FMO DATABASE

FMODB ID: 5N8YZ

Calculation Name: 3L4F-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L4F

Chain ID: A

ChEMBL ID:

UniProt ID: O55043

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-270940.49198
FMO2-HF: Nuclear repulsion	244933.330464
FMO2-HF: Total energy	-26007.161516
FMO2-MP2: Total energy	-26081.334282

3D Structure

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:586:MET)

Summations of interaction energy for fragment #1(A:586:MET)

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.
-14.4	-12.591	0.93	-0.176	-2.561	-0.006

Interaction energy analysis for fragmet #1(A:586:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : -0.028

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].
4	A	587	GLU	-1	-0.969	-0.829	3.882	1.552	2.345	0.009	-0.377	-0.425	-0.001
5	A	588	LYS	0	0.035	-0.072	3.645	-1.135	1.044	-0.017	-1.254	-0.907	0.000
6	A	588	LYS	1	0.761	1.016	3.950	-4.854	-4.663	0.001	-0.060	-0.132	0.000
7	A	589	SER	0	0.130	-0.063	5.404	-0.631	-0.631	0.000	0.000	0.000	0.000
8	A	589	SER	0	0.007	0.099	9.617	0.029	0.029	0.000	0.000	0.000	0.000
9	A	590	LEU	0	0.054	-0.066	7.859	-0.366	-0.366	0.000	0.000	0.000	0.000
10	A	590	LEU	0	-0.085	0.097	8.213	0.045	0.045	0.000	0.000	0.000	0.000
11	A	591	VAL	0	0.084	-0.107	3.820	-0.960	-0.858	0.010	-0.042	-0.070	0.000
12	A	591	VAL	0	-0.063	0.095	2.515	0.112	0.257	0.853	-0.442	-0.556	0.002
13	A	592	ASP	0	0.114	-0.096	4.656	-0.299	-0.279	-0.002	-0.013	-0.004	0.000
14	A	592	ASP	-1	-0.900	-0.816	3.369	-8.118	-9.729	0.078	2.012	-0.478	-0.007
15	A	593	THR	0	0.089	-0.065	5.248	0.022	0.012	-0.002	0.000	0.011	0.000
16	A	593	THR	0	-0.075	0.036	9.569	0.070	0.070	0.000	0.000	0.000	0.000
17	A	594	VAL	0	0.030	-0.088	8.251	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	594	VAL	0	-0.125	0.071	7.962	0.068	0.068	0.000	0.000	0.000	0.000
19	A	595	TYR	0	0.048	-0.082	6.223	0.501	0.501	0.000	0.000	0.000	0.000
20	A	595	TYR	0	-0.019	0.084	5.400	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	596	ALA	0	0.139	-0.073	7.568	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	596	ALA	0	-0.060	0.116	8.914	0.001	0.001	0.000	0.000	0.000	0.000
23	A	597	LEU	0	0.165	-0.041	9.662	0.109	0.109	0.000	0.000	0.000	0.000
24	A	597	LEU	0	-0.089	0.090	12.332	0.041	0.041	0.000	0.000	0.000	0.000
25	A	598	LYS	0	0.097	-0.075	11.229	0.144	0.144	0.000	0.000	0.000	0.000
26	A	598	LYS	1	0.783	1.027	9.138	0.580	0.580	0.000	0.000	0.000	0.000
27	A	599	ASP	0	0.075	-0.125	11.292	0.215	0.215	0.000	0.000	0.000	0.000
28	A	599	ASP	-1	-1.017	-0.844	10.209	-1.536	-1.536	0.000	0.000	0.000	0.000
29	A	600	GLU	0	0.060	-0.152	12.820	0.112	0.112	0.000	0.000	0.000	0.000
30	A	600	GLU	-1	-1.007	-0.851	13.533	-0.801	-0.801	0.000	0.000	0.000	0.000
31	A	601	VAL	0	0.022	-0.117	15.252	0.076	0.076	0.000	0.000	0.000	0.000
32	A	601	VAL	0	-0.130	0.084	16.019	0.021	0.021	0.000	0.000	0.000	0.000
33	A	602	GLN	0	0.080	-0.119	16.079	0.094	0.094	0.000	0.000	0.000	0.000
34	A	602	GLN	0	-0.037	0.125	16.088	0.076	0.076	0.000	0.000	0.000	0.000
35	A	603	GLU	0	0.076	-0.132	17.468	0.068	0.068	0.000	0.000	0.000	0.000
36	A	603	GLU	-1	-0.906	-0.781	17.347	-0.517	-0.517	0.000	0.000	0.000	0.000
