FMO DATABASE

FMODB ID: GNJM1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1457089.600108
FMO2-HF: Nuclear repulsion	1397070.916102
FMO2-HF: Total energy	-60018.684006
FMO2-MP2: Total energy	-60193.78714

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.
-13.423	-18.612	16.535	-4.178	-7.17	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 : -0.008 / q_NPA : -0.011

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	0.018	0.021	3.101	-1.627	0.806	0.112	-1.146	-1.401	-0.005
4	A	334	THR	0	-0.019	-0.018	4.942	0.873	0.873	0.000	0.000	0.000	0.000
5	A	335	PRO	0	0.051	0.011	7.055	-0.062	-0.062	0.000	0.000	0.000	0.000
6	A	336	GLU	-1	-0.895	-0.944	7.962	0.819	0.819	0.000	0.000	0.000	0.000
7	A	337	LYS	1	0.906	0.954	2.162	-12.216	-20.390	16.414	-2.893	-5.347	0.019
8	A	338	LEU	0	0.025	0.007	5.791	-0.340	-0.340	0.000	0.000	0.000	0.000
9	A	339	LEU	0	0.040	0.025	8.164	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	340	GLU	-1	-0.990	-0.984	5.452	2.103	2.103	0.000	0.000	0.000	0.000
11	A	341	ALA	0	-0.023	-0.020	7.073	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.004	0.001	8.766	0.047	0.047	0.000	0.000	0.000	0.000
13	A	343	ASN	0	-0.030	-0.013	12.045	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	344	LYS	1	0.899	0.963	7.254	0.645	0.645	0.000	0.000	0.000	0.000
15	A	345	GLN	0	-0.043	-0.024	13.191	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	346	GLY	0	-0.020	-0.008	10.411	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	347	THR	0	-0.052	-0.054	9.677	0.145	0.145	0.000	0.000	0.000	0.000
18	A	348	VAL	0	-0.032	-0.010	6.154	-0.319	-0.319	0.000	0.000	0.000	0.000
19	A	349	PRO	0	-0.007	0.010	6.741	0.287	0.287	0.000	0.000	0.000	0.000
20	A	350	SER	0	0.052	0.020	9.937	-0.146	-0.146	0.000	0.000	0.000	0.000
21	A	351	ARG	1	0.966	1.004	12.662	0.983	0.983	0.000	0.000	0.000	0.000
22	A	352	VAL	0	-0.017	0.001	15.334	0.137	0.137	0.000	0.000	0.000	0.000
23	A	353	ARG	1	0.757	0.856	16.336	0.663	0.663	0.000	0.000	0.000	0.000
24	A	354	TYR	0	0.058	0.023	19.028	0.036	0.036	0.000	0.000	0.000	0.000
25	A	355	GLN	0	-0.006	-0.022	22.240	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	356	TRP	0	-0.040	-0.010	25.096	0.020	0.020	0.000	0.000	0.000	0.000
27	A	357	MET	0	-0.008	-0.004	28.607	0.003	0.003	0.000	0.000	0.000	0.000
28	A	358	GLU	-1	-0.910	-0.979	30.965	-0.193	-0.193	0.000	0.000	0.000	0.000
29	A	359	ASP	-1	-0.861	-0.909	34.380	-0.175	-0.175	0.000	0.000	0.000	0.000
30	A	360	GLU	-1	-0.945	-0.981	37.859	-0.164	-0.164	0.000	0.000	0.000	0.000
31	A	361	GLU	-1	-0.941	-0.960	39.627	-0.139	-0.139	0.000	0.000	0.000	0.000
32	A	362	THR	0	-0.141	-0.087	41.035	0.007	0.007	0.000	0.000	0.000	0.000
33	A	363	GLY	0	-0.004	0.008	38.894	0.005	0.005	0.000	0.000	0.000	0.000
34	A	364	ARG	1	0.888	0.945	37.716	0.157	0.157	0.000	0.000	0.000	0.000
35	A	365	LEU	0	0.026	0.018	32.201	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	366	LYS	1	0.905	0.946	32.000	0.254	0.254	0.000	0.000	0.000	0.000
