FMO DATABASE

FMODB ID: 8587Y

Calculation Name: 3TNU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TNU

Chain ID: B

ChEMBL ID:

UniProt ID: P02533

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455456.128873
FMO2-HF: Nuclear repulsion	416264.116727
FMO2-HF: Total energy	-39192.012146
FMO2-MP2: Total energy	-39303.968308

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:382:THR)

Summations of interaction energy for fragment #1(B:382:THR)

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.
-29.718	-21.208	10.768	-9.474	-9.803	-0.073

Interaction energy analysis for fragmet #1(B:382:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.026

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	384	HIS	0	-0.034	-0.022	3.420	-5.270	-2.894	0.020	-1.099	-1.297	0.005
4	B	385	GLU	-1	-0.784	-0.909	2.083	-23.883	-18.928	10.697	-8.048	-7.604	-0.079
5	B	386	ILE	0	0.018	0.006	3.090	-0.354	0.668	0.053	-0.317	-0.758	0.001
6	B	387	SER	0	-0.037	-0.009	5.327	-0.036	0.029	-0.001	-0.003	-0.061	0.000
7	B	388	GLU	-1	-0.905	-0.955	7.026	-0.404	-0.404	0.000	0.000	0.000	0.000
8	B	389	MET	0	0.011	0.009	4.575	0.052	0.144	-0.001	-0.007	-0.083	0.000
9	B	390	ASN	0	-0.013	-0.016	9.144	-0.038	-0.038	0.000	0.000	0.000	0.000
10	B	391	ARG	1	0.964	0.986	10.557	-0.373	-0.373	0.000	0.000	0.000	0.000
11	B	392	MET	0	0.015	0.025	12.058	0.076	0.076	0.000	0.000	0.000	0.000
12	B	393	ILE	0	0.048	0.021	11.451	0.053	0.053	0.000	0.000	0.000	0.000
13	B	394	GLN	0	-0.020	-0.004	14.865	0.039	0.039	0.000	0.000	0.000	0.000
14	B	395	ARG	1	0.936	0.949	14.755	0.207	0.207	0.000	0.000	0.000	0.000
15	B	396	LEU	0	0.021	0.015	15.399	0.012	0.012	0.000	0.000	0.000	0.000
16	B	397	ARG	1	0.847	0.924	18.937	0.217	0.217	0.000	0.000	0.000	0.000
17	B	398	ALA	0	0.004	0.006	20.788	0.020	0.020	0.000	0.000	0.000	0.000
18	B	399	GLU	-1	-0.918	-0.959	22.326	-0.191	-0.191	0.000	0.000	0.000	0.000
19	B	400	ILE	0	-0.025	-0.006	21.061	0.011	0.011	0.000	0.000	0.000	0.000
20	B	401	ASP	-1	-0.773	-0.895	24.702	-0.132	-0.132	0.000	0.000	0.000	0.000
21	B	402	ASN	0	-0.015	0.000	26.526	0.028	0.028	0.000	0.000	0.000	0.000
22	B	403	VAL	0	0.081	0.028	27.519	0.012	0.012	0.000	0.000	0.000	0.000
23	B	404	LYS	1	0.866	0.938	26.490	0.161	0.161	0.000	0.000	0.000	0.000
24	B	405	LYS	1	0.893	0.949	28.972	0.080	0.080	0.000	0.000	0.000	0.000
25	B	406	GLN	0	0.004	-0.001	30.629	0.002	0.002	0.000	0.000	0.000	0.000
26	B	407	CYS	0	-0.018	-0.011	32.336	0.002	0.002	0.000	0.000	0.000	0.000
27	B	408	ALA	0	0.022	0.008	35.088	0.004	0.004	0.000	0.000	0.000	0.000
