FMO DATABASE

FMODB ID: 98NJ2

Calculation Name: 2VSV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VSV

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IUC4

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-673171.289104
FMO2-HF: Nuclear repulsion	634979.702243
FMO2-HF: Total energy	-38191.586861
FMO2-MP2: Total energy	-38300.873156

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:-15:SER)

Summations of interaction energy for fragment #1(A:-15:SER)

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.
-0.388	3.005	0.532	-1.588	-2.339	0.01

Interaction energy analysis for fragmet #1(A:-15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.006

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	-13	GLY	0	0.071	0.026	3.800	0.172	2.460	-0.017	-1.143	-1.129	0.005
4	A	-12	VAL	0	0.001	-0.002	6.021	0.475	0.475	0.000	0.000	0.000	0.000
5	A	-11	ASP	-1	-0.887	-0.931	4.517	-0.572	-0.406	-0.001	-0.007	-0.158	0.000
6	A	-10	LEU	0	0.017	0.006	2.737	-1.254	-0.315	0.550	-0.438	-1.052	0.005
7	A	-9	GLY	0	-0.005	0.005	6.478	-0.213	-0.213	0.000	0.000	0.000	0.000
8	A	-8	THR	0	-0.059	-0.063	9.545	-0.047	-0.047	0.000	0.000	0.000	0.000
9	A	-7	GLU	-1	-0.915	-0.947	8.252	1.046	1.046	0.000	0.000	0.000	0.000
10	A	-6	ASN	0	-0.008	-0.018	9.361	0.000	0.000	0.000	0.000	0.000	0.000
11	A	-5	LEU	0	-0.016	-0.004	12.219	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	-4	TYR	0	0.022	0.011	14.233	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	-3	PHE	0	-0.019	-0.011	11.400	-0.057	-0.057	0.000	0.000	0.000	0.000
14	A	-2	GLN	0	-0.002	0.004	16.033	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	-1	SER	0	-0.038	-0.030	18.461	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	0	MET	0	-0.062	-0.019	19.159	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	514	PRO	0	-0.064	-0.040	21.300	0.008	0.008	0.000	0.000	0.000	0.000
18	A	515	ARG	1	0.853	0.923	21.256	-0.178	-0.178	0.000	0.000	0.000	0.000
19	A	516	SER	0	-0.103	-0.072	24.183	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	517	ILE	0	0.013	0.014	25.343	0.012	0.012	0.000	0.000	0.000	0.000
21	A	518	ARG	1	0.895	0.934	28.608	-0.129	-0.129	0.000	0.000	0.000	0.000
22	A	519	PHE	0	0.010	-0.007	31.378	0.007	0.007	0.000	0.000	0.000	0.000
23	A	520	THR	0	0.041	0.026	33.660	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	521	ALA	0	0.018	0.020	36.707	0.003	0.003	0.000	0.000	0.000	0.000
25	A	522	GLU	-1	-0.808	-0.906	36.473	0.086	0.086	0.000	0.000	0.000	0.000
26	A	523	GLU	-1	-0.938	-0.966	40.476	0.059	0.059	0.000	0.000	0.000	0.000
27	A	524	GLY	0	-0.059	-0.028	43.139	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	525	ASP	-1	-0.972	-0.989	40.642	0.059	0.059	0.000	0.000	0.000	0.000
29	A	526	LEU	0	-0.041	-0.023	36.512	0.004	0.004	0.000	0.000	0.000	0.000
30	A	527	GLY	0	0.077	0.042	36.025	0.006	0.006	0.000	0.000	0.000	0.000
31	A	528	PHE	0	-0.010	-0.021	33.276	0.003	0.003	0.000	0.000	0.000	0.000
32	A	529	THR	0	-0.031	-0.005	35.371	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	530	LEU	0	0.018	0.013	34.686	0.003	0.003	0.000	0.000	0.000	0.000
34	A	531	ARG	1	0.898	0.943	31.529	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	532	GLY	0	0.018	0.012	35.367	0.002	0.002	0.000	0.000	0.000	0.000
36	A	533	ASN	0	-0.025	-0.033	36.906	0.003	0.003	0.000	0.000	0.000	0.000
37	A	534	ALA	0	-0.019	0.038	36.409	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	535	PRO	0	0.021	0.014	30.963	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	536	VAL	0	-0.031	-0.014	33.962	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	537	GLN	0	-0.045	-0.032	28.331	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	538	VAL	0	0.046	0.023	29.635	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	539	HIS	0	-0.056	-0.035	30.631	0.001	0.001	0.000	0.000	0.000	0.000
43	A	540	PHE	0	-0.019	-0.009	31.532	0.003	0.003	0.000	0.000	0.000	0.000
44	A	541	LEU	0	0.014	0.003	28.199	0.001	0.001	0.000	0.000	0.000	0.000
45	A	542	ASP	-1	-0.839	-0.915	31.793	0.080	0.080	0.000	0.000	0.000	0.000
