FMO DATABASE

FMODB ID: 5J8LZ

Calculation Name: 4EMG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y7M4

Base Structure: X-ray

Registration Date: 2023-09-23

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-448316.867277
FMO2-HF: Nuclear repulsion	419548.872443
FMO2-HF: Total energy	-28767.994834
FMO2-MP2: Total energy	-28852.331248

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:9:GLU)

Summations of interaction energy for fragment #1(A:9:GLU)

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.
47.396	53.993	4.711	-5.574	-5.733	-0.033

Interaction energy analysis for fragmet #1(A:9:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.929 / q_NPA : -0.966

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	11	LEU	0	0.031	-0.003	3.571	-6.625	-4.547	-0.004	-0.967	-1.106	0.004
4	A	12	ASP	-1	-0.885	-0.935	2.222	52.264	56.610	4.716	-4.594	-4.468	-0.037
5	A	13	LEU	0	-0.031	-0.012	4.790	-3.903	-3.730	-0.001	-0.013	-0.159	0.000
6	A	14	VAL	0	0.002	0.002	7.574	-3.219	-3.219	0.000	0.000	0.000	0.000
7	A	15	ARG	1	0.966	0.981	6.279	-31.609	-31.609	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.051	-0.034	6.666	-2.163	-2.163	0.000	0.000	0.000	0.000
9	A	17	SER	0	-0.016	-0.007	10.364	-1.904	-1.904	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.030	-0.012	11.981	-1.437	-1.437	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.918	-0.970	14.571	14.798	14.798	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.955	-0.956	15.521	16.154	16.154	0.000	0.000	0.000	0.000
13	A	21	ILE	0	-0.064	-0.045	18.057	-0.339	-0.339	0.000	0.000	0.000	0.000
14	A	22	VAL	0	-0.012	-0.004	14.866	0.528	0.528	0.000	0.000	0.000	0.000
15	A	23	TYR	0	-0.061	-0.048	17.667	-0.697	-0.697	0.000	0.000	0.000	0.000
16	A	24	VAL	0	0.015	-0.003	16.917	1.127	1.127	0.000	0.000	0.000	0.000
17	A	25	LYS	1	0.902	0.985	18.388	-13.677	-13.677	0.000	0.000	0.000	0.000
18	A	26	LEU	0	0.020	-0.003	19.325	0.546	0.546	0.000	0.000	0.000	0.000
19	A	27	ARG	1	0.887	0.906	19.328	-14.373	-14.373	0.000	0.000	0.000	0.000
20	A	28	GLY	0	-0.049	-0.014	23.516	-0.264	-0.264	0.000	0.000	0.000	0.000
21	A	29	ASP	-1	-0.932	-0.969	26.855	10.249	10.249	0.000	0.000	0.000	0.000
22	A	30	ARG	1	0.893	0.930	25.467	-10.904	-10.904	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.869	-0.912	23.010	12.981	12.981	0.000	0.000	0.000	0.000
24	A	32	LEU	0	-0.013	-0.012	21.123	-0.579	-0.579	0.000	0.000	0.000	0.000
25	A	33	ASN	0	0.007	0.008	21.916	1.030	1.030	0.000	0.000	0.000	0.000
26	A	34	GLY	0	0.072	0.039	21.393	-0.690	-0.690	0.000	0.000	0.000	0.000
27	A	35	ARG	1	0.882	0.963	20.354	-12.756	-12.756	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.013	0.007	13.043	-0.524	-0.524	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.065	0.026	17.533	0.169	0.169	0.000	0.000	0.000	0.000
30	A	38	ALA	0	-0.023	-0.017	15.959	0.072	0.072	0.000	0.000	0.000	0.000
