FMO DATABASE

FMODB ID: K2JR3

Calculation Name: 4YVQ-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YVQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-576444.324428
FMO2-HF: Nuclear repulsion	539055.192904
FMO2-HF: Total energy	-37389.131525
FMO2-MP2: Total energy	-37492.250613

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:439:MET)

Summations of interaction energy for fragment #1(A:439: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.
-33.827	-33.179	8.536	-3.599	-5.59	0.052

Interaction energy analysis for fragmet #1(A:439:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.122 / q_NPA : -0.013

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	440	LEU	0	-0.022	0.134	3.111	-0.263	0.295	0.133	-0.297	-0.395	0.000
5	A	441	GLU	0	0.066	-0.136	3.744	0.601	2.167	-0.011	-0.819	-0.736	0.001
6	A	441	GLU	-1	-0.885	-0.796	3.363	-8.803	-9.524	0.001	1.041	-0.321	-0.002
7	A	442	THR	0	0.027	-0.119	4.668	0.844	0.946	-0.002	-0.014	-0.086	0.000
8	A	442	THR	0	-0.039	0.063	4.098	-0.100	-0.023	-0.001	-0.026	-0.051	0.000
9	A	443	VAL	0	0.009	-0.093	6.139	0.640	0.640	0.000	0.000	0.000	0.000
10	A	443	VAL	0	-0.078	0.126	5.296	0.081	0.113	-0.001	-0.007	-0.024	0.000
11	A	444	PRO	0	0.036	-0.121	7.560	0.171	0.171	0.000	0.000	0.000	0.000
12	A	445	THR	0	0.009	0.006	9.828	0.162	0.162	0.000	0.000	0.000	0.000
13	A	445	THR	0	0.039	0.094	9.501	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	446	ILE	0	0.134	-0.057	9.644	-0.085	-0.085	0.000	0.000	0.000	0.000
15	A	446	ILE	0	-0.096	0.100	6.741	0.068	0.068	0.000	0.000	0.000	0.000
16	A	447	LYS	0	0.108	-0.086	10.913	0.029	0.029	0.000	0.000	0.000	0.000
17	A	447	LYS	1	0.853	1.064	13.005	-0.174	-0.174	0.000	0.000	0.000	0.000
18	A	448	LYS	0	-0.018	-0.153	13.701	0.036	0.036	0.000	0.000	0.000	0.000
19	A	448	LYS	1	0.770	1.005	14.439	0.334	0.334	0.000	0.000	0.000	0.000
20	A	449	LEU	0	0.120	-0.106	14.166	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	449	LEU	0	-0.054	0.143	13.616	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	450	ARG	0	0.105	-0.085	15.166	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	450	ARG	1	0.847	1.059	14.262	-0.499	-0.499	0.000	0.000	0.000	0.000
24	A	451	ALA	0	0.095	-0.083	16.899	0.004	0.004	0.000	0.000	0.000	0.000
25	A	451	ALA	0	-0.095	0.091	19.009	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	452	TYR	0	0.054	-0.093	18.829	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	452	TYR	0	-0.086	0.089	18.918	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	453	ALA	0	0.084	-0.107	19.451	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	453	ALA	0	-0.063	0.114	19.211	0.009	0.009	0.000	0.000	0.000	0.000
30	A	454	GLU	0	0.097	-0.103	21.029	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	454	GLU	-1	-0.908	-0.774	21.651	0.224	0.224	0.000	0.000	0.000	0.000
32	A	455	ARG	0	0.120	-0.081	23.015	0.002	0.002	0.000	0.000	0.000	0.000
33	A	455	ARG	1	0.844	1.062	24.090	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	456	ILE	0	0.046	-0.107	24.571	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	456	ILE	0	-0.073	0.098	23.455	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	457	ARG	0	0.126	-0.095	25.187	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	457	ARG	1	0.665	0.917	24.500	-0.188	-0.188	0.000	0.000	0.000	0.000