37	A	367	ALA	0	-0.012	0.014	27.663	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	368	VAL	0	-0.026	-0.015	26.955	0.014	0.014	0.000	0.000	0.000	0.000
39	A	369	GLY	0	0.063	0.019	23.651	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	370	TYR	0	-0.044	-0.044	22.125	0.038	0.038	0.000	0.000	0.000	0.000
41	A	371	HIS	0	-0.028	-0.010	19.808	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	372	THR	0	-0.060	-0.057	15.589	0.047	0.047	0.000	0.000	0.000	0.000
43	A	373	SER	0	0.023	0.002	17.560	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	374	MET	0	-0.010	-0.018	9.597	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	375	GLU	-1	-0.956	-0.962	14.750	-0.566	-0.566	0.000	0.000	0.000	0.000
46	A	376	SER	0	-0.090	-0.037	17.779	0.039	0.039	0.000	0.000	0.000	0.000
47	A	377	GLY	0	0.058	0.033	15.492	0.050	0.050	0.000	0.000	0.000	0.000
48	A	378	ARG	1	0.815	0.899	16.220	0.503	0.503	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.835	-0.934	12.197	-1.396	-1.396	0.000	0.000	0.000	0.000
50	A	380	GLN	0	0.004	0.019	9.236	-0.231	-0.231	0.000	0.000	0.000	0.000
51	A	381	VAL	0	0.047	0.031	11.940	0.176	0.176	0.000	0.000	0.000	0.000
52	A	382	ARG	1	0.874	0.927	12.044	0.399	0.399	0.000	0.000	0.000	0.000
53	A	383	VAL	0	0.014	0.020	9.529	0.034	0.034	0.000	0.000	0.000	0.000
54	A	384	ARG	1	0.861	0.928	12.806	0.581	0.581	0.000	0.000	0.000	0.000
55	A	385	LEU	0	0.015	0.023	15.517	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	386	LEU	0	-0.027	-0.009	16.720	0.018	0.018	0.000	0.000	0.000	0.000
57	A	387	LYS	1	0.966	0.977	20.140	0.154	0.154	0.000	0.000	0.000	0.000
58	A	388	HIS	1	0.921	0.956	22.919	0.043	0.043	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.825	-0.912	25.450	-0.052	-0.052	0.000	0.000	0.000	0.000
60	A	390	PHE	0	-0.013	-0.036	26.856	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	391	PRO	0	-0.028	0.002	31.237	0.000	0.000	0.000	0.000	0.000	0.000
62	A	392	ASN	0	-0.018	-0.008	32.277	0.001	0.001	0.000	0.000	0.000	0.000
63	A	393	ASN	0	-0.056	-0.018	31.469	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	394	ARG	1	0.949	0.979	28.927	0.096	0.096	0.000	0.000	0.000	0.000
65	A	395	TYR	0	-0.059	-0.014	23.145	0.022	0.022	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.804	-0.908	24.798	-0.122	-0.122	0.000	0.000	0.000	0.000
67	A	397	PHE	0	0.001	-0.011	20.178	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	398	TRP	0	-0.057	-0.032	23.313	0.003	0.003	0.000	0.000	0.000	0.000
69	A	399	GLU	-1	-0.757	-0.808	23.089	-0.307	-0.307	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.918	-0.977	21.899	-0.195	-0.195	0.000	0.000	0.000	0.000
71	A	401	GLY	0	-0.028	-0.010	24.632	0.000	0.000	0.000	0.000	0.000	0.000
72	A	402	ALA	0	-0.029	0.006	27.552	0.009	0.009	0.000	0.000	0.000	0.000
73	A	403	THR	0	-0.032	-0.032	29.324	0.007	0.007	0.000	0.000	0.000	0.000
74	A	404	GLY	0	0.019	-0.002	30.872	0.013	0.013	0.000	0.000	0.000	0.000
