Prediction of protonation states of ChEMBL33 compounds with MW <= 500

These are structures retrieved from ChEMBL33, which were filtered by MW <= 500, for each compounds the stable tautomer was generated by chemaxon and all stereoisomers were enumerated by RDKit. chembl_stereo.smi is a tab-separated file with SMILES for all enumerated stereoisomers, which can be used to predict protonation states by approaches using 3D representation for which stereoinformation should be important. Example of the content start_smi id base_id stereo_idO=c1oc(Nc2ccc(I)cc2)nc2ccccc12 CHEMBL10000_1 CHEMBL10000 1N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O CHEMBL100001_1 CHEMBL100001 1CCC[C@@H]1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CHEMBL100003_1 CHEMBL100003 1CCC[C@H]1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CHEMBL100003_2 CHEMBL100003 2O=C(O)COCCN1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)CC1 CHEMBL1000_1 CHEMBL1000 1O=C(O)COCCN1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)CC1 CHEMBL1000_2 CHEMBL1000 2 chembl_nostereo.smi is a tab-separated file with unsteric SMILES for the same ChEMBL compounds as above and predicted protonation states at pH 7.4 by Chemaxon, MolGpKa and MolGpKa integrated in EasyDock (there some fixes were implemented) Example of the content start_smi_nostereo base_id chemaxon_nostereo molgpka_nostereo molgpka_easydock_nostereoCS(=O)c1ccc(-c2nc(-c3ccc(F)cc3)c(-c3ccncc3)[nH]2)cc1 CHEMBL10 CS(=O)c1ccc(-c2nc(-c3ccc(F)cc3)c(-c3ccncc3)[nH]2)cc1 CS(=O)c1ccc(-c2nc(-c3ccc(F)cc3)c(-c3ccncc3)[nH]2)cc1 CS(=O)c1ccc(-c2nc(-c3ccc(F)cc3)c(-c3ccncc3)[nH]2)cc1CC1(C)Oc2ccc(C#N)cc2C(N2CCCC2=O)C1O CHEMBL100 CC1(C)Oc2ccc(C#N)cc2C(N2CCCC2=O)C1O CC1(C)Oc2ccc(C#N)cc2C(N2CCCC2=O)C1O CC1(C)Oc2ccc(C#N)cc2C(N2CCCC2=O)C1OO=C(O)COCCN1CCN(C(c2ccccc2)c2ccc(Cl)cc2)CC1 CHEMBL1000 O=C([O-])COCC[NH+]1CCN(C(c2ccccc2)c2ccc(Cl)cc2)CC1 O=C([O-])COCCN1CCN(C(c2ccccc2)c2ccc(Cl)cc2)CC1 O=C([O-])COCCN1CCN(C(c2ccccc2)c2ccc(Cl)cc2)CC1O=c1oc(Nc2ccc(I)cc2)nc2ccccc12 CHEMBL10000 O=c1oc(Nc2ccc(I)cc2)nc2ccccc12 O=c1oc(Nc2ccc(I)cc2)nc2ccccc12 O=c1oc(Nc2ccc(I)cc2)nc2ccccc12NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)O CHEMBL100001 [NH3+]C(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)[O-] NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]c[nH+]1)C(=O)[O-] NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)NC(Cc1c[nH]cn1)C(=O)[O-]CCCC1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CHEMBL100003 CCCC1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CCCC1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CCCC1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC