FMO DATABASE

FMODB ID: R8268

Calculation Name: 3V46-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V46

Chain ID: A

ChEMBL ID:

UniProt ID: Q06697

Base Structure: X-ray

Registration Date: 2023-09-23

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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1783369.874231
FMO2-HF: Nuclear repulsion	1717730.264686
FMO2-HF: Total energy	-65639.609546
FMO2-MP2: Total energy	-65835.981016

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:234:PRO)

Summations of interaction energy for fragment #1(A:234:PRO)

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.
-17.424	-7.438	6.135	-5.798	-10.323	-0.042

Interaction energy analysis for fragmet #1(A:234:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.032

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	236	LYS	1	0.918	0.947	3.879	-3.937	-1.781	-0.020	-1.074	-1.063	0.002
4	A	237	ASP	-1	-0.849	-0.918	4.519	-0.641	-0.541	-0.001	-0.010	-0.088	0.000
5	A	238	PRO	0	0.013	0.029	5.132	0.188	0.188	0.000	0.000	0.000	0.000
6	A	239	ILE	0	-0.033	-0.022	6.582	0.265	0.265	0.000	0.000	0.000	0.000
7	A	240	ILE	0	-0.004	0.000	10.018	-0.142	-0.142	0.000	0.000	0.000	0.000
8	A	241	LEU	0	-0.004	0.007	13.031	0.092	0.092	0.000	0.000	0.000	0.000
9	A	242	ILE	0	-0.017	-0.015	15.888	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	243	PRO	0	0.002	0.015	19.210	0.034	0.034	0.000	0.000	0.000	0.000
11	A	244	SER	0	-0.051	-0.033	22.030	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	245	ALA	0	0.041	0.015	25.526	0.011	0.011	0.000	0.000	0.000	0.000
13	A	246	ALA	0	0.014	0.000	29.017	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	247	SER	0	0.010	0.014	29.780	0.006	0.006	0.000	0.000	0.000	0.000
15	A	248	SER	0	-0.012	-0.005	25.515	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	249	ILE	0	0.009	0.029	26.686	0.006	0.006	0.000	0.000	0.000	0.000
17	A	250	LEU	0	-0.014	0.006	22.336	0.004	0.004	0.000	0.000	0.000	0.000
18	A	251	THR	0	0.042	0.007	23.119	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	252	VAL	0	0.036	0.006	19.786	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	253	ALA	0	0.010	0.016	22.123	0.003	0.003	0.000	0.000	0.000	0.000
21	A	254	ASN	0	-0.005	-0.019	24.705	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	255	ILE	0	0.011	0.015	18.925	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	256	LYS	1	0.927	0.962	19.768	0.181	0.181	0.000	0.000	0.000	0.000
24	A	257	GLN	0	0.003	-0.014	21.792	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	258	PHE	0	0.014	0.009	21.730	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	259	LEU	0	0.025	-0.004	16.916	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	260	LEU	0	-0.031	-0.011	18.366	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	261	GLU	-1	-0.837	-0.888	21.795	-0.143	-0.143	0.000	0.000	0.000	0.000
29	A	262	SER	0	-0.048	-0.014	24.387	0.006	0.006	0.000	0.000	0.000	0.000
30	A	263	LYS	1	0.849	0.911	25.877	0.169	0.169	0.000	0.000	0.000	0.000
31	A	264	TYR	0	-0.055	-0.040	27.046	0.001	0.001	0.000	0.000	0.000	0.000
32	A	265	VAL	0	0.007	0.002	28.525	0.015	0.015	0.000	0.000	0.000	0.000
