FMO DATABASE

FMODB ID: 16M2Z

Calculation Name: 4YII-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YII

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UJX6

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-482708.833333
FMO2-HF: Nuclear repulsion	453056.955113
FMO2-HF: Total energy	-29651.878219
FMO2-MP2: Total energy	-29737.878193

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:747:LYS)

Summations of interaction energy for fragment #1(A:747:LYS)

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.
-1.75	-0.073000000000001	7.8	-4.84	-4.637	-0.016

Interaction energy analysis for fragmet #1(A:747:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.196 / q_NPA : 0.044

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	748	GLU	-1	-1.022	-0.855	4.660	1.770	2.141	-0.001	-0.115	-0.255	0.000
5	A	749	GLU	0	0.068	-0.103	3.583	-2.644	-1.306	-0.003	-0.658	-0.677	0.002
6	A	749	GLU	-1	-0.962	-0.871	3.947	0.874	0.960	-0.001	-0.017	-0.069	0.000
7	A	750	GLU	0	-0.016	-0.107	3.177	0.463	0.083	0.114	0.634	-0.367	0.000
8	A	750	GLU	-1	-0.899	-0.835	2.369	-1.391	-1.423	7.693	-4.557	-3.104	-0.018
9	A	751	LEU	0	0.105	-0.080	4.141	0.423	0.635	-0.001	-0.113	-0.099	0.000
10	A	751	LEU	0	-0.078	0.098	4.492	0.007	0.089	-0.001	-0.014	-0.066	0.000
11	A	752	LEU	0	0.035	-0.147	6.090	0.189	0.189	0.000	0.000	0.000	0.000
12	A	752	LEU	0	-0.005	0.151	8.067	0.005	0.005	0.000	0.000	0.000	0.000
13	A	753	LEU	0	0.138	-0.105	7.497	0.106	0.106	0.000	0.000	0.000	0.000
14	A	753	LEU	0	-0.070	0.140	7.822	0.004	0.004	0.000	0.000	0.000	0.000
15	A	754	PHE	0	0.074	-0.124	8.132	0.141	0.141	0.000	0.000	0.000	0.000
16	A	754	PHE	0	-0.089	0.117	5.641	0.053	0.053	0.000	0.000	0.000	0.000
17	A	755	TRP	0	0.068	-0.077	9.886	0.072	0.072	0.000	0.000	0.000	0.000
18	A	755	TRP	0	-0.133	0.063	11.672	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	756	THR	0	0.060	-0.064	12.075	0.023	0.023	0.000	0.000	0.000	0.000
20	A	756	THR	0	-0.016	0.070	12.420	0.033	0.033	0.000	0.000	0.000	0.000
21	A	757	TYR	0	0.082	-0.122	12.985	0.043	0.043	0.000	0.000	0.000	0.000
22	A	757	TYR	0	-0.086	0.098	12.417	0.002	0.002	0.000	0.000	0.000	0.000
23	A	758	ILE	0	0.050	-0.065	14.059	0.035	0.035	0.000	0.000	0.000	0.000
24	A	758	ILE	0	-0.086	0.081	12.655	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	759	GLN	0	0.083	-0.118	15.830	0.013	0.013	0.000	0.000	0.000	0.000
26	A	759	GLN	0	-0.065	0.105	16.155	0.001	0.001	0.000	0.000	0.000	0.000
27	A	760	ALA	0	0.106	-0.064	17.713	0.016	0.016	0.000	0.000	0.000	0.000
28	A	760	ALA	0	-0.025	0.113	18.485	0.004	0.004	0.000	0.000	0.000	0.000
29	A	761	MET	0	0.068	-0.135	18.578	0.023	0.023	0.000	0.000	0.000	0.000
30	A	761	MET	0	-0.155	0.109	15.477	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	762	LEU	0	0.067	-0.102	20.020	0.013	0.013	0.000	0.000	0.000	0.000
32	A	762	LEU	0	-0.086	0.106	19.614	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	763	THR	0	0.033	-0.063	21.880	0.005	0.005	0.000	0.000	0.000	0.000
34	A	763	THR	0	-0.071	0.024	21.882	0.006	0.006	0.000	0.000	0.000	0.000
35	A	764	ASN	0	0.034	-0.079	23.451	0.009	0.009	0.000	0.000	0.000	0.000
36	A	764	ASN	0	-0.181	0.028	22.654	0.009	0.009	0.000	0.000	0.000	0.000
37	A	765	LEU	0	0.043	-0.083	24.244	0.011	0.011	0.000	0.000	0.000	0.000
38	A	765	LEU	0	-0.094	0.074	22.589	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	766	GLU	0	0.078	-0.080	25.483	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	766	GLU	-1	-0.911	-0.837	28.156	-0.106	-0.106	0.000	0.000	0.000	0.000
41	A	767	SER	0	0.022	-0.094	24.705	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	767	SER	0	-0.068	0.026	26.243	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	768	LEU	0	-0.030	-0.139	22.172	0.013	0.013	0.000	0.000	0.000	0.000
