FMO DATABASE

FMODB ID: 5Y2NZ

Calculation Name: 3D5J-B-Xray547

Preferred Name:

Target Type:

Ligand Name: glutathione

Ligand 3-letter code: GSH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D5J

Chain ID: B

ChEMBL ID:

UniProt ID: P17695

Base Structure: X-ray

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-803823.250257
FMO2-HF: Nuclear repulsion	763193.004672
FMO2-HF: Total energy	-40630.245585
FMO2-MP2: Total energy	-40750.100248

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-98.202	-95.198	0.101	-1.683	-1.422	-0.005

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.933

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	4	GLN	0	0.043	0.017	3.049	-14.466	-11.462	0.101	-1.683	-1.422	-0.005
4	A	5	GLU	-1	-0.906	-0.946	5.715	-25.737	-25.737	0.000	0.000	0.000	0.000
5	A	6	THR	0	0.014	-0.004	7.060	2.696	2.696	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.039	0.026	6.099	2.828	2.828	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.035	-0.019	8.471	3.178	3.178	0.000	0.000	0.000	0.000
8	A	9	HIS	0	0.029	0.012	11.026	2.068	2.068	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.018	0.002	11.186	1.854	1.854	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.938	0.965	11.488	25.840	25.840	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.878	-0.910	14.394	-15.382	-15.382	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.032	-0.026	15.517	1.215	1.215	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.066	-0.035	14.955	0.988	0.988	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.004	0.002	18.494	0.791	0.791	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.099	-0.058	19.646	1.231	1.231	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.830	0.918	22.548	12.770	12.770	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.789	-0.874	24.339	-10.574	-10.574	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.018	-0.005	25.508	-0.090	-0.090	0.000	0.000	0.000	0.000
19	A	20	PHE	0	0.025	0.017	16.425	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.002	-0.018	21.859	0.091	0.091	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.025	0.033	17.255	0.013	0.013	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.008	-0.009	19.167	0.360	0.360	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.883	0.927	16.669	16.522	16.522	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.006	-0.004	22.047	0.716	0.716	0.000	0.000	0.000	0.000
25	A	26	TYR	0	0.012	-0.002	23.775	0.769	0.769	0.000	0.000	0.000	0.000
26	A	27	CYS	0	-0.084	-0.015	23.062	0.429	0.429	0.000	0.000	0.000	0.000
27	A	28	PRO	0	0.036	0.006	25.374	0.126	0.126	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.041	0.005	25.393	0.169	0.169	0.000	0.000	0.000	0.000
29	A	30	SER	0	0.092	0.042	23.992	-0.223	-0.223	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.876	0.945	25.791	10.922	10.922	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.021	0.025	29.310	0.255	0.255	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.027	0.006	25.059	0.123	0.123	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.025	-0.012	25.825	0.205	0.205	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.031	-0.014	29.181	0.326	0.326	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.004	-0.009	30.810	0.309	0.309	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.006	-0.007	26.752	0.193	0.193	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.001	-0.019	27.352	0.110	0.110	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.044	-0.014	33.048	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.851	-0.906	35.617	-8.583	-8.583	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.032	-0.029	32.737	0.208	0.208	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.071	-0.027	36.058	0.082	0.082	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.049	0.038	30.372	0.069	0.069	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.013	0.011	33.530	-0.051	-0.051	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.892	0.940	28.647	10.397	10.397	0.000	0.000	0.000	0.000
45	A	46	SER	0	0.006	0.002	29.763	-0.333	-0.333	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.839	0.916	29.737	9.238	9.238	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.004	-0.002	26.501	-0.273	-0.273	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.024	0.000	19.798	0.222	0.222	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.019	-0.016	22.974	-0.104	-0.104	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.002	0.003	16.903	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.819	-0.930	19.822	-13.277	-13.277	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.040	-0.029	14.793	-0.085	-0.085	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.835	-0.898	16.861	-14.581	-14.581	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.925	-0.955	19.391	-11.957	-11.957	0.000	0.000	0.000	0.000
55	A	56	MET	0	-0.069	-0.022	16.592	0.029	0.029	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.031	0.009	16.132	-0.449	-0.449	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.009	0.003	11.834	0.417	0.417	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.041	0.010	12.137	-1.356	-1.356	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.028	-0.006	10.048	0.694	0.694	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.858	-0.935	7.454	-27.631	-27.631	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.007	-0.008	8.654	-2.292	-2.292	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.016	-0.013	11.441	0.905	0.905	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.888	-0.950	6.874	-32.096	-32.096	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.036	-0.029	7.366	-2.300	-2.300	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.007	-0.010	8.248	1.173	1.173	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.818	-0.849	9.914	-25.590	-25.590	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.957	-0.973	5.720	-45.979	-45.979	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.105	-0.048	8.892	1.859	1.859	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.018	-0.036	11.694	2.150	2.150	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.004	0.014	12.928	1.483	1.483	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.084	-0.048	14.126	0.847	0.847	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.869	0.912	11.041	25.700	25.700	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.033	-0.013	14.797	0.036	0.036	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.037	0.029	17.308	-0.315	-0.315	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.042	-0.032	19.763	0.609	0.609	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.041	-0.023	15.720	0.680	0.680	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.002	0.006	19.361	-0.091	-0.091	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.059	0.017	16.191	-0.471	-0.471	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.017	-0.008	21.742	0.419	0.419	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.002	-0.010	25.085	-0.097	-0.097	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.030	0.025	21.100	0.090	0.090	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.907	0.962	20.733	11.286	11.286	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.007	0.006	18.674	0.306	0.306	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.088	-0.053	20.910	0.648	0.648	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.053	0.037	20.918	0.410	0.410	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.048	0.017	21.842	-0.265	-0.265	0.000	0.000	0.000	0.000
87	A	88	ASN	0	0.024	0.008	23.101	0.479	0.479	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.007	0.003	25.827	0.403	0.403	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.840	-0.892	23.951	-12.623	-12.623	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.041	0.016	26.681	0.385	0.385	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.808	-0.899	28.260	-9.046	-9.046	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.041	-0.025	29.703	0.493	0.493	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.030	-0.025	27.320	0.348	0.348	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.797	0.883	31.505	9.429	9.429	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.830	0.908	34.060	9.351	9.351	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.007	0.001	32.118	0.243	0.243	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.038	0.028	36.114	0.119	0.119	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.948	0.956	31.767	8.973	8.973	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.003	0.009	29.453	-0.185	-0.185	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.034	0.013	32.184	-0.061	-0.061	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.920	-0.946	33.888	-8.504	-8.504	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.034	-0.030	28.071	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.028	0.008	30.274	-0.225	-0.225	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.865	0.936	32.734	8.481	8.481	0.000	0.000	0.000	0.000
105	A	106	PRO	0	-0.048	-0.023	31.683	0.165	0.165	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.035	-0.007	30.003	-0.138	-0.138	0.000	0.000	0.000	0.000
107	A	108	PHE	-1	-0.943	-0.951	33.034	-8.539	-8.539	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:2:VAL)