28	B	409	ASN	0	-0.011	-0.006	36.814	0.009	0.009	0.000	0.000	0.000	0.000
29	B	410	LEU	0	-0.022	-0.006	36.430	0.004	0.004	0.000	0.000	0.000	0.000
30	B	411	GLN	0	0.001	0.000	38.702	0.004	0.004	0.000	0.000	0.000	0.000
31	B	412	ASN	0	0.006	0.007	41.065	0.002	0.002	0.000	0.000	0.000	0.000
32	B	413	ALA	0	0.013	0.001	42.854	0.002	0.002	0.000	0.000	0.000	0.000
33	B	414	ILE	0	-0.036	-0.015	42.012	0.003	0.003	0.000	0.000	0.000	0.000
34	B	415	ALA	0	0.075	0.042	45.570	0.003	0.003	0.000	0.000	0.000	0.000
35	B	416	ASP	-1	-0.919	-0.963	46.925	-0.048	-0.048	0.000	0.000	0.000	0.000
36	B	417	ALA	0	-0.079	-0.045	48.565	0.003	0.003	0.000	0.000	0.000	0.000
37	B	418	GLU	-1	-0.908	-0.944	48.793	-0.066	-0.066	0.000	0.000	0.000	0.000
38	B	419	GLN	0	-0.025	-0.006	51.627	0.003	0.003	0.000	0.000	0.000	0.000
39	B	420	ARG	1	0.926	0.959	49.089	0.051	0.051	0.000	0.000	0.000	0.000
40	B	421	GLY	0	0.005	0.000	54.150	0.002	0.002	0.000	0.000	0.000	0.000
41	B	422	GLU	-1	-0.738	-0.868	55.601	-0.045	-0.045	0.000	0.000	0.000	0.000
42	B	423	LEU	0	-0.043	0.008	57.540	0.001	0.001	0.000	0.000	0.000	0.000
43	B	424	ALA	0	0.061	0.035	58.943	0.001	0.001	0.000	0.000	0.000	0.000
44	B	425	LEU	0	-0.030	-0.015	58.337	0.001	0.001	0.000	0.000	0.000	0.000
45	B	426	LYS	1	0.811	0.887	59.292	0.044	0.044	0.000	0.000	0.000	0.000
46	B	427	ASP	-1	-0.873	-0.935	63.066	-0.032	-0.032	0.000	0.000	0.000	0.000
47	B	428	ALA	0	-0.047	-0.031	64.634	0.001	0.001	0.000	0.000	0.000	0.000
48	B	429	ARG	1	0.805	0.870	60.423	0.045	0.045	0.000	0.000	0.000	0.000
49	B	430	ASN	0	0.022	0.024	67.652	0.000	0.000	0.000	0.000	0.000	0.000
50	B	431	LYS	1	1.003	1.014	69.574	0.029	0.029	0.000	0.000	0.000	0.000
51	B	432	LEU	0	-0.037	-0.009	69.673	0.001	0.001	0.000	0.000	0.000	0.000
52	B	433	ALA	0	0.038	0.016	71.966	0.001	0.001	0.000	0.000	0.000	0.000
53	B	434	GLU	-1	-0.916	-0.954	73.811	-0.025	-0.025	0.000	0.000	0.000	0.000
54	B	435	LEU	0	-0.046	-0.036	73.404	0.001	0.001	0.000	0.000	0.000	0.000
55	B	436	GLU	-1	-0.941	-0.976	75.545	-0.030	-0.030	0.000	0.000	0.000	0.000
56	B	437	GLU	-1	-0.938	-0.954	77.511	-0.024	-0.024	0.000	0.000	0.000	0.000
57	B	438	ALA	0	0.012	-0.001	79.718	0.001	0.001	0.000	0.000	0.000	0.000
58	B	439	LEU	0	-0.045	-0.029	79.420	0.001	0.001	0.000	0.000	0.000	0.000
59	B	440	GLN	0	-0.052	-0.038	79.881	0.001	0.001	0.000	0.000	0.000	0.000
60	B	441	LYS	1	0.907	0.951	83.898	0.020	0.020	0.000	0.000	0.000	0.000
61	B	442	ALA	0	0.001	0.001	85.146	0.001	0.001	0.000	0.000	0.000	0.000