31	A	39	TYR	0	-0.006	-0.011	8.029	0.081	0.081	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.784	-0.881	12.789	16.505	16.505	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.892	-0.959	10.409	18.925	18.925	0.000	0.000	0.000	0.000
34	A	42	HIS	0	-0.070	-0.028	11.410	0.939	0.939	0.000	0.000	0.000	0.000
35	A	43	LEU	0	0.003	-0.004	10.190	-0.194	-0.194	0.000	0.000	0.000	0.000
36	A	44	ASN	0	-0.074	-0.023	13.266	-0.995	-0.995	0.000	0.000	0.000	0.000
37	A	45	MET	0	-0.012	-0.001	14.889	0.996	0.996	0.000	0.000	0.000	0.000
38	A	46	VAL	0	-0.011	0.000	17.257	-0.902	-0.902	0.000	0.000	0.000	0.000
39	A	47	LEU	0	-0.015	-0.009	18.282	0.543	0.543	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.006	-0.016	21.287	-0.652	-0.652	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.956	-0.986	24.023	10.894	10.894	0.000	0.000	0.000	0.000
42	A	50	ALA	0	-0.015	-0.004	24.403	0.229	0.229	0.000	0.000	0.000	0.000
43	A	51	GLU	-1	-0.863	-0.930	25.749	10.164	10.164	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.827	-0.907	25.946	10.841	10.841	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.049	-0.037	26.902	-0.510	-0.510	0.000	0.000	0.000	0.000
46	A	54	VAL	0	0.004	0.012	28.275	0.275	0.275	0.000	0.000	0.000	0.000
47	A	55	THR	0	0.010	0.007	28.857	-0.299	-0.299	0.000	0.000	0.000	0.000
48	A	70	THR	0	0.008	0.003	32.459	0.173	0.173	0.000	0.000	0.000	0.000
49	A	71	ILE	0	-0.068	-0.043	33.638	-0.303	-0.303	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.874	0.934	29.916	-9.830	-9.830	0.000	0.000	0.000	0.000
51	A	73	LYS	1	0.895	0.953	31.127	-9.613	-9.613	0.000	0.000	0.000	0.000
52	A	74	HIS	0	0.001	0.013	29.769	0.105	0.105	0.000	0.000	0.000	0.000
53	A	75	TYR	0	-0.038	-0.038	27.645	-0.493	-0.493	0.000	0.000	0.000	0.000
54	A	76	GLU	-1	-0.882	-0.926	28.290	9.766	9.766	0.000	0.000	0.000	0.000
55	A	77	MET	0	-0.013	-0.003	23.446	0.529	0.529	0.000	0.000	0.000	0.000
56	A	78	LEU	0	-0.034	-0.003	23.862	-0.375	-0.375	0.000	0.000	0.000	0.000
57	A	79	PHE	0	-0.003	0.012	20.736	0.521	0.521	0.000	0.000	0.000	0.000
58	A	80	VAL	0	-0.007	-0.011	19.315	-0.463	-0.463	0.000	0.000	0.000	0.000
59	A	81	ARG	1	0.908	0.951	19.456	-12.045	-12.045	0.000	0.000	0.000	0.000
60	A	82	GLY	0	0.105	0.037	16.449	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	83	ASP	-1	-0.864	-0.931	17.063	14.301	14.301	0.000	0.000	0.000	0.000
62	A	84	SER	0	-0.154	-0.072	18.908	-0.269	-0.269	0.000	0.000	0.000	0.000
63	A	85	VAL	0	0.044	0.017	14.955	-0.514	-0.514	0.000	0.000	0.000	0.000
64	A	86	ILE	0	-0.077	-0.026	16.512	0.301	0.301	0.000	0.000	0.000	0.000
65	A	87	LEU	0	-0.037	-0.024	14.698	1.021	1.021	0.000	0.000	0.000	0.000
66	A	88	ILE	0	0.054	0.020	11.898	-0.896	-0.896	0.000	0.000	0.000	0.000
67	A	89	ALA	0	-0.049	-0.016	12.895	1.476	1.476	0.000	0.000	0.000	0.000
68	A	90	PRO	0	0.037	0.031	11.513	-1.143	-1.143	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.043	0.032	14.585	-0.670	-0.670	0.000	0.000	0.000	0.000
70	A	92	ARG	1	0.939	0.947	15.852	-15.114	-15.114	0.000	0.000	0.000	0.000
71	A	93	ASN	0	-0.016	0.008	15.414	-0.144	-0.144	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLU)