FMO DATABASE

FMODB ID: YN832

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	OptAll
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	-644898.221312
FMO2-HF: Nuclear repulsion	608819.499039
FMO2-HF: Total energy	-36078.722273
FMO2-MP2: Total energy	-36184.392834

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.
1.7	3.613	0.028	-0.403	-1.538	-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 : 0.122 / q_NPA : 0.041

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	-0.042	0.044	3.360	-0.481	0.278	0.024	-0.411	-0.371	-0.002
5	A	3	ASP	0	0.137	-0.065	3.854	-0.634	1.276	-0.005	-1.013	-0.892	-0.002
6	A	3	ASP	-1	-0.978	-0.858	5.852	-2.217	-2.217	0.000	0.000	0.000	0.000
7	A	4	PHE	0	0.092	-0.088	6.037	0.104	0.104	0.000	0.000	0.000	0.000
8	A	4	PHE	0	-0.109	0.113	10.028	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	5	ASN	0	0.080	-0.059	6.863	-0.130	-0.130	0.000	0.000	0.000	0.000
10	A	5	ASN	0	-0.089	0.047	4.640	0.506	0.558	-0.001	-0.019	-0.032	0.000
11	A	6	LEU	0	0.127	-0.124	8.125	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	6	LEU	0	-0.079	0.121	10.568	0.000	0.000	0.000	0.000	0.000	0.000
13	A	7	VAL	0	0.029	-0.103	11.493	0.037	0.037	0.000	0.000	0.000	0.000
14	A	7	VAL	0	-0.089	0.084	14.518	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	8	GLY	0	0.050	-0.080	14.946	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	9	VAL	0	0.062	0.023	18.297	0.010	0.010	0.000	0.000	0.000	0.000
17	A	9	VAL	0	-0.143	0.068	21.675	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	10	ILE	0	0.085	-0.119	21.761	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	10	ILE	0	-0.083	0.113	20.289	0.001	0.001	0.000	0.000	0.000	0.000
20	A	11	ARG	0	0.110	-0.087	23.884	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	11	ARG	1	0.678	0.932	27.791	0.061	0.061	0.000	0.000	0.000	0.000
22	A	12	VAL	0	0.039	-0.093	27.599	0.002	0.002	0.000	0.000	0.000	0.000
23	A	12	VAL	0	-0.065	0.105	27.827	0.001	0.001	0.000	0.000	0.000	0.000
24	A	13	MET	0	0.081	-0.132	30.216	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	13	MET	0	-0.083	0.130	33.518	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	14	PRO	0	0.003	-0.104	34.026	0.004	0.004	0.000	0.000	0.000	0.000
27	A	15	THR	0	0.023	0.023	36.384	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	15	THR	0	-0.065	0.055	38.223	0.001	0.001	0.000	0.000	0.000	0.000
29	A	16	ASP	0	-0.012	-0.104	39.438	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	16	ASP	-1	-0.845	-0.813	42.210	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	17	PRO	0	-0.081	-0.172	40.588	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	18	ASP	0	0.079	0.008	42.399	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	18	ASP	-1	-1.021	-0.853	44.673	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	19	VAL	0	0.027	-0.132	39.217	0.002	0.002	0.000	0.000	0.000	0.000
35	A	19	VAL	0	-0.077	0.129	37.435	0.000	0.000	0.000	0.000	0.000	0.000
36	A	20	ASN	0	0.154	-0.057	39.192	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	20	ASN	0	-0.173	0.029	38.539	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	21	LEU	0	0.073	-0.106	35.721	0.004	0.004	0.000	0.000	0.000	0.000
39	A	21	LEU	0	-0.044	0.104	35.350	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	22	ASP	0	0.130	-0.080	33.736	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	22	ASP	-1	-0.935	-0.803	34.844	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	23	GLU	0	0.064	-0.124	33.163	0.001	0.001	0.000	0.000	0.000	0.000
43	A	23	GLU	-1	-0.925	-0.810	36.220	0.010	0.010	0.000	0.000	0.000	0.000
44	A	24	LEU	0	0.073	-0.100	33.226	0.006	0.006	0.000	0.000	0.000	0.000
45	A	24	LEU	0	-0.066	0.126	32.768	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	25	GLU	0	0.169	-0.074	29.752	0.004	0.004	0.000	0.000	0.000	0.000
47	A	25	GLU	-1	-0.949	-0.802	28.594	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	26	GLU	0	0.041	-0.122	28.548	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	26	GLU	-1	-0.905	-0.804	29.350	0.005	0.005	0.000	0.000	0.000	0.000
50	A	27	LYS	0	0.042	-0.100	28.782	0.008	0.008	0.000	0.000	0.000	0.000
51	A	27	LYS	1	0.761	0.987	31.686	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	28	LEU	0	0.104	-0.096	27.694	0.012	0.012	0.000	0.000	0.000	0.000
53	A	28	LEU	0	-0.092	0.124	27.069	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	29	LYS	0	0.099	-0.090	24.478	0.006	0.006	0.000	0.000	0.000	0.000
55	A	29	LYS	1	0.705	0.958	24.780	0.018	0.018	0.000	0.000	0.000	0.000
56	A	30	LYS	0	0.023	-0.052	23.652	0.005	0.005	0.000	0.000	0.000	0.000
57	A	30	LYS	1	0.678	0.954	26.420	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	31	VAL	0	0.043	-0.129	25.297	0.015	0.015	0.000	0.000	0.000	0.000
59	A	31	VAL	0	-0.061	0.128	25.790	0.000	0.000	0.000	0.000	0.000	0.000
60	A	32	ILE	0	0.131	-0.113	21.160	0.009	0.009	0.000	0.000	0.000	0.000
61	A	32	ILE	0	-0.129	0.096	19.110	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	33	PRO	0	-0.064	-0.117	18.579	0.013	0.013	0.000	0.000	0.000	0.000
63	A	34	GLU	0	0.062	-0.034	17.642	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	34	GLU	-1	-0.941	-0.843	17.119	0.246	0.246	0.000	0.000	0.000	0.000
65	A	35	LYS	0	-0.006	-0.085	13.577	0.008	0.008	0.000	0.000	0.000	0.000
66	A	35	LYS	1	0.743	0.988	12.928	-0.255	-0.255	0.000	0.000	0.000	0.000
67	A	36	TYR	0	0.029	-0.101	12.758	0.046	0.046	0.000	0.000	0.000	0.000
68	A	36	TYR	0	-0.059	0.066	14.747	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	37	GLY	0	0.023	-0.106	14.840	0.017	0.017	0.000	0.000	0.000	0.000
70	A	38	LEU	0	0.086	-0.027	15.626	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	38	LEU	0	-0.094	0.123	19.740	0.005	0.005	0.000	0.000	0.000	0.000
72	A	39	ALA	0	0.089	-0.098	17.888	0.007	0.007	0.000	0.000	0.000	0.000
73	A	39	ALA	0	-0.078	0.089	16.822	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	40	LYS	0	0.054	-0.104	18.585	0.000	0.000	0.000	0.000	0.000	0.000
75	A	40	LYS	1	0.739	1.001	21.785	0.132	0.132	0.000	0.000	0.000	0.000
76	A	41	VAL	0	0.063	-0.101	22.309	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	41	VAL	0	-0.047	0.128	24.308	0.002	0.002	0.000	0.000	0.000	0.000
78	A	42	GLU	0	0.092	-0.086	25.442	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	42	GLU	-1	-0.906	-0.784	26.954	-0.114	-0.114	0.000	0.000	0.000	0.000
80	A	43	ARG	0	0.059	-0.095	28.292	0.004	0.004	0.000	0.000	0.000	0.000
81	A	43	ARG	1	0.735	0.960	31.467	0.034	0.034	0.000	0.000	0.000	0.000
82	A	44	GLU	0	0.055	-0.104	31.808	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	44	GLU	-1	-0.908	-0.775	31.204	-0.075	-0.075	0.000	0.000	0.000	0.000
84	A	45	PRO	0	0.012	-0.117	33.909	0.003	0.003	0.000	0.000	0.000	0.000
85	A	46	ILE	0	0.053	0.006	37.634	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	46	ILE	0	-0.075	0.098	37.192	0.000	0.000	0.000	0.000	0.000	0.000
87	A	47	ALA	0	0.145	-0.084	39.863	0.003	0.003	0.000	0.000	0.000	0.000
88	A	47	ALA	0	-0.110	0.082	43.914	0.000	0.000	0.000	0.000	0.000	0.000
89	A	48	PHE	0	-0.063	-0.133	43.001	0.001	0.001	0.000	0.000	0.000	0.000
90	A	48	PHE	0	-0.074	0.087	41.991	0.000	0.000	0.000	0.000	0.000	0.000
91	A	49	GLY	0	0.044	-0.095	43.239	0.003	0.003	0.000	0.000	0.000	0.000
92	A	50	LEU	0	0.117	0.037	39.814	0.001	0.001	0.000	0.000	0.000	0.000
93	A	50	LEU	0	-0.051	0.098	38.784	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	51	VAL	0	0.047	-0.113	36.798	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	51	VAL	0	-0.083	0.100	34.914	0.000	0.000	0.000	0.000	0.000	0.000
96	A	52	ALA	0	0.122	-0.075	33.021	0.005	0.005	0.000	0.000	0.000	0.000
97	A	52	ALA	0	-0.049	0.106	32.181	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	53	LEU	0	0.013	-0.128	30.387	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	53	LEU	0	-0.051	0.102	29.829	0.001	0.001	0.000	0.000	0.000	0.000
100	A	54	LYS	0	0.134	-0.065	26.706	0.005	0.005	0.000	0.000	0.000	0.000
101	A	54	LYS	1	0.709	0.981	26.072	0.092	0.092	0.000	0.000	0.000	0.000
102	A	55	PHE	0	0.028	-0.111	23.535	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	55	PHE	0	-0.055	0.112	22.777	0.003	0.003	0.000	0.000	0.000	0.000
104	A	56	TYR	0	0.136	-0.043	20.358	0.005	0.005	0.000	0.000	0.000	0.000
105	A	56	TYR	0	-0.212	-0.009	19.565	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	57	VAL	0	0.175	-0.103	18.088	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	57	VAL	0	-0.085	0.128	16.849	0.004	0.004	0.000	0.000	0.000	0.000
108	A	58	LEU	0	0.058	-0.126	13.908	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	58	LEU	0	-0.100	0.101	12.829	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	59	GLY	0	0.092	-0.078	11.878	0.106	0.106	0.000	0.000	0.000	0.000
111	A	60	ARG	0	0.029	-0.023	7.982	-0.284	-0.284	0.000	0.000	0.000	0.000
112	A	60	ARG	1	0.681	0.914	3.078	2.314	1.506	0.010	1.040	-0.243	0.001
113	A	61	ASP	0	0.099	-0.048	8.385	0.209	0.209	0.000	0.000	0.000	0.000
114	A	61	ASP	-1	-0.920	-0.806	8.796	-0.540	-0.540	0.000	0.000	0.000	0.000
115	A	62	GLU	0	0.054	-0.102	8.951	-0.174	-0.174	0.000	0.000	0.000	0.000
116	A	62	GLU	-1	-0.885	-0.798	6.453	1.745	1.745	0.000	0.000	0.000	0.000
117	A	63	GLU	0	0.117	-0.101	10.207	-0.038	-0.038	0.000	0.000	0.000	0.000
118	A	63	GLU	-1	-1.001	-0.853	13.434	0.321	0.321	0.000	0.000	0.000	0.000
119	A	64	GLY	0	-0.004	-0.107	12.294	0.147	0.147	0.000	0.000	0.000	0.000
120	A	65	TYR	0	0.025	-0.018	13.283	0.016	0.016	0.000	0.000	0.000	0.000
121	A	65	TYR	0	-0.109	0.075	8.909	-0.101	-0.101	0.000	0.000	0.000	0.000
122	A	66	SER	0	0.062	-0.101	14.588	-0.036	-0.036	0.000	0.000	0.000	0.000
123	A	66	SER	0	-0.068	0.077	18.544	0.006	0.006	0.000	0.000	0.000	0.000
124	A	67	PHE	0	0.056	-0.077	17.606	0.024	0.024	0.000	0.000	0.000	0.000
125	A	67	PHE	0	-0.089	0.074	14.105	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	68	ASP	0	0.094	-0.085	19.100	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	68	ASP	-1	-0.874	-0.811	20.737	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	69	GLU	0	0.199	-0.046	20.899	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	69	GLU	-1	-0.854	-0.763	18.899	0.177	0.177	0.000	0.000	0.000	0.000