38	A	458	VAL	0	0.034	-0.103	26.729	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	458	VAL	0	-0.077	0.115	26.761	0.002	0.002	0.000	0.000	0.000	0.000
40	A	459	ALA	0	0.168	-0.071	28.910	0.000	0.000	0.000	0.000	0.000	0.000
41	A	459	ALA	0	-0.086	0.104	29.785	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	460	GLU	0	0.020	-0.137	30.098	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	460	GLU	-1	-0.887	-0.777	30.082	0.041	0.041	0.000	0.000	0.000	0.000
44	A	461	LEU	0	0.110	-0.097	30.903	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	461	LEU	0	-0.105	0.098	30.277	0.003	0.003	0.000	0.000	0.000	0.000
46	A	462	GLU	0	0.043	-0.154	32.442	0.001	0.001	0.000	0.000	0.000	0.000
47	A	462	GLU	-1	-0.978	-0.819	32.974	0.083	0.083	0.000	0.000	0.000	0.000
48	A	463	LYS	0	0.104	-0.077	34.726	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	463	LYS	1	0.716	0.967	33.931	-0.037	-0.037	0.000	0.000	0.000	0.000
50	A	464	CYS	0	0.073	-0.127	35.525	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	464	CYS	0	-0.145	0.104	35.211	0.001	0.001	0.000	0.000	0.000	0.000
52	A	465	MET	0	0.052	-0.124	36.697	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	465	MET	0	-0.059	0.115	35.950	0.002	0.002	0.000	0.000	0.000	0.000
54	A	466	SER	0	0.050	-0.085	38.519	0.000	0.000	0.000	0.000	0.000	0.000
55	A	466	SER	0	-0.057	0.063	38.842	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	467	LYS	0	-0.016	-0.085	40.359	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	467	LYS	1	0.837	1.034	38.078	-0.048	-0.048	0.000	0.000	0.000	0.000
58	A	468	MET	0	0.092	-0.087	41.972	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	468	MET	0	-0.115	0.087	39.733	0.004	0.004	0.000	0.000	0.000	0.000
60	A	469	GLY	0	0.003	-0.100	43.072	0.000	0.000	0.000	0.000	0.000	0.000
61	A	470	ASP	0	0.056	-0.024	45.142	0.005	0.005	0.000	0.000	0.000	0.000
62	A	470	ASP	-1	-0.955	-0.828	48.698	0.056	0.056	0.000	0.000	0.000	0.000
63	A	471	ASP	0	0.090	-0.119	45.116	0.003	0.003	0.000	0.000	0.000	0.000
64	A	471	ASP	-1	-1.021	-0.839	44.114	0.071	0.071	0.000	0.000	0.000	0.000
65	A	472	ILE	0	-0.006	-0.122	41.780	0.005	0.005	0.000	0.000	0.000	0.000
66	A	472	ILE	0	-0.058	0.111	39.529	0.001	0.001	0.000	0.000	0.000	0.000
67	A	473	ASN	0	0.111	-0.056	41.997	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	473	ASN	0	0.001	0.108	42.869	0.007	0.007	0.000	0.000	0.000	0.000
69	A	474	LYS	0	0.083	-0.066	39.869	0.003	0.003	0.000	0.000	0.000	0.000
70	A	474	LYS	1	0.897	1.043	40.151	-0.117	-0.117	0.000	0.000	0.000	0.000
71	A	475	LYS	0	0.118	-0.043	38.405	0.008	0.008	0.000	0.000	0.000	0.000
72	A	475	LYS	1	0.913	1.069	39.710	-0.115	-0.115	0.000	0.000	0.000	0.000
73	A	476	THR	0	0.042	-0.121	37.996	0.009	0.009	0.000	0.000	0.000	0.000
74	A	476	THR	0	-0.038	0.094	39.920	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	477	THR	0	0.049	-0.091	37.303	0.001	0.001	0.000	0.000	0.000	0.000
76	A	477	THR	0	-0.044	0.057	35.949	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	478	ARG	0	0.079	-0.076	34.160	0.004	0.004	0.000	0.000	0.000	0.000
78	A	478	ARG	1	0.710	0.953	29.324	-0.222	-0.222	0.000	0.000	0.000	0.000
79	A	479	ALA	0	0.070	-0.104	33.056	0.015	0.015	0.000	0.000	0.000	0.000
80	A	479	ALA	0	-0.073	0.107	35.863	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	480	VAL	0	0.068	-0.112	33.045	0.009	0.009	0.000	0.000	0.000	0.000
