FMO DATABASE

FMODB ID: 9GNG2

Calculation Name: 3MFB-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1459165.150998
FMO2-HF: Nuclear repulsion	1399127.361783
FMO2-HF: Total energy	-60037.789215
FMO2-MP2: Total energy	-60212.987479

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.
-13.631	-19.315	17.535	-4.428	-7.424	0.014

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 : -0.009

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	0.016	0.020	3.065	-1.810	0.686	0.134	-1.194	-1.436	-0.006
4	A	334	THR	0	-0.017	-0.018	4.900	0.957	0.957	0.000	0.000	0.000	0.000
5	A	335	PRO	0	0.051	0.012	7.010	-0.071	-0.071	0.000	0.000	0.000	0.000
6	A	336	GLU	-1	-0.895	-0.944	7.969	0.796	0.796	0.000	0.000	0.000	0.000
7	A	337	LYS	1	0.904	0.952	2.148	-12.214	-20.960	17.389	-3.094	-5.550	0.020
8	A	338	LEU	0	0.025	0.007	5.618	-0.363	-0.363	0.000	0.000	0.000	0.000
9	A	339	LEU	0	0.044	0.026	8.000	0.008	0.008	0.000	0.000	0.000	0.000
10	A	340	GLU	-1	-0.991	-0.983	5.368	2.054	2.054	0.000	0.000	0.000	0.000
11	A	341	ALA	0	-0.025	-0.020	6.972	-0.091	-0.091	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.005	0.002	8.663	0.070	0.070	0.000	0.000	0.000	0.000
13	A	343	ASN	0	-0.031	-0.013	11.919	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	344	LYS	1	0.899	0.964	7.181	0.695	0.695	0.000	0.000	0.000	0.000
15	A	345	GLN	0	-0.042	-0.025	13.063	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	346	GLY	0	-0.019	-0.007	10.277	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	347	THR	0	-0.057	-0.056	9.549	0.144	0.144	0.000	0.000	0.000	0.000
18	A	348	VAL	0	-0.030	-0.010	6.088	-0.363	-0.363	0.000	0.000	0.000	0.000
19	A	349	PRO	0	-0.009	0.010	6.743	0.304	0.304	0.000	0.000	0.000	0.000
20	A	350	SER	0	0.054	0.020	9.945	-0.151	-0.151	0.000	0.000	0.000	0.000
21	A	351	ARG	1	0.964	1.004	12.655	1.016	1.016	0.000	0.000	0.000	0.000
22	A	352	VAL	0	-0.012	0.004	15.241	0.147	0.147	0.000	0.000	0.000	0.000
23	A	353	ARG	1	0.750	0.854	16.331	0.683	0.683	0.000	0.000	0.000	0.000
24	A	354	TYR	0	0.061	0.023	19.000	0.040	0.040	0.000	0.000	0.000	0.000
25	A	355	GLN	0	-0.010	-0.024	22.195	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	356	TRP	0	-0.035	-0.009	25.051	0.022	0.022	0.000	0.000	0.000	0.000
27	A	357	MET	0	-0.005	-0.003	28.553	0.004	0.004	0.000	0.000	0.000	0.000
28	A	358	GLU	-1	-0.908	-0.978	30.927	-0.200	-0.200	0.000	0.000	0.000	0.000
29	A	359	ASP	-1	-0.860	-0.910	34.340	-0.180	-0.180	0.000	0.000	0.000	0.000
30	A	360	GLU	-1	-0.946	-0.980	37.824	-0.169	-0.169	0.000	0.000	0.000	0.000
31	A	361	GLU	-1	-0.941	-0.960	39.598	-0.143	-0.143	0.000	0.000	0.000	0.000
32	A	362	THR	0	-0.142	-0.088	40.990	0.007	0.007	0.000	0.000	0.000	0.000
33	A	363	GLY	0	-0.002	0.008	38.842	0.005	0.005	0.000	0.000	0.000	0.000
34	A	364	ARG	1	0.885	0.945	37.655	0.163	0.163	0.000	0.000	0.000	0.000
35	A	365	LEU	0	0.029	0.019	32.132	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	366	LYS	1	0.902	0.945	31.956	0.263	0.263	0.000	0.000	0.000	0.000
