{"id":1866,"date":"2022-01-24T11:06:00","date_gmt":"2022-01-24T02:06:00","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1866"},"modified":"2022-02-22T14:26:37","modified_gmt":"2022-02-22T05:26:37","slug":"ligand_minimization_in_pocket","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2022\/01\/24\/ligand_minimization_in_pocket\/","title":{"rendered":"\u30bf\u30f3\u30d1\u30af\u8cea\u30dd\u30b1\u30c3\u30c8\u5185\u3067\u30ea\u30ac\u30f3\u30c9\u69cb\u9020\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316"},"content":{"rendered":"\n

\u4eca\u56de\u306e\u8a71\u984c\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30dd\u30b1\u30c3\u30c8\u5185\u306b\u3042\u308b\u30ea\u30ac\u30f3\u30c9\u306b\u3064\u3044\u3066\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3059\u308b\u65b9\u6cd5\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u7279\u306b\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u69cb\u9020\u3092\u56fa\u5b9a\u3059\u308b\u5834\u5408\u306b\u3064\u3044\u3066\u3069\u3046\u3059\u308c\u3070\u3088\u3044\u304b\u7d39\u4ecb\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u3042\u3068\u3001\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u529b\u5834\u30a8\u30cd\u30eb\u30ae\u30fc\u8a08\u7b97\u306b\u3064\u3044\u3066\u3082\u89e6\u308c\u307e\u3059\u3002<\/p>\n\n\n\n

\u306f\u3058\u3081\u306b<\/h2>\n\n\n\n

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\u8a08\u7b97\u5bfe\u8c61\u306a\u3069<\/h2>\n\n\n\n

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\"\"
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\u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac<\/h2>\n\n\n\n

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\n
ZIP\u30d5\u30a1\u30a4\u30eb<\/a>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/a><\/div>\n<\/div><\/div>\n\n\n\n

ZIP\u30d5\u30a1\u30a4\u30eb\u3092\u89e3\u51cd\u3059\u308b\u30683\u3064\u306e\u30d5\u30a1\u30a4\u30eb\u304c\u5c55\u958b\u3055\u308c\u307e\u3059\u3002Protein-Ligand.cpp<\/code>\u306fC++\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u3001protein.pdb<\/code>\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u306ePDB\u30d5\u30a1\u30a4\u30eb\u3067\u3059\u3002\u305d\u3057\u3066ligand.sdf<\/code>\u306f\u30ea\u30ac\u30f3\u30c9\u306eSD\u30d5\u30a1\u30a4\u30eb\u3067\u3059\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30f3\u30d1\u30a4\u30eb\u65b9\u6cd5\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n

