FMO DATABASE

FMODB ID: 5N49Z

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	OptH
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	-575664.880316
FMO2-HF: Nuclear repulsion	538277.321031
FMO2-HF: Total energy	-37387.559285
FMO2-MP2: Total energy	-37490.697084

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.
-12.487	-9.776	0.175	-0.847	-2.038	0.002

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 : 0.092 / q_NPA : -0.042

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	-0.041	0.132	3.483	-0.075	0.424	0.048	-0.242	-0.304	0.000
5	A	441	GLU	0	0.073	-0.140	3.689	0.447	1.924	-0.010	-0.807	-0.660	0.002
6	A	441	GLU	-1	-0.892	-0.784	3.795	-7.565	-7.444	0.001	0.064	-0.186	-0.001
7	A	442	THR	0	0.022	-0.107	4.532	1.303	1.406	-0.002	-0.013	-0.089	0.000
8	A	442	THR	0	-0.059	0.052	4.133	-0.321	-0.230	-0.001	-0.029	-0.061	0.000
9	A	443	VAL	0	0.016	-0.106	5.922	0.821	0.821	0.000	0.000	0.000	0.000
10	A	443	VAL	0	-0.067	0.116	5.220	0.200	0.200	0.000	0.000	0.000	0.000
11	A	444	PRO	0	0.035	-0.114	7.269	0.373	0.373	0.000	0.000	0.000	0.000
12	A	445	THR	0	0.009	0.007	9.625	0.267	0.267	0.000	0.000	0.000	0.000
13	A	445	THR	0	0.049	0.109	9.271	0.021	0.021	0.000	0.000	0.000	0.000
14	A	446	ILE	0	0.164	-0.073	9.406	0.048	0.048	0.000	0.000	0.000	0.000
15	A	446	ILE	0	-0.101	0.103	6.583	0.075	0.075	0.000	0.000	0.000	0.000
16	A	447	LYS	0	0.095	-0.095	10.663	0.112	0.112	0.000	0.000	0.000	0.000
17	A	447	LYS	1	0.848	1.068	12.827	0.145	0.145	0.000	0.000	0.000	0.000
18	A	448	LYS	0	-0.037	-0.156	13.419	0.084	0.084	0.000	0.000	0.000	0.000
19	A	448	LYS	1	0.769	1.016	14.349	0.579	0.579	0.000	0.000	0.000	0.000
20	A	449	LEU	0	0.126	-0.113	13.947	0.027	0.027	0.000	0.000	0.000	0.000
21	A	449	LEU	0	-0.054	0.151	13.507	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	450	ARG	0	0.089	-0.092	14.913	0.017	0.017	0.000	0.000	0.000	0.000
23	A	450	ARG	1	0.841	1.060	13.886	-0.212	-0.212	0.000	0.000	0.000	0.000
24	A	451	ALA	0	0.118	-0.084	16.640	0.029	0.029	0.000	0.000	0.000	0.000
25	A	451	ALA	0	-0.094	0.101	18.826	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	452	TYR	0	0.037	-0.104	18.603	0.021	0.021	0.000	0.000	0.000	0.000
27	A	452	TYR	0	-0.067	0.096	18.765	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	453	ALA	0	0.078	-0.115	19.235	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	453	ALA	0	-0.054	0.117	18.989	0.006	0.006	0.000	0.000	0.000	0.000
30	A	454	GLU	0	0.093	-0.112	20.806	0.003	0.003	0.000	0.000	0.000	0.000
31	A	454	GLU	-1	-0.899	-0.764	21.436	0.084	0.084	0.000	0.000	0.000	0.000
32	A	455	ARG	0	0.102	-0.105	22.760	0.013	0.013	0.000	0.000	0.000	0.000
33	A	455	ARG	1	0.842	1.063	23.787	0.097	0.097	0.000	0.000	0.000	0.000
34	A	456	ILE	0	0.049	-0.105	24.351	0.004	0.004	0.000	0.000	0.000	0.000
35	A	456	ILE	0	-0.056	0.109	23.493	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	457	ARG	0	0.132	-0.078	24.959	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	457	ARG	1	0.676	0.955	24.182	-0.073	-0.073	0.000	0.000	0.000	0.000
38	A	458	VAL	0	0.020	-0.124	26.497	0.006	0.006	0.000	0.000	0.000	0.000
39	A	458	VAL	0	-0.061	0.117	26.485	0.001	0.001	0.000	0.000	0.000	0.000
40	A	459	ALA	0	0.167	-0.075	28.653	0.007	0.007	0.000	0.000	0.000	0.000
