FMO DATABASE

FMODB ID: 763LK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-674512.513165
FMO2-HF: Nuclear repulsion	636320.323707
FMO2-HF: Total energy	-38192.189459
FMO2-MP2: Total energy	-38301.441548

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.
-2.005	0.412	1.032	-1.301	-2.148	0.003

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 : -0.001 / q_NPA : -0.010

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	0.061	0.019	3.870	-1.442	-0.021	-0.005	-0.628	-0.788	0.002
4	A	-12	VAL	0	-0.007	0.000	5.465	1.010	1.010	0.000	0.000	0.000	0.000
5	A	-11	ASP	-1	-0.837	-0.880	4.939	-1.554	-1.554	0.000	0.000	0.000	0.000
6	A	-10	LEU	0	0.050	0.026	2.453	-0.928	0.068	1.037	-0.673	-1.360	0.001
7	A	-9	GLY	0	0.003	0.018	6.106	0.558	0.558	0.000	0.000	0.000	0.000
8	A	-8	THR	0	-0.064	-0.057	9.431	0.339	0.339	0.000	0.000	0.000	0.000
9	A	-7	GLU	-1	-0.917	-0.950	7.679	-0.575	-0.575	0.000	0.000	0.000	0.000
10	A	-6	ASN	0	-0.032	-0.033	8.916	0.288	0.288	0.000	0.000	0.000	0.000
11	A	-5	LEU	0	-0.014	-0.002	11.909	0.108	0.108	0.000	0.000	0.000	0.000
12	A	-4	TYR	0	-0.004	0.003	13.867	0.095	0.095	0.000	0.000	0.000	0.000
13	A	-3	PHE	0	-0.001	-0.020	11.095	0.056	0.056	0.000	0.000	0.000	0.000
14	A	-2	GLN	0	0.005	0.010	15.865	0.064	0.064	0.000	0.000	0.000	0.000
15	A	-1	SER	0	-0.050	-0.041	18.039	0.034	0.034	0.000	0.000	0.000	0.000
16	A	0	MET	0	-0.038	-0.011	18.661	0.027	0.027	0.000	0.000	0.000	0.000
17	A	514	PRO	0	-0.056	-0.036	20.858	0.007	0.007	0.000	0.000	0.000	0.000
18	A	515	ARG	1	0.827	0.914	20.857	0.173	0.173	0.000	0.000	0.000	0.000
19	A	516	SER	0	-0.084	-0.077	23.527	0.007	0.007	0.000	0.000	0.000	0.000
20	A	517	ILE	0	-0.006	0.002	25.064	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	518	ARG	1	0.853	0.905	28.159	0.056	0.056	0.000	0.000	0.000	0.000
22	A	519	PHE	0	0.010	-0.015	30.780	0.000	0.000	0.000	0.000	0.000	0.000
23	A	520	THR	0	-0.003	-0.011	33.264	0.002	0.002	0.000	0.000	0.000	0.000
24	A	521	ALA	0	0.004	0.003	36.598	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	522	GLU	-1	-0.738	-0.827	36.366	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	523	GLU	-1	-0.949	-0.966	40.427	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	524	GLY	0	-0.048	-0.019	43.072	0.001	0.001	0.000	0.000	0.000	0.000
28	A	525	ASP	-1	-0.972	-0.983	40.209	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	526	LEU	0	-0.032	-0.015	36.519	0.000	0.000	0.000	0.000	0.000	0.000
30	A	527	GLY	0	0.035	0.014	35.910	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	528	PHE	0	-0.019	-0.023	33.269	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	529	THR	0	-0.025	-0.010	35.151	0.001	0.001	0.000	0.000	0.000	0.000
33	A	530	LEU	0	0.015	0.009	34.555	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	531	ARG	1	0.869	0.920	30.599	0.123	0.123	0.000	0.000	0.000	0.000
35	A	532	GLY	0	0.023	0.014	35.125	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	533	ASN	0	-0.026	-0.034	36.394	0.009	0.009	0.000	0.000	0.000	0.000
37	A	534	ALA	0	-0.024	0.023	36.063	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	535	PRO	0	0.034	0.027	30.421	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	536	VAL	0	-0.052	-0.017	33.598	0.000	0.000	0.000	0.000	0.000	0.000
40	A	537	GLN	0	-0.011	0.004	28.310	0.004	0.004	0.000	0.000	0.000	0.000
41	A	538	VAL	0	0.044	0.024	29.538	0.009	0.009	0.000	0.000	0.000	0.000
42	A	539	HIS	0	-0.054	-0.037	30.694	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	540	PHE	0	-0.012	-0.005	31.460	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	541	LEU	0	0.002	-0.006	28.344	0.000	0.000	0.000	0.000	0.000	0.000
45	A	542	ASP	-1	-0.800	-0.895	32.029	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	543	PRO	0	-0.007	-0.005	29.677	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	544	TYR	0	-0.056	-0.026	30.033	0.003	0.003	0.000	0.000	0.000	0.000