62	B	443	LYS	1	0.935	0.963	81.353	0.028	0.028	0.000	0.000	0.000	0.000
63	B	444	GLN	0	-0.001	0.003	86.738	0.001	0.001	0.000	0.000	0.000	0.000
64	B	445	ASP	-1	-0.759	-0.858	89.918	-0.018	-0.018	0.000	0.000	0.000	0.000
65	B	446	MET	0	-0.018	-0.007	90.354	0.001	0.001	0.000	0.000	0.000	0.000
66	B	447	ALA	0	-0.005	-0.006	91.960	0.000	0.000	0.000	0.000	0.000	0.000
67	B	448	ARG	1	0.753	0.841	93.758	0.018	0.018	0.000	0.000	0.000	0.000
68	B	449	LEU	0	0.006	0.009	93.500	0.000	0.000	0.000	0.000	0.000	0.000
69	B	450	LEU	0	-0.015	-0.004	94.170	0.000	0.000	0.000	0.000	0.000	0.000
70	B	451	ARG	1	0.924	0.966	95.991	0.019	0.019	0.000	0.000	0.000	0.000
71	B	452	GLU	-1	-0.775	-0.884	99.249	-0.016	-0.016	0.000	0.000	0.000	0.000
72	B	453	TYR	0	-0.034	-0.008	100.664	0.000	0.000	0.000	0.000	0.000	0.000
73	B	454	GLN	0	0.010	-0.001	101.574	0.001	0.001	0.000	0.000	0.000	0.000
74	B	455	GLU	-1	-0.952	-0.963	103.913	-0.016	-0.016	0.000	0.000	0.000	0.000
75	B	456	LEU	0	0.014	0.008	105.402	0.000	0.000	0.000	0.000	0.000	0.000
76	B	457	MET	0	-0.010	-0.011	106.074	0.000	0.000	0.000	0.000	0.000	0.000
77	B	458	ASN	0	-0.014	-0.016	107.867	0.000	0.000	0.000	0.000	0.000	0.000
78	B	459	THR	0	-0.016	-0.010	110.313	0.000	0.000	0.000	0.000	0.000	0.000
79	B	460	LYS	1	0.831	0.907	110.757	0.014	0.014	0.000	0.000	0.000	0.000
80	B	461	LEU	0	0.003	-0.002	110.578	0.000	0.000	0.000	0.000	0.000	0.000
81	B	462	ALA	0	-0.030	-0.021	114.257	0.000	0.000	0.000	0.000	0.000	0.000
82	B	463	LEU	0	0.039	0.017	115.537	0.000	0.000	0.000	0.000	0.000	0.000
83	B	464	ASP	-1	-0.814	-0.886	114.749	-0.013	-0.013	0.000	0.000	0.000	0.000
84	B	465	VAL	0	-0.057	-0.022	118.123	0.000	0.000	0.000	0.000	0.000	0.000
85	B	466	GLU	-1	-0.844	-0.904	120.754	-0.011	-0.011	0.000	0.000	0.000	0.000
86	B	467	ILE	0	0.016	0.009	118.981	0.000	0.000	0.000	0.000	0.000	0.000
87	B	468	ALA	0	-0.009	-0.004	122.322	0.000	0.000	0.000	0.000	0.000	0.000
88	B	469	THR	0	-0.087	-0.059	124.074	0.000	0.000	0.000	0.000	0.000	0.000
89	B	470	TYR	0	-0.037	-0.047	124.145	0.000	0.000	0.000	0.000	0.000	0.000
90	B	471	ARG	1	0.919	0.978	120.770	0.012	0.012	0.000	0.000	0.000	0.000
91	B	472	LYS	1	0.990	1.007	126.064	0.012	0.012	0.000	0.000	0.000	0.000
92	B	473	LEU	0	-0.049	-0.021	130.401	0.000	0.000	0.000	0.000	0.000	0.000
93	B	474	LEU	0	-0.063	-0.032	129.528	0.000	0.000	0.000	0.000	0.000	0.000
94	B	475	GLU	-1	-0.990	-0.982	129.275	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	476	GLY	0	-0.020	-0.005	134.078	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:382:THR)