37	A	604	LEU	0	0.113	-0.094	19.264	0.047	0.047	0.000	0.000	0.000	0.000
38	A	604	LEU	0	-0.073	0.115	20.304	0.005	0.005	0.000	0.000	0.000	0.000
39	A	605	ARG	0	0.184	-0.046	20.855	0.047	0.047	0.000	0.000	0.000	0.000
40	A	605	ARG	1	0.755	1.015	17.874	0.308	0.308	0.000	0.000	0.000	0.000
41	A	606	GLN	0	-0.031	-0.163	22.022	0.049	0.049	0.000	0.000	0.000	0.000
42	A	606	GLN	0	-0.127	0.065	20.440	0.022	0.022	0.000	0.000	0.000	0.000
43	A	607	ASP	0	0.155	-0.107	23.516	0.033	0.033	0.000	0.000	0.000	0.000
44	A	607	ASP	-1	-0.891	-0.750	24.166	-0.346	-0.346	0.000	0.000	0.000	0.000
45	A	608	ASN	0	0.045	-0.086	25.326	0.019	0.019	0.000	0.000	0.000	0.000
46	A	608	ASN	0	-0.165	0.046	25.053	0.021	0.021	0.000	0.000	0.000	0.000
47	A	609	LYS	0	0.100	-0.082	26.679	0.022	0.022	0.000	0.000	0.000	0.000
48	A	609	LYS	1	0.864	1.051	24.646	0.200	0.200	0.000	0.000	0.000	0.000
49	A	610	LYS	0	0.023	-0.114	28.025	0.021	0.021	0.000	0.000	0.000	0.000
50	A	610	LYS	1	0.806	1.019	24.108	0.327	0.327	0.000	0.000	0.000	0.000
51	A	611	MET	0	0.127	-0.069	29.409	0.014	0.014	0.000	0.000	0.000	0.000
52	A	611	MET	0	-0.100	0.104	29.484	0.000	0.000	0.000	0.000	0.000	0.000
53	A	612	LYS	0	0.080	-0.079	31.078	0.011	0.011	0.000	0.000	0.000	0.000
54	A	612	LYS	1	0.843	1.047	31.860	0.108	0.108	0.000	0.000	0.000	0.000
55	A	613	LYS	0	0.052	-0.148	32.576	0.015	0.015	0.000	0.000	0.000	0.000
56	A	613	LYS	1	0.779	1.024	32.811	0.128	0.128	0.000	0.000	0.000	0.000
57	A	614	SER	0	0.092	-0.056	33.967	0.011	0.011	0.000	0.000	0.000	0.000
58	A	614	SER	0	0.002	0.094	34.368	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	615	LEU	0	0.065	-0.073	35.740	0.006	0.006	0.000	0.000	0.000	0.000
60	A	615	LEU	0	-0.086	0.095	34.915	0.001	0.001	0.000	0.000	0.000	0.000
61	A	616	GLU	0	0.084	-0.088	37.229	0.008	0.008	0.000	0.000	0.000	0.000
62	A	616	GLU	-1	-0.906	-0.814	36.134	-0.114	-0.114	0.000	0.000	0.000	0.000
63	A	617	GLU	0	0.052	-0.136	38.574	0.011	0.011	0.000	0.000	0.000	0.000
64	A	617	GLU	-1	-0.972	-0.842	36.953	-0.140	-0.140	0.000	0.000	0.000	0.000
65	A	618	GLU	0	0.132	-0.092	39.819	0.007	0.007	0.000	0.000	0.000	0.000
66	A	618	GLU	-1	-1.021	-0.852	40.102	-0.112	-0.112	0.000	0.000	0.000	0.000
67	A	619	GLN	0	0.056	-0.102	41.519	0.005	0.005	0.000	0.000	0.000	0.000
68	A	619	GLN	0	-0.157	0.048	40.120	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	620	ARG	0	0.026	-0.116	43.169	0.006	0.006	0.000	0.000	0.000	0.000
70	A	620	ARG	1	0.802	1.031	42.808	0.087	0.087	0.000	0.000	0.000	0.000
71	A	621	ALA	0	0.049	-0.142	44.562	0.006	0.006	0.000	0.000	0.000	0.000
72	A	621	ALA	0	-0.019	0.156	44.697	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	622	ARG	0	0.130	-0.079	45.812	0.003	0.003	0.000	0.000	0.000	0.000
74	A	622	ARG	1	0.787	1.037	45.464	0.077	0.077	0.000	0.000	0.000	0.000
75	A	623	LYS	0	0.050	-0.109	47.559	0.004	0.004	0.000	0.000	0.000	0.000
76	A	623	LYS	1	0.862	1.045	47.084	0.067	0.067	0.000	0.000	0.000	0.000
77	A	624	ASP	0	0.056	-0.122	49.244	0.005	0.005	0.000	0.000	0.000	0.000
78	A	624	ASP	-1	-0.859	-0.760	49.237	-0.073	-0.073	0.000	0.000	0.000	0.000
79	A	625	LEU	0	0.097	-0.116	50.575	0.004	0.004	0.000	0.000	0.000	0.000
