FMO DATABASE

FMODB ID: V5881

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

Total energy (hartree)

FMO2-HF: Electronic energy	-611423.415266
FMO2-HF: Nuclear repulsion	576041.485554
FMO2-HF: Total energy	-35381.929713
FMO2-MP2: Total energy	-35484.124874

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.
-26.56	-21.179	13.354	-5.265	-13.469	-0.038

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 : 0.001 / q_NPA : 0.012

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	-0.040	-0.033	3.815	1.133	2.959	0.002	-0.784	-1.044	0.001
4	A	665	TYR	0	0.002	-0.021	6.070	0.557	0.557	0.000	0.000	0.000	0.000
5	A	666	GLU	-1	-0.744	-0.861	2.618	-3.839	-1.088	2.685	-2.233	-3.204	-0.018
6	A	667	LYS	1	0.929	0.951	2.241	-10.087	-8.991	7.572	-2.583	-6.084	0.008
7	A	668	LEU	0	-0.073	-0.029	3.762	-0.890	-3.126	0.053	2.516	-0.333	0.001
8	A	669	VAL	0	0.049	0.031	6.478	-0.553	-0.553	0.000	0.000	0.000	0.000
9	A	670	GLU	-1	-0.952	-0.971	2.538	-13.274	-11.385	3.043	-2.178	-2.754	-0.030
10	A	671	ARG	1	0.980	0.990	4.940	-0.043	0.012	-0.001	-0.003	-0.050	0.000
11	A	672	PHE	0	-0.057	-0.028	7.131	0.097	0.097	0.000	0.000	0.000	0.000
12	A	673	ASN	0	0.055	0.025	8.263	0.110	0.110	0.000	0.000	0.000	0.000
13	A	674	GLU	-1	-0.925	-0.948	7.371	-1.475	-1.475	0.000	0.000	0.000	0.000
14	A	675	MET	0	-0.008	-0.001	10.359	0.136	0.136	0.000	0.000	0.000	0.000
15	A	676	ALA	0	-0.010	-0.011	12.612	0.053	0.053	0.000	0.000	0.000	0.000
16	A	677	ALA	0	-0.003	0.006	13.551	0.044	0.044	0.000	0.000	0.000	0.000
17	A	678	GLU	-1	-0.920	-0.952	14.123	-0.325	-0.325	0.000	0.000	0.000	0.000
18	A	679	PHE	0	-0.027	-0.023	16.517	0.046	0.046	0.000	0.000	0.000	0.000
19	A	680	LEU	0	-0.014	-0.022	17.518	0.023	0.023	0.000	0.000	0.000	0.000
20	A	681	SER	0	-0.086	-0.039	19.348	0.012	0.012	0.000	0.000	0.000	0.000
21	A	682	TYR	0	-0.039	-0.011	19.938	0.021	0.021	0.000	0.000	0.000	0.000
22	A	683	PHE	0	-0.039	-0.032	22.299	0.017	0.017	0.000	0.000	0.000	0.000
23	A	684	PRO	0	0.067	0.050	23.394	0.003	0.003	0.000	0.000	0.000	0.000
24	A	685	THR	0	-0.017	-0.012	24.477	0.006	0.006	0.000	0.000	0.000	0.000
25	A	686	VAL	0	0.078	0.048	26.279	0.000	0.000	0.000	0.000	0.000	0.000
26	A	687	LYS	1	0.944	0.964	27.890	0.030	0.030	0.000	0.000	0.000	0.000
27	A	688	SER	0	-0.030	-0.027	27.416	0.000	0.000	0.000	0.000	0.000	0.000
28	A	689	VAL	0	0.030	0.017	26.225	0.000	0.000	0.000	0.000	0.000	0.000
29	A	690	GLY	0	-0.050	-0.030	29.120	0.003	0.003	0.000	0.000	0.000	0.000
30	A	691	ASN	0	-0.012	-0.008	32.383	0.005	0.005	0.000	0.000	0.000	0.000
31	A	692	LEU	0	-0.046	0.002	27.937	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	693	GLU	-1	-0.906	-0.945	32.533	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	694	SER	0	-0.044	-0.049	32.726	0.005	0.005	0.000	0.000	0.000	0.000
34	A	695	GLU	-1	-0.727	-0.862	33.113	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	696	LEU	0	-0.011	-0.005	30.726	0.002	0.002	0.000	0.000	0.000	0.000
36	A	697	ASP	-1	-0.789	-0.857	28.722	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	698	LYS	1	0.871	0.919	28.075	0.012	0.012	0.000	0.000	0.000	0.000
38	A	699	ARG	1	0.829	0.900	28.326	0.005	0.005	0.000	0.000	0.000	0.000
39	A	700	ARG	1	0.891	0.940	23.657	0.066	0.066	0.000	0.000	0.000	0.000
