FMO DATABASE

FMODB ID: 5N6MZ

Calculation Name: 2YY3-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YY3

Chain ID: A

ChEMBL ID:

UniProt ID: P58748

Base Structure: X-ray

Registration Date: 2025-07-10

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-645935.725097
FMO2-HF: Nuclear repulsion	609857.389994
FMO2-HF: Total energy	-36078.335104
FMO2-MP2: Total energy	-36184.03231

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
1.143	3.816	0.09	-1.025	-1.737	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.111 / q_NPA : 0.034

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	2	SER	0	-0.033	0.051	3.433	-0.042	0.602	0.018	-0.348	-0.313	-0.002
5	A	3	ASP	0	0.137	-0.029	3.792	-1.286	1.228	-0.005	-1.387	-1.121	-0.002
6	A	3	ASP	-1	-1.042	-0.907	5.659	-2.005	-2.005	0.000	0.000	0.000	0.000
7	A	4	PHE	0	0.119	-0.084	5.910	0.278	0.296	-0.002	-0.001	-0.015	0.000
8	A	4	PHE	0	-0.073	0.121	9.551	0.009	0.009	0.000	0.000	0.000	0.000
9	A	5	ASN	0	0.094	-0.053	7.253	-0.098	-0.098	0.000	0.000	0.000	0.000
10	A	5	ASN	0	-0.104	0.047	5.100	0.445	0.467	-0.001	-0.004	-0.018	0.000
11	A	6	LEU	0	0.116	-0.128	8.339	0.029	0.029	0.000	0.000	0.000	0.000
12	A	6	LEU	0	-0.076	0.117	10.688	0.006	0.006	0.000	0.000	0.000	0.000
13	A	7	VAL	0	0.078	-0.094	11.731	0.013	0.013	0.000	0.000	0.000	0.000
14	A	7	VAL	0	-0.100	0.090	14.780	0.003	0.003	0.000	0.000	0.000	0.000
15	A	8	GLY	0	0.051	-0.083	15.069	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	9	VAL	0	0.058	0.009	18.039	0.015	0.015	0.000	0.000	0.000	0.000
17	A	9	VAL	0	-0.156	0.066	21.235	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	10	ILE	0	0.107	-0.111	21.443	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	10	ILE	0	-0.087	0.106	20.187	0.001	0.001	0.000	0.000	0.000	0.000
20	A	11	ARG	0	0.111	-0.089	23.911	0.001	0.001	0.000	0.000	0.000	0.000
21	A	11	ARG	1	0.729	0.998	27.695	0.083	0.083	0.000	0.000	0.000	0.000
22	A	12	VAL	0	0.060	-0.088	27.578	0.002	0.002	0.000	0.000	0.000	0.000
23	A	12	VAL	0	-0.098	0.081	27.337	0.000	0.000	0.000	0.000	0.000	0.000
24	A	13	MET	0	0.085	-0.144	29.830	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	13	MET	0	-0.073	0.131	33.066	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	14	PRO	0	-0.023	-0.115	33.600	0.004	0.004	0.000	0.000	0.000	0.000
27	A	15	THR	0	0.025	0.003	35.856	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	15	THR	0	-0.062	0.059	37.596	0.001	0.001	0.000	0.000	0.000	0.000
29	A	16	ASP	0	-0.011	-0.094	38.888	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	16	ASP	-1	-0.868	-0.828	41.982	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	17	PRO	0	-0.082	-0.168	40.453	0.000	0.000	0.000	0.000	0.000	0.000
32	A	18	ASP	0	0.055	0.000	41.933	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	18	ASP	-1	-1.021	-0.849	44.260	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	19	VAL	0	0.064	-0.108	38.820	0.003	0.003	0.000	0.000	0.000	0.000
35	A	19	VAL	0	-0.111	0.127	36.905	0.000	0.000	0.000	0.000	0.000	0.000
36	A	20	ASN	0	0.191	-0.069	38.856	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	20	ASN	0	-0.187	0.031	38.267	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	21	LEU	0	0.065	-0.113	35.234	0.003	0.003	0.000	0.000	0.000	0.000
