FMO DATABASE

FMODB ID: N1KRQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1459593.4521
FMO2-HF: Nuclear repulsion	1399573.472185
FMO2-HF: Total energy	-60019.979915
FMO2-MP2: Total energy	-60195.018005

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.
-12.284	-11.755	9.613	-3.409	-6.734	0.007

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 : 0.005 / q_NPA : 0.005

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	0.001	-0.001	2.910	-2.527	0.623	0.339	-1.636	-1.853	-0.003
4	A	334	THR	0	-0.010	-0.010	4.730	0.918	1.098	-0.001	-0.011	-0.168	0.000
5	A	335	PRO	0	0.051	0.012	6.852	0.244	0.244	0.000	0.000	0.000	0.000
6	A	336	GLU	-1	-0.877	-0.929	7.517	0.794	0.794	0.000	0.000	0.000	0.000
7	A	337	LYS	1	0.830	0.899	2.638	-9.933	-13.399	9.266	-1.637	-4.163	0.010
8	A	338	LEU	0	0.037	0.019	6.379	-0.164	-0.164	0.000	0.000	0.000	0.000
9	A	339	LEU	0	0.053	0.026	9.004	0.031	0.031	0.000	0.000	0.000	0.000
10	A	340	GLU	-1	-0.822	-0.878	5.942	3.787	3.921	-0.001	-0.004	-0.130	0.000
11	A	341	ALA	0	-0.021	-0.022	7.784	-0.097	-0.097	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.010	0.010	9.426	-0.057	-0.057	0.000	0.000	0.000	0.000
13	A	343	ASN	0	-0.053	-0.033	12.617	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	344	LYS	1	0.806	0.897	6.228	-0.937	-0.937	0.000	0.000	0.000	0.000
15	A	345	GLN	0	-0.029	-0.014	13.124	-0.092	-0.092	0.000	0.000	0.000	0.000
16	A	346	GLY	0	0.020	0.023	10.787	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	347	THR	0	-0.055	-0.047	9.951	0.054	0.054	0.000	0.000	0.000	0.000
18	A	348	VAL	0	-0.021	-0.010	6.175	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	349	PRO	0	0.001	0.007	6.243	0.195	0.195	0.000	0.000	0.000	0.000
20	A	350	SER	0	0.026	0.018	9.241	-0.249	-0.249	0.000	0.000	0.000	0.000
21	A	351	ARG	1	0.823	0.902	11.990	1.065	1.065	0.000	0.000	0.000	0.000
22	A	352	VAL	0	-0.043	-0.020	14.748	0.139	0.139	0.000	0.000	0.000	0.000
23	A	353	ARG	1	0.759	0.848	15.872	0.494	0.494	0.000	0.000	0.000	0.000
24	A	354	TYR	0	0.028	0.015	18.713	0.012	0.012	0.000	0.000	0.000	0.000
25	A	355	GLN	0	-0.001	-0.004	21.979	0.008	0.008	0.000	0.000	0.000	0.000
26	A	356	TRP	0	-0.029	-0.015	24.947	0.009	0.009	0.000	0.000	0.000	0.000
27	A	357	MET	0	0.005	0.011	28.482	0.008	0.008	0.000	0.000	0.000	0.000
28	A	358	GLU	-1	-0.921	-0.978	30.504	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	359	ASP	-1	-0.846	-0.888	33.994	-0.148	-0.148	0.000	0.000	0.000	0.000
30	A	360	GLU	-1	-0.946	-0.977	37.463	-0.125	-0.125	0.000	0.000	0.000	0.000
31	A	361	GLU	-1	-0.977	-0.982	39.376	-0.116	-0.116	0.000	0.000	0.000	0.000
32	A	362	THR	0	-0.144	-0.112	41.206	0.005	0.005	0.000	0.000	0.000	0.000
33	A	363	GLY	0	0.037	0.027	38.688	0.003	0.003	0.000	0.000	0.000	0.000
34	A	364	ARG	1	0.870	0.944	37.922	0.146	0.146	0.000	0.000	0.000	0.000
35	A	365	LEU	0	0.024	0.011	31.676	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	366	LYS	1	0.871	0.923	31.159	0.271	0.271	0.000	0.000	0.000	0.000
