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M END
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$$$$
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trimethyl phosphate
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-OEChem-01020923443D
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17 16 0 0 0 0 0 0 0999 V2000
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1.0022 -0.2850 -0.3279 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.1533 -0.7794 -4.7427 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.3408 1.8571 -2.0448 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.8147 -2.0294 -2.3083 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.0804 -0.1386 -1.7355 O 0 0 0 0 0 0 0 0 0 0 0 0
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2.1854 -0.1335 -4.0172 O 0 0 0 0 0 0 0 0 0 0 0 0
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3.5625 0.4610 -1.9406 O 0 0 0 0 0 0 0 0 0 0 0 0
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2.4477 -0.5829 -2.4828 P 0 0 0 0 0 0 0 0 0 0 0 0
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0.0244 0.0561 0.0209 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.7944 0.3010 0.1448 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.1301 -1.3396 -0.0726 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.1041 -0.3667 -5.7534 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.1992 -0.6316 -4.2305 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.3730 -1.8482 -4.7984 H 0 0 0 0 0 0 0 0 0 0 0 0
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4.1965 2.3947 -1.6292 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.4306 2.1239 -1.5018 H 0 0 0 0 0 0 0 0 0 0 0 0
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3.2245 2.1208 -3.0987 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 5 1 0 0 0 0
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2 6 1 0 0 0 0
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3 7 1 0 0 0 0
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4 8 2 0 0 0 0
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5 8 1 0 0 0 0
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6 8 1 0 0 0 0
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7 8 1 0 0 0 0
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1 9 1 0 0 0 0
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1 10 1 0 0 0 0
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1 11 1 0 0 0 0
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2 12 1 0 0 0 0
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2 13 1 0 0 0 0
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2 14 1 0 0 0 0
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3 15 1 0 0 0 0
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3 16 1 0 0 0 0
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3 17 1 0 0 0 0
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M END
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$$$$
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4-nitroaniline
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-OEChem-01020923443D
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16 16 0 0 0 0 0 0 0999 V2000
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1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.0115 -2.2108 -0.0727 N 0 0 0 0 0 0 0 0 0 0 0 0
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-0.3339 0.0998 2.6407 N 0 3 0 0 0 0 0 0 0 0 0 0
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-1.2552 0.6297 1.9737 O 0 5 0 0 0 0 0 0 0 0 0 0
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-0.3531 0.0697 3.8950 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.9088 -1.0152 -1.1990 H 0 0 0 0 0 0 0 0 0 0 0 0
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3.6806 -2.1125 2.5730 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.0059 -0.0034 -0.0132 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.7796 -1.1017 3.7625 H 0 0 0 0 0 0 0 0 0 0 0 0
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4.0075 -2.2312 -1.0725 H 0 0 0 0 0 0 0 0 0 0 0 0
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4.7239 -2.6751 0.4536 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 3 1 0 0 0 0
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1 5 2 0 0 0 0
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2 4 2 0 0 0 0
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2 5 1 0 0 0 0
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3 6 2 0 0 0 0
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4 6 1 0 0 0 0
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5 7 1 0 0 0 0
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6 8 1 0 0 0 0
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8 9 1 0 0 0 0
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8 10 2 0 0 0 0
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1 11 1 0 0 0 0
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2 12 1 0 0 0 0
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3 13 1 0 0 0 0
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4 14 1 0 0 0 0
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7 15 1 0 0 0 0
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7 16 1 0 0 0 0
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M CHG 2 8 1 9 -1
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M END
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$$$$
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glycerol
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-OEChem-01020923443D
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14 13 0 0 0 0 0 0 0999 V2000
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0.9523 0.5385 -0.0326 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.9856 0.2573 -2.5348 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.1440 1.2331 -1.3744 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.1387 1.4891 1.0107 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.1659 0.9422 -3.7700 O 0 0 0 0 0 0 0 0 0 0 0 0
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2.4671 1.7733 -1.4064 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.6854 -0.2628 0.1078 H 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0587 0.1293 0.0585 H 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0085 -0.2005 -2.5434 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.7391 -0.5353 -2.4895 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.4552 2.0798 -1.4720 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.0096 1.0133 1.8463 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.0559 0.2819 -4.4722 H 0 0 0 0 0 0 0 0 0 0 0 0
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3.0699 1.0224 -1.3025 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 3 1 0 0 0 0
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1 4 1 0 0 0 0
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2 3 1 0 0 0 0
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2 5 1 0 0 0 0
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3 6 1 0 0 0 0
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1 7 1 0 0 0 0
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1 8 1 0 0 0 0
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2 9 1 0 0 0 0
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2 10 1 0 0 0 0
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3 11 1 0 0 0 0
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4 12 1 0 0 0 0
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5 13 1 0 0 0 0
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6 14 1 0 0 0 0
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M END
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$$$$
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pentachloronitrobenzene
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-OEChem-01020923443D
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14 14 0 0 0 0 0 0 0999 V2000
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1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.9288 -1.0153 -1.5411 N 0 3 0 0 0 0 0 0 0 0 0 0
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1.4171 -1.9673 -2.1696 O 0 5 0 0 0 0 0 0 0 0 0 0
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2.4768 -0.0457 -2.1090 O 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4773 0.2751 -0.3572 Cl 0 0 0 0 0 0 0 0 0 0 0 0
252+
4.2594 -2.3438 -0.2512 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5869 0.2320 2.7925 Cl 0 0 0 0 0 0 0 0 0 0 0 0
254+
4.1739 -2.3974 2.8987 Cl 0 0 0 0 0 0 0 0 0 0 0 0
255+
1.7468 -1.1035 4.4182 Cl 0 0 0 0 0 0 0 0 0 0 0 0
256+
1 2 2 0 0 0 0
257+
1 3 1 0 0 0 0
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1 7 1 0 0 0 0
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2 4 1 0 0 0 0
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2 10 1 0 0 0 0
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3 5 2 0 0 0 0
262+
3 11 1 0 0 0 0
263+
4 6 2 0 0 0 0
264+
4 12 1 0 0 0 0
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5 6 1 0 0 0 0
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5 13 1 0 0 0 0
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6 14 1 0 0 0 0
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7 8 1 0 0 0 0
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7 9 2 0 0 0 0
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M CHG 2 7 1 8 -1
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M END
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$$$$

‎solvation_energy/xfer.09/investigate.ism‎

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CN(C)P(=O)(N(C)C)N(C)C hexamethyl phosphoramide
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CP(=O)(OC)OC dimethyl methylphosphonate
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CP(=O)(C)OC methyl dimethylphosphinate
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CS(=O)c1ccccc1 methyl phenyl sulfoxide
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FC(F)(F)S(=O)c1ccccc1 trifluoromethyl phenyl sulfoxide
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CS(=O)(=O)c1ccccc1 methyl phenyl sulfone
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FC(F)(F)S(=O)(=O)c1ccccc1 trifluoromethyl phenyl sulfone
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n1cocc1 oxazole
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n1cscc1 thiazole
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n1sccc1 isothiazole

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