FMO DATABASE

FMODB ID: 8527Y

Calculation Name: 3E9U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E9U

Chain ID: A

ChEMBL ID:

UniProt ID: Q24413

Base Structure: X-ray

Registration Date: 2023-06-21

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1484556.975981
FMO2-HF: Nuclear repulsion	1421030.012052
FMO2-HF: Total energy	-63526.963929
FMO2-MP2: Total energy	-63715.384329

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:548:MET)

Summations of interaction energy for fragment #1(A:548: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.
5.434	-5.876	1.529	12.988	-3.208	-0.014

Interaction energy analysis for fragmet #1(A:548:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.038

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].
3	A	550	ARG	1	0.954	0.948	2.696	6.377	-6.471	1.407	13.499	-2.057	-0.011
4	A	551	GLY	0	0.015	0.016	4.681	-1.472	-1.364	0.013	-0.033	-0.089	0.000
5	A	552	SER	0	-0.026	-0.017	6.175	-0.435	-0.435	0.000	0.000	0.000	0.000
6	A	553	GLU	-1	-0.892	-0.948	8.758	0.078	0.078	0.000	0.000	0.000	0.000
7	A	554	PHE	0	0.034	0.022	11.581	0.051	0.051	0.000	0.000	0.000	0.000
8	A	555	GLY	0	0.032	0.037	10.949	0.048	0.048	0.000	0.000	0.000	0.000
9	A	556	ILE	0	-0.049	-0.026	6.143	-0.213	-0.213	0.000	0.000	0.000	0.000
10	A	557	PHE	0	0.024	0.012	9.923	0.192	0.192	0.000	0.000	0.000	0.000
11	A	558	ALA	0	0.008	0.015	11.877	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	559	PHE	0	0.031	0.028	13.932	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	560	THR	0	-0.040	-0.029	16.166	0.041	0.041	0.000	0.000	0.000	0.000
14	A	561	ASP	-1	-0.847	-0.943	17.841	0.321	0.321	0.000	0.000	0.000	0.000
15	A	562	SER	0	-0.002	0.001	18.296	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	563	VAL	0	-0.045	-0.016	19.796	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	564	PHE	0	0.035	0.021	21.372	0.003	0.003	0.000	0.000	0.000	0.000
18	A	565	GLU	-1	-0.826	-0.902	26.344	0.110	0.110	0.000	0.000	0.000	0.000
19	A	566	ILE	0	-0.007	0.017	30.182	0.002	0.002	0.000	0.000	0.000	0.000
20	A	567	THR	0	-0.032	0.012	33.186	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	568	GLU	-1	-0.688	-0.840	35.928	0.040	0.040	0.000	0.000	0.000	0.000
22	A	569	SER	0	-0.007	-0.026	37.896	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	570	VAL	0	-0.057	-0.022	33.718	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	571	GLY	0	0.034	0.033	36.655	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	572	ARG	1	0.752	0.862	32.435	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	573	PHE	0	-0.013	-0.014	26.943	0.005	0.005	0.000	0.000	0.000	0.000
27	A	574	GLU	-1	-0.869	-0.922	28.088	0.037	0.037	0.000	0.000	0.000	0.000
28	A	575	LEU	0	-0.015	-0.002	22.249	0.015	0.015	0.000	0.000	0.000	0.000
29	A	576	LYS	1	0.804	0.887	20.503	-0.171	-0.171	0.000	0.000	0.000	0.000
30	A	577	VAL	0	-0.009	-0.001	16.969	0.015	0.015	0.000	0.000	0.000	0.000
31	A	578	MET	0	-0.034	-0.015	15.882	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	579	ARG	1	0.745	0.853	14.407	0.108	0.108	0.000	0.000	0.000	0.000
33	A	580	TYR	0	-0.022	-0.033	11.268	0.087	0.087	0.000	0.000	0.000	0.000
34	A	581	SER	0	-0.076	-0.052	10.232	0.025	0.025	0.000	0.000	0.000	0.000
35	A	582	GLY	0	0.041	0.027	11.911	-0.088	-0.088	0.000	0.000	0.000	0.000
