FMO DATABASE

FMODB ID: M318Z

Calculation Name: 4DHX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DHX

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NPA8

Base Structure: X-ray

Registration Date: 2023-06-19

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-572125.527309
FMO2-HF: Nuclear repulsion	535775.032272
FMO2-HF: Total energy	-36350.495037
FMO2-MP2: Total energy	-36456.69862

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(B:9:ASP)

Summations of interaction energy for fragment #1(B:9:ASP)

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.
-212.272	-207.434	17.322	-9.265	-12.895	0.134

Interaction energy analysis for fragmet #1(B:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.790 / q_NPA : -0.913

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	B	11	GLN	0	0.032	0.021	2.176	-42.884	-39.738	9.351	-5.532	-6.965	0.066
4	B	12	MET	0	0.014	0.007	1.953	-37.703	-36.645	7.961	-3.422	-5.597	0.066
5	B	13	ARG	1	0.930	0.965	3.987	-49.674	-49.040	0.010	-0.311	-0.333	0.002
6	B	14	ALA	0	-0.012	-0.005	5.829	-6.535	-6.535	0.000	0.000	0.000	0.000
7	B	15	ALA	0	0.037	0.024	6.556	-5.039	-5.039	0.000	0.000	0.000	0.000
8	B	16	ILE	0	0.005	-0.001	8.069	-4.275	-4.275	0.000	0.000	0.000	0.000
9	B	17	ASN	0	-0.039	-0.029	9.902	-4.253	-4.253	0.000	0.000	0.000	0.000
10	B	18	GLN	0	0.009	0.009	11.285	-1.469	-1.469	0.000	0.000	0.000	0.000
11	B	19	LYS	1	0.991	1.015	12.619	-20.621	-20.621	0.000	0.000	0.000	0.000
12	B	20	LEU	0	-0.040	-0.021	13.097	-1.598	-1.598	0.000	0.000	0.000	0.000
13	B	21	ILE	0	-0.061	-0.029	15.194	-1.368	-1.368	0.000	0.000	0.000	0.000
14	B	22	GLU	-1	-0.864	-0.934	17.202	16.000	16.000	0.000	0.000	0.000	0.000
15	B	23	THR	0	-0.050	-0.033	18.151	-0.908	-0.908	0.000	0.000	0.000	0.000
16	B	24	GLY	0	0.047	0.034	20.424	-0.694	-0.694	0.000	0.000	0.000	0.000
17	B	25	GLU	-1	-0.830	-0.899	18.544	13.817	13.817	0.000	0.000	0.000	0.000
18	B	26	ARG	1	0.907	0.940	15.860	-18.163	-18.163	0.000	0.000	0.000	0.000
19	B	27	GLU	-1	-0.950	-0.979	19.388	12.135	12.135	0.000	0.000	0.000	0.000
20	B	28	ARG	1	0.938	0.967	22.564	-13.305	-13.305	0.000	0.000	0.000	0.000
21	B	29	LEU	0	-0.035	-0.025	18.238	-0.446	-0.446	0.000	0.000	0.000	0.000
22	B	30	LYS	1	0.933	0.969	21.767	-13.472	-13.472	0.000	0.000	0.000	0.000
23	B	31	GLU	-1	-0.940	-0.965	22.969	10.262	10.262	0.000	0.000	0.000	0.000
24	B	32	LEU	0	0.025	0.002	25.034	-0.389	-0.389	0.000	0.000	0.000	0.000
