FMO DATABASE

FMODB ID: Y1GN2

Calculation Name: 5T0H-X-Other547

Preferred Name: 26S proteasome

Target Type: PROTEIN COMPLEX

Ligand Name: adenosine-5'-diphosphate

Ligand 3-letter code: ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5T0H

Chain ID: X

ChEMBL ID: CHEMBL2364701

UniProt ID: P62333

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-420790.139543
FMO2-HF: Nuclear repulsion	388812.656444
FMO2-HF: Total energy	-31977.483099
FMO2-MP2: Total energy	-32071.376415

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:342:PHE)

Summations of interaction energy for fragment #1(A:342:PHE)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-30.91	-24.329	4.415	-3	-7.996	-0.015

Interaction energy analysis for fragmet #1(A:342:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.913

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	344	ARG	1	1.018	1.016	3.842	35.920	37.671	-0.012	-0.713	-1.026	-0.002
4	A	345	VAL	0	-0.067	-0.029	2.263	-11.451	-8.262	2.753	-1.725	-4.217	-0.009
5	A	346	GLN	0	0.088	0.050	4.300	0.240	0.410	0.000	-0.034	-0.136	0.000
9	A	350	ILE	0	0.017	0.016	2.282	-2.231	-1.780	1.285	-0.304	-1.432	-0.002
10	A	351	SER	0	-0.058	-0.040	5.260	1.437	1.470	-0.001	0.000	-0.032	0.000
12	A	353	LEU	0	-0.046	-0.027	2.733	-0.192	0.449	0.392	-0.189	-0.844	-0.002
44	A	385	LEU	0	-0.022	-0.005	4.405	1.559	1.700	-0.001	-0.007	-0.133	0.000
46	A	387	ILE	0	-0.050	-0.012	4.557	1.380	1.585	-0.001	-0.028	-0.176	0.000
6	A	347	ILE	0	0.009	-0.003	6.548	-1.691	-1.691	0.000	0.000	0.000	0.000
7	A	348	GLU	-1	-0.841	-0.930	8.546	-22.132	-22.132	0.000	0.000	0.000	0.000
8	A	349	HIS	0	0.049	0.041	7.121	-0.771	-0.771	0.000	0.000	0.000	0.000
11	A	352	SER	0	-0.014	-0.027	8.518	1.884	1.884	0.000	0.000	0.000	0.000
13	A	354	ILE	0	-0.037	-0.001	6.483	0.781	0.781	0.000	0.000	0.000	0.000
14	A	355	LYS	1	0.875	0.939	8.593	19.057	19.057	0.000	0.000	0.000	0.000
15	A	356	LEU	0	-0.028	0.002	11.537	1.371	1.371	0.000	0.000	0.000	0.000
16	A	357	SER	0	0.042	0.023	12.766	-0.539	-0.539	0.000	0.000	0.000	0.000
17	A	358	LYS	1	1.000	0.988	12.184	17.902	17.902	0.000	0.000	0.000	0.000
18	A	359	ALA	0	0.046	0.033	13.210	-0.290	-0.290	0.000	0.000	0.000	0.000
19	A	360	ASP	-1	-0.889	-0.967	15.486	-16.148	-16.148	0.000	0.000	0.000	0.000
20	A	361	VAL	0	0.024	0.020	8.719	-0.458	-0.458	0.000	0.000	0.000	0.000
21	A	362	GLU	-1	-0.840	-0.923	11.414	-19.146	-19.146	0.000	0.000	0.000	0.000
22	A	363	ARG	1	0.915	0.969	12.808	14.698	14.698	0.000	0.000	0.000	0.000
23	A	364	LYS	1	0.932	0.985	12.792	17.549	17.549	0.000	0.000	0.000	0.000
24	A	365	LEU	0	0.027	-0.005	6.834	-0.166	-0.166	0.000	0.000	0.000	0.000
25	A	366	SER	0	0.011	-0.014	11.218	0.166	0.166	0.000	0.000	0.000	0.000
26	A	367	GLN	0	0.012	0.000	14.160	0.323	0.323	0.000	0.000	0.000	0.000
27	A	368	MET	0	-0.062	-0.029	11.933	0.611	0.611	0.000	0.000	0.000	0.000
28	A	369	ILE	0	0.019	0.029	11.291	0.005	0.005	0.000	0.000	0.000	0.000
29	A	370	LEU	0	-0.067	-0.032	15.289	0.988	0.988	0.000	0.000	0.000	0.000
30	A	371	ASP	-1	-0.893	-0.962	17.158	-15.628	-15.628	0.000	0.000	0.000	0.000
31	A	372	LYS	1	0.858	0.927	16.711	16.998	16.998	0.000	0.000	0.000	0.000
32	A	373	LYS	1	0.927	0.965	15.105	15.931	15.931	0.000	0.000	0.000	0.000
33	A	374	PHE	0	-0.012	0.012	6.885	-1.506	-1.506	0.000	0.000	0.000	0.000
34	A	375	HIS	0	-0.018	-0.005	10.521	2.293	2.293	0.000	0.000	0.000	0.000
