FMO DATABASE

FMODB ID: N918Q

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	OptAll
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	-1488247.249724
FMO2-HF: Nuclear repulsion	1424719.46497
FMO2-HF: Total energy	-63527.784754
FMO2-MP2: Total energy	-63716.204115

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.
2.544	-4.231	4.175	6.957	-4.357	-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 : 0.018 / q_NPA : 0.029

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	0.929	0.942	2.703	3.389	-5.425	3.943	7.620	-2.749	-0.010
4	A	551	GLY	0	0.033	0.018	4.488	-1.297	-1.180	0.027	-0.022	-0.123	0.001
5	A	552	SER	0	-0.040	-0.018	5.793	-0.606	-0.606	0.000	0.000	0.000	0.000
6	A	553	GLU	-1	-0.828	-0.912	8.688	0.116	0.116	0.000	0.000	0.000	0.000
7	A	554	PHE	0	0.023	0.026	11.689	0.050	0.050	0.000	0.000	0.000	0.000
8	A	555	GLY	0	0.037	0.022	10.677	0.057	0.057	0.000	0.000	0.000	0.000
9	A	556	ILE	0	-0.036	-0.018	5.878	-0.203	-0.203	0.000	0.000	0.000	0.000
10	A	557	PHE	0	0.004	-0.002	9.290	0.201	0.201	0.000	0.000	0.000	0.000
11	A	558	ALA	0	0.000	0.001	10.930	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	559	PHE	0	0.044	0.028	13.231	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	560	THR	0	-0.025	-0.020	15.723	0.042	0.042	0.000	0.000	0.000	0.000
14	A	561	ASP	-1	-0.856	-0.946	17.582	0.319	0.319	0.000	0.000	0.000	0.000
15	A	562	SER	0	0.018	0.002	17.608	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	563	VAL	0	-0.070	-0.032	19.399	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	564	PHE	0	0.020	0.018	20.833	0.001	0.001	0.000	0.000	0.000	0.000
18	A	565	GLU	-1	-0.817	-0.893	25.996	0.109	0.109	0.000	0.000	0.000	0.000
19	A	566	ILE	0	-0.024	0.006	29.812	0.001	0.001	0.000	0.000	0.000	0.000
20	A	567	THR	0	-0.016	-0.003	32.936	0.000	0.000	0.000	0.000	0.000	0.000
21	A	568	GLU	-1	-0.701	-0.851	35.698	0.040	0.040	0.000	0.000	0.000	0.000
22	A	569	SER	0	-0.017	-0.037	37.232	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	570	VAL	0	-0.057	-0.018	33.027	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	571	GLY	0	0.034	0.033	35.953	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	572	ARG	1	0.714	0.822	30.493	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	573	PHE	0	-0.009	-0.002	25.944	0.005	0.005	0.000	0.000	0.000	0.000
27	A	574	GLU	-1	-0.859	-0.928	27.504	0.031	0.031	0.000	0.000	0.000	0.000
28	A	575	LEU	0	-0.013	0.001	21.528	0.014	0.014	0.000	0.000	0.000	0.000
29	A	576	LYS	1	0.815	0.892	20.370	-0.156	-0.156	0.000	0.000	0.000	0.000
30	A	577	VAL	0	-0.022	-0.009	16.426	0.013	0.013	0.000	0.000	0.000	0.000
31	A	578	MET	0	-0.030	-0.007	15.682	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	579	ARG	1	0.735	0.858	13.814	0.126	0.126	0.000	0.000	0.000	0.000
33	A	580	TYR	0	0.001	-0.004	11.182	0.078	0.078	0.000	0.000	0.000	0.000
34	A	581	SER	0	-0.057	-0.042	9.641	0.019	0.019	0.000	0.000	0.000	0.000
35	A	582	GLY	0	0.017	0.013	11.611	-0.118	-0.118	0.000	0.000	0.000	0.000
36	A	583	ALA	0	0.013	-0.007	14.394	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	584	ARG	1	0.810	0.910	16.067	0.077	0.077	0.000	0.000	0.000	0.000
38	A	585	GLY	0	0.064	0.019	16.672	-0.053	-0.053	0.000	0.000	0.000	0.000
