FMO DATABASE

FMODB ID: 3JNVL

Calculation Name: 4F8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F8A

Chain ID: A

ChEMBL ID:

UniProt ID: Q60603

Base Structure: X-ray

Registration Date: 2023-09-20

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1372597.599075
FMO2-HF: Nuclear repulsion	1314208.208016
FMO2-HF: Total energy	-58389.391059
FMO2-MP2: Total energy	-58556.987334

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:562:ASP)

Summations of interaction energy for fragment #1(A:562:ASP)

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.
-82.243	-74.887	0.371	-4.16	-3.568	0.037

Interaction energy analysis for fragmet #1(A:562:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.975

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	564	ARG	1	0.995	1.005	2.697	-67.316	-60.232	0.370	-4.081	-3.374	0.037
4	A	565	ALA	0	0.066	0.017	4.408	-11.156	-10.884	0.001	-0.079	-0.194	0.000
5	A	566	ASP	-1	-0.833	-0.927	6.716	31.364	31.364	0.000	0.000	0.000	0.000
6	A	567	ILE	0	-0.017	-0.005	6.967	-4.960	-4.960	0.000	0.000	0.000	0.000
7	A	568	CYS	0	0.002	0.001	8.391	-4.049	-4.049	0.000	0.000	0.000	0.000
8	A	569	VAL	0	0.030	0.031	10.722	-3.074	-3.074	0.000	0.000	0.000	0.000
9	A	570	HIS	0	-0.041	-0.015	12.117	-2.592	-2.592	0.000	0.000	0.000	0.000
10	A	571	LEU	0	-0.026	-0.029	11.824	-2.187	-2.187	0.000	0.000	0.000	0.000
11	A	572	ASN	0	0.041	0.019	14.263	-2.485	-2.485	0.000	0.000	0.000	0.000
12	A	573	ARG	1	0.885	0.939	17.021	-18.766	-18.766	0.000	0.000	0.000	0.000
13	A	574	LYS	1	0.950	0.966	18.775	-14.772	-14.772	0.000	0.000	0.000	0.000
14	A	575	VAL	0	0.071	0.055	20.430	-0.737	-0.737	0.000	0.000	0.000	0.000
15	A	576	PHE	0	-0.043	-0.031	15.203	-0.430	-0.430	0.000	0.000	0.000	0.000
16	A	577	LYS	1	0.907	0.949	16.366	-18.284	-18.284	0.000	0.000	0.000	0.000
17	A	578	GLU	-1	-0.951	-0.950	22.315	12.383	12.383	0.000	0.000	0.000	0.000
18	A	579	HIS	0	0.028	0.011	24.684	-0.306	-0.306	0.000	0.000	0.000	0.000
19	A	580	PRO	0	0.056	0.025	25.676	0.408	0.408	0.000	0.000	0.000	0.000
20	A	581	ALA	0	-0.022	-0.010	26.189	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	582	PHE	0	-0.007	-0.021	20.975	0.349	0.349	0.000	0.000	0.000	0.000
22	A	583	ARG	1	0.957	0.997	22.641	-10.607	-10.607	0.000	0.000	0.000	0.000
23	A	584	LEU	0	-0.038	-0.033	24.223	-0.049	-0.049	0.000	0.000	0.000	0.000
24	A	585	ALA	0	-0.046	-0.006	19.267	0.125	0.125	0.000	0.000	0.000	0.000
25	A	586	SER	0	0.033	0.023	17.741	0.459	0.459	0.000	0.000	0.000	0.000
26	A	587	ASP	-1	-0.820	-0.925	13.367	19.813	19.813	0.000	0.000	0.000	0.000
27	A	588	GLY	0	-0.060	-0.030	12.575	1.618	1.618	0.000	0.000	0.000	0.000
28	A	589	CYS	0	-0.050	-0.013	13.605	0.826	0.826	0.000	0.000	0.000	0.000
29	A	590	LEU	0	0.042	0.012	15.200	0.233	0.233	0.000	0.000	0.000	0.000
30	A	591	ARG	1	0.925	0.954	8.207	-28.553	-28.553	0.000	0.000	0.000	0.000
