FMO DATABASE

FMODB ID: MN6GZ

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	OptHSide
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	-673376.325961
FMO2-HF: Nuclear repulsion	635184.328741
FMO2-HF: Total energy	-38191.99722
FMO2-MP2: Total energy	-38301.285062

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.
-0.805	2.543	0.489	-1.54	-2.298	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 : 0.025 / q_NPA : 0.009

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	0.065	0.023	3.800	-0.171	2.054	-0.017	-1.114	-1.095	0.005
4	A	-12	VAL	0	0.005	-0.001	6.266	0.628	0.628	0.000	0.000	0.000	0.000
5	A	-11	ASP	-1	-0.844	-0.895	4.434	-1.273	-1.118	-0.001	-0.007	-0.147	0.000
6	A	-10	LEU	0	0.037	0.019	2.728	-1.097	-0.129	0.507	-0.419	-1.056	0.005
7	A	-9	GLY	0	0.011	0.020	6.288	0.060	0.060	0.000	0.000	0.000	0.000
8	A	-8	THR	0	-0.061	-0.054	9.389	0.060	0.060	0.000	0.000	0.000	0.000
9	A	-7	GLU	-1	-0.928	-0.953	8.373	0.846	0.846	0.000	0.000	0.000	0.000
10	A	-6	ASN	0	-0.047	-0.049	9.293	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	-5	LEU	0	-0.010	0.003	12.180	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	-4	TYR	0	0.019	0.015	14.095	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	-3	PHE	0	-0.004	-0.006	11.355	-0.033	-0.033	0.000	0.000	0.000	0.000
14	A	-2	GLN	0	-0.005	0.001	16.195	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	-1	SER	0	-0.035	-0.037	18.309	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	0	MET	0	-0.066	-0.017	18.988	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	514	PRO	0	-0.052	-0.035	21.181	0.012	0.012	0.000	0.000	0.000	0.000
18	A	515	ARG	1	0.827	0.898	21.229	-0.147	-0.147	0.000	0.000	0.000	0.000
19	A	516	SER	0	-0.090	-0.075	24.071	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	517	ILE	0	0.008	0.008	25.423	0.013	0.013	0.000	0.000	0.000	0.000
21	A	518	ARG	1	0.851	0.907	28.590	-0.116	-0.116	0.000	0.000	0.000	0.000
22	A	519	PHE	0	0.002	-0.017	31.476	0.007	0.007	0.000	0.000	0.000	0.000
23	A	520	THR	0	0.008	-0.010	33.780	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	521	ALA	0	0.008	0.016	36.830	0.003	0.003	0.000	0.000	0.000	0.000
25	A	522	GLU	-1	-0.775	-0.862	36.688	0.085	0.085	0.000	0.000	0.000	0.000
26	A	523	GLU	-1	-0.940	-0.967	40.572	0.058	0.058	0.000	0.000	0.000	0.000
27	A	524	GLY	0	-0.070	-0.033	43.274	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	525	ASP	-1	-0.962	-0.985	40.595	0.055	0.055	0.000	0.000	0.000	0.000
29	A	526	LEU	0	-0.046	-0.022	36.805	0.004	0.004	0.000	0.000	0.000	0.000
30	A	527	GLY	0	0.067	0.035	36.190	0.006	0.006	0.000	0.000	0.000	0.000
31	A	528	PHE	0	-0.012	-0.022	33.542	0.003	0.003	0.000	0.000	0.000	0.000
32	A	529	THR	0	-0.035	-0.009	35.601	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	530	LEU	0	0.021	0.015	34.837	0.003	0.003	0.000	0.000	0.000	0.000
34	A	531	ARG	1	0.870	0.916	31.579	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	532	GLY	0	0.020	0.013	35.651	0.001	0.001	0.000	0.000	0.000	0.000
36	A	533	ASN	0	-0.030	-0.037	37.053	0.005	0.005	0.000	0.000	0.000	0.000
37	A	534	ALA	0	-0.017	0.041	36.244	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	535	PRO	0	0.021	0.013	30.755	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	536	VAL	0	-0.041	-0.021	33.894	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	537	GLN	0	-0.008	0.005	28.760	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	538	VAL	0	0.045	0.025	29.949	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	539	HIS	0	-0.047	-0.030	30.954	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	540	PHE	0	-0.014	-0.008	31.814	0.003	0.003	0.000	0.000	0.000	0.000
44	A	541	LEU	0	0.007	0.004	28.426	0.000	0.000	0.000	0.000	0.000	0.000
45	A	542	ASP	-1	-0.843	-0.913	31.980	0.081	0.081	0.000	0.000	0.000	0.000
46	A	543	PRO	0	0.006	0.000	29.494	0.005	0.005	0.000	0.000	0.000	0.000
47	A	544	TYR	0	-0.033	-0.030	30.362	0.012	0.012	0.000	0.000	0.000	0.000