25	B	33	LEU	0	-0.025	-0.011	20.173	-0.257	-0.257	0.000	0.000	0.000	0.000
26	B	34	ARG	1	0.914	0.953	24.898	-11.277	-11.277	0.000	0.000	0.000	0.000
27	B	35	ALA	0	0.031	0.018	27.501	-0.337	-0.337	0.000	0.000	0.000	0.000
28	B	36	LYS	1	0.976	0.990	27.492	-10.163	-10.163	0.000	0.000	0.000	0.000
29	B	37	LEU	0	-0.036	-0.021	25.047	-0.209	-0.209	0.000	0.000	0.000	0.000
30	B	38	ILE	0	-0.055	-0.042	29.254	-0.260	-0.260	0.000	0.000	0.000	0.000
31	B	39	GLU	-1	-0.923	-0.950	32.371	8.772	8.772	0.000	0.000	0.000	0.000
32	B	40	CYS	0	-0.099	-0.027	30.077	-0.151	-0.151	0.000	0.000	0.000	0.000
33	B	41	GLY	0	0.092	0.054	33.367	-0.114	-0.114	0.000	0.000	0.000	0.000
34	B	42	TRP	0	-0.017	-0.020	26.864	-0.050	-0.050	0.000	0.000	0.000	0.000
35	B	43	LYS	1	0.951	0.962	31.934	-9.073	-9.073	0.000	0.000	0.000	0.000
36	B	44	ASP	-1	-0.880	-0.947	32.976	8.067	8.067	0.000	0.000	0.000	0.000
37	B	45	GLN	0	-0.005	-0.008	32.809	0.060	0.060	0.000	0.000	0.000	0.000
38	B	46	LEU	0	-0.031	-0.003	29.485	-0.074	-0.074	0.000	0.000	0.000	0.000
39	B	47	LYS	1	0.928	0.965	33.842	-8.303	-8.303	0.000	0.000	0.000	0.000
40	B	48	ALA	0	0.009	0.010	37.130	-0.156	-0.156	0.000	0.000	0.000	0.000
41	B	49	HIS	0	0.028	0.007	33.504	-0.290	-0.290	0.000	0.000	0.000	0.000
42	B	50	CYS	0	0.003	0.001	35.155	-0.010	-0.010	0.000	0.000	0.000	0.000
43	B	51	LYS	1	0.947	0.982	37.809	-7.002	-7.002	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.915	-0.964	40.222	6.929	6.929	0.000	0.000	0.000	0.000
45	B	53	VAL	0	0.040	0.024	36.649	-0.102	-0.102	0.000	0.000	0.000	0.000
46	B	54	ILE	0	-0.030	-0.016	40.031	-0.084	-0.084	0.000	0.000	0.000	0.000
47	B	55	LYS	1	0.880	0.942	42.200	-6.857	-6.857	0.000	0.000	0.000	0.000
48	B	56	GLU	-1	-0.960	-0.970	42.257	6.902	6.902	0.000	0.000	0.000	0.000
49	B	57	LYS	1	0.910	0.966	39.115	-7.921	-7.921	0.000	0.000	0.000	0.000
50	B	58	GLY	0	0.066	0.038	43.427	-0.119	-0.119	0.000	0.000	0.000	0.000
51	B	59	LEU	0	-0.024	-0.038	43.589	0.148	0.148	0.000	0.000	0.000	0.000
52	B	60	GLU	-1	-0.989	-0.980	45.020	6.401	6.401	0.000	0.000	0.000	0.000
53	B	61	HIS	0	-0.031	-0.012	43.373	0.092	0.092	0.000	0.000	0.000	0.000
54	B	62	VAL	0	-0.071	-0.013	38.683	0.190	0.190	0.000	0.000	0.000	0.000
55	B	63	THR	0	0.031	0.007	36.627	0.060	0.060	0.000	0.000	0.000	0.000
56	B	64	VAL	0	-0.008	-0.033	32.798	0.054	0.054	0.000	0.000	0.000	0.000
57	B	65	ASP	-1	-0.883	-0.943	31.665	10.224	10.224	0.000	0.000	0.000	0.000
58	B	66	ASP	-1	-0.836	-0.909	32.220	8.863	8.863	0.000	0.000	0.000	0.000
