| 1L2Y-A-MD4 | 1L2Y | | 100 - 100000 ps | 991 | 2018-02-27 | | | |
| 1L2Y-A-MD49 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-09 | | | |
| 1L2Y-A-MD50 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-09 | | | |
| 1L2Y-A-MD51 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-09 | | | |
| 1L2Y-A-MD52 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-09 | | | |
| 1L2Y-A-MD53 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 1L2Y-A-MD54 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 1L2Y-A-MD55 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 1L2Y-A-MD56 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 1L2Y-A-MD57 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 1L2Y-A-MD58 | 2OTU | | 100 - 100000 ps | 1000 | 2019-08-13 | | | |
| 2AXA-A-MD59 | 2AXA | FHM | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 3ALZ-A-MD467 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-27 | | | |
| 3ALZ-A-MD470 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-27 | | | |
| 3ALZ-A-MD471 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD472 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD473 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD474 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD475 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD476 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD477 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD478 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD479 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD480 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD481 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD482 | 3ALZ | | 50 - 50 ns | 1 | 2024-03-28 | | | |
| 3ALZ-A-MD483 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-05 | | | |
| 3ALZ-A-MD484 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD485 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD486 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD487 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD488 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD489 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD490 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD491 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-22 | | | |
| 3ALZ-A-MD492 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD493 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD494 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD495 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD496 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD497 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD498 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD499 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-23 | | | |
| 3ALZ-A-MD500 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-24 | | | |
| 3ALZ-A-MD501 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-24 | | | |
| 3ALZ-A-MD502 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-24 | | | |
| 3ALZ-A-MD503 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-24 | | | |
| 3ALZ-A-MD504 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-25 | | | |
| 3ALZ-A-MD505 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-25 | | | |
| 3ALZ-A-MD506 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-25 | | | |
| 3ALZ-A-MD507 | 3ALZ | | 50 - 50 ns | 1 | 2024-04-25 | | | |
| 3B5R-A-MD59 | 3B5R | B5R | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 3B66-A-MD59 | 3B66 | B66 | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 3B67-A-MD59 | 3B67 | B67 | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 3B68-A-MD59 | 3B68 | B68 | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 3RLJ-A-MD59 | 3RLJ | RLJ | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 4EIY-A-MD542 | 4EIY | ZMA | 55 - 55 ns | 1 | 2025-07-23 | Ueda, T., Tsuchida, T., Kurita, M., Mizumura, T., Imai, S., Shiraishi, Y., Kofuku, Y., Miyakawa, S., Fukuzawa, K., Takeuchi, K., & Shimada, I. (2025). Structural basis of the residence time of adenosine A?A receptor ligands revealed by NMR. Chemical Science, 16, 17948?17955. | 10.1039/D5SC02398J | |
| 4EIY-A-MD543 | 4EIY | ZMA | 76 - 76 ns | 1 | 2025-07-23 | Ueda, T., Tsuchida, T., Kurita, M., Mizumura, T., Imai, S., Shiraishi, Y., Kofuku, Y., Miyakawa, S., Fukuzawa, K., Takeuchi, K., & Shimada, I. (2025). Structural basis of the residence time of adenosine A?A receptor ligands revealed by NMR. Chemical Science, 16, 17948?17955. | 10.1039/D5SC02398J | |
| 4EIY-A-MD544 | 4EIY | ZMA | 78 - 78 ns | 1 | 2025-07-23 | Ueda, T., Tsuchida, T., Kurita, M., Mizumura, T., Imai, S., Shiraishi, Y., Kofuku, Y., Miyakawa, S., Fukuzawa, K., Takeuchi, K., & Shimada, I. (2025). Structural basis of the residence time of adenosine A?A receptor ligands revealed by NMR. Chemical Science, 16, 17948?17955. | 10.1039/D5SC02398J | |
| 4FKG-AB-MD328 | 4FKG | LIG | 12 - 50 ns | 100 | 2022-02-22 | K. Takaba et al., Protein-Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy, To be published. | | |
| 4FKI-AB-MD329 | 4FKI | LIG | 12 - 50 ns | 100 | 2022-03-09 | K. Takaba et al., Protein-Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy, To be published. | | |
| 4FKL-AB-MD339 | 4FKL | LIG | 12 - 50 ns | 100 | 2022-09-01 | K. 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-MD334 | 4FKQ | LIG | 12 - 50 ns | 100 | 2022-08-10 | K. 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-MD335 | 4FKR | LIG | 12 - 50 ns | 100 | 2022-08-19 | K. 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-MD340 | 4FKS | LIG | 12 - 50 ns | 100 | 2022-09-05 | K. 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-MD341 | 4FKW | LIG | 12 - 50 ns | 100 | 2022-09-08 | K. Takaba et al., Protein-Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy, To be published. | | |
| 4JGT-A-MD520 | 4JGT | | 50 - 50 ns | 25 | 2025-03-27 | | | |
| 4O9H-A-MD375 | 4O9H | | 37 - 100 ns | 10 | 2023-03-23 | | | |
| 4OHA-A-MD59 | 4OHA | HFT | 10100 - 11000 ps | 20 | 2019-08-13 | | | |
| 4OKW-A-MD59 | 4OKW | 198 | 10100 - 11000 ps | 10 | 2019-08-13 | | | |
| 4ZS7-A-MD374 | 4ZS7 | | 37 - 100 ns | 10 | 2023-03-23 | | | |
| 6W63-C-MD428 | 6W63 | 1UN | 50100 - 101100 ps | 103 | 2023-07-12 | Handa, 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, 2249-2265 | 10.1021/acs.jpcb.3c05564 | 9MM52 |
| 6W63-C-MD429 | 6W63 | 1UN | 50100 - 101100 ps | 103 | 2023-07-13 | Handa, 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, 2249-2265 | 10.1021/acs.jpcb.3c05564 | L7759 |
| 6W63-C-MD430 | 6W63 | 1UN | 50100 - 101100 ps | 103 | 2023-07-13 | Handa, 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, 2249-2265 | 10.1021/acs.jpcb.3c05564 | 3772L |
| 6W63-C-MD431 | 6W63 | 1UN | 50100 - 101100 ps | 103 | 2023-07-14 | Handa, 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, 2249-2265 | 10.1021/acs.jpcb.3c05564 | M99KZ |
| 6XKI-A-MD433 | 6XKI | V6D | 73 - 100 ns | 40 | 2023-09-19 | Hironori 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. | | |
| UserDefined-MD551 | | | - | 8 | 2025-10-14 | Honoka MATSUMOTO, Koji OKUWAKI, Kenjirou HIGASHI, Takayuki FURUISHI, Kaori FUKUZAWA, Etsuo YONEMOCHI, Analysis of Moisture Stability in Amorphous Solid DispersionsUsing Molecular Dynamics and FMO Methods, Journal of Computer Chemistry, Japan, 2024, Volume 23, Issue 4, Pages 115-125. | 10.2477/jccj.2024-0031 | |