39	A	586	THR	0	0.001	0.015	19.102	0.026	0.026	0.000	0.000	0.000	0.000
40	A	587	VAL	0	-0.036	-0.027	14.079	-0.050	-0.050	0.000	0.000	0.000	0.000
41	A	588	ILE	0	-0.007	0.001	17.203	0.053	0.053	0.000	0.000	0.000	0.000
42	A	589	VAL	0	0.027	0.008	14.557	-0.071	-0.071	0.000	0.000	0.000	0.000
43	A	590	PRO	0	-0.005	0.016	15.904	0.052	0.052	0.000	0.000	0.000	0.000
44	A	591	TYR	0	0.023	0.007	17.787	0.007	0.007	0.000	0.000	0.000	0.000
45	A	592	TRP	0	-0.038	-0.026	17.101	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	593	THR	0	0.070	0.047	22.192	0.015	0.015	0.000	0.000	0.000	0.000
47	A	594	GLU	-1	-0.874	-0.928	23.006	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	595	ASN	0	0.093	0.066	25.953	0.012	0.012	0.000	0.000	0.000	0.000
49	A	596	ASP	-1	-0.873	-0.929	27.384	0.057	0.057	0.000	0.000	0.000	0.000
50	A	597	THR	0	-0.040	-0.012	29.391	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	598	ALA	0	-0.008	0.017	31.353	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	599	THR	0	-0.024	-0.049	31.793	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	600	GLU	-1	-0.750	-0.836	30.248	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	601	SER	0	-0.063	-0.027	33.296	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	602	LYS	1	0.752	0.844	36.478	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	603	ASP	-1	-0.778	-0.870	34.174	0.033	0.033	0.000	0.000	0.000	0.000
57	A	604	TYR	0	-0.042	-0.042	29.175	0.005	0.005	0.000	0.000	0.000	0.000
58	A	605	GLU	-1	-0.873	-0.925	32.313	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	606	GLY	0	0.044	0.013	30.164	0.002	0.002	0.000	0.000	0.000	0.000
60	A	607	ALA	0	-0.035	-0.012	26.590	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	608	ARG	1	0.714	0.798	24.885	0.046	0.046	0.000	0.000	0.000	0.000
62	A	609	GLY	0	0.002	0.014	23.883	0.005	0.005	0.000	0.000	0.000	0.000
63	A	610	GLU	-1	-0.808	-0.879	20.461	-0.270	-0.270	0.000	0.000	0.000	0.000
64	A	611	LEU	0	-0.018	0.003	19.255	0.018	0.018	0.000	0.000	0.000	0.000
65	A	612	VAL	0	0.017	0.005	19.705	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	613	PHE	0	-0.019	-0.008	17.844	0.031	0.031	0.000	0.000	0.000	0.000
67	A	614	GLU	-1	-0.814	-0.940	19.953	-0.149	-0.149	0.000	0.000	0.000	0.000
68	A	615	ASN	0	0.007	0.018	20.687	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	616	ASN	0	-0.031	-0.019	20.947	0.008	0.008	0.000	0.000	0.000	0.000
70	A	617	GLU	-1	-0.816	-0.867	21.370	-0.027	-0.027	0.000	0.000	0.000	0.000
71	A	618	SER	0	0.061	0.016	18.221	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	619	GLU	-1	-0.837	-0.913	18.301	0.155	0.155	0.000	0.000	0.000	0.000
73	A	620	LYS	1	0.799	0.887	20.451	0.033	0.033	0.000	0.000	0.000	0.000
74	A	621	PHE	0	0.008	0.000	21.776	0.024	0.024	0.000	0.000	0.000	0.000
75	A	622	ILE	0	-0.007	0.006	20.765	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	623	ASP	-1	-0.779	-0.851	25.048	0.019	0.019	0.000	0.000	0.000	0.000
77	A	624	LEU	0	-0.056	-0.020	25.919	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	625	PHE	0	0.013	0.006	29.537	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	626	ILE	0	-0.036	-0.037	30.212	0.000	0.000	0.000	0.000	0.000	0.000
