FMO DATABASE

FMODB ID: 52K2Z

Calculation Name: 2VT1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VT1

Chain ID: B

ChEMBL ID:

UniProt ID: P0A1M8

Base Structure: X-ray

Registration Date: 2023-09-20

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533198.267227
FMO2-HF: Nuclear repulsion	501297.136409
FMO2-HF: Total energy	-31901.130817
FMO2-MP2: Total energy	-31996.527081

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(B:258:PRO)

Summations of interaction energy for fragment #1(B:258: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.
-8.609	-1.549	1.169	-2.694	-5.537	-0.003

Interaction energy analysis for fragmet #1(B:258:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.008

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

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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	B	260	HIS	0	-0.011	0.008	3.756	-3.078	-0.932	0.002	-1.025	-1.123	0.005
4	B	261	ILE	0	0.041	0.031	2.935	1.020	1.998	0.138	-0.229	-0.888	0.000
5	B	262	ALA	0	-0.049	-0.026	5.171	-0.257	-0.217	-0.001	-0.003	-0.036	0.000
6	B	263	ILE	0	0.041	0.014	7.287	-0.052	-0.052	0.000	0.000	0.000	0.000
7	B	264	GLY	0	-0.027	0.009	10.646	0.014	0.014	0.000	0.000	0.000	0.000
8	B	265	ILE	0	-0.002	-0.016	14.191	-0.030	-0.030	0.000	0.000	0.000	0.000
9	B	266	TYR	0	0.013	0.010	16.936	0.010	0.010	0.000	0.000	0.000	0.000
10	B	267	PHE	0	0.018	-0.022	20.486	-0.008	-0.008	0.000	0.000	0.000	0.000
11	B	268	ASN	0	0.038	0.014	23.437	0.004	0.004	0.000	0.000	0.000	0.000
12	B	269	PRO	0	0.033	0.022	27.000	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	270	GLU	-1	-0.917	-0.951	29.104	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	271	ILE	0	-0.104	-0.036	27.353	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	272	ALA	0	0.000	-0.018	25.761	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	273	PRO	0	0.011	0.018	26.683	0.003	0.003	0.000	0.000	0.000	0.000
17	B	274	ALA	0	0.018	0.011	21.623	0.001	0.001	0.000	0.000	0.000	0.000
18	B	275	PRO	0	0.004	0.000	18.837	0.004	0.004	0.000	0.000	0.000	0.000
19	B	276	PHE	0	-0.002	0.011	19.083	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	277	ILE	0	0.018	0.011	12.543	0.017	0.017	0.000	0.000	0.000	0.000
21	B	278	SER	0	0.009	-0.002	15.721	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	279	LEU	0	-0.043	-0.023	11.172	0.011	0.011	0.000	0.000	0.000	0.000
23	B	280	ILE	0	0.031	0.007	7.228	-0.016	-0.016	0.000	0.000	0.000	0.000
24	B	281	GLU	-1	-0.921	-0.942	7.934	0.226	0.226	0.000	0.000	0.000	0.000
25	B	282	THR	0	-0.018	-0.033	2.794	-1.523	-0.255	0.309	-0.402	-1.176	0.002
26	B	283	ASN	0	-0.032	-0.050	3.079	-0.353	0.354	0.046	-0.280	-0.474	-0.001
27	B	284	GLN	0	0.079	0.020	5.808	-0.413	-0.413	0.000	0.000	0.000	0.000
28	B	285	CYS	0	0.061	0.031	8.659	-0.118	-0.118	0.000	0.000	0.000	0.000
29	B	286	ALA	0	0.017	0.018	7.009	-0.130	-0.130	0.000	0.000	0.000	0.000
30	B	287	LEU	0	-0.048	-0.024	9.081	-0.165	-0.165	0.000	0.000	0.000	0.000
31	B	288	ALA	0	0.006	0.014	11.550	-0.101	-0.101	0.000	0.000	0.000	0.000
32	B	289	VAL	0	0.018	0.005	11.761	-0.060	-0.060	0.000	0.000	0.000	0.000
33	B	290	ARG	1	0.854	0.930	7.937	-0.713	-0.713	0.000	0.000	0.000	0.000
34	B	291	LYS	1	0.974	0.995	14.298	-0.239	-0.239	0.000	0.000	0.000	0.000
35	B	292	TYR	0	0.053	0.035	17.060	-0.028	-0.028	0.000	0.000	0.000	0.000