37	A	367	ALA	0	-0.011	0.015	27.600	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	368	VAL	0	-0.018	-0.011	26.930	0.014	0.014	0.000	0.000	0.000	0.000
39	A	369	GLY	0	0.049	0.014	23.623	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	370	TYR	0	-0.037	-0.041	22.110	0.040	0.040	0.000	0.000	0.000	0.000
41	A	371	HIS	0	-0.029	-0.010	19.810	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	372	THR	0	-0.058	-0.056	15.494	0.048	0.048	0.000	0.000	0.000	0.000
43	A	373	SER	0	0.019	0.000	17.521	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	374	MET	0	-0.007	-0.017	9.523	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	375	GLU	-1	-0.956	-0.962	14.728	-0.558	-0.558	0.000	0.000	0.000	0.000
46	A	376	SER	0	-0.089	-0.037	17.781	0.041	0.041	0.000	0.000	0.000	0.000
47	A	377	GLY	0	0.058	0.033	15.449	0.050	0.050	0.000	0.000	0.000	0.000
48	A	378	ARG	1	0.814	0.898	16.147	0.511	0.511	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.837	-0.935	12.133	-1.424	-1.424	0.000	0.000	0.000	0.000
50	A	380	GLN	0	0.005	0.020	9.155	-0.251	-0.251	0.000	0.000	0.000	0.000
51	A	381	VAL	0	0.048	0.031	11.917	0.185	0.185	0.000	0.000	0.000	0.000
52	A	382	ARG	1	0.872	0.927	11.992	0.415	0.415	0.000	0.000	0.000	0.000
53	A	383	VAL	0	0.016	0.021	9.423	0.036	0.036	0.000	0.000	0.000	0.000
54	A	384	ARG	1	0.863	0.928	12.703	0.623	0.623	0.000	0.000	0.000	0.000
55	A	385	LEU	0	0.014	0.022	15.373	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	386	LEU	0	-0.028	-0.009	16.576	0.022	0.022	0.000	0.000	0.000	0.000
57	A	387	LYS	1	0.962	0.975	19.990	0.172	0.172	0.000	0.000	0.000	0.000
58	A	388	HIS	1	0.921	0.957	22.767	0.057	0.057	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.825	-0.912	25.288	-0.061	-0.061	0.000	0.000	0.000	0.000
60	A	390	PHE	0	-0.012	-0.036	26.687	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	391	PRO	0	-0.029	0.002	31.072	0.001	0.001	0.000	0.000	0.000	0.000
62	A	392	ASN	0	-0.017	-0.008	32.121	0.002	0.002	0.000	0.000	0.000	0.000
63	A	393	ASN	0	-0.055	-0.018	31.301	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	394	ARG	1	0.948	0.978	28.764	0.106	0.106	0.000	0.000	0.000	0.000
65	A	395	TYR	0	-0.056	-0.013	22.975	0.021	0.021	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.812	-0.910	24.647	-0.134	-0.134	0.000	0.000	0.000	0.000
67	A	397	PHE	0	0.011	-0.009	20.072	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	398	TRP	0	-0.059	-0.034	23.182	0.005	0.005	0.000	0.000	0.000	0.000
69	A	399	GLU	-1	-0.755	-0.808	22.997	-0.323	-0.323	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.919	-0.977	21.803	-0.207	-0.207	0.000	0.000	0.000	0.000
71	A	401	GLY	0	-0.027	-0.010	24.558	0.001	0.001	0.000	0.000	0.000	0.000
72	A	402	ALA	0	-0.031	0.006	27.465	0.010	0.010	0.000	0.000	0.000	0.000
73	A	403	THR	0	-0.031	-0.032	29.233	0.008	0.008	0.000	0.000	0.000	0.000
74	A	404	GLY	0	0.019	-0.003	30.767	0.014	0.014	0.000	0.000	0.000	0.000