37	A	367	ALA	0	0.009	0.029	27.564	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	368	VAL	0	-0.019	-0.019	26.786	0.010	0.010	0.000	0.000	0.000	0.000
39	A	369	GLY	0	0.069	0.020	23.437	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	370	TYR	0	-0.033	-0.037	21.769	0.036	0.036	0.000	0.000	0.000	0.000
41	A	371	HIS	0	-0.040	-0.031	19.441	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	372	THR	0	-0.065	-0.038	15.067	0.055	0.055	0.000	0.000	0.000	0.000
43	A	373	SER	0	0.010	-0.014	16.966	-0.040	-0.040	0.000	0.000	0.000	0.000
44	A	374	MET	0	0.001	0.001	9.214	0.027	0.027	0.000	0.000	0.000	0.000
45	A	375	GLU	-1	-0.947	-0.961	14.654	-0.399	-0.399	0.000	0.000	0.000	0.000
46	A	376	SER	0	-0.077	-0.047	17.662	0.077	0.077	0.000	0.000	0.000	0.000
47	A	377	GLY	0	-0.011	0.011	14.857	0.054	0.054	0.000	0.000	0.000	0.000
48	A	378	ARG	1	0.828	0.903	15.216	0.343	0.343	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.789	-0.904	11.625	-1.068	-1.068	0.000	0.000	0.000	0.000
50	A	380	GLN	0	-0.061	-0.018	9.010	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	381	VAL	0	0.048	0.029	11.736	0.120	0.120	0.000	0.000	0.000	0.000
52	A	382	ARG	1	0.893	0.942	11.981	0.268	0.268	0.000	0.000	0.000	0.000
53	A	383	VAL	0	-0.006	0.004	9.928	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	384	ARG	1	0.764	0.878	13.307	0.213	0.213	0.000	0.000	0.000	0.000
55	A	385	LEU	0	0.005	0.017	15.838	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	386	LEU	0	-0.010	0.001	17.484	0.016	0.016	0.000	0.000	0.000	0.000
57	A	387	LYS	1	0.897	0.943	20.770	0.010	0.010	0.000	0.000	0.000	0.000
58	A	388	HIS	1	0.876	0.934	23.790	0.000	0.000	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.789	-0.877	26.451	0.002	0.002	0.000	0.000	0.000	0.000
60	A	390	PHE	0	0.016	-0.006	27.602	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	391	PRO	0	-0.041	-0.021	31.871	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	392	ASN	0	-0.035	-0.030	33.206	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	393	ASN	0	-0.033	-0.021	31.796	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	394	ARG	1	0.868	0.938	29.372	0.045	0.045	0.000	0.000	0.000	0.000
65	A	395	TYR	0	-0.018	-0.004	23.615	0.027	0.027	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.787	-0.881	25.203	-0.064	-0.064	0.000	0.000	0.000	0.000
67	A	397	PHE	0	0.024	-0.007	20.797	0.017	0.017	0.000	0.000	0.000	0.000
68	A	398	TRP	0	-0.018	0.012	23.748	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	399	GLU	-1	-0.732	-0.804	23.394	-0.168	-0.168	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.837	-0.925	20.113	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	401	GLY	0	-0.023	-0.007	24.423	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	402	ALA	0	-0.029	0.001	27.601	0.001	0.001	0.000	0.000	0.000	0.000
73	A	403	THR	0	-0.037	-0.036	29.525	0.008	0.008	0.000	0.000	0.000	0.000
