FMO DATABASE

FMODB ID: 82R1Y

Calculation Name: 3MFB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MFB

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D6L3

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1457979.893798
FMO2-HF: Nuclear repulsion	1397960.419514
FMO2-HF: Total energy	-60019.474285
FMO2-MP2: Total energy	-60194.521345

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:331:MET)

Summations of interaction energy for fragment #1(A:331: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.
-11.262	-11.241	9.983	-3.523	-6.481	0.008

Interaction energy analysis for fragmet #1(A:331:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.012

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	333	LEU	0	0.006	0.014	3.065	-1.756	1.431	0.140	-1.607	-1.719	-0.001
4	A	334	THR	0	-0.015	-0.016	4.904	0.838	0.838	0.000	0.000	0.000	0.000
5	A	335	PRO	0	0.052	0.014	7.019	0.158	0.158	0.000	0.000	0.000	0.000
6	A	336	GLU	-1	-0.892	-0.941	7.758	0.902	0.902	0.000	0.000	0.000	0.000
7	A	337	LYS	1	0.848	0.912	2.749	-10.092	-13.802	9.835	-1.782	-4.344	0.009
8	A	338	LEU	0	0.035	0.011	6.218	-0.159	-0.159	0.000	0.000	0.000	0.000
9	A	339	LEU	0	0.047	0.029	8.669	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	340	GLU	-1	-0.849	-0.900	5.650	3.469	3.469	0.000	0.000	0.000	0.000
11	A	341	ALA	0	-0.021	-0.018	7.391	-0.096	-0.096	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.008	0.010	9.181	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	343	ASN	0	-0.051	-0.030	12.519	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	344	LYS	1	0.819	0.917	6.578	-0.590	-0.590	0.000	0.000	0.000	0.000
15	A	345	GLN	0	-0.030	-0.016	13.397	-0.084	-0.084	0.000	0.000	0.000	0.000
16	A	346	GLY	0	0.007	0.002	10.541	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	347	THR	0	-0.049	-0.048	9.764	0.079	0.079	0.000	0.000	0.000	0.000
18	A	348	VAL	0	-0.024	-0.013	6.178	-0.126	-0.126	0.000	0.000	0.000	0.000
19	A	349	PRO	0	0.014	0.019	6.572	0.198	0.198	0.000	0.000	0.000	0.000
20	A	350	SER	0	0.017	0.012	9.680	-0.194	-0.194	0.000	0.000	0.000	0.000
21	A	351	ARG	1	0.886	0.953	12.436	1.042	1.042	0.000	0.000	0.000	0.000
22	A	352	VAL	0	-0.032	-0.007	15.028	0.134	0.134	0.000	0.000	0.000	0.000
23	A	353	ARG	1	0.751	0.845	15.892	0.515	0.515	0.000	0.000	0.000	0.000
24	A	354	TYR	0	0.051	0.013	18.883	0.018	0.018	0.000	0.000	0.000	0.000
25	A	355	GLN	0	-0.009	-0.007	22.156	0.006	0.006	0.000	0.000	0.000	0.000
26	A	356	TRP	0	-0.038	-0.020	25.034	0.009	0.009	0.000	0.000	0.000	0.000
27	A	357	MET	0	-0.012	-0.004	28.579	0.007	0.007	0.000	0.000	0.000	0.000
28	A	358	GLU	-1	-0.924	-0.978	30.878	-0.161	-0.161	0.000	0.000	0.000	0.000
29	A	359	ASP	-1	-0.830	-0.878	34.313	-0.153	-0.153	0.000	0.000	0.000	0.000
30	A	360	GLU	-1	-0.948	-0.980	37.765	-0.130	-0.130	0.000	0.000	0.000	0.000
31	A	361	GLU	-1	-0.953	-0.965	39.537	-0.119	-0.119	0.000	0.000	0.000	0.000
32	A	362	THR	0	-0.140	-0.116	41.168	0.005	0.005	0.000	0.000	0.000	0.000
33	A	363	GLY	0	-0.010	0.008	38.876	0.004	0.004	0.000	0.000	0.000	0.000