$ g++ -std=c++11 Protein-Ligand.cpp \\\n      -I${HOME}\/anaconda3\/envs\/ob3\/include\/openbabel3 \\\n      -L${HOME}\/anaconda3\/envs\/ob3\/lib \\\n      -Wl,-rpath=${HOME}\/anaconda3\/envs\/ob3\/lib -l openbabel<\/code><\/pre>\n\n\n\n
a.out<\/code>\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u304c\u51fa\u6765\u3066\u3044\u308c\u3070\u6210\u529f\u3067\u3059\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u5b9f\u884c\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3059\u3002<\/p>\n\n\n\n
$ .\/a.out<\/code><\/pre>\n\n\n\n
\u305d\u308c\u3067\u306f\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u898b\u3066\u3044\u304d\u307e\u3057\u3087\u3046\u3002C++\u306e\u30b3\u30fc\u30c9\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
  1 #include <fstream>\n  2 #include <iostream>\n  3 #include <string>\n  4 \n  5 #include <openbabel\/mol.h>\n  6 #include <openbabel\/obconversion.h>\n  7 #include <openbabel\/forcefield.h>\n  8 #include <openbabel\/parsmart.h>\n  9 #include <openbabel\/generic.h>\n 10 \n 11 using namespace std;\n 12 using namespace OpenBabel;\n 13 \n 14 int main(int argc, char* argv[]) {\n 15   \/\/ \u529b\u5834\u306e\u8a2d\u5b9a\n 16   string ff = \"MMFF94\";\n 17   OBForceField* pFF = OBForceField::FindForceField(ff);\n 18   if (!pFF) {\n 19     cerr << \"\u6307\u5b9a\u306e\u529b\u5834\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 20     return -1;\n 21   }\n 22   pFF->SetLogFile(&cout);\n 23   pFF->SetLogLevel(OBFF_LOGLVL_LOW);\n 24 \n 25   \/\/ \u30d5\u30a1\u30a4\u30eb\u30aa\u30fc\u30d7\u30f3\n 26   ifstream ifs1(\"protein.pdb\");\n 27   if (ifs1.fail()) {\n 28     cerr << \"\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 29     return -1;\n 30   }\n 31 \n 32   ifstream ifs2(\"ligand.sdf\");\n 33   if (ifs2.fail()) {\n 34     cerr << \"\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 35     return -1;\n 36   }\n 37 \n 38   \/\/ \u30bf\u30f3\u30d1\u30af\u8cea\u5206\u5b50\u306e\u8aad\u307f\u8fbc\u307f\n 39   OBConversion conv;\n 40   conv.SetInAndOutFormats(\"PDB\", \"PDB\");\n 41   OBMol mol;\n 42   conv.Read(&mol, &ifs1);\n 43   ifs1.close();\n 44 \n 45   \/\/ \u4f4e\u5206\u5b50\u30ea\u30ac\u30f3\u30c9\u306e\u8aad\u307f\u8fbc\u307f\n 46   OBConversion conv2;\n 47   conv2.SetInAndOutFormats(\"SDF\", \"SDF\");\n 48   OBMol lig;\n 49   conv2.Read(&lig, &ifs2);\n 50   ifs2.close();\n 51 \n 52   \/\/ \u30ea\u30ac\u30f3\u30c9\u306e\u69cb\u6210\u539f\u5b50\u306b\u5370\u3092\u4ed8\u3051\u308b\n 53   for (auto ii = lig.BeginAtoms(); ii != lig.EndAtoms(); ii++) {\n 54     OBGenericData* pd = new OBPairData;\n 55     pd->SetAttribute(\"Ligand\");\n 56     (*ii)->SetData(pd);\n 57   }\n 58 \n 59   mol += lig;  \/\/ \u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u3092\u5408\u308f\u305b\u308b\n 60 \n 61   \/\/ \u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u30b0\u30eb\u30fc\u30d7\u306e\u8a2d\u5b9a\n 62   OBBitVec protein(mol.NumAtoms());\n 63   OBBitVec ligand(mol.NumAtoms());\n 64   for (auto ii = mol.BeginAtoms(); ii != mol.EndAtoms(); ii++) {\n 65     int ix = (*ii)->GetIdx();\n 66     if ((*ii)->HasData(\"Ligand\")) {\n 67       ligand.SetBitOn(ix);\n 68       protein.SetBitOff(ix);\n 69     } else {\n 70       ligand.SetBitOff(ix);\n 71       protein.SetBitOn(ix);\n 72     }\n 73   }\n 74 \n 75   \/\/ \u30bf\u30f3\u30d1\u30af\u8cea\u3092\u56fa\u5b9a\u3059\u308b\u8a2d\u5b9a\n 76   OBFFConstraints constraints;\n 77   for (auto ii = mol.BeginAtoms(); ii != mol.EndAtoms(); ii++) {\n 78     if (protein.BitIsSet((*ii)->GetIdx())) constraints.AddAtomConstraint((*ii)->GetIdx());\n 79   }\n 80 \n 81   \/\/ \u30a8\u30cd\u30eb\u30ae\u30fc\u8a08\u7b97\u306e\u30b0\u30eb\u30fc\u30d7\u306e\u8a2d\u5b9a\n 82   pFF->AddIntraGroup(ligand);\n 83   pFF->AddInterGroup(ligand);\n 84   pFF->AddInterGroups(ligand, protein);\n 85 \n 86   \/\/ \u30bb\u30c3\u30c8\u30a2\u30c3\u30d7\n 87   if (!pFF->Setup(mol, constraints)) {\n 88     cerr << \"ERROR: could not setup force field.