FMO DATABASE

FMODB ID: G6NR1

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1482755.221385
FMO2-HF: Nuclear repulsion	1419229.651355
FMO2-HF: Total energy	-63525.57003
FMO2-MP2: Total energy	-63713.904227

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.
12.766	-3.845	0.341	19.313	-3.042	-0.017

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 : 0.006 / q_NPA : 0.050

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	0.951	0.944	2.513	12.631	-5.307	0.295	19.725	-2.082	-0.016
4	A	551	GLY	0	0.012	0.012	4.923	-0.902	-0.786	0.001	-0.024	-0.092	0.000
5	A	552	SER	0	-0.027	-0.016	6.122	-0.581	-0.581	0.000	0.000	0.000	0.000
6	A	553	GLU	-1	-0.888	-0.943	8.689	-0.101	-0.101	0.000	0.000	0.000	0.000
7	A	554	PHE	0	0.012	0.010	11.497	0.111	0.111	0.000	0.000	0.000	0.000
8	A	555	GLY	0	0.035	0.043	10.864	0.080	0.080	0.000	0.000	0.000	0.000
9	A	556	ILE	0	-0.055	-0.027	6.505	-0.222	-0.222	0.000	0.000	0.000	0.000
10	A	557	PHE	0	0.029	0.013	9.833	0.193	0.193	0.000	0.000	0.000	0.000
11	A	558	ALA	0	0.000	0.011	11.936	0.005	0.005	0.000	0.000	0.000	0.000
12	A	559	PHE	0	0.027	0.028	13.860	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	560	THR	0	-0.045	-0.028	16.117	0.039	0.039	0.000	0.000	0.000	0.000
14	A	561	ASP	-1	-0.877	-0.968	17.836	0.360	0.360	0.000	0.000	0.000	0.000
15	A	562	SER	0	-0.009	-0.007	18.284	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	563	VAL	0	-0.016	-0.001	19.763	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	564	PHE	0	0.042	0.024	21.333	0.001	0.001	0.000	0.000	0.000	0.000
18	A	565	GLU	-1	-0.900	-0.957	26.305	0.136	0.136	0.000	0.000	0.000	0.000
19	A	566	ILE	0	0.002	0.021	30.144	0.000	0.000	0.000	0.000	0.000	0.000
20	A	567	THR	0	-0.037	0.010	33.140	0.000	0.000	0.000	0.000	0.000	0.000
21	A	568	GLU	-1	-0.731	-0.887	35.876	0.050	0.050	0.000	0.000	0.000	0.000
22	A	569	SER	0	-0.027	-0.048	37.967	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	570	VAL	0	-0.064	-0.026	33.658	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	571	GLY	0	0.035	0.034	36.588	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	572	ARG	1	0.843	0.916	32.205	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	573	PHE	0	-0.017	-0.010	26.661	0.005	0.005	0.000	0.000	0.000	0.000
27	A	574	GLU	-1	-0.824	-0.899	27.998	0.022	0.022	0.000	0.000	0.000	0.000
28	A	575	LEU	0	-0.038	-0.007	22.220	0.017	0.017	0.000	0.000	0.000	0.000
29	A	576	LYS	1	0.886	0.949	20.643	-0.166	-0.166	0.000	0.000	0.000	0.000
30	A	577	VAL	0	-0.001	0.004	16.905	0.020	0.020	0.000	0.000	0.000	0.000
31	A	578	MET	0	-0.037	-0.021	15.794	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	579	ARG	1	0.741	0.854	14.332	0.208	0.208	0.000	0.000	0.000	0.000
33	A	580	TYR	0	-0.010	-0.030	11.200	0.069	0.069	0.000	0.000	0.000	0.000
34	A	581	SER	0	-0.085	-0.060	10.202	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	582	GLY	0	0.047	0.033	11.845	-0.112	-0.112	0.000	0.000	0.000	0.000
36	A	583	ALA	0	-0.006	-0.016	14.219	-0.058	-0.058	0.000	0.000	0.000	0.000
37	A	584	ARG	1	0.888	0.971	16.118	0.174	0.174	0.000	0.000	0.000	0.000
38	A	585	GLY	0	0.063	0.022	16.785	-0.065	-0.065	0.000	0.000	0.000	0.000
