FMO DATABASE

FMODB ID: R8VQ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-434416.034112
FMO2-HF: Nuclear repulsion	406564.419824
FMO2-HF: Total energy	-27851.614288
FMO2-MP2: Total energy	-27932.75579

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.
-27.449	-24.188	0.982	-1.221	-3.023	-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 : 1.001 / q_NPA : 0.978

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	0.107	0.061	3.844	0.752	2.039	-0.009	-0.479	-0.799	0.001
4	A	3	HIS	0	0.019	0.001	6.213	1.407	1.407	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.073	-0.052	2.238	0.448	1.282	0.932	-0.478	-1.289	-0.003
6	A	5	TRP	0	-0.070	-0.015	2.973	1.700	2.677	0.061	-0.247	-0.791	-0.001
7	A	6	GLY	0	0.091	0.041	5.364	3.726	3.755	-0.001	-0.002	-0.026	0.000
8	A	7	THR	0	0.023	-0.008	7.867	-0.547	-0.547	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.891	-0.953	10.017	-19.408	-19.408	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.910	-0.943	4.325	-35.165	-35.031	-0.001	-0.015	-0.118	0.000
11	A	10	VAL	0	-0.029	-0.010	7.392	-0.575	-0.575	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.017	0.009	9.741	0.660	0.660	0.000	0.000	0.000	0.000
13	A	12	ALA	0	0.053	0.034	8.409	0.983	0.983	0.000	0.000	0.000	0.000
14	A	13	TRP	0	0.084	0.027	8.639	1.914	1.914	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.004	0.000	10.339	1.189	1.189	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.802	-0.913	13.395	-18.208	-18.208	0.000	0.000	0.000	0.000
17	A	16	HIS	0	-0.092	-0.039	10.014	0.578	0.578	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.079	-0.025	13.517	0.917	0.917	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.051	-0.017	16.122	1.470	1.470	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.072	-0.051	17.331	1.193	1.193	0.000	0.000	0.000	0.000
21	A	20	CYM	-1	-0.754	-0.874	17.424	-16.648	-16.648	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.891	-0.944	18.444	-12.068	-12.068	0.000	0.000	0.000	0.000
23	A	22	TYR	0	-0.049	-0.058	18.790	0.856	0.856	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.809	0.899	14.708	18.027	18.027	0.000	0.000	0.000	0.000
25	A	24	ASP	-1	-0.822	-0.883	17.375	-13.441	-13.441	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.010	0.018	19.328	-0.166	-0.166	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.013	-0.003	15.175	0.103	0.103	0.000	0.000	0.000	0.000
28	A	27	THR	0	0.058	0.030	15.259	-0.806	-0.806	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.828	0.892	16.562	12.515	12.515	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.106	-0.054	18.993	0.678	0.678	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.782	-0.850	14.463	-17.582	-17.582	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.031	-0.002	13.425	-0.190	-0.190	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.778	0.844	10.499	17.500	17.500	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.031	0.001	7.866	0.341	0.341	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.004	-0.022	8.786	1.360	1.360	0.000	0.000	0.000	0.000
36	A	35	GLY	0	0.037	0.035	11.311	0.903	0.903	0.000	0.000	0.000	0.000
37	A	36	LEU	0	0.036	0.019	10.187	1.034	1.034	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.097	-0.047	10.053	0.788	0.788	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.099	-0.050	14.192	1.011	1.011	0.000	0.000	0.000	0.000
40	A	39	LEU	0	-0.017	0.023	16.351	0.811	0.811	0.000	0.000	0.000	0.000
41	A	40	GLU	-1	-0.928	-0.966	19.061	-11.765	-11.765	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.864	0.909	22.632	10.731	10.731	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.952	0.958	24.919	10.052	10.052	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.684	-0.811	21.134	-12.732	-12.732	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.005	-0.003	19.153	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.916	0.946	22.833	10.070	10.070	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.955	-0.968	24.971	-10.398	-10.398	0.000	0.000	0.000	0.000
48	A	47	LEU	0	-0.059	-0.032	18.634	0.027	0.027	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.013	0.013	23.053	-0.246	-0.246	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.046	-0.018	21.072	0.307	0.307	0.000	0.000	0.000	0.000
51	A	50	THR	0	0.008	-0.005	24.421	0.338	0.338	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.863	0.943	25.852	11.844	11.844	0.000	0.000	0.000	0.000
53	A	52	VAL	0	0.114	0.052	25.862	-0.481	-0.481	0.000	0.000	0.000	0.000
54	A	53	GLY	0	-0.022	-0.019	25.217	-0.396	-0.396	0.000	0.000	0.000	0.000
55	A	54	HIS	0	-0.014	0.013	22.314	-0.401	-0.401	0.000	0.000	0.000	0.000
56	A	55	MET	0	0.020	0.029	21.214	-0.435	-0.435	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.912	0.959	21.123	11.262	11.262	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.940	0.974	18.546	14.161	14.161	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.057	0.025	16.575	-0.701	-0.701	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.023	-0.031	16.621	-0.580	-0.580	0.000	0.000	0.000	0.000
61	A	60	CYS	0	-0.114	-0.069	17.824	-0.079	-0.079	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.094	0.059	15.050	-0.453	-0.453	0.000	0.000	0.000	0.000
63	A	62	ILE	0	0.033	0.022	12.923	-1.502	-1.502	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.922	0.957	13.784	13.443	13.443	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.998	-1.003	13.673	-19.832	-19.832	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.038	-0.012	8.087	-1.772	-1.772	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.028	-0.008	10.824	-1.517	-1.517	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.937	0.984	12.138	15.549	15.549	0.000	0.000	0.000	0.000

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