31	A	592	ALA	0	-0.055	-0.019	11.358	1.325	1.325	0.000	0.000	0.000	0.000
32	A	593	LEU	0	0.018	0.004	13.053	-0.328	-0.328	0.000	0.000	0.000	0.000
33	A	594	ALA	0	-0.016	-0.008	11.744	-0.405	-0.405	0.000	0.000	0.000	0.000
34	A	595	MET	0	-0.097	-0.040	7.885	3.035	3.035	0.000	0.000	0.000	0.000
35	A	596	GLU	-1	-0.923	-0.960	11.588	21.085	21.085	0.000	0.000	0.000	0.000
36	A	597	PHE	0	-0.097	-0.042	15.240	-1.443	-1.443	0.000	0.000	0.000	0.000
37	A	598	GLN	0	-0.028	-0.006	15.757	0.830	0.830	0.000	0.000	0.000	0.000
38	A	599	THR	0	-0.019	-0.004	17.742	-0.437	-0.437	0.000	0.000	0.000	0.000
39	A	600	VAL	0	-0.008	-0.006	19.515	0.155	0.155	0.000	0.000	0.000	0.000
40	A	601	HIS	0	-0.052	-0.045	20.958	0.432	0.432	0.000	0.000	0.000	0.000
41	A	602	CYS	0	-0.030	0.002	24.813	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	603	ALA	0	0.022	-0.001	28.580	0.057	0.057	0.000	0.000	0.000	0.000
43	A	604	PRO	0	-0.022	-0.016	31.532	-0.083	-0.083	0.000	0.000	0.000	0.000
44	A	605	GLY	0	-0.018	-0.013	34.935	-0.096	-0.096	0.000	0.000	0.000	0.000
45	A	606	ASP	-1	-0.831	-0.907	30.727	10.324	10.324	0.000	0.000	0.000	0.000
46	A	607	LEU	0	-0.070	-0.047	33.725	-0.076	-0.076	0.000	0.000	0.000	0.000
47	A	608	ILE	0	-0.061	-0.027	28.959	0.243	0.243	0.000	0.000	0.000	0.000
48	A	609	TYR	0	0.024	0.004	28.407	0.196	0.196	0.000	0.000	0.000	0.000
49	A	610	HIS	1	0.860	0.931	33.456	-9.659	-9.659	0.000	0.000	0.000	0.000
50	A	611	ALA	0	0.035	0.016	36.833	0.122	0.122	0.000	0.000	0.000	0.000
51	A	612	GLY	0	-0.025	-0.023	39.222	-0.088	-0.088	0.000	0.000	0.000	0.000
52	A	613	GLU	-1	-0.881	-0.939	31.660	10.156	10.156	0.000	0.000	0.000	0.000
53	A	614	SER	0	0.005	-0.008	31.861	-0.178	-0.178	0.000	0.000	0.000	0.000
54	A	615	VAL	0	0.016	0.016	31.319	0.330	0.330	0.000	0.000	0.000	0.000
55	A	616	ASP	-1	-0.926	-0.957	27.604	11.816	11.816	0.000	0.000	0.000	0.000
56	A	617	SER	0	-0.007	-0.004	24.735	0.632	0.632	0.000	0.000	0.000	0.000
57	A	618	LEU	0	-0.043	-0.003	24.663	-0.504	-0.504	0.000	0.000	0.000	0.000
58	A	619	CYS	0	-0.017	-0.008	24.519	0.764	0.764	0.000	0.000	0.000	0.000
59	A	620	PHE	0	0.045	0.006	23.628	-0.462	-0.462	0.000	0.000	0.000	0.000
60	A	621	VAL	0	0.054	0.041	25.191	0.507	0.507	0.000	0.000	0.000	0.000
61	A	622	VAL	0	-0.039	-0.024	22.534	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	623	SER	0	-0.060	-0.038	25.859	-0.342	-0.342	0.000	0.000	0.000	0.000
63	A	624	GLY	0	0.045	0.020	27.918	0.060	0.060	0.000	0.000	0.000	0.000
64	A	625	SER	0	-0.022	-0.014	31.245	-0.107	-0.107	0.000	0.000	0.000	0.000
65	A	626	LEU	0	0.006	-0.006	30.748	0.104	0.104	0.000	0.000	0.000	0.000
66	A	627	GLU	-1	-0.783	-0.885	34.943	7.899	7.899	0.000	0.000	0.000	0.000
67	A	628	VAL	0	-0.022	-0.019	36.441	0.191	0.191	0.000	0.000	0.000	0.000
68	A	629	ILE	0	-0.008	-0.004	38.772	-0.221	-0.221	0.000	0.000	0.000	0.000
69	A	630	GLN	0	-0.017	0.004	41.437	0.337	0.337	0.000	0.000	0.000	0.000