44	A	768	LEU	0	-0.023	0.125	20.633	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	769	SER	0	0.097	-0.052	22.654	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	769	SER	0	0.025	0.077	23.669	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	770	LEU	0	0.120	-0.099	19.246	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	770	LEU	0	-0.084	0.120	16.739	0.000	0.000	0.000	0.000	0.000	0.000
49	A	771	ASP	0	0.137	-0.116	18.705	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	771	ASP	-1	-1.013	-0.844	21.751	-0.236	-0.236	0.000	0.000	0.000	0.000
51	A	772	ARG	0	0.019	-0.077	19.990	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	772	ARG	1	0.892	1.061	22.136	0.148	0.148	0.000	0.000	0.000	0.000
53	A	773	ILE	0	0.139	-0.069	17.517	0.018	0.018	0.000	0.000	0.000	0.000
54	A	773	ILE	0	-0.079	0.100	15.319	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	774	TYR	0	0.098	-0.096	15.086	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	774	TYR	0	-0.090	0.086	13.696	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	775	ASN	0	0.070	-0.084	15.559	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	775	ASN	0	-0.096	0.078	19.520	0.018	0.018	0.000	0.000	0.000	0.000
59	A	776	MET	0	0.104	-0.083	17.638	0.008	0.008	0.000	0.000	0.000	0.000
60	A	776	MET	0	-0.099	0.092	17.856	0.004	0.004	0.000	0.000	0.000	0.000
61	A	777	LEU	0	0.048	-0.097	12.901	0.048	0.048	0.000	0.000	0.000	0.000
62	A	777	LEU	0	-0.030	0.092	11.440	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	778	ARG	0	0.139	-0.078	13.004	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	778	ARG	1	0.858	1.069	13.677	0.350	0.350	0.000	0.000	0.000	0.000
65	A	779	MET	0	0.067	-0.104	14.464	0.008	0.008	0.000	0.000	0.000	0.000
66	A	779	MET	0	-0.113	0.092	18.313	0.007	0.007	0.000	0.000	0.000	0.000
67	A	780	PHE	0	0.028	-0.071	15.716	0.023	0.023	0.000	0.000	0.000	0.000
68	A	780	PHE	0	-0.092	0.071	15.873	0.005	0.005	0.000	0.000	0.000	0.000
69	A	781	VAL	0	0.085	-0.080	11.187	0.060	0.060	0.000	0.000	0.000	0.000
70	A	781	VAL	0	-0.088	0.078	9.200	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	782	VAL	0	0.094	-0.092	10.250	0.031	0.031	0.000	0.000	0.000	0.000
72	A	782	VAL	0	-0.121	0.081	9.898	0.004	0.004	0.000	0.000	0.000	0.000
73	A	783	THR	0	-0.056	-0.110	11.231	0.021	0.021	0.000	0.000	0.000	0.000
74	A	783	THR	0	-0.076	0.047	15.080	0.012	0.012	0.000	0.000	0.000	0.000
75	A	784	GLY	0	0.010	-0.077	13.375	0.034	0.034	0.000	0.000	0.000	0.000
76	A	785	PRO	0	-0.012	-0.040	13.393	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	786	ALA	0	0.084	0.035	9.961	0.063	0.063	0.000	0.000	0.000	0.000
78	A	786	ALA	0	-0.064	0.073	8.888	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	787	LEU	0	-0.023	-0.105	8.908	0.026	0.026	0.000	0.000	0.000	0.000
80	A	787	LEU	0	-0.120	0.083	10.357	0.009	0.009	0.000	0.000	0.000	0.000
81	A	788	ALA	0	0.194	-0.085	6.411	0.038	0.038	0.000	0.000	0.000	0.000
82	A	788	ALA	0	-0.090	0.103	5.636	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	789	GLU	0	0.066	-0.089	6.051	0.035	0.035	0.000	0.000	0.000	0.000
84	A	789	GLU	-1	-0.932	-0.852	6.655	-0.587	-0.587	0.000	0.000	0.000	0.000
85	A	790	ILE	0	-0.004	-0.113	6.186	-0.367	-0.367	0.000	0.000	0.000	0.000
86	A	790	ILE	0	-0.116	0.071	7.880	0.038	0.038	0.000	0.000	0.000	0.000
87	A	791	ASP	0	0.070	-0.111	8.754	0.163	0.163	0.000	0.000	0.000	0.000
88	A	791	ASP	-1	-0.884	-0.806	11.562	-0.852	-0.852	0.000	0.000	0.000	0.000
89	A	792	LEU	0	0.141	-0.103	11.984	-0.075	-0.075	0.000	0.000	0.000	0.000
90	A	792	LEU	0	-0.102	0.113	16.232	0.006	0.006	0.000	0.000	0.000	0.000