75	A	405	PRO	0	-0.058	0.002	28.098	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	406	THR	0	0.010	-0.009	25.518	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	407	ILE	0	0.001	0.001	22.326	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	408	LEU	0	-0.021	-0.017	25.748	0.012	0.012	0.000	0.000	0.000	0.000
79	A	409	TRP	0	0.041	0.024	23.392	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	410	THR	0	0.078	0.022	26.541	0.013	0.013	0.000	0.000	0.000	0.000
81	A	411	PRO	0	-0.091	-0.052	27.491	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	412	ASP	-1	-0.891	-0.942	28.961	-0.065	-0.065	0.000	0.000	0.000	0.000
83	A	413	ASN	0	-0.078	0.029	31.131	0.010	0.010	0.000	0.000	0.000	0.000
84	A	414	PRO	0	-0.045	-0.049	27.198	0.002	0.002	0.000	0.000	0.000	0.000
85	A	415	GLY	0	0.057	0.002	26.478	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	416	ILE	0	-0.039	-0.019	22.400	0.009	0.009	0.000	0.000	0.000	0.000
87	A	417	GLU	-1	-0.946	-0.966	26.385	-0.140	-0.140	0.000	0.000	0.000	0.000
88	A	418	LEU	0	-0.003	-0.017	26.926	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.051	-0.005	30.132	0.009	0.009	0.000	0.000	0.000	0.000
90	A	420	THR	0	-0.035	-0.019	31.409	0.008	0.008	0.000	0.000	0.000	0.000
91	A	421	ASP	-1	-0.906	-0.954	33.589	-0.158	-0.158	0.000	0.000	0.000	0.000
92	A	422	THR	0	-0.047	-0.016	29.956	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	423	ALA	0	0.021	0.006	30.279	0.000	0.000	0.000	0.000	0.000	0.000
94	A	424	HIS	1	0.845	0.901	26.045	0.237	0.237	0.000	0.000	0.000	0.000
95	A	425	GLY	0	0.032	0.038	25.207	0.021	0.021	0.000	0.000	0.000	0.000
96	A	426	GLU	-1	-0.859	-0.951	21.882	-0.326	-0.326	0.000	0.000	0.000	0.000
97	A	427	GLN	0	0.052	0.017	19.954	0.047	0.047	0.000	0.000	0.000	0.000
98	A	428	PRO	0	-0.047	-0.019	18.394	-0.056	-0.056	0.000	0.000	0.000	0.000
99	A	429	VAL	0	-0.008	-0.003	11.746	-0.035	-0.035	0.000	0.000	0.000	0.000
100	A	430	ILE	0	-0.051	-0.027	12.754	0.121	0.121	0.000	0.000	0.000	0.000
101	A	431	PRO	0	-0.022	-0.027	11.512	-0.211	-0.211	0.000	0.000	0.000	0.000
102	A	432	SER	0	-0.011	-0.014	7.799	0.019	0.019	0.000	0.000	0.000	0.000
103	A	433	ALA	0	0.062	0.052	8.644	0.064	0.064	0.000	0.000	0.000	0.000
104	A	434	ILE	0	0.002	-0.008	5.249	-1.005	-1.005	0.000	0.000	0.000	0.000
105	A	435	PRO	0	-0.016	-0.015	3.431	0.147	0.699	0.009	-0.139	-0.422	0.000
106	A	436	GLY	0	0.048	0.036	6.700	0.292	0.292	0.000	0.000	0.000	0.000
107	A	437	LEU	0	-0.079	-0.053	9.839	0.478	0.478	0.000	0.000	0.000	0.000
108	A	438	GLU	-1	-0.815	-0.920	9.701	-1.987	-1.987	0.000	0.000	0.000	0.000
109	A	439	ILE	0	0.004	0.015	11.734	0.210	0.210	0.000	0.000	0.000	0.000
110	A	440	PRO	0	-0.034	0.003	15.152	0.005	0.005	0.000	0.000	0.000	0.000
111	A	441	GLU	-1	-0.857	-0.963	18.155	-0.573	-0.573	0.000	0.000	0.000	0.000
112	A	442	MET	0	-0.077	-0.024	19.906	0.050	0.050	0.000	0.000	0.000	0.000