36	A	583	ALA	0	-0.016	-0.018	14.299	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	584	ARG	1	0.885	0.951	16.207	0.043	0.043	0.000	0.000	0.000	0.000
38	A	585	GLY	0	0.060	0.021	16.880	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	586	THR	0	-0.010	0.010	19.388	0.036	0.036	0.000	0.000	0.000	0.000
40	A	587	VAL	0	-0.025	-0.017	14.297	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	588	ILE	0	-0.001	0.006	17.615	0.049	0.049	0.000	0.000	0.000	0.000
42	A	589	VAL	0	0.019	0.006	15.252	-0.068	-0.068	0.000	0.000	0.000	0.000
43	A	590	PRO	0	-0.001	0.017	16.311	0.051	0.051	0.000	0.000	0.000	0.000
44	A	591	TYR	0	0.027	0.002	18.197	0.006	0.006	0.000	0.000	0.000	0.000
45	A	592	TRP	0	-0.036	-0.024	17.294	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	593	THR	0	0.035	0.058	22.602	0.014	0.014	0.000	0.000	0.000	0.000
47	A	594	GLU	-1	-0.869	-0.938	23.365	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	595	ASN	0	0.086	0.059	26.300	0.013	0.013	0.000	0.000	0.000	0.000
49	A	596	ASP	-1	-0.905	-0.952	27.354	0.050	0.050	0.000	0.000	0.000	0.000
50	A	597	THR	0	0.001	0.018	29.335	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	598	ALA	0	-0.068	-0.022	31.318	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	599	THR	0	-0.026	-0.051	31.919	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	600	GLU	-1	-0.744	-0.847	30.866	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	601	SER	0	-0.074	-0.025	33.776	0.000	0.000	0.000	0.000	0.000	0.000
55	A	602	LYS	1	0.774	0.872	36.972	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	603	ASP	-1	-0.738	-0.869	34.609	0.030	0.030	0.000	0.000	0.000	0.000
57	A	604	TYR	0	-0.066	-0.055	29.567	0.003	0.003	0.000	0.000	0.000	0.000
58	A	605	GLU	-1	-0.881	-0.935	33.663	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	606	GLY	0	-0.014	-0.017	30.232	0.002	0.002	0.000	0.000	0.000	0.000
60	A	607	ALA	0	0.026	0.018	27.234	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	608	ARG	1	0.759	0.810	25.346	0.050	0.050	0.000	0.000	0.000	0.000
62	A	609	GLY	0	0.002	0.013	24.220	0.005	0.005	0.000	0.000	0.000	0.000
63	A	610	GLU	-1	-0.816	-0.893	21.090	-0.261	-0.261	0.000	0.000	0.000	0.000
64	A	611	LEU	0	-0.018	0.004	19.908	0.018	0.018	0.000	0.000	0.000	0.000
65	A	612	VAL	0	0.025	0.004	20.502	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	613	PHE	0	-0.026	-0.007	18.572	0.029	0.029	0.000	0.000	0.000	0.000
67	A	614	GLU	-1	-0.839	-0.953	20.757	-0.141	-0.141	0.000	0.000	0.000	0.000
68	A	615	ASN	0	0.025	0.024	21.090	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	616	ASN	0	-0.019	-0.014	20.873	0.003	0.003	0.000	0.000	0.000	0.000
70	A	617	GLU	-1	-0.791	-0.852	21.973	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	618	SER	0	0.045	0.008	18.514	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	619	GLU	-1	-0.838	-0.913	18.794	0.172	0.172	0.000	0.000	0.000	0.000
73	A	620	LYS	1	0.833	0.917	21.107	0.030	0.030	0.000	0.000	0.000	0.000
74	A	621	PHE	0	0.010	-0.003	22.310	0.019	0.019	0.000	0.000	0.000	0.000
75	A	622	ILE	0	-0.008	0.008	21.283	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	623	ASP	-1	-0.784	-0.862	25.556	0.025	0.025	0.000	0.000	0.000	0.000