70	A	631	ASP	-1	-0.909	-0.960	43.772	6.853	6.853	0.000	0.000	0.000	0.000
71	A	632	ASP	-1	-0.975	-0.984	45.535	6.917	6.917	0.000	0.000	0.000	0.000
72	A	633	GLU	-1	-0.917	-0.953	46.167	6.586	6.586	0.000	0.000	0.000	0.000
73	A	634	VAL	0	-0.032	-0.028	42.225	0.201	0.201	0.000	0.000	0.000	0.000
74	A	635	VAL	0	-0.032	-0.020	41.413	-0.108	-0.108	0.000	0.000	0.000	0.000
75	A	636	ALA	0	-0.025	-0.024	39.311	0.011	0.011	0.000	0.000	0.000	0.000
76	A	637	ILE	0	-0.014	-0.002	37.736	0.042	0.042	0.000	0.000	0.000	0.000
77	A	638	LEU	0	-0.032	0.000	33.027	0.032	0.032	0.000	0.000	0.000	0.000
78	A	639	GLY	0	0.008	-0.019	32.894	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	640	LYS	1	0.910	0.958	28.840	-10.704	-10.704	0.000	0.000	0.000	0.000
80	A	641	GLY	0	-0.021	-0.020	28.477	-0.246	-0.246	0.000	0.000	0.000	0.000
81	A	642	ASP	-1	-0.821	-0.884	29.480	9.650	9.650	0.000	0.000	0.000	0.000
82	A	643	VAL	0	-0.029	-0.031	27.771	0.490	0.490	0.000	0.000	0.000	0.000
83	A	644	PHE	0	0.030	0.013	29.540	-0.447	-0.447	0.000	0.000	0.000	0.000
84	A	645	GLY	0	0.050	0.023	29.393	0.535	0.535	0.000	0.000	0.000	0.000
85	A	646	ASP	-1	-0.819	-0.935	30.363	9.109	9.109	0.000	0.000	0.000	0.000
86	A	647	VAL	0	-0.068	-0.025	30.338	0.391	0.391	0.000	0.000	0.000	0.000
87	A	648	PHE	0	0.029	-0.004	27.014	-0.081	-0.081	0.000	0.000	0.000	0.000
88	A	649	TRP	0	0.024	0.006	27.543	0.093	0.093	0.000	0.000	0.000	0.000
89	A	650	LYS	1	0.868	0.925	29.777	-9.442	-9.442	0.000	0.000	0.000	0.000
90	A	651	GLU	-1	-0.886	-0.906	32.658	8.441	8.441	0.000	0.000	0.000	0.000
91	A	652	ALA	0	-0.012	0.001	32.701	0.261	0.261	0.000	0.000	0.000	0.000
92	A	653	THR	0	-0.034	-0.020	33.436	0.196	0.196	0.000	0.000	0.000	0.000
93	A	654	LEU	0	0.015	0.021	31.344	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	655	ALA	0	0.026	0.003	33.558	-0.276	-0.276	0.000	0.000	0.000	0.000
95	A	656	GLN	0	-0.018	-0.011	35.180	0.125	0.125	0.000	0.000	0.000	0.000
96	A	657	SER	0	-0.006	0.002	35.371	-0.094	-0.094	0.000	0.000	0.000	0.000
97	A	658	CYS	0	-0.044	-0.016	37.326	-0.259	-0.259	0.000	0.000	0.000	0.000
98	A	659	ALA	0	0.003	0.002	38.746	-0.205	-0.205	0.000	0.000	0.000	0.000
99	A	660	ASN	0	-0.015	-0.013	37.571	0.386	0.386	0.000	0.000	0.000	0.000
100	A	661	VAL	0	0.019	0.023	32.801	-0.118	-0.118	0.000	0.000	0.000	0.000
101	A	662	ARG	1	0.870	0.942	34.510	-7.931	-7.931	0.000	0.000	0.000	0.000
102	A	663	ALA	0	0.008	0.009	32.068	-0.063	-0.063	0.000	0.000	0.000	0.000
103	A	664	LEU	0	-0.011	0.000	34.059	-0.223	-0.223	0.000	0.000	0.000	0.000
104	A	665	THR	0	-0.021	-0.022	32.410	-0.208	-0.208	0.000	0.000	0.000	0.000
105	A	666	TYR	0	0.012	0.001	29.301	0.087	0.087	0.000	0.000	0.000	0.000
106	A	667	CYS	0	-0.074	-0.014	28.642	-0.184	-0.184	0.000	0.000	0.000	0.000
107	A	668	ASP	-1	-0.844	-0.900	23.083	13.959	13.959	0.000	0.000	0.000	0.000
108	A	669	LEU	0	-0.004	-0.011	24.266	-0.303	-0.303	0.000	0.000	0.000	0.000