40	A	701	PHE	0	0.039	0.024	23.575	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	702	VAL	0	0.002	-0.002	23.485	0.003	0.003	0.000	0.000	0.000	0.000
42	A	703	ILE	0	-0.043	-0.017	21.550	0.010	0.010	0.000	0.000	0.000	0.000
43	A	704	LEU	0	0.026	0.009	18.284	0.009	0.009	0.000	0.000	0.000	0.000
44	A	705	PHE	0	0.023	0.013	18.877	0.004	0.004	0.000	0.000	0.000	0.000
45	A	706	ARG	1	0.934	0.965	20.001	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	707	ALA	0	-0.041	-0.024	16.387	0.026	0.026	0.000	0.000	0.000	0.000
47	A	708	MET	0	0.076	0.046	15.151	0.015	0.015	0.000	0.000	0.000	0.000
48	A	709	LEU	0	-0.024	-0.001	16.016	0.032	0.032	0.000	0.000	0.000	0.000
49	A	710	ARG	1	0.886	0.931	17.436	-0.138	-0.138	0.000	0.000	0.000	0.000
50	A	711	LEU	0	0.015	0.032	9.911	0.032	0.032	0.000	0.000	0.000	0.000
51	A	712	ARG	1	0.814	0.890	13.346	0.024	0.024	0.000	0.000	0.000	0.000
52	A	713	ASN	0	-0.045	-0.039	15.076	0.026	0.026	0.000	0.000	0.000	0.000
53	A	714	GLU	-1	-0.952	-0.967	12.440	0.531	0.531	0.000	0.000	0.000	0.000
54	A	715	VAL	0	0.004	-0.007	10.019	0.067	0.067	0.000	0.000	0.000	0.000
55	A	716	LYS	1	0.846	0.914	12.685	-0.131	-0.131	0.000	0.000	0.000	0.000
56	A	717	GLY	0	-0.044	-0.010	15.379	-0.032	-0.032	0.000	0.000	0.000	0.000
57	A	718	TYR	0	-0.061	-0.030	10.098	0.125	0.125	0.000	0.000	0.000	0.000
58	A	719	ASN	0	-0.025	-0.026	13.632	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	720	GLU	-1	-0.875	-0.932	9.067	0.533	0.533	0.000	0.000	0.000	0.000
60	A	721	PHE	0	-0.014	-0.004	12.347	0.003	0.003	0.000	0.000	0.000	0.000
61	A	722	ASP	-1	-0.816	-0.908	13.333	0.100	0.100	0.000	0.000	0.000	0.000
62	A	723	ALA	0	-0.042	-0.021	14.082	0.004	0.004	0.000	0.000	0.000	0.000
63	A	724	GLU	-1	-0.948	-0.976	15.715	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	725	ASP	-1	-0.896	-0.905	10.454	0.370	0.370	0.000	0.000	0.000	0.000
65	A	726	LEU	0	-0.098	-0.052	10.910	-0.054	-0.054	0.000	0.000	0.000	0.000
66	A	727	THR	0	0.001	-0.011	12.337	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	728	ILE	0	-0.070	-0.033	14.662	0.030	0.030	0.000	0.000	0.000	0.000
68	A	729	GLU	-1	-0.773	-0.883	17.862	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	730	GLU	-1	-0.704	-0.845	18.542	0.095	0.095	0.000	0.000	0.000	0.000
70	A	731	GLN	0	-0.026	-0.010	21.415	0.004	0.004	0.000	0.000	0.000	0.000
71	A	732	ARG	1	0.924	0.962	22.284	0.043	0.043	0.000	0.000	0.000	0.000
72	A	733	PHE	0	0.019	-0.005	17.546	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	734	ALA	0	0.037	0.010	21.861	0.002	0.002	0.000	0.000	0.000	0.000
74	A	735	ASP	-1	-0.860	-0.925	24.929	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	736	TYR	0	-0.075	-0.060	22.442	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	737	GLN	0	0.013	0.006	23.644	0.007	0.007	0.000	0.000	0.000	0.000
77	A	738	SER	0	-0.040	-0.018	25.482	0.004	0.004	0.000	0.000	0.000	0.000
78	A	739	LYS	1	0.970	0.988	28.044	0.009	0.009	0.000	0.000	0.000	0.000
79	A	740	TYR	0	0.017	0.012	24.729	0.001	0.001	0.000	0.000	0.000	0.000
80	A	741	LEU	0	-0.042	-0.025	27.579	0.003	0.003	0.000	0.000	0.000	0.000
81	A	742	ASP	-1	-0.930	-0.948	29.890	0.009	0.009	0.000	0.000	0.000	0.000
82	A	743	MET	0	-0.076	-0.014	29.738	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	744	SER	0	-0.095	-0.054	28.731	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:662:MET)