41	A	459	ALA	0	-0.090	0.111	29.602	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	460	GLU	0	0.018	-0.149	29.877	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	460	GLU	-1	-0.954	-0.816	29.895	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	461	LEU	0	0.119	-0.106	30.666	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	461	LEU	0	-0.101	0.108	30.120	0.002	0.002	0.000	0.000	0.000	0.000
46	A	462	GLU	0	0.031	-0.161	32.201	0.006	0.006	0.000	0.000	0.000	0.000
47	A	462	GLU	-1	-0.978	-0.812	32.634	0.008	0.008	0.000	0.000	0.000	0.000
48	A	463	LYS	0	0.105	-0.092	34.493	0.002	0.002	0.000	0.000	0.000	0.000
49	A	463	LYS	1	0.780	1.026	33.969	0.028	0.028	0.000	0.000	0.000	0.000
50	A	464	CYS	0	0.086	-0.116	35.296	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	464	CYS	0	-0.143	0.104	35.114	0.002	0.002	0.000	0.000	0.000	0.000
52	A	465	MET	0	0.038	-0.129	36.450	0.000	0.000	0.000	0.000	0.000	0.000
53	A	465	MET	0	-0.055	0.113	35.724	0.003	0.003	0.000	0.000	0.000	0.000
54	A	466	SER	0	0.050	-0.082	38.269	0.003	0.003	0.000	0.000	0.000	0.000
55	A	466	SER	0	-0.053	0.073	38.726	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	467	LYS	0	-0.018	-0.084	40.124	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	467	LYS	1	0.837	1.032	38.281	0.005	0.005	0.000	0.000	0.000	0.000
58	A	468	MET	0	0.091	-0.090	41.718	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	468	MET	0	-0.117	0.086	39.401	0.002	0.002	0.000	0.000	0.000	0.000
60	A	469	GLY	0	0.024	-0.092	42.836	0.001	0.001	0.000	0.000	0.000	0.000
61	A	470	ASP	0	0.055	-0.036	44.878	0.002	0.002	0.000	0.000	0.000	0.000
62	A	470	ASP	-1	-0.948	-0.818	48.420	0.023	0.023	0.000	0.000	0.000	0.000
63	A	471	ASP	0	0.104	-0.109	44.807	0.003	0.003	0.000	0.000	0.000	0.000
64	A	471	ASP	-1	-1.030	-0.837	43.967	0.030	0.030	0.000	0.000	0.000	0.000
65	A	472	ILE	0	0.000	-0.158	41.507	0.005	0.005	0.000	0.000	0.000	0.000
66	A	472	ILE	0	-0.067	0.134	39.862	0.001	0.001	0.000	0.000	0.000	0.000
67	A	473	ASN	0	0.103	-0.082	41.712	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	473	ASN	0	-0.061	0.089	43.335	0.005	0.005	0.000	0.000	0.000	0.000
69	A	474	LYS	0	0.091	-0.080	39.585	0.000	0.000	0.000	0.000	0.000	0.000
70	A	474	LYS	1	0.895	1.054	39.844	-0.076	-0.076	0.000	0.000	0.000	0.000
71	A	475	LYS	0	0.102	-0.050	38.127	0.004	0.004	0.000	0.000	0.000	0.000
72	A	475	LYS	1	0.895	1.069	39.666	-0.076	-0.076	0.000	0.000	0.000	0.000
73	A	476	THR	0	0.030	-0.103	37.741	0.006	0.006	0.000	0.000	0.000	0.000
74	A	476	THR	0	0.008	0.109	39.614	0.001	0.001	0.000	0.000	0.000	0.000
75	A	477	THR	0	0.076	-0.078	37.043	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	477	THR	0	-0.039	0.059	35.626	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	478	ARG	0	0.105	-0.075	33.875	0.000	0.000	0.000	0.000	0.000	0.000
78	A	478	ARG	1	0.803	1.048	29.828	-0.144	-0.144	0.000	0.000	0.000	0.000
79	A	479	ALA	0	0.084	-0.102	32.796	0.009	0.009	0.000	0.000	0.000	0.000
80	A	479	ALA	0	-0.080	0.111	35.609	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	480	VAL	0	0.063	-0.118	32.811	0.005	0.005	0.000	0.000	0.000	0.000
82	A	480	VAL	0	-0.016	0.129	33.543	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	481	ASP	0	0.071	-0.104	30.765	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	481	ASP	-1	-0.928	-0.821	29.444	0.109	0.109	0.000	0.000	0.000	0.000