33	A	266	ASN	0	0.029	0.016	29.347	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	267	PRO	0	0.031	0.019	27.576	0.009	0.009	0.000	0.000	0.000	0.000
35	A	268	ARG	1	0.914	0.969	29.620	0.106	0.106	0.000	0.000	0.000	0.000
36	A	269	ASN	0	-0.056	-0.036	32.716	0.011	0.011	0.000	0.000	0.000	0.000
37	A	270	LEU	0	0.026	0.020	28.384	0.002	0.002	0.000	0.000	0.000	0.000
38	A	271	PRO	0	0.000	0.000	29.492	0.003	0.003	0.000	0.000	0.000	0.000
39	A	272	SER	0	0.026	0.019	28.883	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	273	VAL	0	0.010	0.002	22.807	0.004	0.004	0.000	0.000	0.000	0.000
41	A	274	PRO	0	0.004	0.002	25.773	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	275	ASN	0	0.045	0.025	21.901	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	276	GLY	0	0.017	0.017	22.640	0.000	0.000	0.000	0.000	0.000	0.000
44	A	277	LEU	0	-0.070	-0.035	16.206	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	278	VAL	0	0.009	0.005	18.449	0.021	0.021	0.000	0.000	0.000	0.000
46	A	279	ASN	0	0.008	-0.006	14.067	0.006	0.006	0.000	0.000	0.000	0.000
47	A	280	ILE	0	-0.008	-0.006	14.890	0.037	0.037	0.000	0.000	0.000	0.000
48	A	281	GLU	-1	-0.821	-0.882	13.557	-0.212	-0.212	0.000	0.000	0.000	0.000
49	A	282	LYS	1	0.887	0.966	12.711	0.545	0.545	0.000	0.000	0.000	0.000
50	A	283	ASN	0	0.027	0.025	12.764	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	284	PHE	0	-0.031	-0.032	10.554	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	285	GLU	-1	-0.851	-0.901	14.421	-0.336	-0.336	0.000	0.000	0.000	0.000
53	A	286	ARG	1	0.815	0.893	13.362	0.518	0.518	0.000	0.000	0.000	0.000
54	A	287	ILE	0	-0.015	-0.009	7.753	-0.127	-0.127	0.000	0.000	0.000	0.000
55	A	288	SER	0	-0.010	-0.004	10.298	0.093	0.093	0.000	0.000	0.000	0.000
56	A	289	ARG	1	0.818	0.912	3.861	1.257	1.785	-0.001	-0.261	-0.267	0.001
57	A	290	PRO	0	0.036	0.020	10.832	-0.173	-0.173	0.000	0.000	0.000	0.000
58	A	291	ILE	0	-0.034	-0.007	6.435	-0.032	-0.032	0.000	0.000	0.000	0.000
59	A	292	ARG	1	0.862	0.911	9.629	0.153	0.153	0.000	0.000	0.000	0.000
60	A	293	PHE	0	0.047	0.008	9.220	-0.123	-0.123	0.000	0.000	0.000	0.000
61	A	294	ILE	0	0.004	0.000	10.715	0.127	0.127	0.000	0.000	0.000	0.000
62	A	295	ILE	0	-0.007	-0.003	12.694	-0.082	-0.082	0.000	0.000	0.000	0.000
63	A	296	VAL	0	0.025	0.005	15.169	0.055	0.055	0.000	0.000	0.000	0.000
64	A	297	ASP	-1	-0.800	-0.888	17.775	-0.192	-0.192	0.000	0.000	0.000	0.000
65	A	298	ASN	0	-0.070	-0.055	19.384	0.026	0.026	0.000	0.000	0.000	0.000
66	A	299	THR	0	0.040	-0.008	17.446	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	300	ARG	1	0.873	0.936	18.273	0.129	0.129	0.000	0.000	0.000	0.000
68	A	301	MET	0	0.011	0.017	12.435	0.009	0.009	0.000	0.000	0.000	0.000
69	A	302	PHE	0	-0.035	-0.009	11.820	0.038	0.038	0.000	0.000	0.000	0.000
70	A	303	THR	0	-0.017	-0.018	15.472	0.009	0.009	0.000	0.000	0.000	0.000
71	A	304	LYS	1	0.909	0.933	12.822	-0.356	-0.356	0.000	0.000	0.000	0.000
72	A	305	PRO	0	0.084	0.034	13.158	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	306	GLU	-1	-0.803	-0.881	8.532	0.576	0.576	0.000	0.000	0.000	0.000
74	A	307	TYR	0	-0.053	-0.024	7.926	0.017	0.017	0.000	0.000	0.000	0.000
75	A	308	TRP	0	0.043	0.023	9.273	-0.150	-0.150	0.000	0.000	0.000	0.000
76	A	309	ASP	-1	-0.848	-0.916	6.312	-0.673	-0.673	0.000	0.000	0.000	0.000