39	A	21	LEU	0	-0.046	0.103	34.764	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	22	ASP	0	0.138	-0.069	33.595	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	22	ASP	-1	-0.933	-0.804	34.858	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	23	GLU	0	0.066	-0.152	32.872	0.000	0.000	0.000	0.000	0.000	0.000
43	A	23	GLU	-1	-0.937	-0.816	35.796	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	24	LEU	0	0.061	-0.093	32.845	0.006	0.006	0.000	0.000	0.000	0.000
45	A	24	LEU	0	-0.058	0.133	32.223	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	25	GLU	0	0.149	-0.098	29.100	0.003	0.003	0.000	0.000	0.000	0.000
47	A	25	GLU	-1	-0.897	-0.794	28.954	-0.054	-0.054	0.000	0.000	0.000	0.000
48	A	26	GLU	0	0.060	-0.071	28.212	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	26	GLU	-1	-0.974	-0.841	29.144	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	27	LYS	0	0.017	-0.124	28.814	0.009	0.009	0.000	0.000	0.000	0.000
51	A	27	LYS	1	0.765	0.995	31.217	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	28	LEU	0	0.127	-0.103	27.365	0.012	0.012	0.000	0.000	0.000	0.000
53	A	28	LEU	0	-0.097	0.125	26.633	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	29	LYS	0	0.089	-0.102	24.108	0.001	0.001	0.000	0.000	0.000	0.000
55	A	29	LYS	1	0.723	0.976	24.557	0.037	0.037	0.000	0.000	0.000	0.000
56	A	30	LYS	0	0.038	-0.061	23.467	0.003	0.003	0.000	0.000	0.000	0.000
57	A	30	LYS	1	0.779	1.023	26.260	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	31	VAL	0	0.101	-0.127	24.936	0.018	0.018	0.000	0.000	0.000	0.000
59	A	31	VAL	0	-0.090	0.138	25.270	0.000	0.000	0.000	0.000	0.000	0.000
60	A	32	ILE	0	0.049	-0.142	20.975	0.008	0.008	0.000	0.000	0.000	0.000
61	A	32	ILE	0	-0.136	0.088	18.935	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	33	PRO	0	-0.064	-0.108	18.343	0.014	0.014	0.000	0.000	0.000	0.000
63	A	34	GLU	0	0.074	-0.019	17.631	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	34	GLU	-1	-0.955	-0.846	17.054	0.207	0.207	0.000	0.000	0.000	0.000
65	A	35	LYS	0	0.043	-0.075	13.562	0.003	0.003	0.000	0.000	0.000	0.000
66	A	35	LYS	1	0.750	0.995	12.696	-0.164	-0.164	0.000	0.000	0.000	0.000
67	A	36	TYR	0	0.009	-0.112	12.713	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	36	TYR	0	-0.062	0.068	14.721	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	37	GLY	0	0.018	-0.087	14.624	0.028	0.028	0.000	0.000	0.000	0.000
70	A	38	LEU	0	0.112	-0.013	15.426	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	38	LEU	0	-0.082	0.126	19.696	0.004	0.004	0.000	0.000	0.000	0.000
72	A	39	ALA	0	0.072	-0.107	17.776	0.004	0.004	0.000	0.000	0.000	0.000
73	A	39	ALA	0	-0.083	0.092	16.732	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	40	LYS	0	0.076	-0.120	18.609	0.004	0.004	0.000	0.000	0.000	0.000
75	A	40	LYS	1	0.740	1.003	21.620	0.156	0.156	0.000	0.000	0.000	0.000
76	A	41	VAL	0	0.053	-0.100	22.223	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	41	VAL	0	-0.058	0.138	24.172	0.002	0.002	0.000	0.000	0.000	0.000
78	A	42	GLU	0	0.116	-0.088	25.392	0.004	0.004	0.000	0.000	0.000	0.000
79	A	42	GLU	-1	-0.954	-0.801	26.754	-0.137	-0.137	0.000	0.000	0.000	0.000
80	A	43	ARG	0	0.081	-0.097	28.044	0.001	0.001	0.000	0.000	0.000	0.000
81	A	43	ARG	1	0.717	0.959	31.350	0.048	0.048	0.000	0.000	0.000	0.000
82	A	44	GLU	0	0.037	-0.112	31.616	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	44	GLU	-1	-0.920	-0.785	31.042	-0.095	-0.095	0.000	0.000	0.000	0.000
84	A	45	PRO	0	0.040	-0.113	33.402	0.003	0.003	0.000	0.000	0.000	0.000