85	A	482	ASP	0	0.156	-0.105	28.518	0.002	0.002	0.000	0.000	0.000	0.000
86	A	482	ASP	-1	-0.965	-0.821	29.598	0.134	0.134	0.000	0.000	0.000	0.000
87	A	483	LEU	0	0.076	-0.121	27.978	0.012	0.012	0.000	0.000	0.000	0.000
88	A	483	LEU	0	-0.097	0.127	29.874	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	484	SER	0	-0.008	-0.100	27.992	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	484	SER	0	-0.039	0.063	28.248	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	485	ARG	0	0.022	-0.119	24.327	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	485	ARG	1	0.811	1.056	23.790	-0.136	-0.136	0.000	0.000	0.000	0.000
93	A	486	GLY	0	0.006	-0.102	23.318	0.018	0.018	0.000	0.000	0.000	0.000
94	A	487	ILE	0	0.051	-0.031	23.958	0.014	0.014	0.000	0.000	0.000	0.000
95	A	487	ILE	0	-0.046	0.122	25.072	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	488	VAL	0	0.059	-0.106	22.238	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	488	VAL	0	-0.032	0.126	20.462	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	489	ASN	0	0.140	-0.070	19.177	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	489	ASN	0	-0.120	0.060	19.839	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	490	ARG	0	0.044	-0.095	18.581	0.029	0.029	0.000	0.000	0.000	0.000
101	A	490	ARG	1	0.882	1.069	22.164	-0.113	-0.113	0.000	0.000	0.000	0.000
102	A	491	PHE	0	0.083	-0.109	19.794	0.006	0.006	0.000	0.000	0.000	0.000
103	A	491	PHE	0	-0.130	0.100	20.200	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	492	LEU	0	0.024	-0.137	16.389	-0.046	-0.046	0.000	0.000	0.000	0.000
105	A	492	LEU	0	-0.058	0.103	15.606	0.003	0.003	0.000	0.000	0.000	0.000
106	A	493	HIS	0	0.088	-0.084	14.412	0.000	0.000	0.000	0.000	0.000	0.000
107	A	493	HIS	0	-0.059	0.113	15.138	0.017	0.017	0.000	0.000	0.000	0.000
108	A	494	GLY	0	0.017	-0.084	13.430	0.053	0.053	0.000	0.000	0.000	0.000
109	A	495	PRO	0	0.067	0.008	12.569	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	496	MET	0	0.089	0.003	10.018	-0.164	-0.164	0.000	0.000	0.000	0.000
111	A	496	MET	0	-0.112	0.102	10.831	0.020	0.020	0.000	0.000	0.000	0.000
112	A	497	GLN	0	0.158	-0.110	8.754	0.226	0.226	0.000	0.000	0.000	0.000
113	A	497	GLN	0	-0.110	0.115	10.876	-0.098	-0.098	0.000	0.000	0.000	0.000
114	A	498	HIS	0	-0.018	-0.119	8.450	0.309	0.309	0.000	0.000	0.000	0.000
115	A	498	HIS	0	-0.119	0.086	10.184	-0.026	-0.026	0.000	0.000	0.000	0.000
116	A	499	LEU	0	0.103	-0.087	6.527	-0.439	-0.439	0.000	0.000	0.000	0.000
117	A	499	LEU	0	-0.091	0.101	6.620	-0.024	-0.024	0.000	0.000	0.000	0.000
118	A	500	ARG	0	0.094	-0.073	3.421	-1.382	-1.229	0.008	-0.078	-0.083	0.000
119	A	500	ARG	1	0.881	1.065	4.334	-5.840	-5.644	0.000	-0.055	-0.141	0.000
120	A	501	CYS	0	0.124	-0.051	3.646	-1.374	-1.024	0.006	-0.151	-0.205	0.001
121	A	501	CYS	0	-0.201	0.111	6.262	-0.148	-0.148	0.000	0.000	0.000	0.000
122	A	502	ASP	0	0.154	-0.076	4.292	-1.267	-1.156	-0.001	-0.034	-0.075	0.000
123	A	502	ASP	-1	-0.812	-0.815	6.126	0.938	0.938	0.000	0.000	0.000	0.000
124	A	503	GLY	0	-0.124	-0.210	7.093	0.001	0.001	0.000	0.000	0.000	0.000
125	A	504	SER	0	-0.018	0.043	9.899	-0.087	-0.087	0.000	0.000	0.000	0.000
126	A	504	SER	0	-0.073	0.024	12.868	0.032	0.032	0.000	0.000	0.000	0.000
127	A	505	ASP	0	0.067	-0.100	11.663	0.033	0.033	0.000	0.000	0.000	0.000
