FMO DATABASE

FMODB ID: YZ662

Calculation Name: 3EVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EVY

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LEB7

Base Structure: X-ray

Registration Date: 2023-06-21

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-610960.173917
FMO2-HF: Nuclear repulsion	575579.032042
FMO2-HF: Total energy	-35381.141874
FMO2-MP2: Total energy	-35483.378951

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:662:MET)

Summations of interaction energy for fragment #1(A:662:MET)

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.
-22.443	-15.134	13.468	-6.978	-13.802	-0.052

Interaction energy analysis for fragmet #1(A:662:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.002

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	A	664	PRO	0	-0.071	-0.057	2.972	-2.166	0.185	0.200	-1.219	-1.333	-0.004
4	A	665	TYR	0	0.008	-0.024	5.334	-0.125	0.069	-0.001	-0.009	-0.184	0.000
5	A	666	GLU	-1	-0.789	-0.882	2.441	-7.678	-4.136	2.382	-2.370	-3.555	-0.030
6	A	667	LYS	1	0.946	0.969	2.038	1.090	0.229	9.760	-2.962	-5.937	0.010
7	A	668	LEU	0	-0.077	-0.035	2.985	0.618	-0.860	0.024	1.885	-0.432	0.000
8	A	669	VAL	0	0.046	0.036	6.441	-0.061	-0.061	0.000	0.000	0.000	0.000
9	A	670	GLU	-1	-0.919	-0.951	2.578	-13.183	-9.622	1.103	-2.303	-2.361	-0.028
10	A	671	ARG	1	0.991	0.992	5.377	1.047	1.047	0.000	0.000	0.000	0.000
11	A	672	PHE	0	-0.059	-0.029	7.196	0.184	0.184	0.000	0.000	0.000	0.000
12	A	673	ASN	0	0.056	0.007	9.249	0.141	0.141	0.000	0.000	0.000	0.000
13	A	674	GLU	-1	-0.929	-0.948	7.228	-1.739	-1.739	0.000	0.000	0.000	0.000
14	A	675	MET	0	-0.011	0.007	11.039	0.154	0.154	0.000	0.000	0.000	0.000
15	A	676	ALA	0	-0.030	-0.022	13.139	0.083	0.083	0.000	0.000	0.000	0.000
16	A	677	ALA	0	0.006	0.009	14.319	0.067	0.067	0.000	0.000	0.000	0.000
17	A	678	GLU	-1	-0.907	-0.952	13.666	-0.600	-0.600	0.000	0.000	0.000	0.000
18	A	679	PHE	0	-0.033	-0.019	17.004	0.061	0.061	0.000	0.000	0.000	0.000
19	A	680	LEU	0	-0.019	-0.026	18.346	0.038	0.038	0.000	0.000	0.000	0.000
20	A	681	SER	0	-0.087	-0.044	20.061	0.027	0.027	0.000	0.000	0.000	0.000
21	A	682	TYR	0	-0.031	-0.008	20.541	0.034	0.034	0.000	0.000	0.000	0.000
22	A	683	PHE	0	-0.042	-0.034	22.797	0.024	0.024	0.000	0.000	0.000	0.000
23	A	684	PRO	0	0.074	0.048	24.047	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	685	THR	0	-0.025	-0.014	25.267	0.007	0.007	0.000	0.000	0.000	0.000
25	A	686	VAL	0	0.074	0.032	26.739	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	687	LYS	1	0.934	0.961	28.482	0.107	0.107	0.000	0.000	0.000	0.000
27	A	688	SER	0	-0.024	-0.018	27.960	0.001	0.001	0.000	0.000	0.000	0.000
28	A	689	VAL	0	0.050	0.028	26.627	0.001	0.001	0.000	0.000	0.000	0.000
29	A	690	GLY	0	-0.070	-0.046	29.532	0.005	0.005	0.000	0.000	0.000	0.000
30	A	691	ASN	0	0.008	0.007	32.860	0.009	0.009	0.000	0.000	0.000	0.000
31	A	692	LEU	0	-0.042	0.005	28.258	0.001	0.001	0.000	0.000	0.000	0.000
32	A	693	GLU	-1	-0.925	-0.957	32.862	-0.097	-0.097	0.000	0.000	0.000	0.000
33	A	694	SER	0	-0.007	0.002	33.234	0.002	0.002	0.000	0.000	0.000	0.000
34	A	695	GLU	-1	-0.823	-0.946	33.207	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	696	LEU	0	-0.046	-0.026	30.563	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	697	ASP	-1	-0.854	-0.919	28.837	-0.176	-0.176	0.000	0.000	0.000	0.000
37	A	698	LYS	1	0.930	0.965	28.179	0.108	0.108	0.000	0.000	0.000	0.000
38	A	699	ARG	1	0.885	0.942	28.304	0.133	0.133	0.000	0.000	0.000	0.000
