FMO DATABASE

FMODB ID: ZV17N

Calculation Name: 3BQ7-A-Xray372

Preferred Name: Diacylglycerol kinase delta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BQ7

Chain ID: A

ChEMBL ID: CHEMBL1075120

UniProt ID: Q16760

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	68
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-436058.930644
FMO2-HF: Nuclear repulsion	408208.604825
FMO2-HF: Total energy	-27850.325819
FMO2-MP2: Total energy	-27931.57414

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:0:ARG)

Summations of interaction energy for fragment #1(A:0:ARG)

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.
-28.859	-25.309	0.128	-1.111	-2.568	0.006

Interaction energy analysis for fragmet #1(A:0:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.997 / q_NPA : 0.981

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	2	VAL	0	0.127	0.071	3.844	1.265	2.582	-0.011	-0.474	-0.832	0.003
4	A	3	HIS	0	0.009	-0.010	6.137	1.281	1.281	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.075	-0.045	3.447	0.912	2.064	0.085	-0.466	-0.772	0.003
6	A	5	TRP	0	-0.044	0.000	2.983	1.722	2.623	0.056	-0.149	-0.808	0.000
7	A	6	GLY	0	0.086	0.046	5.362	3.834	3.862	-0.001	-0.002	-0.025	0.000
8	A	7	THR	0	0.025	-0.010	7.875	-0.760	-0.760	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.879	-0.951	9.631	-19.946	-19.946	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.942	-0.955	4.155	-35.275	-35.123	-0.001	-0.020	-0.131	0.000
11	A	10	VAL	0	-0.031	-0.015	7.351	-0.819	-0.819	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.017	0.009	9.829	0.663	0.663	0.000	0.000	0.000	0.000
13	A	12	ALA	0	0.052	0.037	8.043	1.008	1.008	0.000	0.000	0.000	0.000
14	A	13	TRP	0	0.074	0.030	9.042	2.157	2.157	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.005	-0.009	10.512	1.300	1.300	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.854	-0.943	12.916	-18.760	-18.760	0.000	0.000	0.000	0.000
17	A	16	HIS	0	-0.094	-0.053	8.732	1.400	1.400	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.108	-0.026	12.934	0.999	0.999	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.055	-0.029	15.666	1.603	1.603	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.078	-0.051	17.328	1.225	1.225	0.000	0.000	0.000	0.000
21	A	20	CYM	-1	-0.765	-0.878	17.219	-17.196	-17.196	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.987	-0.988	18.231	-12.585	-12.585	0.000	0.000	0.000	0.000
23	A	22	TYR	0	-0.035	-0.050	18.997	0.783	0.783	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.865	0.937	14.868	17.913	17.913	0.000	0.000	0.000	0.000
25	A	24	ASP	-1	-0.868	-0.914	17.341	-13.842	-13.842	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.004	0.015	19.302	-0.168	-0.168	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.023	0.001	14.904	0.113	0.113	0.000	0.000	0.000	0.000
28	A	27	THR	0	0.052	0.026	15.518	-0.913	-0.913	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.859	0.918	16.542	12.720	12.720	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.126	-0.068	18.934	0.721	0.721	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.883	-0.941	14.681	-17.140	-17.140	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.041	0.002	13.364	-0.139	-0.139	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.894	0.943	10.255	17.451	17.451	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.029	-0.006	7.879	0.228	0.228	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.012	-0.036	8.781	1.245	1.245	0.000	0.000	0.000	0.000
36	A	35	GLY	0	0.065	0.044	11.318	0.776	0.776	0.000	0.000	0.000	0.000
37	A	36	LEU	0	0.026	0.016	10.289	0.941	0.941	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.121	-0.045	10.065	0.729	0.729	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.091	-0.049	14.176	0.982	0.982	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.005	0.034	16.315	0.790	0.790	0.000	0.000	0.000	0.000
41	A	40	GLU	-1	-0.962	-0.988	19.041	-12.094	-12.094	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.864	0.906	22.621	11.024	11.024	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.934	0.943	24.937	10.007	10.007	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.628	-0.767	21.099	-12.941	-12.941	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.011	-0.004	19.472	0.009	0.009	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.898	0.938	22.892	10.283	10.283	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.938	-0.957	24.768	-10.543	-10.543	0.000	0.000	0.000	0.000
48	A	47	LEU	0	-0.063	-0.043	18.429	0.028	0.028	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.022	0.020	23.022	-0.250	-0.250	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.029	-0.006	21.265	0.311	0.311	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.007	-0.013	24.609	0.363	0.363	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.993	0.998	26.709	11.101	11.101	0.000	0.000	0.000	0.000
53	A	52	VAL	0	0.100	0.045	25.961	-0.489	-0.489	0.000	0.000	0.000	0.000
54	A	53	GLY	0	-0.024	-0.021	25.256	-0.404	-0.404	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.003	0.021	22.473	-0.402	-0.402	0.000	0.000	0.000	0.000
56	A	55	MET	0	0.044	0.038	21.285	-0.456	-0.456	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.890	0.948	21.137	11.420	11.420	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.959	0.992	18.385	14.350	14.350	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.057	0.029	16.504	-0.717	-0.717	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.032	-0.034	16.601	-0.595	-0.595	0.000	0.000	0.000	0.000
61	A	60	CYS	0	-0.108	-0.065	17.711	-0.059	-0.059	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.101	0.056	14.827	-0.483	-0.483	0.000	0.000	0.000	0.000
63	A	62	ILE	0	0.059	0.028	12.978	-1.661	-1.661	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.920	0.952	13.571	13.831	13.831	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-1.002	-1.004	12.758	-20.710	-20.710	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.049	-0.008	8.656	-1.769	-1.769	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.033	-0.014	10.465	-1.144	-1.144	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.931	0.981	11.941	15.913	15.913	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ARG)