FMO DATABASE

FMODB ID: 4J97N

Calculation Name: 3I3U-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3I3U

Chain ID: A

ChEMBL ID:
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UniProt ID: F9UPN6

Base Structure: X-ray

Registration Date: 2023-09-21

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-622605.434952
FMO2-HF: Nuclear repulsion	587009.942
FMO2-HF: Total energy	-35595.492952
FMO2-MP2: Total energy	-35700.367918

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-38.2	-36.859	11.373	-5.949	-6.764	0.065

Interaction energy analysis for fragmet #1(A:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.089 / q_NPA : 0.032

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	4	LYS	1	0.968	0.970	3.885	2.724	3.994	-0.003	-0.519	-0.748	0.001
4	A	5	LYS	1	0.901	0.951	1.765	-40.810	-41.780	11.181	-5.146	-5.064	0.065
5	A	6	ILE	0	0.029	0.017	2.926	-0.240	0.691	0.196	-0.280	-0.847	-0.001
6	A	7	GLU	-1	-0.867	-0.897	5.389	-0.645	-0.535	-0.001	-0.004	-0.105	0.000
7	A	8	LEU	0	0.001	0.004	8.132	0.436	0.436	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.022	-0.022	6.176	0.266	0.266	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.009	-0.013	9.017	0.082	0.082	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.011	-0.014	11.252	0.166	0.166	0.000	0.000	0.000	0.000
11	A	12	TYR	0	-0.026	0.005	12.734	0.085	0.085	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.011	-0.023	11.873	0.056	0.056	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.065	-0.036	15.165	0.007	0.007	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.005	0.013	17.328	0.015	0.015	0.000	0.000	0.000	0.000
15	A	16	TYR	0	-0.045	-0.026	17.786	0.042	0.042	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.006	0.012	20.913	-0.047	-0.047	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.801	-0.887	23.076	0.023	0.023	0.000	0.000	0.000	0.000
18	A	19	HIS	0	0.034	0.009	24.204	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	20	HIS	0	0.002	0.009	27.009	0.007	0.007	0.000	0.000	0.000	0.000
20	A	21	THR	0	-0.017	-0.041	26.325	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.012	-0.004	27.904	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.020	-0.023	30.372	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.020	0.010	31.692	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.774	-0.869	32.517	-0.086	-0.086	0.000	0.000	0.000	0.000
25	A	26	MET	0	-0.003	-0.002	34.354	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.071	-0.027	35.557	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.099	-0.050	36.349	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.014	-0.009	38.089	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.100	-0.052	36.933	0.005	0.005	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.004	0.014	36.975	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.831	0.905	30.636	0.105	0.105	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.020	0.004	27.791	0.001	0.001	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.005	0.012	32.781	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.005	-0.001	32.006	0.003	0.003	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.014	0.008	32.366	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.822	-0.903	32.582	0.107	0.107	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.029	0.016	30.120	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.866	0.926	33.450	-0.111	-0.111	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.030	0.000	34.865	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.015	0.014	37.217	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	51	LYS	1	1.003	1.000	36.914	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	52	GLY	0	-0.060	-0.038	38.000	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.023	0.014	36.036	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	54	ILE	0	0.013	0.009	37.182	0.002	0.002	0.000	0.000	0.000	0.000
45	A	55	ALA	0	-0.003	0.004	37.235	0.005	0.005	0.000	0.000	0.000	0.000
46	A	56	MET	0	0.014	0.013	35.845	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	57	PRO	0	0.023	0.018	35.336	0.003	0.003	0.000	0.000	0.000	0.000
48	A	58	ALA	0	0.029	0.012	31.994	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	59	LYS	1	0.745	0.863	33.790	-0.085	-0.085	0.000	0.000	0.000	0.000
50	A	60	ASP	-1	-0.806	-0.892	36.551	0.057	0.057	0.000	0.000	0.000	0.000
51	A	61	LEU	0	-0.012	-0.005	32.012	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	62	ALA	0	0.014	0.007	35.294	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	63	THR	0	-0.023	-0.017	36.647	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	64	ARG	1	0.736	0.813	39.366	-0.026	-0.026	0.000	0.000	0.000	0.000
55	A	65	ILE	0	0.018	0.027	35.517	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	66	GLY	0	0.002	0.000	38.238	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	67	GLU	-1	-0.840	-0.888	40.229	0.002	0.002	0.000	0.000	0.000	0.000
58	A	68	LEU	0	-0.088	-0.021	34.421	0.001	0.001	0.000	0.000	0.000	0.000
59	A	69	ASP	-1	-0.770	-0.882	37.765	-0.085	-0.085	0.000	0.000	0.000	0.000
60	A	70	PRO	0	-0.015	-0.030	35.280	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	71	ALA	0	-0.044	-0.006	34.848	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	72	LYS	1	0.820	0.899	34.625	0.064	0.064	0.000	0.000	0.000	0.000
63	A	73	THR	0	0.002	-0.001	28.292	0.002	0.002	0.000	0.000	0.000	0.000
64	A	74	TYR	0	-0.014	-0.006	30.284	0.016	0.016	0.000	0.000	0.000	0.000
65	A	75	VAL	0	-0.006	-0.011	27.380	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	76	VAL	0	-0.010	0.008	26.864	0.013	0.013	0.000	0.000	0.000	0.000
67	A	77	TYR	0	0.000	-0.013	27.829	0.013	0.013	0.000	0.000	0.000	0.000
68	A	78	ASP	-1	-0.727	-0.845	26.330	0.240	0.240	0.000	0.000	0.000	0.000
69	A	79	TRP	0	-0.008	-0.019	28.402	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	80	THR	0	-0.075	-0.038	26.957	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	81	GLY	0	-0.033	-0.023	25.492	0.022	0.022	0.000	0.000	0.000	0.000
72	A	82	GLY	0	-0.008	0.014	22.448	0.043	0.043	0.000	0.000	0.000	0.000
73	A	83	THR	0	-0.051	-0.046	22.904	0.015	0.015	0.000	0.000	0.000	0.000
74	A	84	THR	0	0.044	0.002	25.047	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	85	LEU	0	-0.017	0.011	26.185	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	86	GLY	0	0.041	0.038	26.374	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	87	LYS	1	0.847	0.900	20.326	-0.272	-0.272	0.000	0.000	0.000	0.000
78	A	88	THR	0	-0.030	-0.028	24.521	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	89	ALA	0	0.005	-0.007	27.632	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	90	LEU	0	0.017	0.017	22.391	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	91	LEU	0	0.003	0.008	24.074	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	92	VAL	0	-0.018	0.001	26.327	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	93	LEU	0	-0.013	-0.003	28.618	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	94	LEU	0	0.021	0.007	22.959	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	95	SER	0	-0.083	-0.057	27.134	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	96	ALA	0	-0.056	-0.027	28.839	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	97	GLY	0	-0.013	0.008	29.523	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	98	PHE	0	-0.041	-0.021	30.492	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	99	GLU	-1	-0.812	-0.862	26.298	-0.201	-0.201	0.000	0.000	0.000	0.000
90	A	100	ALA	0	-0.020	-0.027	26.286	0.021	0.021	0.000	0.000	0.000	0.000
91	A	101	TYR	0	-0.035	-0.038	21.815	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	102	GLU	-1	-0.825	-0.911	22.864	0.207	0.207	0.000	0.000	0.000	0.000
93	A	103	LEU	0	-0.035	-0.022	23.841	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	104	ALA	0	-0.027	-0.009	21.582	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)