34	A	364	ARG	1	0.885	0.946	37.722	0.148	0.148	0.000	0.000	0.000	0.000
35	A	365	LEU	0	0.036	0.019	32.211	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	366	LYS	1	0.903	0.940	31.916	0.254	0.254	0.000	0.000	0.000	0.000
37	A	367	ALA	0	-0.002	0.022	27.650	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	368	VAL	0	-0.024	-0.020	27.079	0.007	0.007	0.000	0.000	0.000	0.000
39	A	369	GLY	0	0.063	0.023	23.496	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	370	TYR	0	-0.062	-0.056	21.918	0.033	0.033	0.000	0.000	0.000	0.000
41	A	371	HIS	0	-0.034	-0.030	19.709	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	372	THR	0	-0.063	-0.052	15.341	0.054	0.054	0.000	0.000	0.000	0.000
43	A	373	SER	0	0.023	-0.001	17.608	-0.053	-0.053	0.000	0.000	0.000	0.000
44	A	374	MET	0	-0.019	-0.020	9.605	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	375	GLU	-1	-0.951	-0.959	14.824	-0.389	-0.389	0.000	0.000	0.000	0.000
46	A	376	SER	0	-0.098	-0.045	17.780	0.049	0.049	0.000	0.000	0.000	0.000
47	A	377	GLY	0	0.066	0.041	15.537	0.056	0.056	0.000	0.000	0.000	0.000
48	A	378	ARG	1	0.799	0.888	16.067	0.373	0.373	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.786	-0.910	11.914	-1.080	-1.080	0.000	0.000	0.000	0.000
50	A	380	GLN	0	-0.041	-0.009	9.182	-0.134	-0.134	0.000	0.000	0.000	0.000
51	A	381	VAL	0	0.041	0.024	11.855	0.129	0.129	0.000	0.000	0.000	0.000
52	A	382	ARG	1	0.881	0.933	12.105	0.281	0.281	0.000	0.000	0.000	0.000
53	A	383	VAL	0	0.005	0.011	9.736	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	384	ARG	1	0.841	0.928	13.088	0.305	0.305	0.000	0.000	0.000	0.000
55	A	385	LEU	0	0.010	0.019	15.672	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	386	LEU	0	-0.015	-0.005	17.200	0.012	0.012	0.000	0.000	0.000	0.000
57	A	387	LYS	1	0.953	0.971	20.617	0.030	0.030	0.000	0.000	0.000	0.000
58	A	388	HIS	1	0.877	0.935	23.436	0.007	0.007	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.808	-0.896	25.992	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	390	PHE	0	0.021	-0.020	27.371	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	391	PRO	0	-0.031	-0.002	31.794	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	392	ASN	0	-0.041	-0.037	32.714	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	393	ASN	0	-0.055	-0.018	31.870	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	394	ARG	1	0.916	0.958	29.381	0.052	0.052	0.000	0.000	0.000	0.000
65	A	395	TYR	0	-0.055	-0.014	23.636	0.028	0.028	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.773	-0.880	25.254	-0.069	-0.069	0.000	0.000	0.000	0.000
67	A	397	PHE	0	0.018	-0.004	20.310	0.012	0.012	0.000	0.000	0.000	0.000
68	A	398	TRP	0	-0.047	-0.024	23.706	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	399	GLU	-1	-0.753	-0.822	23.348	-0.191	-0.191	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.917	-0.978	21.471	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	401	GLY	0	-0.031	-0.011	24.850	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	402	ALA	0	-0.030	0.006	27.839	0.000	0.000	0.000	0.000	0.000	0.000