39	A	586	THR	0	-0.004	0.012	19.309	0.039	0.039	0.000	0.000	0.000	0.000
40	A	587	VAL	0	-0.025	-0.015	14.303	-0.056	-0.056	0.000	0.000	0.000	0.000
41	A	588	ILE	0	0.013	0.014	17.586	0.054	0.054	0.000	0.000	0.000	0.000
42	A	589	VAL	0	0.008	-0.003	15.519	-0.072	-0.072	0.000	0.000	0.000	0.000
43	A	590	PRO	0	0.001	0.016	16.337	0.052	0.052	0.000	0.000	0.000	0.000
44	A	591	TYR	0	0.033	0.004	18.293	0.011	0.011	0.000	0.000	0.000	0.000
45	A	592	TRP	0	-0.055	-0.030	17.465	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	593	THR	0	0.011	0.042	22.755	0.017	0.017	0.000	0.000	0.000	0.000
47	A	594	GLU	-1	-0.908	-0.955	23.620	0.000	0.000	0.000	0.000	0.000	0.000
48	A	595	ASN	0	0.075	0.073	26.473	0.015	0.015	0.000	0.000	0.000	0.000
49	A	596	ASP	-1	-0.965	-0.975	27.667	0.092	0.092	0.000	0.000	0.000	0.000
50	A	597	THR	0	-0.071	-0.016	29.547	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	598	ALA	0	-0.034	-0.012	31.779	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	599	THR	0	-0.066	-0.047	32.120	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	600	GLU	-1	-0.879	-0.959	31.235	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	601	SER	0	-0.072	-0.024	33.947	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	602	LYS	1	0.889	0.955	37.158	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	603	ASP	-1	-0.776	-0.904	34.859	0.046	0.046	0.000	0.000	0.000	0.000
57	A	604	TYR	0	-0.080	-0.084	29.669	0.003	0.003	0.000	0.000	0.000	0.000
58	A	605	GLU	-1	-0.874	-0.933	33.826	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	606	GLY	0	-0.018	-0.015	30.418	0.002	0.002	0.000	0.000	0.000	0.000
60	A	607	ALA	0	0.027	0.023	27.337	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	608	ARG	1	0.905	0.911	25.403	0.052	0.052	0.000	0.000	0.000	0.000
62	A	609	GLY	0	-0.009	0.010	24.308	0.003	0.003	0.000	0.000	0.000	0.000
63	A	610	GLU	-1	-0.886	-0.942	21.039	-0.263	-0.263	0.000	0.000	0.000	0.000
64	A	611	LEU	0	-0.023	-0.006	19.974	0.017	0.017	0.000	0.000	0.000	0.000
65	A	612	VAL	0	0.031	0.010	20.537	-0.038	-0.038	0.000	0.000	0.000	0.000
66	A	613	PHE	0	-0.037	-0.008	18.838	0.031	0.031	0.000	0.000	0.000	0.000
67	A	614	GLU	-1	-0.832	-0.934	20.745	-0.199	-0.199	0.000	0.000	0.000	0.000
68	A	615	ASN	0	0.033	0.013	20.993	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	616	ASN	0	-0.030	-0.029	20.787	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	617	GLU	-1	-0.852	-0.912	21.870	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	618	SER	0	0.042	0.004	18.335	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	619	GLU	-1	-0.919	-0.972	18.718	0.136	0.136	0.000	0.000	0.000	0.000
73	A	620	LYS	1	0.882	0.951	21.037	0.063	0.063	0.000	0.000	0.000	0.000
74	A	621	PHE	0	0.012	-0.001	22.225	0.023	0.023	0.000	0.000	0.000	0.000
75	A	622	ILE	0	-0.009	0.007	21.401	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	623	ASP	-1	-0.861	-0.921	25.697	0.020	0.020	0.000	0.000	0.000	0.000
77	A	624	LEU	0	-0.080	-0.058	26.650	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	625	PHE	0	0.032	0.029	30.336	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	626	ILE	0	-0.048	-0.045	31.289	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	627	LEU	0	-0.038	-0.006	35.127	0.000	0.000	0.000	0.000	0.000	0.000