82	A	480	VAL	0	-0.025	0.129	33.808	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	481	ASP	0	0.079	-0.095	31.020	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	481	ASP	-1	-0.852	-0.776	29.707	0.200	0.200	0.000	0.000	0.000	0.000
85	A	482	ASP	0	0.113	-0.097	28.760	0.012	0.012	0.000	0.000	0.000	0.000
86	A	482	ASP	-1	-0.881	-0.758	29.387	0.221	0.221	0.000	0.000	0.000	0.000
87	A	483	LEU	0	0.104	-0.104	28.206	0.019	0.019	0.000	0.000	0.000	0.000
88	A	483	LEU	0	-0.087	0.121	30.243	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	484	SER	0	-0.008	-0.092	28.197	0.002	0.002	0.000	0.000	0.000	0.000
90	A	484	SER	0	-0.028	0.082	28.574	0.001	0.001	0.000	0.000	0.000	0.000
91	A	485	ARG	0	0.048	-0.110	24.567	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	485	ARG	1	0.772	1.013	24.119	-0.245	-0.245	0.000	0.000	0.000	0.000
93	A	486	GLY	0	0.000	-0.110	23.543	0.031	0.031	0.000	0.000	0.000	0.000
94	A	487	ILE	0	0.054	-0.018	24.141	0.021	0.021	0.000	0.000	0.000	0.000
95	A	487	ILE	0	-0.056	0.115	25.362	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	488	VAL	0	0.099	-0.103	22.412	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	488	VAL	0	-0.069	0.128	20.865	0.000	0.000	0.000	0.000	0.000	0.000
98	A	489	ASN	0	0.121	-0.080	19.387	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	489	ASN	0	-0.124	0.054	20.070	0.013	0.013	0.000	0.000	0.000	0.000
100	A	490	ARG	0	0.082	-0.090	18.759	0.051	0.051	0.000	0.000	0.000	0.000
101	A	490	ARG	1	0.878	1.069	22.279	-0.205	-0.205	0.000	0.000	0.000	0.000
102	A	491	PHE	0	0.060	-0.099	19.910	0.005	0.005	0.000	0.000	0.000	0.000
103	A	491	PHE	0	-0.117	0.092	20.385	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	492	LEU	0	0.038	-0.135	16.533	-0.048	-0.048	0.000	0.000	0.000	0.000
105	A	492	LEU	0	-0.063	0.099	15.823	0.005	0.005	0.000	0.000	0.000	0.000
106	A	493	HIS	0	0.084	-0.073	14.563	0.054	0.054	0.000	0.000	0.000	0.000
107	A	493	HIS	0	-0.082	0.097	15.209	0.012	0.012	0.000	0.000	0.000	0.000
108	A	494	GLY	0	0.015	-0.090	13.542	0.086	0.086	0.000	0.000	0.000	0.000
109	A	495	PRO	0	0.074	0.014	12.604	0.023	0.023	0.000	0.000	0.000	0.000
110	A	496	MET	0	0.089	0.006	10.177	-0.104	-0.104	0.000	0.000	0.000	0.000
111	A	496	MET	0	-0.108	0.091	11.019	0.012	0.012	0.000	0.000	0.000	0.000
112	A	497	GLN	0	0.139	-0.090	8.910	0.419	0.419	0.000	0.000	0.000	0.000
113	A	497	GLN	0	-0.076	0.119	11.009	-0.129	-0.129	0.000	0.000	0.000	0.000
114	A	498	HIS	0	0.005	-0.108	8.488	0.367	0.367	0.000	0.000	0.000	0.000
115	A	498	HIS	0	-0.139	0.074	10.175	-0.057	-0.057	0.000	0.000	0.000	0.000
116	A	499	LEU	0	0.094	-0.083	6.538	-0.555	-0.555	0.000	0.000	0.000	0.000
117	A	499	LEU	0	-0.085	0.094	6.791	0.000	0.000	0.000	0.000	0.000	0.000
118	A	500	ARG	0	0.069	-0.099	3.530	-0.430	-0.277	0.005	-0.082	-0.077	0.000
119	A	500	ARG	1	0.782	0.989	2.068	-24.588	-25.542	8.286	-3.979	-3.353	0.052
120	A	501	CYS	0	0.177	-0.049	3.733	-1.918	-1.597	0.005	-0.135	-0.192	0.001
121	A	501	CYS	0	-0.212	0.097	6.189	0.100	0.100	0.000	0.000	0.000	0.000
122	A	502	ASP	0	0.045	-0.108	4.361	-1.658	-1.550	-0.002	-0.022	-0.085	0.000
123	A	502	ASP	-1	-0.798	-0.786	6.231	0.620	0.620	0.000	0.000	0.000	0.000
124	A	503	GLY	0	-0.097	-0.195	7.274	0.233	0.233	0.000	0.000	0.000	0.000
125	A	504	SER	0	-0.010	0.018	10.014	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	504	SER	0	-0.050	0.031	13.186	0.032	0.032	0.000	0.000	0.000	0.000
