Merge branch 'master' of https://github.com/foldingathome/covid-moonshot

README.md

@@ -6,5 +6,6 @@ John D. Chodera <[email protected]>
 * `diamond-structures/` - structures of SARS-CoV-2 main viral protease from [DiamondMX/XChem](https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html)
 * `receptors/` - prepared receptor structures (in OpenEye `.oeb.gz` format as well as PDB) with prepared fragments
 * `molecules/` - input molecule sets for docking
-* `scripts/` - scripts for preparing and docking ligands
-* `docked/` - docked structures for use in free energy calculations
+* `scripts/` - scripts for preparing receptors and docking and scoring ligands
+* `docking/` - docked structures (and scores) for use in free energy calculations
+* `simulation_prep/` - scripts used in preparing gromacs expanded ensemble free energy calculations for Folding@home

docking/README.md

@@ -3,8 +3,15 @@
 ![ensemble of docked molecules](https://github.com/foldingathome/covid-moonshot/raw/master/docking/docked-molecules.png "Ensemble of docked molecules")
 
 ## Manifest
-* `covid_submissions_03_26_2020 - docked.sdf` - docked COVID Moonshot molecules as of 2:34 PST March 27, 2020
+* `covid_submissions_03_26_2020 - top docked.{csv,sdf}` - COVID Moonshot molecules as of 2:34 PST March 27, 2020 docked into all structures, with only the best scores (over all fragment structures) preserved
+  * `SMILES`: SMILES for compound
+  * `TITLE`: the compound ID (CID)
+  * `Chemgauss4 Score`: docking score (lower is better)
+  * `fragments`: fragment ID for corresponding fragment X-ray structure for best docked pose; corresponding structures are in `../receptors/Mpro-{fragment}-protein.pdb`
+* `covid_submissions_03_26_2020 - docked.sdf` - COVID Moonshot molecules as of 2:34 PST March 27, 2020 docked into inspiration fragment structures
    * Each molecule was docked into every fragment structure listed as inspirati; the corresponding fragment is listed in the `<fragments>` tag;
      docked structures are found in `f'../receptors/Mpro-{fragment}-protein.pdb'`
    * Some Moonshot molecules failed to dock and were omitted
    * See `../scripts/README.md` for more information on methodology
+* `mpro_fragments_03_25_2020 - docked.sdf` - docked [DiamondMX fragment hits](https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem/Downloads.html) from 2020-03-25 for score comparison
+   * Each compound was redocked into its original fragment structure