80	A	625	LEU	0	-0.039	0.147	50.326	0.000	0.000	0.000	0.000	0.000	0.000
81	A	626	GLU	0	0.084	-0.133	52.048	0.002	0.002	0.000	0.000	0.000	0.000
82	A	626	GLU	-1	-0.910	-0.799	50.753	-0.066	-0.066	0.000	0.000	0.000	0.000
83	A	627	LYS	0	0.041	-0.097	53.781	0.003	0.003	0.000	0.000	0.000	0.000
84	A	627	LYS	1	0.791	1.016	51.067	0.064	0.064	0.000	0.000	0.000	0.000
85	A	628	LEU	0	0.047	-0.095	55.272	0.004	0.004	0.000	0.000	0.000	0.000
86	A	628	LEU	0	-0.074	0.114	54.484	0.000	0.000	0.000	0.000	0.000	0.000
87	A	629	VAL	0	0.125	-0.084	56.466	0.003	0.003	0.000	0.000	0.000	0.000
88	A	629	VAL	0	-0.059	0.117	55.943	0.000	0.000	0.000	0.000	0.000	0.000
89	A	630	ARG	0	0.146	-0.061	57.770	0.002	0.002	0.000	0.000	0.000	0.000
90	A	630	ARG	1	0.824	1.033	54.324	0.052	0.052	0.000	0.000	0.000	0.000
91	A	631	LYS	0	0.078	-0.094	59.594	0.003	0.003	0.000	0.000	0.000	0.000
92	A	631	LYS	1	0.743	1.016	59.654	0.048	0.048	0.000	0.000	0.000	0.000
93	A	632	VAL	0	0.099	-0.101	60.936	0.002	0.002	0.000	0.000	0.000	0.000
94	A	632	VAL	0	-0.079	0.105	60.527	0.000	0.000	0.000	0.000	0.000	0.000
95	A	633	LEU	0	0.039	-0.109	62.365	0.001	0.001	0.000	0.000	0.000	0.000
96	A	633	LEU	0	-0.086	0.099	60.958	0.000	0.000	0.000	0.000	0.000	0.000
97	A	634	LYS	0	0.135	-0.060	63.932	0.002	0.002	0.000	0.000	0.000	0.000
98	A	634	LYS	1	0.857	1.040	64.483	0.038	0.038	0.000	0.000	0.000	0.000
99	A	635	ASN	0	0.042	-0.068	65.771	0.002	0.002	0.000	0.000	0.000	0.000
100	A	635	ASN	0	-0.115	0.033	65.875	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	636	MET	0	0.155	-0.049	66.962	0.001	0.001	0.000	0.000	0.000	0.000
102	A	636	MET	0	-0.109	0.069	65.741	0.000	0.000	0.000	0.000	0.000	0.000
103	A	637	ASN	0	0.103	-0.020	68.562	0.001	0.001	0.000	0.000	0.000	0.000
104	A	637	ASN	0	-0.218	-0.002	69.123	0.000	0.000	0.000	0.000	0.000	0.000
105	A	638	ASP	0	0.141	-0.110	70.107	0.001	0.001	0.000	0.000	0.000	0.000
106	A	638	ASP	-1	-1.064	-0.856	71.180	-0.033	-0.033	0.000	0.000	0.000	0.000
107	A	639	PRO	0	-0.003	-0.108	70.777	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	640	ALA	0	0.142	0.047	70.715	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	640	ALA	0	-0.123	0.071	70.512	0.000	0.000	0.000	0.000	0.000	0.000
110	A	641	TRP	0	0.018	-0.127	72.529	0.001	0.001	0.000	0.000	0.000	0.000
111	A	641	TRP	0	-0.142	0.064	71.137	0.000	0.000	0.000	0.000	0.000	0.000
112	A	642	ASP	0	0.094	-0.098	73.870	0.000	0.000	0.000	0.000	0.000	0.000
113	A	642	ASP	-1	-0.969	-0.828	77.600	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	643	GLU	0	0.057	-0.156	77.609	0.000	0.000	0.000	0.000	0.000	0.000
115	A	643	GLU	-1	-1.018	-0.830	77.219	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	644	THR	0	-0.012	-0.098	80.342	0.000	0.000	0.000	0.000	0.000	0.000
117	A	644	THR	0	-0.001	0.065	83.081	0.000	0.000	0.000	0.000	0.000	0.000
118	A	645	ASN	0	0.070	-0.070	84.108	0.000	0.000	0.000	0.000	0.000	0.000
119	A	645	ASN	0	-0.120	0.063	85.699	0.000	0.000	0.000	0.000	0.000	0.000
120	A	646	LEU	0	-0.071	-0.125	86.986	0.001	0.001	0.000	0.000	0.000	0.000
121	A	646	LEU	0	0.056	0.032	86.417	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:586:MET)