73	A	403	THR	0	-0.034	-0.034	29.611	0.009	0.009	0.000	0.000	0.000	0.000
74	A	404	GLY	0	0.020	0.001	31.206	0.008	0.008	0.000	0.000	0.000	0.000
75	A	405	PRO	0	-0.058	-0.002	28.481	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	406	THR	0	0.000	-0.007	25.811	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	407	ILE	0	-0.011	-0.010	22.519	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	408	LEU	0	-0.012	-0.009	26.128	0.017	0.017	0.000	0.000	0.000	0.000
79	A	409	TRP	0	0.036	0.015	23.801	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	410	THR	0	0.048	0.015	26.954	0.018	0.018	0.000	0.000	0.000	0.000
81	A	411	PRO	0	-0.073	-0.045	27.576	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	412	ASP	-1	-0.893	-0.947	29.011	-0.076	-0.076	0.000	0.000	0.000	0.000
83	A	413	ASN	0	-0.098	-0.008	31.506	0.007	0.007	0.000	0.000	0.000	0.000
84	A	414	PRO	0	-0.056	-0.031	27.188	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	415	GLY	0	0.056	0.002	26.678	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	416	ILE	0	-0.055	-0.029	22.566	0.015	0.015	0.000	0.000	0.000	0.000
87	A	417	GLU	-1	-0.895	-0.936	26.692	-0.132	-0.132	0.000	0.000	0.000	0.000
88	A	418	LEU	0	0.001	-0.012	27.105	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.032	0.003	30.493	0.004	0.004	0.000	0.000	0.000	0.000
90	A	420	THR	0	-0.038	-0.020	31.832	0.008	0.008	0.000	0.000	0.000	0.000
91	A	421	ASP	-1	-0.930	-0.965	33.832	-0.137	-0.137	0.000	0.000	0.000	0.000
92	A	422	THR	0	-0.029	-0.003	30.320	0.000	0.000	0.000	0.000	0.000	0.000
93	A	423	ALA	0	0.017	0.005	30.438	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	424	HIS	1	0.836	0.879	26.292	0.228	0.228	0.000	0.000	0.000	0.000
95	A	425	GLY	0	0.019	0.034	25.334	0.012	0.012	0.000	0.000	0.000	0.000
96	A	426	GLU	-1	-0.821	-0.918	22.032	-0.295	-0.295	0.000	0.000	0.000	0.000
97	A	427	GLN	0	0.035	0.012	20.096	0.035	0.035	0.000	0.000	0.000	0.000
98	A	428	PRO	0	-0.038	-0.014	18.315	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	429	VAL	0	-0.025	-0.007	11.801	-0.047	-0.047	0.000	0.000	0.000	0.000
100	A	430	ILE	0	-0.029	-0.023	12.848	0.090	0.090	0.000	0.000	0.000	0.000
101	A	431	PRO	0	-0.022	-0.026	11.454	-0.211	-0.211	0.000	0.000	0.000	0.000
102	A	432	SER	0	-0.027	-0.020	7.769	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	433	ALA	0	0.058	0.054	8.614	-0.240	-0.240	0.000	0.000	0.000	0.000
104	A	434	ILE	0	0.008	-0.013	5.714	-1.090	-1.090	0.000	0.000	0.000	0.000
105	A	435	PRO	0	-0.017	-0.016	3.476	0.333	0.877	0.008	-0.134	-0.418	0.000
106	A	436	GLY	0	0.039	0.032	6.751	0.238	0.238	0.000	0.000	0.000	0.000
107	A	437	LEU	0	-0.068	-0.048	10.081	0.441	0.441	0.000	0.000	0.000	0.000
108	A	438	GLU	-1	-0.824	-0.919	9.484	-1.933	-1.933	0.000	0.000	0.000	0.000
109	A	439	ILE	0	0.036	0.028	11.663	0.221	0.221	0.000	0.000	0.000	0.000
110	A	440	PRO	0	-0.028	0.003	15.125	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	441	GLU	-1	-0.816	-0.909	18.086	-0.657	-0.657	0.000	0.000	0.000	0.000