\" << endl;\n 89   }\n 90 \n 91   \/\/ \u30ea\u30ac\u30f3\u30c9\u69cb\u9020\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\n 92   pFF->SteepestDescent(1000);\n 93   pFF->ConjugateGradients(1000);\n 94   pFF->GetCoordinates(mol);\n 95 \n 96   \/\/ \u76f8\u4e92\u4f5c\u7528\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u8a08\u7b97\n 97   pFF->ClearGroups();\n 98   pFF->AddInterGroups(ligand, protein);\n 99   pFF->SetupCalculations();\n100   cout << endl;\n101   cout << \"Interaction Energy = \" << pFF->Energy() << \" \" << pFF->GetUnit() << endl;\n102 \n103   \/\/ \u7d50\u679c\u306e\u51fa\u529b\n104   ofstream ofs(\"out.pdb\");\n105   conv.Write(&mol, &ofs);\n106   ofs.close();\n107 \n108   return 0;\n109 }<\/code><\/pre>\n\n\n\n
\u5148\u305a\u300115\uff5e23\u884c\u76ee\u306e\u529b\u5834\u306e\u8a2d\u5b9a\u3084\u30ed\u30b0\u306e\u8a2d\u5b9a\u306f\u4ee5\u524d\u306e\u30d6\u30ed\u30b0\u3067\u7d39\u4ecb\u3057\u305f\u901a\u308a\u3067\u3059\u3002\u305d\u3057\u306625\uff5e50\u884c\u76ee\u307e\u3067\u3067\u30bf\u30f3\u30d1\u30af\u8cea\u5206\u5b50\u3068\u30ea\u30ac\u30f3\u30c9\u5206\u5b50\u3092\u8aad\u307f\u8fbc\u3093\u3067\u3044\u307e\u3059\u3002\u3053\u3053\u307e\u3067\u306f\u7279\u306b\u65b0\u3057\u3044\u8a71\u984c\u306f\u3042\u308a\u307e\u305b\u3093\u3002\u554f\u984c\u306f\u3053\u306e\u5f8c\u304b\u3089\u3067\u3059\u300252\uff5e57\u884c\u76ee\u306f\u539f\u5b50\u306b\u30ea\u30ac\u30f3\u30c9\u3067\u3042\u308b\u3068\u3044\u3046\u5370\u3092\u4ed8\u3051\u3066\u3044\u307e\u3059\u3002\u5177\u4f53\u7684\u306b\u306fOBPairData\u3068\u3044\u3046\u30af\u30e9\u30b9\u306e\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u3092\u5404\u539f\u5b50\u306b\u767b\u9332\u3057\u3066\u3044\u307e\u3059\u300255\u884c\u76ee\u3067\u305d\u306e\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u306b”Ligand”\u3068\u3044\u3046\u5c5e\u6027\u3092SetAttribute<\/code>\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u3067\u30bb\u30c3\u30c8\u3057\u3066\u300156\u884c\u76ee\u3067SetData<\/code>\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u3092\u4f7f\u3063\u3066\u5404\u539f\u5b50\u306b\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u3092\u767b\u9332\u3057\u307e\u3059\u3002\u3061\u306a\u307f\u306bOBPairData\u30af\u30e9\u30b9\u306b\u306fSetValue<\/code>\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u3082\u3042\u3063\u3066\u3001\u4efb\u610f\u306e\u5024\u3092\u6587\u5b57\u5217\u3068\u3057\u3066\u81ea\u7531\u306b\u767b\u9332\u3067\u304d\u307e\u3059\u3002\u4eca\u56de\u306f”Ligand”\u3068\u3044\u3046\u5c5e\u6027\u306b\u5bfe\u3057\u3066\u767b\u9332\u3059\u3079\u304d\u5024\u306f\u7121\u3044\u306e\u3067\u30d7\u30ed\u30b0\u30e9\u30e0\u306b\u306f\u66f8\u3044\u3066\u3044\u307e\u305b\u3093\u304c\u3001OpenBabel\u3092\u4f7f\u3063\u3066\u5206\u5b50\u306b\u5bfe\u3057\u3066\u8272\u3005\u3068\u7d30\u304b\u3044\u64cd\u4f5c\u3092\u3059\u308b\u3068\u304d\u306b\u826f\u304f\u4f7f\u3044\u307e\u3059\u3002RDKit\u306b\u3082\u4f3c\u305f\u3088\u3046\u306a\u30af\u30e9\u30b9\u3084\u30e1\u30bd\u30c3\u30c9\u304c\u3042\u308b\u306e\u3067\u3001\u6a5f\u4f1a\u304c\u3042\u308c\u3070\u7d39\u4ecb\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
59\u884c\u76ee\u3067\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u3092\u30de\u30fc\u30b8\u3057\u3066\u3044\u307e\u3059\u3002OpenBabel\u3067\u306f\u5206\u5b50\u306e\u30de\u30fc\u30b8\u306f+=<\/code>\u3092\u4f7f\u3044\u307e\u3059\u300261\uff5e73\u884c\u76ee\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u90e8\u5206\u304c1\u306b\u306a\u308b\u30d3\u30c3\u30c8\u5217\u3068\u30ea\u30ac\u30f3\u30c9\u90e8\u5206\u304c1\u306b\u306a\u308b\u30d3\u30c3\u30c8\u5217\u3092\u4f5c\u6210\u3057\u3066\u3044\u307e\u3059\u3002\u30d3\u30c3\u30c8\u5217\u306fOBBitVec\u30af\u30e9\u30b9\u3092\u4f7f\u3063\u3066\u4f5c\u6210\u3057\u307e\u3059\u3002SetBitOn<\/code>\u3067\u30d3\u30c3\u30c8\u30921\u306b\u3057\u3066\u3001SetBitOff<\/code>\u3067\u30d3\u30c3\u30c8\u30920\u306b\u3057\u307e\u3059\u3002\u305d\u3057\u306675\uff5e79\u884c\u76ee\u3067\u30bf\u30f3\u30d1\u30af\u8cea\u3092\u56fa\u5b9a\u3059\u308b\u62d8\u675f\u6761\u4ef6\u3092\u8a2d\u5b9a\u3057\u3066\u3044\u307e\u3059\u300281\uff5e84\u884c\u76ee\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u8a08\u7b97\u3059\u308b\u30b0\u30eb\u30fc\u30d7\u3092\u8a2d\u5b9a\u3057\u3066\u3044\u307e\u3059\u3002
