FMO DATABASE | MD

Group	PDB	Ligand	MD Time	Number of Entries	Registration Date	Reference	Reference_DOI
1DD1-A-MD418			1 - 100 ns	49
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
1S2C-A -MD355			10 - 100 ns	10
1UBQ-A-MD61			1 - 10000 fs	446
1ZUA-A-MD353			10 - 100 ns	10
2AXA-A-MD59	2AXA	FHM	10100 - 11000 ps	10	2019-08-13
2FZ8-A-MD352			10 - 100 ns	58
2FZD-A-MD352			10 - 100 ns	10
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
3R43-A -MD355			10 - 100 ns	10
3R58-A -MD355			10 - 100 ns	10
3R6I-A -MD355			10 - 100 ns	10
3R7M-A -MD355			10 - 100 ns	10
3R8G-A -MD355			10 - 100 ns	10
3R8H-A -MD355			10 - 100 ns	10
3R94-A -MD355			10 - 100 ns	10
3RLJ-A-MD59	3RLJ	RLJ	10100 - 11000 ps	10	2019-08-13
3UFY-A -MD355			10 - 100 ns	10
3UG8-A -MD355			10 - 100 ns	10
3UWE-A -MD355			10 - 100 ns	10
4DBS-A -MD355			10 - 100 ns	10
4DBU-A -MD355			10 - 100 ns	10
4DBW-A -MD355			10 - 100 ns	10
4FA3-A -MD355			10 - 100 ns	10
4FAM-A -MD355			10 - 100 ns	10
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 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
4I5X-A-MD353			10 - 100 ns	10
4JIH-A-MD353			10 - 100 ns	10
4JII-A-MD353			10 - 100 ns	10
4JIR-A-MD352			10 - 100 ns	10
4JQ1-A-MD354			10 - 100 ns	109
4JQ2-A-MD354			10 - 100 ns	9
4JQ3-A-MD354			10 - 100 ns	10
4JQA-A-MD354			10 - 100 ns	10
4JTQ-A-MD354			10 - 100 ns	10
4JTR-A-MD354			10 - 100 ns	10
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
4WEV-A-MD353			10 - 100 ns	10
4XZL-A-MD353			10 - 100 ns	10
4ZS7-A-MD374	4ZS7		37 - 100 ns	10	2023-03-23
5IBN-A-MD68			200 - 1100 ps	9
5LIK-A-MD353			10 - 100 ns	10
5LIU-A-MD353			10 - 100 ns	10
5LIW-A-MD353			10 - 100 ns	10
5LIX-A-MD353			10 - 100 ns	10
5M2F-A-MD353			10 - 100 ns	10
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
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
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
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
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 F�rstner, 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.
7BV2-ABCD-MD419			42110 - 51110 ps	10
7BV2-ABCD-MD420			42110 - 51110 ps	10
7BV2-ABCD-MD421			42110 - 51110 ps	10
7BV2-ABCD-MD422			42110 - 51110 ps	10
7BV2-ABCD-MD423			42110 - 51110 ps	10
7BV2-ABCD-MD424			42110 - 51110 ps	10
7BV2-ABCD-MD425			42110 - 51110 ps	10
Group	PDB	Ligand	MD Time	Number of Entries	Registration Date	Reference	Reference_DOI

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