112	A	442	MET	0	-0.074	-0.025	19.700	0.044	0.044	0.000	0.000	0.000	0.000
113	A	443	ASP	-1	-0.898	-0.955	23.685	-0.346	-0.346	0.000	0.000	0.000	0.000
114	A	444	ASP	-1	-0.963	-0.973	26.830	-0.256	-0.256	0.000	0.000	0.000	0.000
115	A	445	VAL	0	-0.047	-0.010	26.087	0.018	0.018	0.000	0.000	0.000	0.000
116	A	446	SER	0	-0.068	-0.035	26.967	-0.029	-0.029	0.000	0.000	0.000	0.000
117	A	447	ILE	0	0.019	0.016	22.461	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	448	LEU	0	-0.013	0.001	26.317	0.020	0.020	0.000	0.000	0.000	0.000
119	A	449	ALA	0	-0.009	-0.010	26.333	-0.027	-0.027	0.000	0.000	0.000	0.000
120	A	450	THR	0	-0.007	0.000	27.656	0.028	0.028	0.000	0.000	0.000	0.000
121	A	451	PRO	0	-0.021	-0.019	26.649	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	452	MET	0	-0.001	0.008	20.894	0.005	0.005	0.000	0.000	0.000	0.000
123	A	453	PRO	0	0.053	0.036	24.143	0.019	0.019	0.000	0.000	0.000	0.000
124	A	454	ASP	-1	-0.777	-0.892	24.080	-0.261	-0.261	0.000	0.000	0.000	0.000
125	A	455	GLU	-1	-0.787	-0.860	19.214	-0.441	-0.441	0.000	0.000	0.000	0.000
126	A	456	LYS	1	0.824	0.901	22.767	0.214	0.214	0.000	0.000	0.000	0.000
127	A	457	ASP	-1	-0.879	-0.935	25.718	-0.215	-0.215	0.000	0.000	0.000	0.000
128	A	458	PHE	0	-0.036	0.007	21.145	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	459	ARG	1	0.807	0.868	22.382	0.215	0.215	0.000	0.000	0.000	0.000
130	A	460	ASP	-1	-0.746	-0.818	18.059	-0.531	-0.531	0.000	0.000	0.000	0.000
131	A	461	TYR	0	-0.083	-0.069	16.774	0.018	0.018	0.000	0.000	0.000	0.000
132	A	462	ILE	0	0.039	0.034	11.643	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	463	LEU	0	-0.022	-0.012	15.064	0.052	0.052	0.000	0.000	0.000	0.000
134	A	464	VAL	0	0.015	-0.007	12.524	-0.041	-0.041	0.000	0.000	0.000	0.000
135	A	465	PHE	0	0.035	0.027	15.873	0.062	0.062	0.000	0.000	0.000	0.000
136	A	466	PRO	0	-0.016	-0.019	17.223	0.020	0.020	0.000	0.000	0.000	0.000
137	A	467	GLU	-1	-0.951	-0.968	17.762	0.064	0.064	0.000	0.000	0.000	0.000
138	A	468	ASN	0	-0.046	-0.036	14.047	-0.087	-0.087	0.000	0.000	0.000	0.000
139	A	469	ALA	0	0.003	0.018	17.783	-0.027	-0.027	0.000	0.000	0.000	0.000
140	A	470	PHE	0	0.012	0.007	19.799	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	471	PRO	0	0.009	0.008	16.642	0.009	0.009	0.000	0.000	0.000	0.000
142	A	472	PRO	0	-0.004	-0.001	12.515	0.020	0.020	0.000	0.000	0.000	0.000
143	A	473	ILE	0	0.015	0.007	15.586	-0.058	-0.058	0.000	0.000	0.000	0.000
144	A	474	TYR	0	-0.024	-0.025	15.976	0.021	0.021	0.000	0.000	0.000	0.000
145	A	475	VAL	0	0.015	0.003	17.655	0.036	0.036	0.000	0.000	0.000	0.000
146	A	476	TYR	0	0.025	0.003	20.363	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	477	LEU	0	0.011	-0.002	22.622	0.020	0.020	0.000	0.000	0.000	0.000
148	A	478	SER	0	0.043	0.021	25.829	-0.010	-0.010	0.000	0.000	0.000	0.000
149	A	479	LYS	1	0.877	0.926	28.434	0.210	0.210	0.000	0.000	0.000	0.000
150	A	480	LEU	0	-0.022	0.008	28.064	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:331:MET)