91	A	793	GLN	0	0.090	-0.118	14.697	0.019	0.019	0.000	0.000	0.000	0.000
92	A	793	GLN	0	-0.079	0.108	14.071	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	794	GLU	0	0.049	-0.132	10.142	0.119	0.119	0.000	0.000	0.000	0.000
94	A	794	GLU	-1	-0.908	-0.796	6.643	-2.324	-2.324	0.000	0.000	0.000	0.000
95	A	795	LEU	0	0.145	-0.115	11.421	-0.054	-0.054	0.000	0.000	0.000	0.000
96	A	795	LEU	0	-0.105	0.122	12.000	0.017	0.017	0.000	0.000	0.000	0.000
97	A	796	GLN	0	0.049	-0.127	12.466	0.040	0.040	0.000	0.000	0.000	0.000
98	A	796	GLN	0	-0.116	0.103	16.779	0.045	0.045	0.000	0.000	0.000	0.000
99	A	797	GLY	0	0.005	-0.094	13.959	0.055	0.055	0.000	0.000	0.000	0.000
100	A	798	TYR	0	0.097	0.007	11.704	0.077	0.077	0.000	0.000	0.000	0.000
101	A	798	TYR	0	-0.026	0.103	10.033	0.003	0.003	0.000	0.000	0.000	0.000
102	A	799	LEU	0	0.071	-0.121	12.816	0.049	0.049	0.000	0.000	0.000	0.000
103	A	799	LEU	0	-0.064	0.104	14.817	0.011	0.011	0.000	0.000	0.000	0.000
104	A	800	GLN	0	0.106	-0.085	15.967	0.057	0.057	0.000	0.000	0.000	0.000
105	A	800	GLN	0	-0.121	0.071	17.259	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	801	LYS	0	0.005	-0.091	15.017	0.069	0.069	0.000	0.000	0.000	0.000
107	A	801	LYS	1	0.822	0.991	13.208	0.321	0.321	0.000	0.000	0.000	0.000
108	A	802	LYS	0	0.096	-0.086	16.008	0.039	0.039	0.000	0.000	0.000	0.000
109	A	802	LYS	1	0.839	1.065	12.643	0.417	0.417	0.000	0.000	0.000	0.000
110	A	803	VAL	0	0.034	-0.093	17.326	0.034	0.034	0.000	0.000	0.000	0.000
111	A	803	VAL	0	-0.088	0.086	20.241	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	804	ARG	0	0.068	-0.076	19.892	0.031	0.031	0.000	0.000	0.000	0.000
113	A	804	ARG	1	0.835	1.032	16.758	0.342	0.342	0.000	0.000	0.000	0.000
114	A	805	ASP	0	0.052	-0.091	19.302	0.028	0.028	0.000	0.000	0.000	0.000
115	A	805	ASP	-1	-0.935	-0.797	17.385	-0.260	-0.260	0.000	0.000	0.000	0.000
116	A	806	GLN	0	0.055	-0.112	20.659	0.014	0.014	0.000	0.000	0.000	0.000
117	A	806	GLN	0	-0.111	0.087	24.077	0.005	0.005	0.000	0.000	0.000	0.000
118	A	807	GLN	0	0.140	-0.093	19.011	0.026	0.026	0.000	0.000	0.000	0.000
119	A	807	GLN	0	-0.115	0.081	16.816	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	808	LEU	0	-0.023	-0.146	20.090	0.012	0.012	0.000	0.000	0.000	0.000
121	A	808	LEU	0	-0.057	0.100	17.161	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	809	VAL	0	0.148	-0.096	21.209	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	809	VAL	0	-0.070	0.138	25.327	0.002	0.002	0.000	0.000	0.000	0.000
124	A	810	TYR	0	0.118	-0.114	23.830	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	810	TYR	0	-0.101	0.114	22.951	0.000	0.000	0.000	0.000	0.000	0.000
126	A	811	SER	0	-0.037	-0.092	24.851	0.005	0.005	0.000	0.000	0.000	0.000
127	A	811	SER	0	-0.022	0.075	28.860	0.001	0.001	0.000	0.000	0.000	0.000
128	A	812	ALA	0	0.092	-0.120	28.324	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	812	ALA	0	-0.065	0.135	30.610	0.002	0.002	0.000	0.000	0.000	0.000
130	A	813	GLY	0	0.011	-0.106	27.194	0.004	0.004	0.000	0.000	0.000	0.000
131	A	814	VAL	0	-0.040	0.001	24.502	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	814	VAL	0	-0.045	0.080	25.259	0.000	0.000	0.000	0.000	0.000	0.000
133	A	815	TYR	0	0.063	-0.085	21.344	0.009	0.009	0.000	0.000	0.000	0.000
134	A	815	TYR	0	-0.040	0.078	19.914	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	816	ARG	0	0.129	-0.125	22.892	0.005	0.005	0.000	0.000	0.000	0.000
136	A	816	ARG	1	0.819	1.101	25.611	0.126	0.126	0.000	0.000	0.000	0.000
137	A	817	LEU	0	0.092	-0.097	22.763	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	817	LEU	0	-0.057	0.133	20.143	0.000	0.000	0.000	0.000	0.000	0.000
139	A	818	PRO	0	-0.068	-0.100	23.032	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:747:LYS)