85	A	46	ILE	0	0.035	0.004	37.041	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	46	ILE	0	-0.099	0.087	36.767	0.000	0.000	0.000	0.000	0.000	0.000
87	A	47	ALA	0	0.151	-0.089	39.326	0.003	0.003	0.000	0.000	0.000	0.000
88	A	47	ALA	0	-0.113	0.084	43.222	0.000	0.000	0.000	0.000	0.000	0.000
89	A	48	PHE	0	-0.073	-0.152	42.495	0.002	0.002	0.000	0.000	0.000	0.000
90	A	48	PHE	0	-0.090	0.082	41.844	0.000	0.000	0.000	0.000	0.000	0.000
91	A	49	GLY	0	0.092	-0.064	42.670	0.003	0.003	0.000	0.000	0.000	0.000
92	A	50	LEU	0	0.092	0.027	39.313	0.002	0.002	0.000	0.000	0.000	0.000
93	A	50	LEU	0	-0.030	0.097	38.338	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	51	VAL	0	0.029	-0.098	36.399	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	51	VAL	0	-0.078	0.113	34.543	0.000	0.000	0.000	0.000	0.000	0.000
96	A	52	ALA	0	0.156	-0.075	32.944	0.005	0.005	0.000	0.000	0.000	0.000
97	A	52	ALA	0	-0.063	0.106	31.901	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	53	LEU	0	0.015	-0.146	29.948	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	53	LEU	0	-0.061	0.110	29.213	0.001	0.001	0.000	0.000	0.000	0.000
100	A	54	LYS	0	0.163	-0.060	26.501	0.003	0.003	0.000	0.000	0.000	0.000
101	A	54	LYS	1	0.692	0.997	25.805	0.117	0.117	0.000	0.000	0.000	0.000
102	A	55	PHE	0	0.046	-0.117	23.370	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	55	PHE	0	-0.051	0.121	22.453	0.003	0.003	0.000	0.000	0.000	0.000
104	A	56	TYR	0	0.125	-0.043	20.093	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	56	TYR	0	-0.214	0.004	19.264	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	57	VAL	0	0.147	-0.118	17.743	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	57	VAL	0	-0.077	0.133	16.518	0.004	0.004	0.000	0.000	0.000	0.000
108	A	58	LEU	0	0.074	-0.129	13.579	-0.038	-0.038	0.000	0.000	0.000	0.000
109	A	58	LEU	0	-0.093	0.107	12.510	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	59	GLY	0	0.083	-0.075	11.519	0.120	0.120	0.000	0.000	0.000	0.000
111	A	60	ARG	0	0.014	-0.021	7.869	-0.249	-0.249	0.000	0.000	0.000	0.000
112	A	60	ARG	1	0.693	0.903	3.089	3.036	2.511	0.080	0.715	-0.270	0.001
113	A	61	ASP	0	0.129	-0.050	8.312	0.220	0.220	0.000	0.000	0.000	0.000
114	A	61	ASP	-1	-0.941	-0.814	9.055	-0.646	-0.646	0.000	0.000	0.000	0.000
115	A	62	GLU	0	0.052	-0.115	8.878	-0.166	-0.166	0.000	0.000	0.000	0.000
116	A	62	GLU	-1	-0.891	-0.796	6.175	0.549	0.549	0.000	0.000	0.000	0.000
117	A	63	GLU	0	0.116	-0.101	10.134	0.014	0.014	0.000	0.000	0.000	0.000
118	A	63	GLU	-1	-1.016	-0.868	13.616	0.213	0.213	0.000	0.000	0.000	0.000
119	A	64	GLY	0	0.010	-0.081	12.308	0.103	0.103	0.000	0.000	0.000	0.000
120	A	65	TYR	0	0.043	-0.014	12.926	0.039	0.039	0.000	0.000	0.000	0.000
121	A	65	TYR	0	-0.129	0.084	9.264	-0.096	-0.096	0.000	0.000	0.000	0.000
122	A	66	SER	0	0.097	-0.076	14.196	-0.045	-0.045	0.000	0.000	0.000	0.000
123	A	66	SER	0	-0.041	0.081	18.140	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	67	PHE	0	0.046	-0.076	17.449	0.027	0.027	0.000	0.000	0.000	0.000
125	A	67	PHE	0	-0.074	0.078	13.997	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	68	ASP	0	0.148	-0.080	18.813	0.003	0.003	0.000	0.000	0.000	0.000
127	A	68	ASP	-1	-0.949	-0.842	21.218	-0.096	-0.096	0.000	0.000	0.000	0.000
128	A	69	GLU	0	0.151	-0.059	20.704	0.004	0.004	0.000	0.000	0.000	0.000
129	A	69	GLU	-1	-0.874	-0.818	18.888	0.092	0.092	0.000	0.000	0.000	0.000