docking/mpro_fragments_03_25_2020 - docked.csv

@@ -0,0 +1,92 @@
+SMILES,TITLE,fragments,Hybrid2
+CS(=O)(=O)NCCc1ccccc1,Z45617795,x0072,-7.050613
+CC(=O)NCCc1c[nH]c2c1cc(cc2)F,Z1220452176,x0104,-10.112116
+Cc1ccncc1NC(=O)C,Z1129283193,x0107,-6.576210
+COC(=O)c1ccc(cc1)S(=O)(=O)N,Z18197050,x0161,-6.763607
+C[NH+]1CCN(CC1)C(=O)Nc2ccccc2,Z2856434890,x0165,-1.649171
+c1ccc(cc1)NC(=O)N2CCC(CC2)C(=O)N,Z33545544,x0177,0.227592
+CC(=O)Nc1ccc(cc1)Oc2ncccn2,Z54571979,x0194,-1.643927
+CN1CCCc2c1cc(cc2)S(=O)(=O)N,Z1367324110,x0195,-7.785241
+CCNc1ccc(cn1)C#N,Z219104216,x0305,-6.523846
+CC(=O)NCc1ccc(cc1)S(=O)(=O)N,Z30932204,x0336,-1.543823
+c1cc(cc(c1)F)C[NH2+]Cc2ccco2,Z2737076969,x0350,-4.714625
+Cc1ccc(cc1)OCC(=O)N2CC[NH+](CC2)C,Z2856434836,x0354,-4.154733
+c1cc2c(cc1C(=O)N3CCCCCC3)OCO2,Z31432226,x0376,0.344451
+c1cscc1C[NH+]2CCC(CC2)O,Z2856434899,x0387,-6.468851
+c1ccc(c(c1)CNc2[nH]c3ccccc3n2)O,Z1587220559,x0390,-4.645006
+Cc1nnc(s1)C[N@@H+]2CCC=C(C2)F,Z1619978933,x0395,-5.711845
+Cc1cc(no1)CN(C)C(=O)NC2CC2,Z369936976,x0397,-7.605450
+c1ccc(cc1)SCC[NH+]2CCOCC2,Z2856434865,x0398,-1.396757
+c1cnc(cn1)N2CC[C@]3(C2)CCOC3,Z1401276297,x0425,-1.879012
+c1ccc(c(c1)C(=O)NCCc2ccncc2)F,Z1310876699,x0426,-3.854048
+c1ccc(cc1)NC(=O)Nc2cccnc2,Z44592329,x0434,-6.273730
+C[C@@H]1[C@@H](CCC[N@H+]1Cc2ccccc2)O,Z2217052426,x0464,-6.373271
+COC(=O)c1cccc(c1)NS(=O)(=O)C,Z24758179,x0478,-4.501690
+c1cc(ccc1C(=O)N)NC(=O)[C@@H]2CCCO2,Z1545313172,x0499,-3.286886
+c1cnccc1CCNC(=O)NC2CCCCC2,Z111507846,x0540,-6.911177
+c1cc(cc(c1)Cl)C[NH+]2CCOCC2,Z2856434856,x0669,-3.508027
+c1cc(cnc1)NC(=O)CC2CCCCC2,Z31792168,x0678,-11.355043
+c1cc(sc1)S(=O)(=O)N2CCN(CC2)C(=O)CCl,PCM-0102241,x0689,-1.434038
+c1cc(cc(c1)S(=O)(=O)N2CCN(CC2)C(=O)CCl)F,PCM-0102327,x0691,-1.737753
+Cc1cccc(c1)C[NH+]2CCN(CC2)C(=O)CCl,PCM-0102340,x0692,-5.727720
+Cc1ccc(cc1)C(=O)N2CCN(CC2)C(=O)CCl,PCM-0102962,x0705,-1.080877
+c1c2c(sc1C(=O)NNC(=O)CCl)CCCC2,PCM-0102142,x0708,-2.875404
+Cc1ccc(cc1)S(=O)(=O)N2CCN(CC2)C(=O)CCl,PCM-0102759,x0731,-2.087135
+c1ccc(c(c1)N2CCN(CC2)C(=O)CCl)N(=O)=O,PCM-0103016,x0734,-4.101091
+c1cc(oc1)C(=O)N2CCN(CC2)C(=O)CCl,PCM-0102248,x0736,-3.104951
+c1ccc2c(c1)nc(s2)[C@@H]3CCCN(C3)C(=O)CCl,PCM-0102425,x0749,-10.101554
+c1cc2c(cc1CNC(=O)CCl)OCO2,PCM-0102578,x0752,-1.739265
+c1cc(c(c(c1)F)S(=O)(=O)N2CCN(CC2)C(=O)CCl)F,PCM-0102201,x0755,-1.588711
+c1cc(ccc1[C@@H]2CN(CCO2)C(=O)CCl)F,PCM-0102615,x0759,-5.831551
+c1ccc(c(c1)F)S(=O)(=O)N2CCN(CC2)C(=O)CCl,PCM-0102281,x0769,-2.620309
+c1cc(cc(c1)Cl)C[NH+]2CCN(CC2)C(=O)CCl,PCM-0102269,x0770,-5.598250
+Cc1ccc(c(c1)C)S(=O)(=O)N2CCN(CC2)C(=O)CCl,PCM-0102628,x0771,-1.831967
+c1ccc(c(c1)C#N)S(=O)(=O)N2CCN(CC2)C(=O)CCl,PCM-0102395,x0774,-5.778869
+c1cc(cc(c1)NC(=O)CCl)C(=O)N2CCSCC2,PCM-0103072,x0786,-0.873283
+C[C@@H](c1cccc2c1cccc2)NC(=O)CCl,PCM-0102275,x0820,-4.013700