75	A	405	PRO	0	-0.057	0.003	27.976	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	406	THR	0	0.013	-0.008	25.407	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	407	ILE	0	-0.006	-0.001	22.208	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	408	LEU	0	-0.020	-0.017	25.612	0.012	0.012	0.000	0.000	0.000	0.000
79	A	409	TRP	0	0.042	0.024	23.247	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	410	THR	0	0.080	0.022	26.387	0.013	0.013	0.000	0.000	0.000	0.000
81	A	411	PRO	0	-0.093	-0.053	27.319	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	412	ASP	-1	-0.889	-0.941	28.792	-0.075	-0.075	0.000	0.000	0.000	0.000
83	A	413	ASN	0	-0.080	0.029	30.975	0.011	0.011	0.000	0.000	0.000	0.000
84	A	414	PRO	0	-0.045	-0.049	27.037	0.002	0.002	0.000	0.000	0.000	0.000
85	A	415	GLY	0	0.056	0.002	26.331	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	416	ILE	0	-0.041	-0.019	22.261	0.009	0.009	0.000	0.000	0.000	0.000
87	A	417	GLU	-1	-0.943	-0.965	26.247	-0.149	-0.149	0.000	0.000	0.000	0.000
88	A	418	LEU	0	-0.003	-0.017	26.812	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.055	-0.006	30.011	0.010	0.010	0.000	0.000	0.000	0.000
90	A	420	THR	0	-0.035	-0.018	31.286	0.008	0.008	0.000	0.000	0.000	0.000
91	A	421	ASP	-1	-0.903	-0.953	33.477	-0.167	-0.167	0.000	0.000	0.000	0.000
92	A	422	THR	0	-0.049	-0.017	29.878	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	423	ALA	0	0.022	0.007	30.198	0.000	0.000	0.000	0.000	0.000	0.000
94	A	424	HIS	1	0.841	0.901	25.938	0.250	0.250	0.000	0.000	0.000	0.000
95	A	425	GLY	0	0.030	0.038	25.111	0.021	0.021	0.000	0.000	0.000	0.000
96	A	426	GLU	-1	-0.855	-0.950	21.760	-0.345	-0.345	0.000	0.000	0.000	0.000
97	A	427	GLN	0	0.050	0.015	19.852	0.048	0.048	0.000	0.000	0.000	0.000
98	A	428	PRO	0	-0.048	-0.019	18.274	-0.060	-0.060	0.000	0.000	0.000	0.000
99	A	429	VAL	0	-0.005	-0.002	11.620	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	430	ILE	0	-0.053	-0.027	12.748	0.124	0.124	0.000	0.000	0.000	0.000
101	A	431	PRO	0	-0.021	-0.026	11.499	-0.222	-0.222	0.000	0.000	0.000	0.000
102	A	432	SER	0	-0.014	-0.015	7.774	0.010	0.010	0.000	0.000	0.000	0.000
103	A	433	ALA	0	0.062	0.052	8.632	0.052	0.052	0.000	0.000	0.000	0.000
104	A	434	ILE	0	0.003	-0.008	5.254	-1.062	-1.062	0.000	0.000	0.000	0.000
105	A	435	PRO	0	-0.019	-0.016	3.385	0.132	0.698	0.012	-0.140	-0.438	0.000
106	A	436	GLY	0	0.052	0.037	6.646	0.352	0.352	0.000	0.000	0.000	0.000
107	A	437	LEU	0	-0.081	-0.054	9.838	0.501	0.501	0.000	0.000	0.000	0.000
108	A	438	GLU	-1	-0.814	-0.920	9.705	-2.058	-2.058	0.000	0.000	0.000	0.000
109	A	439	ILE	0	0.004	0.015	11.741	0.223	0.223	0.000	0.000	0.000	0.000
110	A	440	PRO	0	-0.035	0.002	15.080	0.012	0.012	0.000	0.000	0.000	0.000
111	A	441	GLU	-1	-0.855	-0.963	18.163	-0.590	-0.590	0.000	0.000	0.000	0.000
112	A	442	MET	0	-0.078	-0.024	19.822	0.053	0.053	0.000	0.000	0.000	0.000
113	A	443	ASP	-1	-0.903	-0.961	23.645	-0.288	-0.288	0.000	0.000	0.000	0.000