80	A	627	LEU	0	-0.020	-0.008	34.165	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	628	GLU	-1	-0.782	-0.854	37.667	0.042	0.042	0.000	0.000	0.000	0.000
82	A	629	GLU	-1	-0.856	-0.908	39.839	0.025	0.025	0.000	0.000	0.000	0.000
83	A	630	SER	0	-0.072	-0.053	42.941	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	631	SER	0	-0.023	-0.039	41.208	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	632	TYR	0	-0.074	-0.043	43.710	0.002	0.002	0.000	0.000	0.000	0.000
86	A	633	GLU	-1	-0.958	-0.992	41.731	0.059	0.059	0.000	0.000	0.000	0.000
87	A	634	LYS	1	0.796	0.891	36.996	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	635	ASP	-1	-0.798	-0.857	34.006	0.094	0.094	0.000	0.000	0.000	0.000
89	A	636	VAL	0	-0.022	0.012	33.688	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	637	SER	0	0.004	0.001	28.305	0.009	0.009	0.000	0.000	0.000	0.000
91	A	638	PHE	0	0.015	0.015	26.848	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	639	LYS	1	0.800	0.888	22.148	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	640	VAL	0	0.002	0.010	21.435	-0.019	-0.019	0.000	0.000	0.000	0.000
94	A	641	HIS	1	0.798	0.876	17.562	0.034	0.034	0.000	0.000	0.000	0.000
95	A	642	ILE	0	0.025	0.018	12.984	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	643	GLY	0	0.003	0.002	14.776	0.008	0.008	0.000	0.000	0.000	0.000
97	A	644	GLU	-1	-0.933	-0.976	11.164	-0.563	-0.563	0.000	0.000	0.000	0.000
98	A	645	PRO	0	-0.055	0.001	10.563	0.051	0.051	0.000	0.000	0.000	0.000
99	A	646	ARG	1	0.748	0.837	12.357	0.203	0.203	0.000	0.000	0.000	0.000
100	A	647	LEU	0	-0.003	0.001	14.892	0.055	0.055	0.000	0.000	0.000	0.000
101	A	648	ALA	0	0.031	0.016	16.638	0.002	0.002	0.000	0.000	0.000	0.000
102	A	649	PRO	0	-0.058	-0.046	20.479	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	650	ASP	-1	-0.926	-0.957	22.309	-0.225	-0.225	0.000	0.000	0.000	0.000
104	A	651	ASP	-1	-0.847	-0.920	19.632	-0.326	-0.326	0.000	0.000	0.000	0.000
105	A	652	GLY	0	-0.003	-0.009	21.223	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	653	LEU	0	-0.016	-0.012	16.131	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	654	ALA	0	0.009	0.014	17.114	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	655	ALA	0	-0.050	-0.024	17.774	-0.047	-0.047	0.000	0.000	0.000	0.000
109	A	656	LYS	1	0.896	0.914	17.154	0.480	0.480	0.000	0.000	0.000	0.000
110	A	657	ILE	0	0.023	0.031	12.477	-0.046	-0.046	0.000	0.000	0.000	0.000
111	A	658	LYS	1	0.977	0.988	14.237	0.387	0.387	0.000	0.000	0.000	0.000
112	A	659	GLU	-1	-0.925	-0.946	16.465	-0.412	-0.412	0.000	0.000	0.000	0.000
113	A	660	VAL	0	0.041	0.007	12.708	0.034	0.034	0.000	0.000	0.000	0.000
114	A	661	GLU	-1	-0.873	-0.931	11.444	-1.016	-1.016	0.000	0.000	0.000	0.000
115	A	662	LYS	1	0.853	0.938	12.579	0.510	0.510	0.000	0.000	0.000	0.000
116	A	663	LYS	1	0.761	0.878	14.671	0.742	0.742	0.000	0.000	0.000	0.000
117	A	664	PRO	0	0.017	0.004	14.819	-0.069	-0.069	0.000	0.000	0.000	0.000
118	A	665	VAL	0	0.040	0.007	11.178	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	666	GLN	0	-0.003	-0.009	13.367	-0.094	-0.094	0.000	0.000	0.000	0.000
120	A	667	ASP	-1	-0.866	-0.930	15.960	-0.417	-0.417	0.000	0.000	0.000	0.000
