FMO DATABASE

FMODB ID: QVJKY

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	OptAll
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	-433301.744213
FMO2-HF: Nuclear repulsion	405449.279665
FMO2-HF: Total energy	-27852.464548
FMO2-MP2: Total energy	-27933.465769

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.
-25.422	-22.211	0.326	-1.108	-2.43	-0.003

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 : 0.977 / q_NPA : 0.968

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	0.093	0.048	3.915	0.188	1.368	-0.006	-0.460	-0.714	0.001
4	A	3	HIS	0	0.027	0.010	6.314	1.141	1.141	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.063	-0.036	2.778	1.320	1.863	0.184	-0.190	-0.537	-0.001
6	A	5	TRP	0	-0.071	-0.021	2.887	2.001	3.331	0.149	-0.439	-1.040	-0.003
7	A	6	GLY	0	0.078	0.025	5.653	3.854	3.854	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.025	0.000	8.263	-0.928	-0.928	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.819	-0.903	10.144	-19.400	-19.400	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.873	-0.926	4.174	-35.468	-35.310	-0.001	-0.019	-0.139	0.000
11	A	10	VAL	0	-0.021	-0.002	6.926	-0.394	-0.394	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.001	-0.001	9.316	1.029	1.029	0.000	0.000	0.000	0.000
13	A	12	ALA	0	0.040	0.008	8.227	1.004	1.004	0.000	0.000	0.000	0.000
14	A	13	TRP	0	0.009	-0.002	8.553	0.972	0.972	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.014	-0.011	10.293	1.352	1.352	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.836	-0.924	13.090	-18.196	-18.196	0.000	0.000	0.000	0.000
17	A	16	HIS	0	-0.040	-0.014	10.200	0.384	0.384	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.024	0.005	13.479	1.034	1.034	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.044	-0.022	16.055	1.592	1.592	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.078	-0.050	17.011	1.223	1.223	0.000	0.000	0.000	0.000
21	A	20	CYM	-1	-0.759	-0.868	17.692	-16.690	-16.690	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.833	-0.903	18.708	-12.058	-12.058	0.000	0.000	0.000	0.000
23	A	22	TYR	0	-0.032	-0.045	18.579	0.710	0.710	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.786	0.897	14.475	17.676	17.676	0.000	0.000	0.000	0.000
25	A	24	ASP	-1	-0.796	-0.854	16.666	-13.285	-13.285	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.034	0.008	19.094	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.015	0.000	14.474	0.221	0.221	0.000	0.000	0.000	0.000
28	A	27	THR	0	0.036	0.006	14.277	-0.452	-0.452	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.754	0.851	16.242	12.586	12.586	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.086	-0.046	18.863	0.891	0.891	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.794	-0.847	14.495	-18.085	-18.085	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.012	0.003	13.317	-0.418	-0.418	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.804	0.852	10.492	18.333	18.333	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.032	0.010	8.101	0.870	0.870	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.019	-0.023	8.985	1.233	1.233	0.000	0.000	0.000	0.000
36	A	35	GLY	0	0.008	0.026	11.735	1.213	1.213	0.000	0.000	0.000	0.000
37	A	36	LEU	0	0.008	-0.003	9.715	1.059	1.059	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.072	-0.048	10.505	0.686	0.686	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.084	-0.041	13.905	1.046	1.046	0.000	0.000	0.000	0.000
40	A	39	LEU	0	-0.025	0.016	15.876	0.889	0.889	0.000	0.000	0.000	0.000
41	A	40	GLU	-1	-0.896	-0.946	18.752	-11.708	-11.708	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.878	0.909	22.317	10.635	10.635	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.840	0.905	24.641	10.480	10.480	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.733	-0.858	20.830	-12.897	-12.897	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.006	0.002	18.772	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.923	0.951	22.377	10.070	10.070	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.860	-0.907	25.046	-10.382	-10.382	0.000	0.000	0.000	0.000
48	A	47	LEU	0	-0.002	0.009	18.826	0.056	0.056	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.009	0.009	22.978	-0.095	-0.095	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.035	-0.021	20.742	0.176	0.176	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.017	-0.015	24.126	0.141	0.141	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.794	0.885	25.515	11.930	11.930	0.000	0.000	0.000	0.000
53	A	52	VAL	0	0.041	0.010	25.787	-0.455	-0.455	0.000	0.000	0.000	0.000
54	A	53	GLY	0	0.004	-0.002	25.760	-0.304	-0.304	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.036	0.040	22.047	-0.343	-0.343	0.000	0.000	0.000	0.000
56	A	55	MET	0	0.000	0.014	21.166	-0.465	-0.465	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.910	0.952	21.532	11.308	11.308	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.903	0.949	18.547	14.398	14.398	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.061	0.037	16.411	-0.760	-0.760	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.003	-0.004	16.787	-0.632	-0.632	0.000	0.000	0.000	0.000
61	A	60	CYS	0	-0.105	-0.060	18.294	-0.038	-0.038	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.115	0.062	15.243	-0.411	-0.411	0.000	0.000	0.000	0.000
63	A	62	ILE	0	0.003	0.007	13.292	-1.483	-1.483	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.882	0.937	14.210	13.440	13.440	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.990	-0.999	13.470	-20.052	-20.052	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.007	0.016	8.224	-1.612	-1.612	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.014	-0.019	10.687	-1.909	-1.909	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.914	0.980	12.109	16.443	16.443	0.000	0.000	0.000	0.000

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