(原创,转载请注明出处)
1、查看获取小分子信息

直接打开https://www.rcsb.org/ligand/XPI
下载sdf格式
wget https://files.rcsb.org/ligands/download/XPI_ideal.sdf
obabel -isdf XPI_ideal.sdf -osmi -O 8r2k.smi
[chenfj@login26 testnew01]$ cat 8r2k.smi
C1=C(C(=O)O[C@H]1c1c(OC)cc(OC)c(OC)c1)Nc1ccc(cc1)S(=O)(=O)N XPI
打开https://www.rcsb.org/fasta/entry/8R2K/display fasta文件
生成json格式,其中ZN和GOL等基础分子(离子),为默认的ccd格式,是有的,不需要提供smiles格式:
"modelSeeds": [1,22,333,4444,66666],
"sequence":"MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK"
"smiles":"C1=C(C(=O)O[C@H]1c1c(OC)cc(OC)c(OC)c1)Nc1ccc(cc1)S(=O)(=O)N"
结果偏移了许多,蛋白质rmsd为 2.568,红色圈飘了许多