35	A	376	GLY	0	0.047	0.016	9.750	-3.769	-3.769	0.000	0.000	0.000	0.000
36	A	377	ILE	0	-0.063	-0.020	10.408	2.400	2.400	0.000	0.000	0.000	0.000
37	A	378	LEU	0	-0.010	-0.015	9.714	-2.732	-2.732	0.000	0.000	0.000	0.000
38	A	379	ASP	-1	-0.855	-0.932	11.424	-17.595	-17.595	0.000	0.000	0.000	0.000
39	A	380	GLN	0	-0.075	-0.048	12.854	-0.279	-0.279	0.000	0.000	0.000	0.000
40	A	381	GLY	0	-0.028	0.001	15.556	0.621	0.621	0.000	0.000	0.000	0.000
41	A	382	GLU	-1	-0.918	-0.966	13.939	-16.180	-16.180	0.000	0.000	0.000	0.000
42	A	383	GLY	0	-0.031	0.002	12.589	-0.853	-0.853	0.000	0.000	0.000	0.000
43	A	384	VAL	0	-0.035	-0.025	7.987	-2.342	-2.342	0.000	0.000	0.000	0.000
45	A	386	ILE	0	0.008	-0.016	6.058	-4.626	-4.626	0.000	0.000	0.000	0.000
47	A	388	PHE	0	-0.022	-0.033	7.955	-1.042	-1.042	0.000	0.000	0.000	0.000
48	A	389	ASP	-1	-0.937	-0.975	10.525	-25.925	-25.925	0.000	0.000	0.000	0.000
49	A	390	GLU	-1	-0.886	-0.942	12.931	-18.903	-18.903	0.000	0.000	0.000	0.000
50	A	391	PRO	0	-0.022	-0.002	14.773	1.136	1.136	0.000	0.000	0.000	0.000
51	A	392	PRO	0	-0.030	0.000	17.504	0.726	0.726	0.000	0.000	0.000	0.000
52	A	393	VAL	0	0.024	-0.003	20.974	0.333	0.333	0.000	0.000	0.000	0.000
53	A	394	ASP	-1	-0.844	-0.908	24.100	-11.971	-11.971	0.000	0.000	0.000	0.000
54	A	395	LYS	1	0.996	0.985	26.355	11.529	11.529	0.000	0.000	0.000	0.000
55	A	396	THR	0	-0.079	-0.049	27.251	0.464	0.464	0.000	0.000	0.000	0.000
56	A	397	TYR	0	-0.005	-0.007	24.037	0.397	0.397	0.000	0.000	0.000	0.000
57	A	398	GLU	-1	-0.916	-0.949	30.090	-9.431	-9.431	0.000	0.000	0.000	0.000
58	A	399	ALA	0	0.055	0.026	32.400	0.319	0.319	0.000	0.000	0.000	0.000
59	A	400	ALA	0	-0.015	0.012	32.664	0.334	0.334	0.000	0.000	0.000	0.000
60	A	401	LEU	0	-0.024	-0.021	32.699	0.307	0.307	0.000	0.000	0.000	0.000
61	A	402	GLU	-1	-0.924	-0.948	35.939	-8.122	-8.122	0.000	0.000	0.000	0.000
62	A	403	THR	0	-0.055	-0.059	36.915	0.267	0.267	0.000	0.000	0.000	0.000
63	A	404	ILE	0	-0.005	-0.003	35.498	0.245	0.245	0.000	0.000	0.000	0.000
64	A	405	GLN	0	0.020	0.015	39.251	0.406	0.406	0.000	0.000	0.000	0.000
65	A	406	ASN	0	-0.005	0.006	41.726	0.332	0.332	0.000	0.000	0.000	0.000
66	A	407	MET	0	0.010	0.014	42.242	0.267	0.267	0.000	0.000	0.000	0.000
67	A	408	SER	0	-0.052	-0.040	44.875	0.182	0.182	0.000	0.000	0.000	0.000
68	A	409	LYS	1	1.001	1.003	43.311	7.462	7.462	0.000	0.000	0.000	0.000
69	A	410	VAL	0	-0.005	-0.001	47.693	0.184	0.184	0.000	0.000	0.000	0.000
70	A	411	VAL	0	0.012	0.011	49.373	0.180	0.180	0.000	0.000	0.000	0.000
71	A	412	ASP	-1	-0.878	-0.953	49.456	-6.326	-6.326	0.000	0.000	0.000	0.000
72	A	413	SER	0	-0.142	-0.085	52.240	0.179	0.179	0.000	0.000	0.000	0.000
73	A	414	LEU	0	0.022	0.012	53.021	0.146	0.146	0.000	0.000	0.000	0.000
74	A	415	TYR	0	0.021	0.024	53.069	0.177	0.177	0.000	0.000	0.000	0.000
75	A	416	ASN	0	-0.030	-0.022	57.306	0.192	0.192	0.000	0.000	0.000	0.000
76	A	417	LYS	1	0.921	0.949	54.841	5.924	5.924	0.000	0.000	0.000	0.000
77	A	418	ALA	0	0.027	0.016	59.506	0.061	0.061	0.000	0.000	0.000	0.000
78	A	419	LYS	1	0.966	0.992	60.976	5.351	5.351	0.000	0.000	0.000	0.000
79	A	420	LYS	1	0.885	0.953	62.763	5.083	5.083	0.000	0.000	0.000	0.000
80	A	421	LEU	0	-0.098	-0.051	62.499	0.050	0.050	0.000	0.000	0.000	0.000
81	A	422	THR	-1	-0.904	-0.935	65.678	-4.812	-4.812	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:342:PHE)