39	A	700	ARG	1	0.980	1.005	23.741	0.195	0.195	0.000	0.000	0.000	0.000
40	A	701	PHE	0	0.032	0.020	23.556	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	702	VAL	0	0.002	0.001	23.503	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	703	ILE	0	-0.040	-0.018	21.361	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	704	LEU	0	0.019	0.008	18.393	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	705	PHE	0	0.026	0.014	18.825	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	706	ARG	1	0.941	0.972	19.901	0.188	0.188	0.000	0.000	0.000	0.000
46	A	707	ALA	0	-0.050	-0.026	15.888	0.002	0.002	0.000	0.000	0.000	0.000
47	A	708	MET	0	0.081	0.047	15.093	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	709	LEU	0	-0.008	0.002	15.921	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	710	ARG	1	0.877	0.924	16.909	0.258	0.258	0.000	0.000	0.000	0.000
50	A	711	LEU	0	0.030	0.036	9.413	0.016	0.016	0.000	0.000	0.000	0.000
51	A	712	ARG	1	0.837	0.901	13.038	0.267	0.267	0.000	0.000	0.000	0.000
52	A	713	ASN	0	-0.038	-0.036	14.988	0.024	0.024	0.000	0.000	0.000	0.000
53	A	714	GLU	-1	-0.989	-0.976	11.645	-0.401	-0.401	0.000	0.000	0.000	0.000
54	A	715	VAL	0	0.003	-0.009	9.910	0.009	0.009	0.000	0.000	0.000	0.000
55	A	716	LYS	1	0.867	0.937	12.284	0.215	0.215	0.000	0.000	0.000	0.000
56	A	717	GLY	0	-0.042	-0.008	14.692	0.031	0.031	0.000	0.000	0.000	0.000
57	A	718	TYR	0	-0.063	-0.030	9.832	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	719	ASN	0	-0.019	-0.024	13.185	0.007	0.007	0.000	0.000	0.000	0.000
59	A	720	GLU	-1	-0.894	-0.954	9.025	-0.269	-0.269	0.000	0.000	0.000	0.000
60	A	721	PHE	0	-0.015	-0.006	12.397	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	722	ASP	-1	-0.824	-0.908	13.394	-0.095	-0.095	0.000	0.000	0.000	0.000
62	A	723	ALA	0	-0.049	-0.029	14.455	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	724	GLU	-1	-0.945	-0.975	16.279	-0.176	-0.176	0.000	0.000	0.000	0.000
64	A	725	ASP	-1	-0.870	-0.886	10.830	-0.222	-0.222	0.000	0.000	0.000	0.000
65	A	726	LEU	0	-0.092	-0.053	11.590	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	727	THR	0	0.012	0.009	13.502	0.033	0.033	0.000	0.000	0.000	0.000
67	A	728	ILE	0	-0.089	-0.045	15.599	0.007	0.007	0.000	0.000	0.000	0.000
68	A	729	GLU	-1	-0.832	-0.921	18.583	-0.150	-0.150	0.000	0.000	0.000	0.000
69	A	730	GLU	-1	-0.739	-0.871	19.171	-0.204	-0.204	0.000	0.000	0.000	0.000
70	A	731	GLN	0	0.006	0.015	21.952	0.002	0.002	0.000	0.000	0.000	0.000
71	A	732	ARG	1	0.999	0.998	23.057	0.167	0.167	0.000	0.000	0.000	0.000
72	A	733	PHE	0	0.018	0.000	17.952	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	734	ALA	0	0.038	0.009	22.320	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	735	ASP	-1	-0.901	-0.949	25.257	-0.123	-0.123	0.000	0.000	0.000	0.000
75	A	736	TYR	0	-0.087	-0.061	23.189	0.005	0.005	0.000	0.000	0.000	0.000
76	A	737	GLN	0	0.009	-0.002	23.619	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	738	SER	0	-0.024	-0.006	25.635	0.008	0.008	0.000	0.000	0.000	0.000
78	A	739	LYS	1	0.934	0.974	28.178	0.129	0.129	0.000	0.000	0.000	0.000
79	A	740	TYR	0	-0.001	-0.001	24.600	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	741	LEU	0	-0.043	-0.032	27.602	0.003	0.003	0.000	0.000	0.000	0.000
81	A	742	ASP	-1	-0.915	-0.938	29.810	-0.104	-0.104	0.000	0.000	0.000	0.000
82	A	743	MET	0	-0.091	-0.023	29.585	0.003	0.003	0.000	0.000	0.000	0.000
83	A	744	SER	0	-0.097	-0.055	28.514	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:662:MET)