128	A	505	ASP	-1	-0.947	-0.818	14.848	0.405	0.405	0.000	0.000	0.000	0.000
129	A	506	SER	0	0.059	-0.062	11.046	-0.101	-0.101	0.000	0.000	0.000	0.000
130	A	506	SER	0	-0.084	0.033	11.522	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	507	ARG	0	0.118	-0.095	8.832	-0.117	-0.117	0.000	0.000	0.000	0.000
132	A	507	ARG	1	0.696	1.032	6.241	0.125	0.125	0.000	0.000	0.000	0.000
133	A	508	THR	0	0.135	-0.094	7.575	-0.149	-0.149	0.000	0.000	0.000	0.000
134	A	508	THR	0	-0.030	0.098	10.569	-0.097	-0.097	0.000	0.000	0.000	0.000
135	A	509	LEU	0	0.168	-0.086	5.842	0.101	0.101	0.000	0.000	0.000	0.000
136	A	509	LEU	0	-0.089	0.117	3.223	0.247	-0.200	0.127	0.507	-0.187	0.000
137	A	510	SER	0	0.036	-0.088	6.521	-0.597	-0.597	0.000	0.000	0.000	0.000
138	A	510	SER	0	0.025	0.090	10.624	0.115	0.115	0.000	0.000	0.000	0.000
139	A	511	GLU	0	0.039	-0.157	9.466	-0.082	-0.082	0.000	0.000	0.000	0.000
140	A	511	GLU	-1	-0.968	-0.804	10.414	-0.628	-0.628	0.000	0.000	0.000	0.000
141	A	512	THR	0	0.005	-0.087	6.135	0.463	0.463	0.000	0.000	0.000	0.000
142	A	512	THR	0	-0.035	0.078	4.266	0.053	0.110	-0.001	-0.009	-0.047	0.000
143	A	513	LEU	0	0.084	-0.107	7.575	0.005	0.005	0.000	0.000	0.000	0.000
144	A	513	LEU	0	-0.075	0.117	5.716	-0.038	-0.038	0.000	0.000	0.000	0.000
145	A	514	GLU	0	0.069	-0.117	8.457	0.174	0.174	0.000	0.000	0.000	0.000
146	A	514	GLU	-1	-0.966	-0.826	12.122	-1.065	-1.065	0.000	0.000	0.000	0.000
147	A	515	ASN	0	0.086	-0.101	10.550	0.206	0.206	0.000	0.000	0.000	0.000
148	A	515	ASN	0	-0.123	0.076	9.377	0.093	0.093	0.000	0.000	0.000	0.000
149	A	516	MET	0	0.073	-0.095	9.492	0.337	0.337	0.000	0.000	0.000	0.000
150	A	516	MET	0	-0.091	0.095	8.527	-0.235	-0.235	0.000	0.000	0.000	0.000
151	A	517	HIS	0	0.034	-0.124	10.544	0.192	0.192	0.000	0.000	0.000	0.000
152	A	517	HIS	0	-0.060	0.116	11.524	0.068	0.068	0.000	0.000	0.000	0.000
153	A	518	ALA	0	0.121	-0.137	13.705	0.126	0.126	0.000	0.000	0.000	0.000
154	A	518	ALA	0	-0.068	0.145	14.867	0.012	0.012	0.000	0.000	0.000	0.000
155	A	519	LEU	0	0.048	-0.126	13.920	0.118	0.118	0.000	0.000	0.000	0.000
156	A	519	LEU	0	-0.067	0.112	11.496	0.020	0.020	0.000	0.000	0.000	0.000
157	A	520	ASN	0	0.065	-0.088	14.471	0.119	0.119	0.000	0.000	0.000	0.000
158	A	520	ASN	0	-0.070	0.086	12.749	0.078	0.078	0.000	0.000	0.000	0.000
159	A	521	ARG	0	0.043	-0.090	16.038	0.064	0.064	0.000	0.000	0.000	0.000
160	A	521	ARG	1	0.891	1.062	16.837	0.666	0.666	0.000	0.000	0.000	0.000
161	A	522	MET	0	0.050	-0.112	18.460	0.044	0.044	0.000	0.000	0.000	0.000
162	A	522	MET	0	-0.109	0.102	18.528	-0.005	-0.005	0.000	0.000	0.000	0.000
163	A	523	TYR	0	0.064	-0.103	18.659	0.046	0.046	0.000	0.000	0.000	0.000
164	A	523	TYR	0	-0.105	0.097	17.098	0.016	0.016	0.000	0.000	0.000	0.000
165	A	524	GLY	0	0.035	-0.087	19.904	0.037	0.037	0.000	0.000	0.000	0.000
166	A	525	LEU	0	0.040	-0.016	16.415	0.061	0.061	0.000	0.000	0.000	0.000
167	A	525	LEU	0	-0.059	0.114	14.389	0.002	0.002	0.000	0.000	0.000	0.000
168	A	526	GLU	0	-0.066	-0.153	17.543	0.049	0.049	0.000	0.000	0.000	0.000
169	A	526	GLU	-1	-0.858	-0.778	14.417	-0.745	-0.745	0.000	0.000	0.000	0.000
170	A	527	LYS	0	0.018	-0.101	18.349	-0.002	-0.002	0.000	0.000	0.000	0.000
171	A	527	LYS	1	0.911	0.968	21.702	0.283	0.283	0.000	0.000	0.000	0.000

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