113	A	443	ASP	-1	-0.903	-0.961	23.717	-0.276	-0.276	0.000	0.000	0.000	0.000
114	A	444	ASP	-1	-0.953	-0.965	26.902	-0.232	-0.232	0.000	0.000	0.000	0.000
115	A	445	VAL	0	-0.054	-0.010	25.978	0.008	0.008	0.000	0.000	0.000	0.000
116	A	446	SER	0	-0.073	-0.041	27.111	-0.025	-0.025	0.000	0.000	0.000	0.000
117	A	447	ILE	0	0.029	0.021	22.624	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	448	LEU	0	-0.021	-0.006	26.552	0.025	0.025	0.000	0.000	0.000	0.000
119	A	449	ALA	0	-0.014	-0.009	26.640	-0.030	-0.030	0.000	0.000	0.000	0.000
120	A	450	THR	0	-0.007	-0.001	27.896	0.030	0.030	0.000	0.000	0.000	0.000
121	A	451	PRO	0	-0.040	-0.021	26.843	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	452	MET	0	-0.014	-0.008	21.140	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	453	PRO	0	0.057	0.045	24.273	0.013	0.013	0.000	0.000	0.000	0.000
124	A	454	ASP	-1	-0.828	-0.918	24.323	-0.366	-0.366	0.000	0.000	0.000	0.000
125	A	455	GLU	-1	-0.835	-0.899	19.423	-0.601	-0.601	0.000	0.000	0.000	0.000
126	A	456	LYS	1	0.864	0.932	22.917	0.367	0.367	0.000	0.000	0.000	0.000
127	A	457	ASP	-1	-0.907	-0.955	25.863	-0.288	-0.288	0.000	0.000	0.000	0.000
128	A	458	PHE	0	-0.032	0.015	21.197	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	459	ARG	1	0.798	0.866	22.360	0.289	0.289	0.000	0.000	0.000	0.000
130	A	460	ASP	-1	-0.755	-0.841	18.183	-0.655	-0.655	0.000	0.000	0.000	0.000
131	A	461	TYR	0	-0.096	-0.091	16.616	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	462	ILE	0	0.036	0.036	11.384	0.011	0.011	0.000	0.000	0.000	0.000
133	A	463	LEU	0	-0.033	-0.020	14.748	0.019	0.019	0.000	0.000	0.000	0.000
134	A	464	VAL	0	0.038	0.005	12.052	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	465	PHE	0	0.029	0.022	15.408	0.055	0.055	0.000	0.000	0.000	0.000
136	A	466	PRO	0	-0.020	-0.019	16.887	0.014	0.014	0.000	0.000	0.000	0.000
137	A	467	GLU	-1	-0.946	-0.972	17.520	0.073	0.073	0.000	0.000	0.000	0.000
138	A	468	ASN	0	-0.047	-0.032	14.217	-0.014	-0.014	0.000	0.000	0.000	0.000
139	A	469	ALA	0	-0.004	0.015	17.831	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	470	PHE	0	0.005	-0.001	19.847	0.004	0.004	0.000	0.000	0.000	0.000
141	A	471	PRO	0	0.004	0.005	16.696	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	472	PRO	0	-0.004	0.004	12.620	0.010	0.010	0.000	0.000	0.000	0.000
143	A	473	ILE	0	0.028	0.008	15.482	-0.027	-0.027	0.000	0.000	0.000	0.000
144	A	474	TYR	0	-0.032	-0.026	15.759	0.000	0.000	0.000	0.000	0.000	0.000
145	A	475	VAL	0	0.023	0.006	17.479	0.056	0.056	0.000	0.000	0.000	0.000
146	A	476	TYR	0	0.014	0.000	20.233	-0.035	-0.035	0.000	0.000	0.000	0.000
147	A	477	LEU	0	0.003	-0.014	22.538	0.032	0.032	0.000	0.000	0.000	0.000
148	A	478	SER	0	0.052	0.032	25.720	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	479	LYS	1	0.959	0.969	28.346	0.269	0.269	0.000	0.000	0.000	0.000
150	A	480	LEU	0	-0.029	0.006	28.193	0.016	0.016	0.000	0.000	0.000	0.000

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