130	A	70	VAL	0	-0.010	-0.096	20.626	0.015	0.015	0.000	0.000	0.000	0.000
131	A	70	VAL	0	-0.081	0.078	18.943	0.000	0.000	0.000	0.000	0.000	0.000
132	A	71	ALA	0	0.129	-0.067	21.940	0.006	0.006	0.000	0.000	0.000	0.000
133	A	71	ALA	0	-0.073	0.104	23.781	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	72	GLU	0	0.065	-0.115	24.550	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	72	GLU	-1	-1.004	-0.869	25.277	0.001	0.001	0.000	0.000	0.000	0.000
136	A	73	LYS	0	0.160	-0.039	24.961	0.002	0.002	0.000	0.000	0.000	0.000
137	A	73	LYS	1	0.752	0.987	21.648	-0.079	-0.079	0.000	0.000	0.000	0.000
138	A	74	PHE	0	-0.054	-0.138	25.865	0.008	0.008	0.000	0.000	0.000	0.000
139	A	74	PHE	0	-0.071	0.046	22.838	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	75	GLU	0	0.068	-0.126	27.382	0.000	0.000	0.000	0.000	0.000	0.000
141	A	75	GLU	-1	-0.892	-0.797	28.920	-0.029	-0.029	0.000	0.000	0.000	0.000
142	A	76	GLU	0	0.050	-0.098	29.695	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	76	GLU	-1	-1.005	-0.870	28.512	0.036	0.036	0.000	0.000	0.000	0.000
144	A	77	VAL	0	0.002	-0.108	30.760	0.005	0.005	0.000	0.000	0.000	0.000
145	A	77	VAL	0	-0.129	0.067	29.349	0.000	0.000	0.000	0.000	0.000	0.000
146	A	78	GLU	0	0.103	-0.100	32.168	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	78	GLU	-1	-0.975	-0.831	35.635	0.006	0.006	0.000	0.000	0.000	0.000
148	A	79	ASN	0	0.063	-0.070	35.467	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	79	ASN	0	-0.121	0.047	36.544	0.000	0.000	0.000	0.000	0.000	0.000
150	A	80	VAL	0	0.107	-0.128	32.761	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	80	VAL	0	-0.086	0.127	30.794	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	81	GLU	0	0.166	-0.083	34.161	0.004	0.004	0.000	0.000	0.000	0.000
153	A	81	GLU	-1	-1.039	-0.898	35.692	-0.026	-0.026	0.000	0.000	0.000	0.000
154	A	82	SER	0	-0.032	-0.091	32.397	0.003	0.003	0.000	0.000	0.000	0.000
155	A	82	SER	0	-0.033	0.076	32.190	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	83	ALA	0	0.061	-0.099	28.062	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	83	ALA	0	-0.107	0.086	27.066	0.000	0.000	0.000	0.000	0.000	0.000
158	A	84	GLU	0	0.079	-0.115	27.020	0.006	0.006	0.000	0.000	0.000	0.000
159	A	84	GLU	-1	-0.998	-0.842	27.847	-0.065	-0.065	0.000	0.000	0.000	0.000
160	A	85	VAL	0	0.079	-0.112	22.742	-0.003	-0.003	0.000	0.000	0.000	0.000
161	A	85	VAL	0	-0.089	0.104	20.671	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	86	GLU	0	0.121	-0.051	23.856	-0.001	-0.001	0.000	0.000	0.000	0.000
163	A	86	GLU	-1	-1.010	-0.862	24.727	-0.104	-0.104	0.000	0.000	0.000	0.000
164	A	87	THR	0	-0.027	-0.113	21.930	0.003	0.003	0.000	0.000	0.000	0.000
165	A	87	THR	0	-0.049	0.044	21.461	-0.010	-0.010	0.000	0.000	0.000	0.000
166	A	88	VAL	0	0.145	-0.085	17.731	0.009	0.009	0.000	0.000	0.000	0.000
167	A	88	VAL	0	-0.061	0.140	15.716	-0.004	-0.004	0.000	0.000	0.000	0.000
168	A	89	SER	0	0.000	-0.117	16.260	0.006	0.006	0.000	0.000	0.000	0.000
169	A	89	SER	0	-0.051	0.077	16.240	0.016	0.016	0.000	0.000	0.000	0.000
170	A	90	ARG	0	0.116	-0.050	12.349	-0.017	-0.017	0.000	0.000	0.000	0.000
171	A	90	ARG	1	0.724	0.947	10.659	0.739	0.739	0.000	0.000	0.000	0.000
172	A	91	ILE	0	-0.138	-0.153	9.425	0.113	0.113	0.000	0.000	0.000	0.000
173	A	91	ILE	0	0.045	0.047	10.682	0.017	0.017	0.000	0.000	0.000	0.000

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