121	A	668	LEU	0	-0.058	-0.001	10.114	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	669	THR	0	-0.003	-0.002	14.019	0.045	0.045	0.000	0.000	0.000	0.000
123	A	670	GLU	-1	-0.828	-0.898	11.932	-0.795	-0.795	0.000	0.000	0.000	0.000
124	A	671	LEU	0	0.031	-0.003	12.097	-0.093	-0.093	0.000	0.000	0.000	0.000
125	A	672	ASP	-1	-0.786	-0.887	13.407	-0.846	-0.846	0.000	0.000	0.000	0.000
126	A	673	ARG	1	0.873	0.908	8.642	0.670	0.670	0.000	0.000	0.000	0.000
127	A	674	ILE	0	-0.002	0.005	8.303	-0.402	-0.402	0.000	0.000	0.000	0.000
128	A	675	LEU	0	0.009	0.008	9.401	-0.111	-0.111	0.000	0.000	0.000	0.000
129	A	676	LEU	0	-0.010	-0.001	7.080	-0.063	-0.063	0.000	0.000	0.000	0.000
130	A	677	LEU	0	-0.057	-0.016	3.211	-1.186	-0.555	0.069	-0.172	-0.528	-0.001
131	A	678	SER	0	-0.070	-0.045	5.975	-0.037	-0.037	0.000	0.000	0.000	0.000
132	A	679	LYS	1	0.909	0.960	8.001	1.766	1.766	0.000	0.000	0.000	0.000
133	A	680	PRO	0	-0.004	0.013	8.032	-0.222	-0.222	0.000	0.000	0.000	0.000
134	A	681	ARG	1	0.854	0.917	3.110	1.625	2.916	0.136	-0.469	-0.957	-0.004
135	A	682	ASN	0	0.029	0.004	7.436	0.336	0.336	0.000	0.000	0.000	0.000
136	A	683	GLY	0	-0.020	-0.006	6.312	-0.239	-0.239	0.000	0.000	0.000	0.000
137	A	684	GLU	-1	-0.917	-0.975	8.265	1.276	1.276	0.000	0.000	0.000	0.000
138	A	685	LEU	0	-0.010	0.016	9.914	-0.097	-0.097	0.000	0.000	0.000	0.000
139	A	686	THR	0	0.028	0.002	11.021	-0.049	-0.049	0.000	0.000	0.000	0.000
140	A	687	THR	0	-0.046	-0.019	13.593	-0.069	-0.069	0.000	0.000	0.000	0.000
141	A	688	ALA	0	-0.001	0.015	17.157	0.050	0.050	0.000	0.000	0.000	0.000
142	A	689	TYR	0	-0.027	-0.014	19.630	-0.037	-0.037	0.000	0.000	0.000	0.000
143	A	690	VAL	0	0.002	-0.003	23.553	0.016	0.016	0.000	0.000	0.000	0.000
144	A	691	ARG	1	0.757	0.820	26.707	-0.119	-0.119	0.000	0.000	0.000	0.000
145	A	692	ILE	0	-0.034	-0.026	29.836	0.001	0.001	0.000	0.000	0.000	0.000
146	A	693	ARG	1	0.813	0.890	33.245	-0.087	-0.087	0.000	0.000	0.000	0.000
147	A	694	GLU	-1	-0.746	-0.863	36.376	0.066	0.066	0.000	0.000	0.000	0.000
148	A	695	SER	0	-0.027	-0.003	39.139	0.005	0.005	0.000	0.000	0.000	0.000
149	A	696	GLN	0	-0.033	-0.031	39.230	0.002	0.002	0.000	0.000	0.000	0.000
150	A	697	GLU	-1	-0.880	-0.957	41.658	0.062	0.062	0.000	0.000	0.000	0.000
151	A	698	PHE	0	-0.014	0.001	44.644	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	699	LYS	1	0.897	0.928	43.079	-0.059	-0.059	0.000	0.000	0.000	0.000
153	A	700	ALA	0	0.013	0.031	46.045	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	701	THR	0	-0.080	-0.052	47.910	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	702	VAL	0	-0.009	-0.003	48.822	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	703	ASP	-1	-0.796	-0.879	47.906	0.052	0.052	0.000	0.000	0.000	0.000
157	A	704	LYS	1	0.883	0.930	51.027	-0.044	-0.044	0.000	0.000	0.000	0.000
158	A	705	LEU	0	-0.048	-0.017	53.664	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	706	VAL	0	0.023	0.006	52.472	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	707	ALA	0	-0.034	-0.007	55.160	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	708	LYS	1	0.861	0.940	56.828	-0.032	-0.032	0.000	0.000	0.000	0.000
162	A	709	ALA	0	0.010	0.007	59.878	-0.002	-0.002	0.000	0.000	0.000	0.000

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