46	A	543	PRO	0	-0.026	-0.021	29.372	0.006	0.006	0.000	0.000	0.000	0.000
47	A	544	TYR	0	-0.035	-0.032	30.280	0.010	0.010	0.000	0.000	0.000	0.000
48	A	545	CYS	0	-0.042	0.029	32.637	0.002	0.002	0.000	0.000	0.000	0.000
49	A	546	SER	0	0.064	0.005	31.732	0.010	0.010	0.000	0.000	0.000	0.000
50	A	547	ALA	0	0.015	0.003	30.797	0.009	0.009	0.000	0.000	0.000	0.000
51	A	548	SER	0	-0.004	-0.004	28.198	0.014	0.014	0.000	0.000	0.000	0.000
52	A	549	VAL	0	-0.033	-0.006	26.796	0.017	0.017	0.000	0.000	0.000	0.000
53	A	550	ALA	0	-0.022	-0.003	26.563	0.015	0.015	0.000	0.000	0.000	0.000
54	A	551	GLY	0	-0.064	-0.038	23.949	0.013	0.013	0.000	0.000	0.000	0.000
55	A	552	ALA	0	-0.014	0.004	24.099	0.005	0.005	0.000	0.000	0.000	0.000
56	A	553	ARG	1	0.861	0.915	22.139	-0.169	-0.169	0.000	0.000	0.000	0.000
57	A	554	GLU	-1	-0.855	-0.924	25.858	0.098	0.098	0.000	0.000	0.000	0.000
58	A	555	GLY	0	-0.079	-0.044	25.999	0.004	0.004	0.000	0.000	0.000	0.000
59	A	556	ASP	-1	-0.742	-0.852	24.454	0.138	0.138	0.000	0.000	0.000	0.000
60	A	557	TYR	0	-0.020	-0.023	26.130	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	558	ILE	0	0.034	0.012	28.524	0.009	0.009	0.000	0.000	0.000	0.000
62	A	559	VAL	0	-0.055	-0.039	28.105	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	560	SER	0	0.006	-0.006	31.231	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	561	ILE	0	0.056	0.041	32.735	0.006	0.006	0.000	0.000	0.000	0.000
65	A	562	GLN	0	0.029	0.014	34.581	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	563	LEU	0	-0.083	-0.042	34.198	0.002	0.002	0.000	0.000	0.000	0.000
67	A	564	VAL	0	-0.010	0.008	36.351	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	565	ASP	-1	-0.851	-0.942	34.626	0.058	0.058	0.000	0.000	0.000	0.000
69	A	566	CYS	0	-0.020	-0.023	34.415	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	567	LYS	1	0.910	0.956	29.213	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	568	TRP	0	-0.025	-0.014	34.508	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	569	LEU	0	-0.010	0.032	37.750	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	570	THR	0	-0.014	-0.032	38.639	0.000	0.000	0.000	0.000	0.000	0.000
74	A	571	LEU	0	0.050	0.010	38.298	0.003	0.003	0.000	0.000	0.000	0.000
75	A	572	SER	0	-0.057	-0.026	40.285	0.003	0.003	0.000	0.000	0.000	0.000
76	A	573	GLU	-1	-0.846	-0.933	42.034	0.035	0.035	0.000	0.000	0.000	0.000
77	A	574	VAL	0	0.034	0.029	36.401	0.002	0.002	0.000	0.000	0.000	0.000
78	A	575	MET	0	0.008	0.006	39.739	0.001	0.001	0.000	0.000	0.000	0.000
79	A	576	LYS	1	0.892	0.947	41.485	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	577	LEU	0	0.041	0.017	39.668	0.000	0.000	0.000	0.000	0.000	0.000
81	A	578	LEU	0	0.033	0.022	36.155	0.001	0.001	0.000	0.000	0.000	0.000
82	A	579	LYS	1	0.933	0.964	40.314	-0.044	-0.044	0.000	0.000	0.000	0.000
83	A	580	SER	0	-0.129	-0.073	43.003	0.000	0.000	0.000	0.000	0.000	0.000
84	A	581	PHE	0	0.043	0.027	39.137	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	582	GLY	0	-0.041	-0.004	42.897	0.000	0.000	0.000	0.000	0.000	0.000
86	A	583	GLU	-1	-0.946	-0.980	42.392	0.060	0.060	0.000	0.000	0.000	0.000
87	A	584	ASP	-1	-0.960	-0.968	41.857	0.065	0.065	0.000	0.000	0.000	0.000
88	A	585	GLU	-1	-0.955	-0.994	34.769	0.106	0.106	0.000	0.000	0.000	0.000
89	A	586	ILE	0	0.000	0.012	35.254	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	587	GLU	-1	-0.826	-0.877	30.535	0.117	0.117	0.000	0.000	0.000	0.000
91	A	588	MET	0	0.002	0.004	30.338	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	589	LYS	1	0.807	0.891	27.694	-0.101	-0.101	0.000	0.000	0.000	0.000
93	A	590	VAL	0	0.030	0.012	25.140	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	591	VAL	0	-0.002	0.009	23.737	0.013	0.013	0.000	0.000	0.000	0.000
95	A	592	SER	0	0.012	0.000	20.715	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	593	LEU	0	-0.065	-0.024	18.545	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	594	LEU	0	-0.008	0.006	22.791	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-15:SER)