109	A	670	HIS	0	-0.057	-0.024	18.852	0.331	0.331	0.000	0.000	0.000	0.000
110	A	671	VAL	0	0.031	0.004	21.064	-0.556	-0.556	0.000	0.000	0.000	0.000
111	A	672	ILE	0	0.024	0.025	18.575	0.890	0.890	0.000	0.000	0.000	0.000
112	A	673	LYS	1	0.980	0.980	20.814	-14.484	-14.484	0.000	0.000	0.000	0.000
113	A	674	ARG	1	0.947	0.975	22.377	-10.982	-10.982	0.000	0.000	0.000	0.000
114	A	675	ASP	-1	-0.938	-0.968	22.561	12.854	12.854	0.000	0.000	0.000	0.000
115	A	676	ALA	0	0.004	-0.003	17.960	0.119	0.119	0.000	0.000	0.000	0.000
116	A	677	LEU	0	-0.004	-0.001	19.391	0.442	0.442	0.000	0.000	0.000	0.000
117	A	678	GLN	0	0.055	0.001	21.471	-0.374	-0.374	0.000	0.000	0.000	0.000
118	A	679	LYS	1	1.013	1.022	15.821	-18.555	-18.555	0.000	0.000	0.000	0.000
119	A	680	VAL	0	-0.025	-0.016	16.734	0.138	0.138	0.000	0.000	0.000	0.000
120	A	681	LEU	0	-0.043	-0.027	19.482	-0.160	-0.160	0.000	0.000	0.000	0.000
121	A	682	GLU	-1	-0.927	-0.965	23.097	12.137	12.137	0.000	0.000	0.000	0.000
122	A	683	PHE	0	-0.039	-0.001	18.531	-0.138	-0.138	0.000	0.000	0.000	0.000
123	A	684	TYR	0	-0.006	0.000	15.035	-0.354	-0.354	0.000	0.000	0.000	0.000
124	A	685	THR	0	0.040	0.003	21.951	-0.391	-0.391	0.000	0.000	0.000	0.000
125	A	686	ALA	0	-0.008	-0.003	25.072	-0.391	-0.391	0.000	0.000	0.000	0.000
126	A	687	PHE	0	0.009	-0.007	21.726	-0.308	-0.308	0.000	0.000	0.000	0.000
127	A	688	SER	0	0.084	0.035	24.699	-0.237	-0.237	0.000	0.000	0.000	0.000
128	A	689	HIS	0	-0.019	0.002	26.073	-0.313	-0.313	0.000	0.000	0.000	0.000
129	A	690	SER	0	-0.046	-0.034	27.304	-0.485	-0.485	0.000	0.000	0.000	0.000
130	A	691	PHE	0	0.027	0.021	24.185	-0.214	-0.214	0.000	0.000	0.000	0.000
131	A	692	SER	0	-0.005	-0.002	27.348	-0.313	-0.313	0.000	0.000	0.000	0.000
132	A	693	ARG	1	0.894	0.932	30.344	-10.053	-10.053	0.000	0.000	0.000	0.000
133	A	694	ASN	0	-0.046	-0.016	29.434	-0.405	-0.405	0.000	0.000	0.000	0.000
134	A	695	LEU	0	-0.038	0.002	26.884	0.010	0.010	0.000	0.000	0.000	0.000
135	A	696	ILE	0	-0.035	-0.010	30.321	-0.192	-0.192	0.000	0.000	0.000	0.000
136	A	697	LEU	0	-0.053	-0.019	30.659	0.105	0.105	0.000	0.000	0.000	0.000
137	A	698	THR	0	0.011	0.013	32.956	-0.155	-0.155	0.000	0.000	0.000	0.000
138	A	699	TYR	0	0.042	0.013	34.196	-0.277	-0.277	0.000	0.000	0.000	0.000
139	A	700	ASN	0	-0.003	-0.015	34.297	0.400	0.400	0.000	0.000	0.000	0.000
140	A	701	LEU	0	0.031	0.008	32.843	-0.251	-0.251	0.000	0.000	0.000	0.000
141	A	702	ARG	1	0.887	0.952	35.325	-9.143	-9.143	0.000	0.000	0.000	0.000
142	A	703	LYN	0	-0.060	-0.016	38.061	-0.152	-0.152	0.000	0.000	0.000	0.000
143	A	704	ARG	1	0.991	0.987	40.991	-7.168	-7.168	0.000	0.000	0.000	0.000
144	A	705	ILE	0	-0.031	-0.005	42.998	-0.103	-0.103	0.000	0.000	0.000	0.000
145	A	706	VAL	0	-0.012	-0.003	45.871	-0.070	-0.070	0.000	0.000	0.000	0.000
146	A	707	PHE	0	0.008	0.010	46.802	-0.083	-0.083	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:562:ASP)