59	B	67	LEU	0	-0.030	-0.016	34.084	0.093	0.093	0.000	0.000	0.000	0.000
60	B	68	VAL	0	-0.011	-0.007	28.182	0.144	0.144	0.000	0.000	0.000	0.000
61	B	69	ALA	0	-0.006	0.008	29.383	0.322	0.322	0.000	0.000	0.000	0.000
62	B	70	GLU	-1	-0.924	-0.955	30.324	8.984	8.984	0.000	0.000	0.000	0.000
63	B	71	ILE	0	-0.050	-0.035	30.617	0.034	0.034	0.000	0.000	0.000	0.000
64	B	72	THR	0	-0.074	-0.044	25.090	0.316	0.316	0.000	0.000	0.000	0.000
65	B	73	PRO	0	-0.034	-0.018	26.461	0.319	0.319	0.000	0.000	0.000	0.000
66	B	74	LYS	1	1.012	1.006	27.204	-8.710	-8.710	0.000	0.000	0.000	0.000
67	B	75	GLY	0	0.056	0.027	28.275	-0.023	-0.023	0.000	0.000	0.000	0.000
68	B	76	ARG	1	0.925	0.949	21.016	-12.962	-12.962	0.000	0.000	0.000	0.000
69	B	77	ALA	0	-0.038	-0.020	24.353	0.288	0.288	0.000	0.000	0.000	0.000
70	B	78	LEU	0	0.008	0.012	26.412	-0.184	-0.184	0.000	0.000	0.000	0.000
71	B	79	VAL	0	-0.069	-0.014	22.874	-0.131	-0.131	0.000	0.000	0.000	0.000
72	B	80	PRO	0	0.066	0.027	25.280	0.183	0.183	0.000	0.000	0.000	0.000
73	B	81	ASP	-1	-0.846	-0.954	23.434	12.108	12.108	0.000	0.000	0.000	0.000
74	B	82	SER	0	-0.013	-0.003	23.425	0.428	0.428	0.000	0.000	0.000	0.000
75	B	83	VAL	0	0.075	0.027	23.117	0.264	0.264	0.000	0.000	0.000	0.000
76	B	84	LYS	1	0.910	0.975	19.705	-12.358	-12.358	0.000	0.000	0.000	0.000
77	B	85	LYS	1	0.949	0.984	19.331	-11.219	-11.219	0.000	0.000	0.000	0.000
78	B	86	GLU	-1	-0.938	-0.971	20.564	11.569	11.569	0.000	0.000	0.000	0.000
79	B	87	LEU	0	0.012	0.001	17.418	0.305	0.305	0.000	0.000	0.000	0.000
80	B	88	LEU	0	-0.009	-0.005	13.896	0.637	0.637	0.000	0.000	0.000	0.000
81	B	89	GLN	0	-0.012	-0.016	16.345	0.998	0.998	0.000	0.000	0.000	0.000
82	B	90	ARG	1	0.954	0.985	18.848	-12.090	-12.090	0.000	0.000	0.000	0.000
83	B	91	ILE	0	0.012	0.011	12.599	0.299	0.299	0.000	0.000	0.000	0.000
84	B	92	ARG	1	0.956	0.973	13.713	-16.336	-16.336	0.000	0.000	0.000	0.000
85	B	93	THR	0	0.012	0.013	15.349	0.041	0.041	0.000	0.000	0.000	0.000
86	B	94	PHE	0	0.014	0.003	14.289	0.092	0.092	0.000	0.000	0.000	0.000
87	B	95	LEU	0	-0.016	-0.028	10.363	0.416	0.416	0.000	0.000	0.000	0.000
88	B	96	ALA	0	-0.004	-0.002	14.246	0.287	0.287	0.000	0.000	0.000	0.000
89	B	97	GLN	0	-0.042	-0.017	16.758	-0.171	-0.171	0.000	0.000	0.000	0.000
90	B	98	HIS	0	-0.048	-0.013	15.841	-0.782	-0.782	0.000	0.000	0.000	0.000
91	B	99	ALA	0	-0.037	0.004	12.539	1.196	1.196	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:ASP)