+c1ccc2c(c1)cccc2C[NH+]3CCN(CC3)C(=O)CCl,PCM-0102287,x0830,-9.263649
+Cc1ccccc1C[N@@H+]2CCCN(CC2)C(=O)CCl,PCM-0102911,x0831,-7.894884
+c1cscc1[C@@H]2CCC[C@@H]2C(=O)N,POB0129,x0874,-7.257104
+c1ccnc(c1)C2(CCCC2)CO,POB0073,x0887,-1.444870
+c1cc(ccc1S(=O)(=O)N)Br,NCL-00023830,x0946,-4.741473
+CC(=O)N[C@H](Cc1ccc(cc1)O)C(=O)NCC#CBr,NCL-00024905,x0967,-6.092483
+C[C@@H]([C@@H](C(=O)NCC#CBr)NC(=O)C)O,NCL-00025058,x0978,-4.174518
+CC(=O)N[C@H](CC(=O)N)C(=O)NCC#CBr,NCL-00025412,x0981,-3.172795
+CCC(=[NH2+])N,Z1741969146,x0387,-4.595698
+c1c(cncn1)N,Z1741970824,x0387,-3.957347
+c1cc[nH]c(=O)c1,Z1741982125,x0387,-4.679280
+C1C(CS1(=O)=O)O,Z3241250482,x0387,-3.273957
+c1cc(ncc1N2CCCOCC2)C#N,Z1348371854,x1077,-7.238197
+Cc1cc(ccc1CS(=O)(=O)N)F,Z1849009686,x1086,-8.643620
+C[NH+]1CCN(CC1)C(=O)Cc2c[nH]c3c2cccn3,Z316425948_minor,x1093,-6.186084
+CC(C)N(C)c1c2cnn(c2ncn1)C,Z328695024,x1101,-1.664622
+c1ccnc(c1)NS(=O)(=O)c2ccc(cc2)N,Z271004858,x1119,-0.886664
+C[C@H]1CN(CCO1)C(=O)Cn2cccn2,Z217038356,x1132,-4.214947
+c1ccc(cc1)C[N@@H+]2CCO[C@@H](C2)CO,Z1259086950,x1163,-4.460948
+Cn1ccc(n1)C(=O)NC[C@@H]2CCCO2,Z2643472210,x1187,-4.117119
+CC[NH2+]Cc1cn(nn1)C,Z1271660837,x1226,-2.522496
+Cc1nc(c(s1)NC(=O)OC)c2ccccc2,Z979145504,x1235,-4.372152
+CS(=O)(=O)Cc1[nH]c2ccccc2n1,Z126932614,x1237,-3.544934
+c1cc(ccc1CNC(=O)N2CCOCC2)C#N,Z509756472,x1249,-4.906038
+c1cc(ccc1S(=O)(=O)N2CCN(CC2)C(=O)CCl)Cl,PCM-0102704,x1308,-2.028034
+c1ccc(cc1)N([C@H]2CS(=O)(=O)C=C2)C(=O)CCl,PCM-0102372,x1311,-6.172644
+c1cc(sc1C[NH+]2CCN(CC2)C(=O)CCl)Cl,PCM-0102277,x1334,-6.128600
+Cc1ccc(c(c1)S(=O)(=O)N2CCN(CC2)C(=O)CCl)C,PCM-0102353,x1336,-5.511868
+COc1cccc2c1nc(s2)NC(=O)CCl,PCM-0103067,x1348,-4.544401
+c1ccc(cc1)C(=O)NC2CCN(CC2)C(=O)CCl,PCM-0102575,x1351,-1.651460
+c1ccc(c(c1)NC(=O)C2CCN(CC2)C(=O)CCl)O,PCM-0102389,x1358,-3.659343
+Cc1ccc(cc1)N([C@H]2CS(=O)(=O)C=C2)C(=O)CCl,PCM-0102539,x1374,-4.032683
+c1cc(ccc1N([C@H]2CS(=O)(=O)C=C2)C(=O)CCl)F,PCM-0102868,x1375,-4.463304
+C1CCN(CC1)C(=O)C2CCN(CC2)C(=O)CCl,PCM-0102972,x1380,-3.441131
+C[C@@H](c1cccc(c1)Cl)NC(=O)CCl,PCM-0102190,x1382,-5.739811
+c1cc(cc(c1)N2CCCC2=O)NC(=O)CCl,PCM-0102179,x1384,-2.839446
+c1cc(sc1C[NH+]2CCN(CC2)C(=O)CCl)Br,PCM-0102169,x1385,-6.422934
+c1cscc1C[NH+]2CCN(CC2)C(=O)CCl,PCM-0102739,x1386,-6.591770
+c1ccc(cc1)[C@H]2CN(Cc3c2cccc3)C(=O)CCl,PCM-0102432,x1392,-8.119668
+c1cc(sc1S(=O)(=O)N2CCN(CC2)C(=O)CCl)Cl,PCM-0102121,x1402,-2.153136
+c1cc(sc1)C(=O)N2CCN(CC2)C(=O)CCl,PCM-0102306,x1412,-4.936234
+c1cc(sc1)C[NH+]2CCN(CC2)C(=O)CCl,PCM-0102243,x1418,-6.103490
+COc1ccc(cc1)N2CCN(CC2)C(=O)CCl,PCM-0102254,x1425,-1.256195
+CC(C)N(C)C(=O)C1CCN(CC1)C(=O)CCl,PCM-0102974,x1458,-3.005788
+c1cc(c(nc1)Cl)NC(=O)CCl,PCM-0102274,x1478,-3.614936
+CC(=O)N1CCN(CC1)C(=O)CCl,PCM-0102535,x1493,-3.740527