127	A	505	ASP	0	0.018	-0.091	11.749	0.007	0.007	0.000	0.000	0.000	0.000
128	A	505	ASP	-1	-0.923	-0.817	14.570	0.264	0.264	0.000	0.000	0.000	0.000
129	A	506	SER	0	0.063	-0.055	10.879	-0.096	-0.096	0.000	0.000	0.000	0.000
130	A	506	SER	0	-0.094	0.029	11.417	0.015	0.015	0.000	0.000	0.000	0.000
131	A	507	ARG	0	0.120	-0.076	9.070	-0.150	-0.150	0.000	0.000	0.000	0.000
132	A	507	ARG	1	0.721	1.011	6.098	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	508	THR	0	0.070	-0.089	7.704	-0.305	-0.305	0.000	0.000	0.000	0.000
134	A	508	THR	0	-0.091	0.031	10.662	-0.096	-0.096	0.000	0.000	0.000	0.000
135	A	509	LEU	0	0.182	-0.080	5.837	0.185	0.202	-0.002	0.000	-0.015	0.000
136	A	509	LEU	0	-0.081	0.112	3.214	0.464	-0.209	0.126	0.753	-0.206	0.000
137	A	510	SER	0	0.042	-0.091	6.525	-0.474	-0.474	0.000	0.000	0.000	0.000
138	A	510	SER	0	0.019	0.089	10.637	0.094	0.094	0.000	0.000	0.000	0.000
139	A	511	GLU	0	0.022	-0.153	9.510	-0.011	-0.011	0.000	0.000	0.000	0.000
140	A	511	GLU	-1	-0.846	-0.746	10.172	-0.805	-0.805	0.000	0.000	0.000	0.000
141	A	512	THR	0	-0.011	-0.065	5.955	0.504	0.504	0.000	0.000	0.000	0.000
142	A	512	THR	0	-0.066	0.077	4.076	0.096	0.158	-0.001	-0.012	-0.049	0.000
143	A	513	LEU	0	0.114	-0.101	7.364	0.209	0.209	0.000	0.000	0.000	0.000
144	A	513	LEU	0	-0.087	0.110	5.797	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	514	GLU	0	0.075	-0.105	8.578	0.223	0.223	0.000	0.000	0.000	0.000
146	A	514	GLU	-1	-0.883	-0.791	12.476	-0.923	-0.923	0.000	0.000	0.000	0.000
147	A	515	ASN	0	0.068	-0.100	10.464	0.193	0.193	0.000	0.000	0.000	0.000
148	A	515	ASN	0	-0.108	0.067	9.136	0.082	0.082	0.000	0.000	0.000	0.000
149	A	516	MET	0	0.078	-0.069	9.401	0.344	0.344	0.000	0.000	0.000	0.000
150	A	516	MET	0	-0.092	0.099	8.532	-0.180	-0.180	0.000	0.000	0.000	0.000
151	A	517	HIS	0	0.067	-0.118	10.514	0.195	0.195	0.000	0.000	0.000	0.000
152	A	517	HIS	0	-0.079	0.108	11.744	0.092	0.092	0.000	0.000	0.000	0.000
153	A	518	ALA	0	0.075	-0.134	13.634	0.115	0.115	0.000	0.000	0.000	0.000
154	A	518	ALA	0	-0.026	0.131	14.743	0.006	0.006	0.000	0.000	0.000	0.000
155	A	519	LEU	0	0.070	-0.099	13.960	0.083	0.083	0.000	0.000	0.000	0.000
156	A	519	LEU	0	-0.075	0.106	11.539	0.028	0.028	0.000	0.000	0.000	0.000
157	A	520	ASN	0	0.073	-0.073	14.483	0.111	0.111	0.000	0.000	0.000	0.000
158	A	520	ASN	0	-0.075	0.071	12.798	0.088	0.088	0.000	0.000	0.000	0.000
159	A	521	ARG	0	0.037	-0.085	16.073	0.057	0.057	0.000	0.000	0.000	0.000
160	A	521	ARG	1	0.796	0.995	16.079	0.648	0.648	0.000	0.000	0.000	0.000
161	A	522	MET	0	0.072	-0.108	18.455	0.033	0.033	0.000	0.000	0.000	0.000
162	A	522	MET	0	-0.103	0.096	18.498	0.004	0.004	0.000	0.000	0.000	0.000
163	A	523	TYR	0	0.040	-0.096	18.716	0.031	0.031	0.000	0.000	0.000	0.000
164	A	523	TYR	0	-0.097	0.094	16.994	0.013	0.013	0.000	0.000	0.000	0.000
165	A	524	GLY	0	0.040	-0.089	19.958	0.035	0.035	0.000	0.000	0.000	0.000
166	A	525	LEU	0	0.015	-0.012	16.526	0.044	0.044	0.000	0.000	0.000	0.000
167	A	525	LEU	0	-0.057	0.099	14.441	0.010	0.010	0.000	0.000	0.000	0.000
168	A	526	GLU	0	-0.011	-0.127	17.620	0.055	0.055	0.000	0.000	0.000	0.000
169	A	526	GLU	-1	-0.879	-0.772	14.521	-0.484	-0.484	0.000	0.000	0.000	0.000
170	A	527	LYS	0	0.019	-0.107	18.449	-0.019	-0.019	0.000	0.000	0.000	0.000
171	A	527	LYS	1	0.898	0.960	21.737	0.157	0.157	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:439:MET)