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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-09-03

All entries: 45600

Number of unique PDB entries: 8613

MD Entries
Group PDB Ligand MD Time Number of Entries Registration Date Reference Reference_DOI InitialStructure
1L2Y-A-MD41L2Y100 - 100000 ps9912018-02-27
1L2Y-A-MD492OTU100 - 100000 ps10002019-08-09
1L2Y-A-MD502OTU100 - 100000 ps10002019-08-09
1L2Y-A-MD512OTU100 - 100000 ps10002019-08-09
1L2Y-A-MD522OTU100 - 100000 ps10002019-08-09
1L2Y-A-MD532OTU100 - 100000 ps10002019-08-13
1L2Y-A-MD542OTU100 - 100000 ps10002019-08-13
1L2Y-A-MD552OTU100 - 100000 ps10002019-08-13
1L2Y-A-MD562OTU100 - 100000 ps10002019-08-13
1L2Y-A-MD572OTU100 - 100000 ps10002019-08-13
1L2Y-A-MD582OTU100 - 100000 ps10002019-08-13
2AXA-A-MD592AXAFHM10100 - 11000 ps102019-08-13
3ALZ-A-MD4673ALZ50 - 50 ns12024-03-27
3ALZ-A-MD4703ALZ50 - 50 ns12024-03-27
3ALZ-A-MD4713ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4723ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4733ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4743ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4753ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4763ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4773ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4783ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4793ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4803ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4813ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4823ALZ50 - 50 ns12024-03-28
3ALZ-A-MD4833ALZ50 - 50 ns12024-04-05
3ALZ-A-MD4843ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4853ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4863ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4873ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4883ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4893ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4903ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4913ALZ50 - 50 ns12024-04-22
3ALZ-A-MD4923ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4933ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4943ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4953ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4963ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4973ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4983ALZ50 - 50 ns12024-04-23
3ALZ-A-MD4993ALZ50 - 50 ns12024-04-23
3ALZ-A-MD5003ALZ50 - 50 ns12024-04-24
3ALZ-A-MD5013ALZ50 - 50 ns12024-04-24
3ALZ-A-MD5023ALZ50 - 50 ns12024-04-24
3ALZ-A-MD5033ALZ50 - 50 ns12024-04-24
3ALZ-A-MD5043ALZ50 - 50 ns12024-04-25
3ALZ-A-MD5053ALZ50 - 50 ns12024-04-25
3ALZ-A-MD5063ALZ50 - 50 ns12024-04-25
3ALZ-A-MD5073ALZ50 - 50 ns12024-04-25
3B5R-A-MD593B5RB5R10100 - 11000 ps102019-08-13
3B66-A-MD593B66B6610100 - 11000 ps102019-08-13
3B67-A-MD593B67B6710100 - 11000 ps102019-08-13
3B68-A-MD593B68B6810100 - 11000 ps102019-08-13
3RLJ-A-MD593RLJRLJ10100 - 11000 ps102019-08-13
4EIY-A-MD5424EIYZMA55 - 55 ns12025-07-23Takumi Ueda, Tomoki Tsuchida, Masatoshi Kurita, Takuya Mizumura, Shunsuke Imai, Yutaro Shiraishi, Yutaka Kofuku, Shuhei Miyakawa, Kaori Fukuzawa, Koh Takeuchi, Ichio Shimada, Structural basis of the residence time of adenosine A2A receptor ligands revealed by NMR, To be published.
4EIY-A-MD5434EIYZMA76 - 76 ns12025-07-23Takumi Ueda, Tomoki Tsuchida, Masatoshi Kurita, Takuya Mizumura, Shunsuke Imai, Yutaro Shiraishi, Yutaka Kofuku, Shuhei Miyakawa, Kaori Fukuzawa, Koh Takeuchi, Ichio Shimada, Structural basis of the residence time of adenosine A2A receptor ligands revealed by NMR, To be published.