74	A	404	GLY	0	0.019	0.001	31.132	0.007	0.007	0.000	0.000	0.000	0.000
75	A	405	PRO	0	-0.063	-0.015	28.158	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	406	THR	0	-0.012	-0.020	25.757	0.003	0.003	0.000	0.000	0.000	0.000
77	A	407	ILE	0	-0.016	-0.016	22.502	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	408	LEU	0	-0.025	-0.013	26.056	0.020	0.020	0.000	0.000	0.000	0.000
79	A	409	TRP	0	0.028	0.008	24.075	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	410	THR	0	-0.011	-0.024	26.886	0.021	0.021	0.000	0.000	0.000	0.000
81	A	411	PRO	0	-0.070	-0.040	27.762	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	412	ASP	-1	-0.898	-0.959	29.025	-0.081	-0.081	0.000	0.000	0.000	0.000
83	A	413	ASN	0	-0.094	-0.022	31.582	0.005	0.005	0.000	0.000	0.000	0.000
84	A	414	PRO	0	-0.035	-0.007	27.207	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	415	GLY	0	0.030	-0.011	27.188	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	416	ILE	0	-0.048	-0.016	22.516	0.014	0.014	0.000	0.000	0.000	0.000
87	A	417	GLU	-1	-0.833	-0.892	26.645	-0.124	-0.124	0.000	0.000	0.000	0.000
88	A	418	LEU	0	0.019	-0.009	27.403	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.051	-0.005	30.573	0.003	0.003	0.000	0.000	0.000	0.000
90	A	420	THR	0	-0.033	-0.029	31.719	0.009	0.009	0.000	0.000	0.000	0.000
91	A	421	ASP	-1	-0.936	-0.956	33.233	-0.137	-0.137	0.000	0.000	0.000	0.000
92	A	422	THR	0	-0.018	-0.009	30.713	0.002	0.002	0.000	0.000	0.000	0.000
93	A	423	ALA	0	0.013	0.010	30.671	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	424	HIS	1	0.859	0.895	26.282	0.225	0.225	0.000	0.000	0.000	0.000
95	A	425	GLY	0	0.015	0.023	25.272	0.012	0.012	0.000	0.000	0.000	0.000
96	A	426	GLU	-1	-0.811	-0.901	21.730	-0.297	-0.297	0.000	0.000	0.000	0.000
97	A	427	GLN	0	0.026	0.006	19.650	0.030	0.030	0.000	0.000	0.000	0.000
98	A	428	PRO	0	-0.037	-0.017	18.079	-0.035	-0.035	0.000	0.000	0.000	0.000
99	A	429	VAL	0	-0.026	-0.006	11.512	-0.056	-0.056	0.000	0.000	0.000	0.000
100	A	430	ILE	0	-0.011	-0.007	12.662	0.085	0.085	0.000	0.000	0.000	0.000
101	A	431	PRO	0	-0.016	-0.020	11.290	-0.239	-0.239	0.000	0.000	0.000	0.000
102	A	432	SER	0	-0.030	-0.028	7.625	0.023	0.023	0.000	0.000	0.000	0.000
103	A	433	ALA	0	0.059	0.057	8.178	-0.410	-0.410	0.000	0.000	0.000	0.000
104	A	434	ILE	0	-0.001	-0.009	5.554	-1.245	-1.245	0.000	0.000	0.000	0.000
105	A	435	PRO	0	-0.013	-0.014	3.590	0.418	0.949	0.010	-0.121	-0.420	0.000
106	A	436	GLY	0	0.015	0.019	6.454	0.167	0.167	0.000	0.000	0.000	0.000
107	A	437	LEU	0	-0.055	-0.035	9.899	0.431	0.431	0.000	0.000	0.000	0.000
108	A	438	GLU	-1	-0.777	-0.896	9.133	-2.038	-2.038	0.000	0.000	0.000	0.000
109	A	439	ILE	0	-0.001	0.001	11.382	0.235	0.235	0.000	0.000	0.000	0.000
110	A	440	PRO	0	-0.031	-0.001	14.631	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	441	GLU	-1	-0.771	-0.876	17.722	-0.688	-0.688	0.000	0.000	0.000	0.000
112	A	442	MET	0	-0.071	-0.022	19.818	0.039	0.039	0.000	0.000	0.000	0.000