81	A	628	GLU	-1	-0.805	-0.872	38.551	0.050	0.050	0.000	0.000	0.000	0.000
82	A	629	GLU	-1	-0.929	-0.981	40.482	0.030	0.030	0.000	0.000	0.000	0.000
83	A	630	SER	0	-0.065	-0.029	43.595	0.001	0.001	0.000	0.000	0.000	0.000
84	A	631	SER	0	-0.029	-0.019	42.449	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	632	TYR	0	-0.048	-0.043	44.596	0.002	0.002	0.000	0.000	0.000	0.000
86	A	633	GLU	-1	-0.973	-1.005	42.131	0.074	0.074	0.000	0.000	0.000	0.000
87	A	634	LYS	1	0.833	0.935	37.272	-0.055	-0.055	0.000	0.000	0.000	0.000
88	A	635	ASP	-1	-0.814	-0.887	34.178	0.117	0.117	0.000	0.000	0.000	0.000
89	A	636	VAL	0	0.001	0.012	34.090	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	637	SER	0	0.021	0.002	29.040	0.003	0.003	0.000	0.000	0.000	0.000
91	A	638	PHE	0	0.057	0.048	27.442	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	639	LYS	1	0.943	0.976	22.731	-0.061	-0.061	0.000	0.000	0.000	0.000
93	A	640	VAL	0	0.026	0.021	21.773	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	641	HIS	1	0.787	0.868	18.206	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	642	ILE	0	0.024	0.016	14.139	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	643	GLY	0	-0.001	-0.004	15.211	0.011	0.011	0.000	0.000	0.000	0.000
97	A	644	GLU	-1	-0.953	-0.984	10.599	-0.635	-0.635	0.000	0.000	0.000	0.000
98	A	645	PRO	0	-0.060	-0.006	10.812	0.040	0.040	0.000	0.000	0.000	0.000
99	A	646	ARG	1	0.844	0.920	12.577	0.236	0.236	0.000	0.000	0.000	0.000
100	A	647	LEU	0	-0.004	-0.009	14.735	0.046	0.046	0.000	0.000	0.000	0.000
101	A	648	ALA	0	0.043	0.027	16.514	0.012	0.012	0.000	0.000	0.000	0.000
102	A	649	PRO	0	-0.072	-0.056	20.328	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	650	ASP	-1	-0.931	-0.960	22.071	-0.285	-0.285	0.000	0.000	0.000	0.000
104	A	651	ASP	-1	-0.874	-0.922	19.361	-0.436	-0.436	0.000	0.000	0.000	0.000
105	A	652	GLY	0	-0.008	-0.029	20.928	-0.035	-0.035	0.000	0.000	0.000	0.000
106	A	653	LEU	0	0.002	0.003	15.825	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	654	ALA	0	0.033	0.045	16.981	-0.089	-0.089	0.000	0.000	0.000	0.000
108	A	655	ALA	0	-0.052	-0.032	17.258	-0.059	-0.059	0.000	0.000	0.000	0.000
109	A	656	LYS	1	1.009	0.992	16.989	0.658	0.658	0.000	0.000	0.000	0.000
110	A	657	ILE	0	0.004	0.025	12.020	-0.038	-0.038	0.000	0.000	0.000	0.000
111	A	658	LYS	1	0.993	0.996	14.043	0.449	0.449	0.000	0.000	0.000	0.000
112	A	659	GLU	-1	-1.018	-1.018	16.084	-0.537	-0.537	0.000	0.000	0.000	0.000
113	A	660	VAL	0	-0.002	-0.015	12.330	0.025	0.025	0.000	0.000	0.000	0.000
114	A	661	GLU	-1	-0.889	-0.956	11.096	-1.281	-1.281	0.000	0.000	0.000	0.000
115	A	662	LYS	1	0.899	0.960	12.572	0.571	0.571	0.000	0.000	0.000	0.000
116	A	663	LYS	1	0.913	0.980	15.132	0.857	0.857	0.000	0.000	0.000	0.000
117	A	664	PRO	0	0.016	0.013	14.874	-0.085	-0.085	0.000	0.000	0.000	0.000
118	A	665	VAL	0	0.075	0.019	11.041	-0.032	-0.032	0.000	0.000	0.000	0.000
119	A	666	GLN	0	-0.047	-0.027	13.214	-0.106	-0.106	0.000	0.000	0.000	0.000
120	A	667	ASP	-1	-0.877	-0.941	15.640	-0.491	-0.491	0.000	0.000	0.000	0.000