48	A	545	CYS	0	-0.050	0.012	32.717	0.001	0.001	0.000	0.000	0.000	0.000
49	A	546	SER	0	0.035	-0.025	31.828	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	547	ALA	0	0.021	0.007	30.679	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	548	SER	0	-0.041	-0.027	28.269	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	549	VAL	0	-0.038	-0.010	26.829	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	550	ALA	0	-0.016	-0.002	26.331	0.000	0.000	0.000	0.000	0.000	0.000
54	A	551	GLY	0	-0.021	0.000	23.902	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	552	ALA	0	-0.005	0.006	24.129	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	553	ARG	1	0.834	0.883	22.942	0.106	0.106	0.000	0.000	0.000	0.000
57	A	554	GLU	-1	-0.866	-0.936	26.205	-0.115	-0.115	0.000	0.000	0.000	0.000
58	A	555	GLY	0	-0.036	-0.016	26.129	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	556	ASP	-1	-0.767	-0.850	24.428	-0.165	-0.165	0.000	0.000	0.000	0.000
60	A	557	TYR	0	-0.028	-0.024	26.095	0.012	0.012	0.000	0.000	0.000	0.000
61	A	558	ILE	0	0.050	0.014	28.067	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	559	VAL	0	-0.041	-0.036	27.530	0.002	0.002	0.000	0.000	0.000	0.000
63	A	560	SER	0	-0.073	-0.052	30.663	0.001	0.001	0.000	0.000	0.000	0.000
64	A	561	ILE	0	0.078	0.039	32.388	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	562	GLN	0	0.023	0.009	34.296	0.005	0.005	0.000	0.000	0.000	0.000
66	A	563	LEU	0	-0.057	-0.023	33.670	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	564	VAL	0	-0.004	0.013	35.918	0.000	0.000	0.000	0.000	0.000	0.000
68	A	565	ASP	-1	-0.799	-0.887	34.299	-0.106	-0.106	0.000	0.000	0.000	0.000
69	A	566	CYS	0	-0.023	-0.012	33.725	0.006	0.006	0.000	0.000	0.000	0.000
70	A	567	LYS	1	0.842	0.894	29.886	0.113	0.113	0.000	0.000	0.000	0.000
71	A	568	TRP	0	-0.028	-0.009	33.964	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	569	LEU	0	-0.010	0.023	37.358	0.005	0.005	0.000	0.000	0.000	0.000
73	A	570	THR	0	-0.017	-0.060	38.341	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	571	LEU	0	0.029	0.002	38.402	0.001	0.001	0.000	0.000	0.000	0.000
75	A	572	SER	0	-0.023	-0.008	40.068	0.003	0.003	0.000	0.000	0.000	0.000
76	A	573	GLU	-1	-0.836	-0.889	41.617	-0.064	-0.064	0.000	0.000	0.000	0.000
77	A	574	VAL	0	0.063	0.030	35.769	0.002	0.002	0.000	0.000	0.000	0.000
78	A	575	MET	0	0.014	0.012	39.072	0.003	0.003	0.000	0.000	0.000	0.000
79	A	576	LYS	1	0.876	0.930	40.925	0.056	0.056	0.000	0.000	0.000	0.000
80	A	577	LEU	0	0.009	0.006	38.886	0.003	0.003	0.000	0.000	0.000	0.000
81	A	578	LEU	0	0.034	0.029	35.427	0.002	0.002	0.000	0.000	0.000	0.000
82	A	579	LYS	1	0.951	0.975	39.544	0.045	0.045	0.000	0.000	0.000	0.000
83	A	580	SER	0	-0.109	-0.071	42.290	0.003	0.003	0.000	0.000	0.000	0.000
84	A	581	PHE	0	0.026	0.017	38.044	0.001	0.001	0.000	0.000	0.000	0.000
85	A	582	GLY	0	-0.028	-0.008	42.571	0.002	0.002	0.000	0.000	0.000	0.000
86	A	583	GLU	-1	-0.909	-0.960	41.883	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	584	ASP	-1	-0.962	-0.970	41.008	-0.032	-0.032	0.000	0.000	0.000	0.000
88	A	585	GLU	-1	-0.885	-0.940	34.064	-0.050	-0.050	0.000	0.000	0.000	0.000
89	A	586	ILE	0	-0.014	0.005	35.210	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	587	GLU	-1	-0.835	-0.874	30.223	-0.085	-0.085	0.000	0.000	0.000	0.000
91	A	588	MET	0	-0.020	-0.008	29.848	0.001	0.001	0.000	0.000	0.000	0.000
92	A	589	LYS	1	0.821	0.904	27.670	0.086	0.086	0.000	0.000	0.000	0.000
93	A	590	VAL	0	0.012	0.006	24.676	0.002	0.002	0.000	0.000	0.000	0.000
94	A	591	VAL	0	0.002	0.017	23.149	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	592	SER	0	0.025	-0.001	20.710	0.011	0.011	0.000	0.000	0.000	0.000
96	A	593	LEU	0	-0.059	-0.018	18.331	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	594	LEU	0	-0.001	0.006	22.471	0.007	0.007	0.000	0.000	0.000	0.000

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