113	A	443	ASP	-1	-0.857	-0.932	23.417	-0.343	-0.343	0.000	0.000	0.000	0.000
114	A	444	ASP	-1	-0.957	-0.969	26.784	-0.260	-0.260	0.000	0.000	0.000	0.000
115	A	445	VAL	0	-0.087	-0.035	25.797	0.018	0.018	0.000	0.000	0.000	0.000
116	A	446	SER	0	-0.049	-0.033	26.344	-0.035	-0.035	0.000	0.000	0.000	0.000
117	A	447	ILE	0	-0.003	0.004	22.462	0.001	0.001	0.000	0.000	0.000	0.000
118	A	448	LEU	0	-0.010	-0.005	26.245	0.021	0.021	0.000	0.000	0.000	0.000
119	A	449	ALA	0	-0.006	-0.004	26.253	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	450	THR	0	-0.025	-0.011	26.979	0.035	0.035	0.000	0.000	0.000	0.000
121	A	451	PRO	0	-0.035	-0.021	26.153	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	452	MET	0	0.010	0.014	20.073	0.014	0.014	0.000	0.000	0.000	0.000
123	A	453	PRO	0	0.061	0.043	24.260	0.020	0.020	0.000	0.000	0.000	0.000
124	A	454	ASP	-1	-0.762	-0.859	23.852	-0.249	-0.249	0.000	0.000	0.000	0.000
125	A	455	GLU	-1	-0.750	-0.860	18.948	-0.429	-0.429	0.000	0.000	0.000	0.000
126	A	456	LYS	1	0.768	0.863	22.477	0.196	0.196	0.000	0.000	0.000	0.000
127	A	457	ASP	-1	-0.858	-0.921	25.256	-0.205	-0.205	0.000	0.000	0.000	0.000
128	A	458	PHE	0	-0.031	0.011	20.983	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	459	ARG	1	0.789	0.856	22.515	0.205	0.205	0.000	0.000	0.000	0.000
130	A	460	ASP	-1	-0.742	-0.819	18.020	-0.505	-0.505	0.000	0.000	0.000	0.000
131	A	461	TYR	0	-0.065	-0.062	16.710	0.015	0.015	0.000	0.000	0.000	0.000
132	A	462	ILE	0	0.012	0.010	11.431	-0.030	-0.030	0.000	0.000	0.000	0.000
133	A	463	LEU	0	-0.005	0.007	15.075	0.070	0.070	0.000	0.000	0.000	0.000
134	A	464	VAL	0	0.017	-0.002	12.656	-0.056	-0.056	0.000	0.000	0.000	0.000
135	A	465	PHE	0	0.040	0.019	15.996	0.067	0.067	0.000	0.000	0.000	0.000
136	A	466	PRO	0	-0.040	-0.023	17.294	0.014	0.014	0.000	0.000	0.000	0.000
137	A	467	GLU	-1	-0.911	-0.958	18.126	0.079	0.079	0.000	0.000	0.000	0.000
138	A	468	ASN	0	-0.076	-0.052	14.029	-0.096	-0.096	0.000	0.000	0.000	0.000
139	A	469	ALA	0	0.006	0.016	17.756	-0.034	-0.034	0.000	0.000	0.000	0.000
140	A	470	PHE	0	0.008	0.017	20.281	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	471	PRO	0	0.018	0.008	16.782	0.014	0.014	0.000	0.000	0.000	0.000
142	A	472	PRO	0	-0.008	-0.001	12.579	0.026	0.026	0.000	0.000	0.000	0.000
143	A	473	ILE	0	0.015	0.003	15.548	-0.075	-0.075	0.000	0.000	0.000	0.000
144	A	474	TYR	0	-0.019	-0.030	15.679	0.020	0.020	0.000	0.000	0.000	0.000
145	A	475	VAL	0	0.003	-0.005	17.309	0.034	0.034	0.000	0.000	0.000	0.000
146	A	476	TYR	0	0.028	-0.004	20.025	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	477	LEU	0	-0.007	-0.002	22.497	0.018	0.018	0.000	0.000	0.000	0.000
148	A	478	SER	0	0.042	0.026	25.844	-0.012	-0.012	0.000	0.000	0.000	0.000
149	A	479	LYS	1	0.884	0.920	28.001	0.198	0.198	0.000	0.000	0.000	0.000
150	A	480	LEU	0	-0.011	0.008	28.043	0.009	0.009	0.000	0.000	0.000	0.000

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