121	A	668	LEU	0	-0.115	-0.038	9.937	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	669	THR	0	-0.013	-0.011	13.944	0.078	0.078	0.000	0.000	0.000	0.000
123	A	670	GLU	-1	-0.961	-0.989	13.213	-0.816	-0.816	0.000	0.000	0.000	0.000
124	A	671	LEU	0	0.073	0.007	12.598	-0.135	-0.135	0.000	0.000	0.000	0.000
125	A	672	ASP	-1	-0.856	-0.921	13.285	-1.128	-1.128	0.000	0.000	0.000	0.000
126	A	673	ARG	1	0.976	0.981	8.624	1.021	1.021	0.000	0.000	0.000	0.000
127	A	674	ILE	0	-0.011	0.005	8.322	-0.507	-0.507	0.000	0.000	0.000	0.000
128	A	675	LEU	0	0.004	-0.007	9.940	-0.121	-0.121	0.000	0.000	0.000	0.000
129	A	676	LEU	0	-0.013	-0.006	7.060	-0.046	-0.046	0.000	0.000	0.000	0.000
130	A	677	LEU	0	-0.081	-0.032	3.743	-1.059	-0.563	0.009	-0.173	-0.332	0.000
131	A	678	SER	0	-0.080	-0.034	6.440	0.081	0.081	0.000	0.000	0.000	0.000
132	A	679	LYS	1	0.928	0.970	7.066	2.355	2.355	0.000	0.000	0.000	0.000
133	A	680	PRO	0	-0.006	0.015	8.301	-0.228	-0.228	0.000	0.000	0.000	0.000
134	A	681	ARG	1	0.929	0.955	3.639	1.344	2.059	0.036	-0.215	-0.536	-0.001
135	A	682	ASN	0	0.033	0.021	7.909	0.327	0.327	0.000	0.000	0.000	0.000
136	A	683	GLY	0	-0.030	-0.028	7.491	-0.047	-0.047	0.000	0.000	0.000	0.000
137	A	684	GLU	-1	-0.929	-0.980	8.143	1.649	1.649	0.000	0.000	0.000	0.000
138	A	685	LEU	0	-0.038	0.005	10.420	-0.071	-0.071	0.000	0.000	0.000	0.000
139	A	686	THR	0	0.015	0.002	11.622	-0.050	-0.050	0.000	0.000	0.000	0.000
140	A	687	THR	0	-0.036	-0.018	14.602	-0.078	-0.078	0.000	0.000	0.000	0.000
141	A	688	ALA	0	0.010	0.030	18.117	0.051	0.051	0.000	0.000	0.000	0.000
142	A	689	TYR	0	-0.042	-0.039	20.391	-0.037	-0.037	0.000	0.000	0.000	0.000
143	A	690	VAL	0	0.015	0.004	24.298	0.015	0.015	0.000	0.000	0.000	0.000
144	A	691	ARG	1	0.774	0.868	27.425	-0.144	-0.144	0.000	0.000	0.000	0.000
145	A	692	ILE	0	-0.003	-0.024	30.430	0.001	0.001	0.000	0.000	0.000	0.000
146	A	693	ARG	1	0.836	0.909	33.804	-0.105	-0.105	0.000	0.000	0.000	0.000
147	A	694	GLU	-1	-0.842	-0.931	36.847	0.078	0.078	0.000	0.000	0.000	0.000
148	A	695	SER	0	0.027	0.035	39.879	0.006	0.006	0.000	0.000	0.000	0.000
149	A	696	GLN	0	0.028	0.012	40.006	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	697	GLU	-1	-1.020	-1.057	41.966	0.075	0.075	0.000	0.000	0.000	0.000
151	A	698	PHE	0	0.023	0.023	44.952	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	699	LYS	1	0.953	0.988	43.632	-0.078	-0.078	0.000	0.000	0.000	0.000
153	A	700	ALA	0	0.099	0.056	46.592	0.000	0.000	0.000	0.000	0.000	0.000
154	A	701	THR	0	-0.071	-0.027	48.492	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	702	VAL	0	0.013	-0.003	49.144	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	703	ASP	-1	-0.831	-0.908	48.376	0.062	0.062	0.000	0.000	0.000	0.000
157	A	704	LYS	1	0.863	0.924	51.720	-0.050	-0.050	0.000	0.000	0.000	0.000
158	A	705	LEU	0	-0.066	-0.040	54.384	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	706	VAL	0	0.014	0.013	52.927	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	707	ALA	0	-0.018	-0.003	55.700	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	708	LYS	1	0.845	0.933	57.350	-0.043	-0.043	0.000	0.000	0.000	0.000
162	A	709	ALA	0	0.014	0.022	60.360	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:548:MET)