82\u884c\u76ee\u306f\u5206\u5b50\u5185\u306e\u529b\u5834\uff08\u7d50\u5408\u3057\u3066\u3044\u308b\u90e8\u5206\uff09\u30a8\u30cd\u30eb\u30ae\u30fc\u3067\u300183\u884c\u76ee\u306f\u5206\u5b50\u5185\u306evdw\u76f8\u4e92\u4f5c\u7528\u3068\u9759\u96fb\u76f8\u4e92\u4f5c\u7528\u306e\u8a08\u7b97\u3059\u308b\u8a2d\u5b9a\u3067\u3059\u300284\u884c\u76ee\u306f\u5206\u5b50\u9593\u3001\u3053\u306e\u5834\u5408\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u5206\u5b50\u306e\u8a2d\u5b9a\u3067\u3059\u3002\u305d\u3057\u3066\u8a2d\u5b9a\u306e\u6700\u5f8c\u306b87\u884c\u76ee\u3067\u529b\u5834\u306e\u30bb\u30c3\u30c8\u30a2\u30c3\u30d7\u3092\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
91\uff5e94\u884c\u76ee\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u8a08\u7b97\u3092\u3084\u3063\u3066\u3044\u307e\u3059\u3002\u6700\u7d42\u7684\u306b\u8a08\u7b97\u3057\u305f\u3044\u306e\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u76f8\u4e92\u4f5c\u7528\u30a8\u30cd\u30eb\u30ae\u30fc\u306a\u306e\u3067\u3001\u5206\u5b50\u5185\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u5024\u306f\u5dee\u3057\u5f15\u304d\u305f\u3044\u306e\u3067\u3001\u6539\u3081\u306697\uff5e99\u884c\u76ee\u3067\u5206\u5b50\u9593\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u307f\u8a08\u7b97\u3059\u308b\u3088\u3046\u306b\u3001\u518d\u8a2d\u5b9a\u3092\u884c\u3063\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u3066101\u884c\u76ee\u3067\u7d50\u679c\u3092\u6a19\u6e96\u51fa\u529b\u3057\u3066\u3044\u307e\u3059\u3002\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3057\u305f\u69cb\u9020\u3082104\uff5e106\u884c\u76ee\u3067\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9conv<\/code>\u3092\u4f7f\u3046\u3053\u3068\u306b\u3088\u3063\u3066PDB\u5f62\u5f0f\u3067\u51fa\u529b\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u8a08\u7b97\u7d50\u679c<\/h2>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u52d5\u304b\u3059\u3068\u8272\u3005\u3068\u51fa\u529b\u3055\u308c\u3066\u3001\u6700\u5f8c\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u51fa\u529b\u3068\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
S E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nSETTING UP ANGLE & STRETCH-BEND CALCULATIONS...\nSETTING UP TORSION CALCULATIONS...\nSETTING UP OOP CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nInteraction Energy = -19.6935 kcal\/mol<\/code><\/pre>\n\n\n\n
\u76f8\u4e92\u4f5c\u7528\u30a8\u30cd\u30eb\u30ae\u30fc\u306f-19.6935 kcal\/mol\u3068\u306a\u308a\u307e\u3057\u305f\u3002\u3068\u308a\u3042\u3048\u305a\u8ca0\u306e\u5024\u306b\u306a\u3063\u3066\u826f\u304b\u3063\u305f\u3067\u3059\u3002\u3042\u3068\u3001\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3057\u305f\u30ea\u30ac\u30f3\u30c9\u69cb\u9020\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u56f3\u306b\u306a\u308a\u307e\u3059\u3002\u6c34\u8272\u304c\u8a08\u7b97\u524d\u306e\u30ea\u30ac\u30f3\u30c9\u69cb\u9020\u3067\u3001\u30aa\u30ec\u30f3\u30b8\u8272\u304c\u6975\u5c0f\u5316\u5f8c\u306e\u69cb\u9020\u3067\u3059\u3002\u3053\u3046\u3057\u3066\u898b\u308b\u3068\u6bcd\u6838\u90e8\u5206\u306f\u3042\u307e\u308a\u52d5\u3044\u3066\u3044\u306a\u3044\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
\"\"
\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3059\u308b\u524d\u3068\u5f8c\u306e\u30ea\u30ac\u30f3\u30c9\u306e\u56f3<\/figcaption><\/figure><\/div>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n\n\n\n
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