77	A	624	LEU	0	-0.081	-0.052	26.342	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	625	PHE	0	0.026	0.026	30.173	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	626	ILE	0	-0.036	-0.037	31.017	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	627	LEU	0	-0.027	0.000	34.938	0.001	0.001	0.000	0.000	0.000	0.000
81	A	628	GLU	-1	-0.792	-0.855	38.363	0.041	0.041	0.000	0.000	0.000	0.000
82	A	629	GLU	-1	-0.867	-0.929	40.156	0.022	0.022	0.000	0.000	0.000	0.000
83	A	630	SER	0	-0.082	-0.050	43.389	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	631	SER	0	-0.010	-0.026	41.882	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	632	TYR	0	-0.072	-0.049	44.397	0.002	0.002	0.000	0.000	0.000	0.000
86	A	633	GLU	-1	-0.945	-0.994	42.019	0.058	0.058	0.000	0.000	0.000	0.000
87	A	634	LYS	1	0.781	0.877	37.263	-0.043	-0.043	0.000	0.000	0.000	0.000
88	A	635	ASP	-1	-0.788	-0.850	34.208	0.093	0.093	0.000	0.000	0.000	0.000
89	A	636	VAL	0	-0.030	0.006	33.985	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	637	SER	0	0.024	0.015	28.680	0.008	0.008	0.000	0.000	0.000	0.000
91	A	638	PHE	0	0.037	0.033	27.394	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	639	LYS	1	0.800	0.902	22.518	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	640	VAL	0	0.004	0.004	21.758	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	641	HIS	1	0.807	0.882	18.056	0.037	0.037	0.000	0.000	0.000	0.000
95	A	642	ILE	0	0.015	0.011	13.914	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	643	GLY	0	-0.006	-0.001	15.110	0.000	0.000	0.000	0.000	0.000	0.000
97	A	644	GLU	-1	-0.939	-0.968	10.695	-0.593	-0.593	0.000	0.000	0.000	0.000
98	A	645	PRO	0	-0.055	-0.007	10.740	0.053	0.053	0.000	0.000	0.000	0.000
99	A	646	ARG	1	0.780	0.865	12.608	0.204	0.204	0.000	0.000	0.000	0.000
100	A	647	LEU	0	-0.021	-0.010	15.020	0.051	0.051	0.000	0.000	0.000	0.000
101	A	648	ALA	0	0.038	0.019	16.607	0.004	0.004	0.000	0.000	0.000	0.000
102	A	649	PRO	0	-0.068	-0.055	20.418	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	650	ASP	-1	-0.939	-0.962	22.192	-0.229	-0.229	0.000	0.000	0.000	0.000
104	A	651	ASP	-1	-0.865	-0.926	19.644	-0.343	-0.343	0.000	0.000	0.000	0.000
105	A	652	GLY	0	-0.001	-0.022	21.094	-0.031	-0.031	0.000	0.000	0.000	0.000
106	A	653	LEU	0	0.006	0.006	16.111	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	654	ALA	0	0.024	0.039	17.177	-0.083	-0.083	0.000	0.000	0.000	0.000
108	A	655	ALA	0	-0.056	-0.036	17.433	-0.060	-0.060	0.000	0.000	0.000	0.000
109	A	656	LYS	1	0.905	0.920	16.854	0.540	0.540	0.000	0.000	0.000	0.000
110	A	657	ILE	0	0.015	0.025	12.145	-0.045	-0.045	0.000	0.000	0.000	0.000
111	A	658	LYS	1	0.982	0.994	14.243	0.401	0.401	0.000	0.000	0.000	0.000
112	A	659	GLU	-1	-0.929	-0.952	16.258	-0.497	-0.497	0.000	0.000	0.000	0.000
113	A	660	VAL	0	0.022	0.000	12.265	0.017	0.017	0.000	0.000	0.000	0.000
114	A	661	GLU	-1	-0.880	-0.936	11.260	-1.144	-1.144	0.000	0.000	0.000	0.000
115	A	662	LYS	1	0.895	0.956	12.702	0.519	0.519	0.000	0.000	0.000	0.000
116	A	663	LYS	1	0.785	0.898	14.709	0.807	0.807	0.000	0.000	0.000	0.000
117	A	664	PRO	0	0.017	0.005	14.740	-0.078	-0.078	0.000	0.000	0.000	0.000
118	A	665	VAL	0	0.074	0.022	11.047	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	666	GLN	0	-0.030	-0.016	13.148	-0.105	-0.105	0.000	0.000	0.000	0.000