77	A	310	ARG	1	0.810	0.906	4.507	-0.704	-0.532	-0.001	-0.009	-0.162	0.000
78	A	311	VAL	0	-0.012	0.002	6.005	-0.140	-0.140	0.000	0.000	0.000	0.000
79	A	312	VAL	0	-0.002	-0.002	5.947	-0.237	-0.237	0.000	0.000	0.000	0.000
80	A	313	ALA	0	0.003	0.005	9.095	0.046	0.046	0.000	0.000	0.000	0.000
81	A	314	ILE	0	0.005	0.010	12.783	0.077	0.077	0.000	0.000	0.000	0.000
82	A	315	PHE	0	0.014	0.009	15.992	0.016	0.016	0.000	0.000	0.000	0.000
83	A	316	THR	0	-0.050	-0.033	19.190	0.034	0.034	0.000	0.000	0.000	0.000
84	A	317	THR	0	-0.002	-0.016	22.129	0.016	0.016	0.000	0.000	0.000	0.000
85	A	318	GLY	0	0.009	0.011	25.216	0.015	0.015	0.000	0.000	0.000	0.000
86	A	319	HIS	0	0.005	0.008	26.823	0.011	0.011	0.000	0.000	0.000	0.000
87	A	320	THR	0	0.042	-0.002	25.441	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	321	TRP	0	0.034	0.018	25.105	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	322	GLN	0	-0.010	0.003	20.018	0.024	0.024	0.000	0.000	0.000	0.000
90	A	323	PHE	0	0.017	-0.001	19.627	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	324	ASN	0	-0.017	0.005	21.122	0.005	0.005	0.000	0.000	0.000	0.000
92	A	325	ASN	0	0.030	0.013	20.912	0.000	0.000	0.000	0.000	0.000	0.000
93	A	326	TYR	0	0.021	-0.001	16.949	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	327	GLN	0	-0.034	-0.012	13.969	0.050	0.050	0.000	0.000	0.000	0.000
95	A	328	TRP	0	0.055	0.016	9.851	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	329	ASN	0	-0.050	-0.005	17.105	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	330	SER	0	0.018	0.005	19.705	0.017	0.017	0.000	0.000	0.000	0.000
98	A	331	PRO	0	0.004	-0.016	19.447	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	332	GLN	0	-0.018	0.006	19.250	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	333	GLU	-1	-0.789	-0.893	15.066	-0.413	-0.413	0.000	0.000	0.000	0.000
101	A	334	LEU	0	-0.025	-0.002	14.385	-0.077	-0.077	0.000	0.000	0.000	0.000
102	A	335	PHE	0	-0.009	-0.020	14.165	-0.075	-0.075	0.000	0.000	0.000	0.000
103	A	336	GLN	0	-0.006	0.005	15.166	0.009	0.009	0.000	0.000	0.000	0.000
104	A	337	ARG	1	0.827	0.922	9.884	0.527	0.527	0.000	0.000	0.000	0.000
105	A	338	CYS	0	-0.075	-0.031	9.559	-0.198	-0.198	0.000	0.000	0.000	0.000
106	A	339	LYS	1	0.878	0.948	11.161	0.922	0.922	0.000	0.000	0.000	0.000
107	A	340	GLY	0	0.035	0.017	13.227	0.033	0.033	0.000	0.000	0.000	0.000
108	A	341	TYR	0	-0.016	-0.025	14.493	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	342	TYR	0	-0.003	0.005	19.324	0.028	0.028	0.000	0.000	0.000	0.000
110	A	343	PHE	0	0.031	0.012	20.056	0.001	0.001	0.000	0.000	0.000	0.000
111	A	344	HIS	0	-0.024	-0.016	24.919	0.001	0.001	0.000	0.000	0.000	0.000
112	A	345	PHE	0	-0.006	-0.022	28.735	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	346	ALA	0	0.038	0.018	31.695	0.002	0.002	0.000	0.000	0.000	0.000
114	A	347	GLY	0	-0.020	-0.008	33.631	0.010	0.010	0.000	0.000	0.000	0.000
115	A	348	ASP	-1	-0.852	-0.905	33.189	-0.148	-0.148	0.000	0.000	0.000	0.000
116	A	349	SER	0	0.001	-0.008	32.734	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	350	VAL	0	-0.008	0.008	28.120	0.001	0.001	0.000	0.000	0.000	0.000
118	A	351	PRO	0	0.014	0.012	29.597	0.009	0.009	0.000	0.000	0.000	0.000