36	B	293	ALA	0	0.017	0.003	16.705	-0.022	-0.022	0.000	0.000	0.000	0.000
37	B	294	ASN	0	-0.051	-0.029	18.472	-0.020	-0.020	0.000	0.000	0.000	0.000
38	B	295	GLU	-1	-0.934	-0.969	20.336	0.137	0.137	0.000	0.000	0.000	0.000
39	B	296	VAL	0	-0.075	-0.026	21.403	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	297	GLY	0	-0.004	0.006	23.221	-0.010	-0.010	0.000	0.000	0.000	0.000
41	B	298	ILE	0	-0.035	-0.011	18.601	-0.010	-0.010	0.000	0.000	0.000	0.000
42	B	299	PRO	0	0.029	0.010	19.671	0.017	0.017	0.000	0.000	0.000	0.000
43	B	300	THR	0	-0.047	-0.018	15.151	0.015	0.015	0.000	0.000	0.000	0.000
44	B	301	VAL	0	0.056	0.024	15.601	0.001	0.001	0.000	0.000	0.000	0.000
45	B	302	ARG	1	0.881	0.940	9.698	-0.189	-0.189	0.000	0.000	0.000	0.000
46	B	303	ASP	-1	-0.727	-0.874	12.425	-0.036	-0.036	0.000	0.000	0.000	0.000
47	B	304	VAL	0	-0.043	-0.028	8.421	-0.014	-0.014	0.000	0.000	0.000	0.000
48	B	305	LYS	1	0.947	0.970	8.939	0.058	0.058	0.000	0.000	0.000	0.000
49	B	306	LEU	0	0.100	0.064	10.661	-0.049	-0.049	0.000	0.000	0.000	0.000
50	B	307	ALA	0	-0.012	-0.008	7.499	-0.027	-0.027	0.000	0.000	0.000	0.000
51	B	308	ARG	1	0.949	0.959	4.961	0.171	0.171	0.000	0.000	0.000	0.000
52	B	309	LYS	1	0.914	0.966	7.043	0.012	0.012	0.000	0.000	0.000	0.000
53	B	310	LEU	0	0.052	0.044	9.912	-0.037	-0.037	0.000	0.000	0.000	0.000
54	B	311	TYR	0	-0.019	-0.012	2.816	-3.116	-1.195	0.675	-0.755	-1.840	-0.009
55	B	312	LYS	1	0.851	0.919	5.290	0.698	0.698	0.000	0.000	0.000	0.000
56	B	313	THR	0	0.005	-0.003	8.259	0.046	0.046	0.000	0.000	0.000	0.000
57	B	314	HIS	0	0.017	0.032	10.659	0.065	0.065	0.000	0.000	0.000	0.000
58	B	315	THR	0	0.016	0.013	10.473	-0.061	-0.061	0.000	0.000	0.000	0.000
59	B	316	LYS	1	0.908	0.966	12.363	0.032	0.032	0.000	0.000	0.000	0.000
60	B	317	TYR	0	-0.022	-0.029	13.694	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	318	SER	0	-0.003	-0.001	15.370	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	319	PHE	0	0.008	-0.003	17.520	0.006	0.006	0.000	0.000	0.000	0.000
63	B	320	VAL	0	-0.040	-0.012	15.955	-0.013	-0.013	0.000	0.000	0.000	0.000
64	B	321	ASP	-1	-0.780	-0.888	17.183	-0.123	-0.123	0.000	0.000	0.000	0.000
65	B	322	PHE	0	0.020	-0.017	19.542	0.004	0.004	0.000	0.000	0.000	0.000
66	B	323	GLU	-1	-0.963	-0.956	18.991	-0.104	-0.104	0.000	0.000	0.000	0.000
67	B	324	HIS	0	-0.088	-0.075	15.609	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	325	LEU	0	-0.021	0.000	18.196	0.008	0.008	0.000	0.000	0.000	0.000
69	B	326	ASP	-1	-0.820	-0.926	20.590	-0.024	-0.024	0.000	0.000	0.000	0.000
70	B	327	GLU	-1	-0.928	-0.957	15.806	-0.076	-0.076	0.000	0.000	0.000	0.000
71	B	328	VAL	0	-0.011	-0.007	15.564	0.010	0.010	0.000	0.000	0.000	0.000
72	B	329	LEU	0	0.028	0.015	18.177	0.013	0.013	0.000	0.000	0.000	0.000
73	B	330	ARG	1	0.862	0.915	17.015	0.020	0.020	0.000	0.000	0.000	0.000
74	B	331	LEU	0	-0.071	-0.035	16.028	0.008	0.008	0.000	0.000	0.000	0.000
75	B	332	ILE	0	0.000	-0.001	20.479	0.007	0.007	0.000	0.000	0.000	0.000
76	B	333	VAL	0	0.046	0.023	22.693	0.003	0.003	0.000	0.000	0.000	0.000
77	B	334	TRP	0	-0.032	-0.007	22.786	0.001	0.001	0.000	0.000	0.000	0.000
78	B	335	LEU	0	-0.047	-0.041	20.536	0.004	0.004	0.000	0.000	0.000	0.000
79	B	336	GLU	-1	-0.989	-0.979	24.910	0.017	0.017	0.000	0.000	0.000	0.000
80	B	337	GLN	0	-0.020	-0.008	28.082	0.001	0.001	0.000	0.000	0.000	0.000
81	B	338	VAL	0	-0.072	-0.015	27.704	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:258:PRO)