120	A	667	ASP	-1	-0.866	-0.939	15.612	-0.438	-0.438	0.000	0.000	0.000	0.000
121	A	668	LEU	0	-0.085	-0.011	9.767	0.008	0.008	0.000	0.000	0.000	0.000
122	A	669	THR	0	-0.025	-0.017	13.838	0.063	0.063	0.000	0.000	0.000	0.000
123	A	670	GLU	-1	-0.861	-0.927	12.712	-0.843	-0.843	0.000	0.000	0.000	0.000
124	A	671	LEU	0	0.041	-0.002	12.429	-0.096	-0.096	0.000	0.000	0.000	0.000
125	A	672	ASP	-1	-0.780	-0.885	13.043	-0.984	-0.984	0.000	0.000	0.000	0.000
126	A	673	ARG	1	0.926	0.952	8.394	0.789	0.789	0.000	0.000	0.000	0.000
127	A	674	ILE	0	-0.006	0.004	8.157	-0.410	-0.410	0.000	0.000	0.000	0.000
128	A	675	LEU	0	-0.003	-0.005	9.831	-0.084	-0.084	0.000	0.000	0.000	0.000
129	A	676	LEU	0	-0.010	-0.005	6.933	-0.041	-0.041	0.000	0.000	0.000	0.000
130	A	677	LEU	0	-0.079	-0.029	3.604	-1.063	-0.525	0.016	-0.177	-0.377	-0.001
131	A	678	SER	0	-0.087	-0.044	6.440	0.171	0.171	0.000	0.000	0.000	0.000
132	A	679	LYS	1	0.906	0.947	7.685	1.991	1.991	0.000	0.000	0.000	0.000
133	A	680	PRO	0	0.001	0.018	8.398	-0.183	-0.183	0.000	0.000	0.000	0.000
134	A	681	ARG	1	0.892	0.937	3.346	1.141	2.033	0.093	-0.301	-0.685	-0.002
135	A	682	ASN	0	0.025	0.005	7.834	0.339	0.339	0.000	0.000	0.000	0.000
136	A	683	GLY	0	-0.022	-0.022	7.317	-0.109	-0.109	0.000	0.000	0.000	0.000
137	A	684	GLU	-1	-0.919	-0.977	8.917	1.196	1.196	0.000	0.000	0.000	0.000
138	A	685	LEU	0	-0.036	-0.002	10.456	-0.069	-0.069	0.000	0.000	0.000	0.000
139	A	686	THR	0	0.021	0.005	11.479	-0.035	-0.035	0.000	0.000	0.000	0.000
140	A	687	THR	0	-0.040	-0.024	14.395	-0.066	-0.066	0.000	0.000	0.000	0.000
141	A	688	ALA	0	0.003	0.027	17.898	0.046	0.046	0.000	0.000	0.000	0.000
142	A	689	TYR	0	-0.041	-0.036	20.118	-0.035	-0.035	0.000	0.000	0.000	0.000
143	A	690	VAL	0	0.001	-0.003	24.071	0.016	0.016	0.000	0.000	0.000	0.000
144	A	691	ARG	1	0.747	0.815	27.284	-0.119	-0.119	0.000	0.000	0.000	0.000
145	A	692	ILE	0	-0.012	-0.025	30.356	0.002	0.002	0.000	0.000	0.000	0.000
146	A	693	ARG	1	0.798	0.870	33.711	-0.088	-0.088	0.000	0.000	0.000	0.000
147	A	694	GLU	-1	-0.793	-0.886	36.878	0.067	0.067	0.000	0.000	0.000	0.000
148	A	695	SER	0	-0.021	-0.004	39.920	0.005	0.005	0.000	0.000	0.000	0.000
149	A	696	GLN	0	-0.051	-0.026	39.351	0.002	0.002	0.000	0.000	0.000	0.000
150	A	697	GLU	-1	-0.959	-1.029	42.004	0.065	0.065	0.000	0.000	0.000	0.000
151	A	698	PHE	0	0.028	0.026	44.994	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	699	LYS	1	0.848	0.929	43.846	-0.060	-0.060	0.000	0.000	0.000	0.000
153	A	700	ALA	0	0.085	0.047	46.598	0.000	0.000	0.000	0.000	0.000	0.000
154	A	701	THR	0	-0.091	-0.040	48.524	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	702	VAL	0	0.022	0.003	49.616	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	703	ASP	-1	-0.789	-0.872	48.631	0.052	0.052	0.000	0.000	0.000	0.000
157	A	704	LYS	1	0.894	0.937	51.749	-0.044	-0.044	0.000	0.000	0.000	0.000
158	A	705	LEU	0	-0.066	-0.032	54.424	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	706	VAL	0	-0.003	0.001	53.144	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	707	ALA	0	-0.020	-0.002	55.801	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	708	LYS	1	0.866	0.947	57.488	-0.035	-0.035	0.000	0.000	0.000	0.000
162	A	709	ALA	0	0.031	0.023	60.410	-0.001	-0.001	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:548:MET)