119	A	352	GLN	0	0.059	0.028	30.054	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	353	HIS	0	0.004	-0.009	27.737	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	354	VAL	0	0.020	0.010	25.019	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	355	GLN	0	-0.005	-0.024	25.512	-0.040	-0.040	0.000	0.000	0.000	0.000
123	A	356	GLN	0	-0.019	-0.017	26.563	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	357	TRP	0	0.008	0.010	22.016	-0.018	-0.018	0.000	0.000	0.000	0.000
125	A	358	ASN	0	-0.015	-0.006	17.259	0.034	0.034	0.000	0.000	0.000	0.000
126	A	359	VAL	0	-0.049	-0.017	18.638	-0.054	-0.054	0.000	0.000	0.000	0.000
127	A	360	GLU	-1	-0.731	-0.827	18.264	-0.551	-0.551	0.000	0.000	0.000	0.000
128	A	361	LYS	1	0.827	0.940	20.576	0.324	0.324	0.000	0.000	0.000	0.000
129	A	362	VAL	0	-0.029	-0.015	21.542	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	363	GLU	-1	-0.846	-0.914	24.823	-0.197	-0.197	0.000	0.000	0.000	0.000
131	A	364	LEU	0	-0.032	-0.020	26.061	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	365	ASP	-1	-0.805	-0.880	29.760	-0.159	-0.159	0.000	0.000	0.000	0.000
133	A	366	LYS	1	0.849	0.917	33.101	0.144	0.144	0.000	0.000	0.000	0.000
134	A	367	ASN	0	0.017	0.002	35.220	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	368	LYS	1	0.902	0.946	35.753	0.125	0.125	0.000	0.000	0.000	0.000
136	A	369	ARG	1	0.838	0.878	30.601	0.173	0.173	0.000	0.000	0.000	0.000
137	A	370	PHE	0	0.023	0.013	31.584	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	371	LYS	1	0.894	0.930	30.044	0.171	0.171	0.000	0.000	0.000	0.000
139	A	372	ASP	-1	-0.728	-0.829	27.476	-0.219	-0.219	0.000	0.000	0.000	0.000
140	A	373	VAL	0	0.032	0.005	25.872	-0.022	-0.022	0.000	0.000	0.000	0.000
141	A	374	GLU	-1	-0.851	-0.895	25.075	-0.301	-0.301	0.000	0.000	0.000	0.000
142	A	375	VAL	0	0.017	0.005	23.708	-0.028	-0.028	0.000	0.000	0.000	0.000
143	A	376	VAL	0	-0.011	0.001	20.881	-0.042	-0.042	0.000	0.000	0.000	0.000
144	A	377	ARG	1	0.863	0.921	20.211	0.224	0.224	0.000	0.000	0.000	0.000
145	A	378	TYR	0	-0.022	-0.027	19.344	-0.046	-0.046	0.000	0.000	0.000	0.000
146	A	379	PHE	0	0.015	0.002	15.841	-0.063	-0.063	0.000	0.000	0.000	0.000
147	A	380	TRP	0	-0.019	-0.038	13.195	-0.105	-0.105	0.000	0.000	0.000	0.000
148	A	381	HIS	0	0.047	0.031	14.556	-0.085	-0.085	0.000	0.000	0.000	0.000
149	A	382	SER	0	-0.062	-0.061	14.751	-0.110	-0.110	0.000	0.000	0.000	0.000
150	A	383	LEU	0	0.011	0.005	10.507	-0.101	-0.101	0.000	0.000	0.000	0.000
151	A	384	GLU	-1	-0.820	-0.932	10.224	-0.972	-0.972	0.000	0.000	0.000	0.000
152	A	385	LYS	1	0.887	0.939	9.889	0.426	0.426	0.000	0.000	0.000	0.000
153	A	386	GLU	-1	-0.806	-0.885	8.106	-1.764	-1.764	0.000	0.000	0.000	0.000
154	A	387	LEU	0	-0.028	-0.012	5.828	-0.494	-0.494	0.000	0.000	0.000	0.000
155	A	388	ILE	0	0.009	0.001	4.919	-1.363	-1.286	-0.001	-0.001	-0.074	0.000
156	A	389	SER	0	-0.077	-0.033	6.607	-0.216	-0.216	0.000	0.000	0.000	0.000
157	A	390	ARG	1	0.813	0.889	3.993	2.168	2.404	0.001	-0.045	-0.192	0.000
158	A	391	GLY	0	0.024	0.012	2.341	-5.986	-3.473	1.835	-1.808	-2.540	-0.018
159	A	392	TYR	0	-0.085	-0.049	2.575	-5.597	-1.762	4.320	-2.561	-5.594	-0.027
160	A	393	ARG	1	0.984	0.993	3.858	0.602	0.971	0.003	-0.029	-0.343	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:234:PRO)