130	A	70	VAL	0	-0.016	-0.098	21.080	0.012	0.012	0.000	0.000	0.000	0.000
131	A	70	VAL	0	-0.098	0.069	19.175	0.000	0.000	0.000	0.000	0.000	0.000
132	A	71	ALA	0	0.148	-0.075	22.241	0.001	0.001	0.000	0.000	0.000	0.000
133	A	71	ALA	0	-0.097	0.096	24.287	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	72	GLU	0	0.098	-0.118	25.045	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	72	GLU	-1	-1.032	-0.877	25.190	0.052	0.052	0.000	0.000	0.000	0.000
136	A	73	LYS	0	0.121	-0.056	25.387	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	73	LYS	1	0.765	1.000	21.685	-0.129	-0.129	0.000	0.000	0.000	0.000
138	A	74	PHE	0	-0.012	-0.127	26.306	0.004	0.004	0.000	0.000	0.000	0.000
139	A	74	PHE	0	-0.081	0.051	23.336	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	75	GLU	0	0.113	-0.096	27.847	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	75	GLU	-1	-0.931	-0.810	29.575	0.001	0.001	0.000	0.000	0.000	0.000
142	A	76	GLU	0	0.039	-0.115	29.963	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	76	GLU	-1	-1.006	-0.870	28.572	0.069	0.069	0.000	0.000	0.000	0.000
144	A	77	VAL	0	-0.011	-0.120	31.168	0.004	0.004	0.000	0.000	0.000	0.000
145	A	77	VAL	0	-0.116	0.084	29.581	0.000	0.000	0.000	0.000	0.000	0.000
146	A	78	GLU	0	0.137	-0.082	32.417	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	78	GLU	-1	-0.943	-0.821	35.588	0.019	0.019	0.000	0.000	0.000	0.000
148	A	79	ASN	0	0.028	-0.081	35.512	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	79	ASN	0	-0.149	0.020	37.021	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	80	VAL	0	0.149	-0.113	33.186	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	80	VAL	0	-0.096	0.120	31.306	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	81	GLU	0	0.126	-0.080	34.633	0.005	0.005	0.000	0.000	0.000	0.000
153	A	81	GLU	-1	-1.039	-0.897	36.154	-0.008	-0.008	0.000	0.000	0.000	0.000
154	A	82	SER	0	-0.016	-0.100	32.774	0.003	0.003	0.000	0.000	0.000	0.000
155	A	82	SER	0	-0.039	0.072	32.524	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	83	ALA	0	0.040	-0.124	28.438	-0.005	-0.005	0.000	0.000	0.000	0.000
157	A	83	ALA	0	-0.092	0.086	27.460	0.001	0.001	0.000	0.000	0.000	0.000
158	A	84	GLU	0	0.105	-0.094	27.356	0.007	0.007	0.000	0.000	0.000	0.000
159	A	84	GLU	-1	-1.007	-0.842	28.192	-0.036	-0.036	0.000	0.000	0.000	0.000
160	A	85	VAL	0	0.072	-0.106	23.050	-0.005	-0.005	0.000	0.000	0.000	0.000
161	A	85	VAL	0	-0.085	0.102	20.981	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	86	GLU	0	0.120	-0.075	24.035	-0.006	-0.006	0.000	0.000	0.000	0.000
163	A	86	GLU	-1	-0.947	-0.817	25.184	-0.071	-0.071	0.000	0.000	0.000	0.000
164	A	87	THR	0	-0.035	-0.092	22.330	0.001	0.001	0.000	0.000	0.000	0.000
165	A	87	THR	0	-0.052	0.036	21.831	-0.010	-0.010	0.000	0.000	0.000	0.000
166	A	88	VAL	0	0.135	-0.090	18.083	0.009	0.009	0.000	0.000	0.000	0.000
167	A	88	VAL	0	-0.049	0.131	16.062	-0.001	-0.001	0.000	0.000	0.000	0.000
168	A	89	SER	0	0.011	-0.107	16.348	0.008	0.008	0.000	0.000	0.000	0.000
169	A	89	SER	0	-0.056	0.067	15.946	0.012	0.012	0.000	0.000	0.000	0.000
170	A	90	ARG	0	0.084	-0.054	12.226	0.008	0.008	0.000	0.000	0.000	0.000
171	A	90	ARG	1	0.728	0.946	10.317	0.642	0.642	0.000	0.000	0.000	0.000
172	A	91	ILE	0	-0.124	-0.147	9.325	0.067	0.067	0.000	0.000	0.000	0.000
173	A	91	ILE	0	0.061	0.051	10.539	0.017	0.017	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:1:MET)