114	A	444	ASP	-1	-0.953	-0.965	26.908	-0.241	-0.241	0.000	0.000	0.000	0.000
115	A	445	VAL	0	-0.054	-0.010	25.923	0.008	0.008	0.000	0.000	0.000	0.000
116	A	446	SER	0	-0.074	-0.042	27.070	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	447	ILE	0	0.031	0.022	22.625	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	448	LEU	0	-0.022	-0.007	26.539	0.027	0.027	0.000	0.000	0.000	0.000
119	A	449	ALA	0	-0.015	-0.009	26.548	-0.031	-0.031	0.000	0.000	0.000	0.000
120	A	450	THR	0	-0.008	-0.001	27.810	0.032	0.032	0.000	0.000	0.000	0.000
121	A	451	PRO	0	-0.040	-0.021	26.765	-0.032	-0.032	0.000	0.000	0.000	0.000
122	A	452	MET	0	-0.014	-0.008	21.069	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	453	PRO	0	0.055	0.044	24.285	0.014	0.014	0.000	0.000	0.000	0.000
124	A	454	ASP	-1	-0.826	-0.917	24.326	-0.374	-0.374	0.000	0.000	0.000	0.000
125	A	455	GLU	-1	-0.836	-0.899	19.413	-0.620	-0.620	0.000	0.000	0.000	0.000
126	A	456	LYS	1	0.867	0.935	22.923	0.376	0.376	0.000	0.000	0.000	0.000
127	A	457	ASP	-1	-0.906	-0.954	25.856	-0.297	-0.297	0.000	0.000	0.000	0.000
128	A	458	PHE	0	-0.033	0.015	21.167	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	459	ARG	1	0.797	0.866	22.306	0.303	0.303	0.000	0.000	0.000	0.000
130	A	460	ASP	-1	-0.756	-0.842	18.135	-0.682	-0.682	0.000	0.000	0.000	0.000
131	A	461	TYR	0	-0.093	-0.090	16.530	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	462	ILE	0	0.036	0.036	11.289	0.011	0.011	0.000	0.000	0.000	0.000
133	A	463	LEU	0	-0.034	-0.019	14.624	0.020	0.020	0.000	0.000	0.000	0.000
134	A	464	VAL	0	0.037	0.004	11.894	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	465	PHE	0	0.027	0.022	15.249	0.063	0.063	0.000	0.000	0.000	0.000
136	A	466	PRO	0	-0.020	-0.019	16.714	0.014	0.014	0.000	0.000	0.000	0.000
137	A	467	GLU	-1	-0.943	-0.971	17.347	0.057	0.057	0.000	0.000	0.000	0.000
138	A	468	ASN	0	-0.049	-0.032	14.119	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	469	ALA	0	-0.003	0.016	17.781	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	470	PHE	0	0.008	-0.001	19.771	0.005	0.005	0.000	0.000	0.000	0.000
141	A	471	PRO	0	0.003	0.004	16.658	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	472	PRO	0	-0.007	0.004	12.586	0.009	0.009	0.000	0.000	0.000	0.000
143	A	473	ILE	0	0.029	0.009	15.325	-0.028	-0.028	0.000	0.000	0.000	0.000
144	A	474	TYR	0	-0.036	-0.027	15.671	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	475	VAL	0	0.029	0.007	17.368	0.061	0.061	0.000	0.000	0.000	0.000
146	A	476	TYR	0	0.015	0.000	20.142	-0.036	-0.036	0.000	0.000	0.000	0.000
147	A	477	LEU	0	0.002	-0.015	22.456	0.035	0.035	0.000	0.000	0.000	0.000
148	A	478	SER	0	0.051	0.030	25.637	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	479	LYS	1	0.961	0.967	28.275	0.278	0.278	0.000	0.000	0.000	0.000
150	A	480	LEU	0	-0.037	-0.007	28.122	0.014	0.014	0.000	0.000	0.000	0.000
151	A	1	NME	0	0.005	0.015	30.453	0.003	0.003	0.000	0.000	0.000	0.000

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