48	A	545	CYS	0	-0.056	0.018	32.771	0.002	0.002	0.000	0.000	0.000	0.000
49	A	546	SER	0	0.065	-0.005	31.829	0.010	0.010	0.000	0.000	0.000	0.000
50	A	547	ALA	0	0.026	0.010	30.900	0.009	0.009	0.000	0.000	0.000	0.000
51	A	548	SER	0	-0.030	-0.018	28.348	0.012	0.012	0.000	0.000	0.000	0.000
52	A	549	VAL	0	-0.038	-0.009	26.910	0.017	0.017	0.000	0.000	0.000	0.000
53	A	550	ALA	0	-0.015	0.001	26.618	0.016	0.016	0.000	0.000	0.000	0.000
54	A	551	GLY	0	-0.050	-0.025	24.081	0.011	0.011	0.000	0.000	0.000	0.000
55	A	552	ALA	0	-0.017	0.009	24.295	0.001	0.001	0.000	0.000	0.000	0.000
56	A	553	ARG	1	0.853	0.896	22.691	-0.159	-0.159	0.000	0.000	0.000	0.000
57	A	554	GLU	-1	-0.852	-0.923	26.103	0.090	0.090	0.000	0.000	0.000	0.000
58	A	555	GLY	0	-0.077	-0.045	26.314	0.002	0.002	0.000	0.000	0.000	0.000
59	A	556	ASP	-1	-0.735	-0.834	24.682	0.112	0.112	0.000	0.000	0.000	0.000
60	A	557	TYR	0	-0.027	-0.026	26.377	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	558	ILE	0	0.033	0.017	28.498	0.007	0.007	0.000	0.000	0.000	0.000
62	A	559	VAL	0	-0.026	-0.031	28.051	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	560	SER	0	-0.074	-0.047	31.089	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	561	ILE	0	0.086	0.054	32.607	0.006	0.006	0.000	0.000	0.000	0.000
65	A	562	GLN	0	0.042	0.020	34.514	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	563	LEU	0	-0.067	-0.032	34.142	0.001	0.001	0.000	0.000	0.000	0.000
67	A	564	VAL	0	-0.004	0.011	36.264	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	565	ASP	-1	-0.808	-0.893	34.672	0.035	0.035	0.000	0.000	0.000	0.000
69	A	566	CYS	0	-0.017	-0.022	34.320	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	567	LYS	1	0.849	0.905	30.281	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	568	TRP	0	-0.028	-0.014	34.359	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	569	LEU	0	-0.014	0.027	37.593	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	570	THR	0	-0.011	-0.058	38.560	0.000	0.000	0.000	0.000	0.000	0.000
74	A	571	LEU	0	0.040	0.009	38.810	0.003	0.003	0.000	0.000	0.000	0.000
75	A	572	SER	0	-0.038	-0.017	40.427	0.003	0.003	0.000	0.000	0.000	0.000
76	A	573	GLU	-1	-0.828	-0.896	42.047	0.022	0.022	0.000	0.000	0.000	0.000
77	A	574	VAL	0	0.040	0.030	36.437	0.002	0.002	0.000	0.000	0.000	0.000
78	A	575	MET	0	0.005	0.000	39.745	0.002	0.002	0.000	0.000	0.000	0.000
79	A	576	LYS	1	0.872	0.936	41.628	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	577	LEU	0	0.035	0.015	39.460	0.001	0.001	0.000	0.000	0.000	0.000
81	A	578	LEU	0	0.045	0.037	36.228	0.002	0.002	0.000	0.000	0.000	0.000
82	A	579	LYS	1	0.937	0.965	40.369	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	580	SER	0	-0.126	-0.080	43.032	0.000	0.000	0.000	0.000	0.000	0.000
84	A	581	PHE	0	0.033	0.022	38.880	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	582	GLY	0	-0.032	0.000	42.888	0.001	0.001	0.000	0.000	0.000	0.000
86	A	583	GLU	-1	-0.919	-0.967	42.501	0.058	0.058	0.000	0.000	0.000	0.000
87	A	584	ASP	-1	-0.960	-0.970	41.962	0.061	0.061	0.000	0.000	0.000	0.000
88	A	585	GLU	-1	-0.908	-0.954	34.612	0.099	0.099	0.000	0.000	0.000	0.000
89	A	586	ILE	0	-0.012	0.003	35.620	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	587	GLU	-1	-0.819	-0.863	30.390	0.097	0.097	0.000	0.000	0.000	0.000
91	A	588	MET	0	-0.017	-0.004	30.313	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	589	LYS	1	0.823	0.902	27.654	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	590	VAL	0	0.024	0.009	25.146	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	591	VAL	0	0.011	0.018	23.636	0.010	0.010	0.000	0.000	0.000	0.000
95	A	592	SER	0	0.013	-0.011	20.912	0.000	0.000	0.000	0.000	0.000	0.000
96	A	593	LEU	0	-0.077	-0.028	18.800	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	594	LEU	0	0.000	0.009	22.823	-0.001	-0.001	0.000	0.000	0.000	0.000

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