4EIY-A-MD5444EIYZMA78 - 78 ns12025-07-23Takumi Ueda, Tomoki Tsuchida, Masatoshi Kurita, Takuya Mizumura, Shunsuke Imai, Yutaro Shiraishi, Yutaka Kofuku, Shuhei Miyakawa, Kaori Fukuzawa, Koh Takeuchi, Ichio Shimada, Structural basis of the residence time of adenosine A2A receptor ligands revealed by NMR, To be published.
4FKG-AB-MD3284FKGLIG12 - 50 ns1002022-02-22K. Takaba et al., Protein-Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy, To be published.
4FKI-AB-MD3294FKILIG12 - 50 ns1002022-03-09K. Takaba et al., Protein-Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy, To be published.
4FKL-AB-MD3394FKLLIG12 - 50 ns1002022-09-01K. Takaba et al., Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy, J. Comput. Chem., 43, 1362-1371, 2022.10.1002/jcc.26940
4FKQ-AB-MD3344FKQLIG12 - 50 ns1002022-08-10K. Takaba et al., Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy, J. Comput. Chem., 43, 1362-1371, 2022.10.1002/jcc.26940
4FKR-AB-MD3354FKRLIG12 - 50 ns1002022-08-19K. Takaba et al., Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy, J. Comput. Chem., 43, 1362-1371, 2022.10.1002/jcc.26940
4FKS-AB-MD3404FKSLIG12 - 50 ns1002022-09-05K. Takaba et al., Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy, J Comput Chem. 2022;43:1362-1371.10.1002/jcc.26940
4FKW-AB-MD3414FKWLIG12 - 50 ns1002022-09-08K. Takaba et al., Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy, J Comput Chem. 2022;43:1362-1371.10.1002/jcc.26940
4JGT-A-MD5204JGT50 - 50 ns252025-03-27
4O9H-A-MD3754O9H37 - 100 ns102023-03-23
4OHA-A-MD594OHAHFT10100 - 11000 ps202019-08-13
4OKW-A-MD594OKW19810100 - 11000 ps102019-08-13
4ZS7-A-MD3744ZS737 - 100 ns102023-03-23
6W63-C-MD4286W631UN50100 - 101100 ps1032023-07-12Handa, Y.; Okuwaki, K.; Kawashima, Y.; Hatada, R.; Mochizuki, Y.; Komeiji, Y.; Tanaka, S.; Furuishi, T.; Yonemochi, E.; Honma, T.; Fukuzawa, K. Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. J. Phys. Chem. B 2024, 128, 10, 2249-226510.1021/acs.jpcb.3c055649MM52
6W63-C-MD4296W631UN50100 - 101100 ps1032023-07-13Handa, Y.; Okuwaki, K.; Kawashima, Y.; Hatada, R.; Mochizuki, Y.; Komeiji, Y.; Tanaka, S.; Furuishi, T.; Yonemochi, E.; Honma, T.; Fukuzawa, K. Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. J. Phys. Chem. B 2024, 128, 10, 2249-226510.1021/acs.jpcb.3c05564L7759
6W63-C-MD4306W631UN50100 - 101100 ps1032023-07-13Handa, Y.; Okuwaki, K.; Kawashima, Y.; Hatada, R.; Mochizuki, Y.; Komeiji, Y.; Tanaka, S.; Furuishi, T.; Yonemochi, E.; Honma, T.; Fukuzawa, K. Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. J. Phys. Chem. B 2024, 128, 10, 2249-226510.1021/acs.jpcb.3c055643772L
6W63-C-MD4316W631UN50100 - 101100 ps1032023-07-14Handa, Y.; Okuwaki, K.; Kawashima, Y.; Hatada, R.; Mochizuki, Y.; Komeiji, Y.; Tanaka, S.; Furuishi, T.; Yonemochi, E.; Honma, T.; Fukuzawa, K. Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. J. Phys. Chem. B 2024, 128, 10, 2249-226510.1021/acs.jpcb.3c05564M99KZ
6XKI-A-MD4336XKIV6D73 - 100 ns402023-09-19Hironori Saito, Yuma Handa, Mingming Chen, Tilman Schneider-Poetsch, Yuichi Shichino, Mari Takahashi, Daniel Romo, Minoru Yoshida, Alois Frstner, Takuhiro Ito, Kaori Fukuzawa, Shintaro Iwasaki Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs, To be published.
Group PDB Ligand MD Time Number of Entries Registration Date Reference Reference_DOI InitialStructure

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