FMO DATABASE

FMODB ID: JL6Y9

Calculation Name: 3TNU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TNU

Chain ID: A

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:

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-440420.134781
FMO2-HF: Nuclear repulsion	401739.198953
FMO2-HF: Total energy	-38680.935828
FMO2-MP2: Total energy	-38788.982339

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:332:SER)

Summations of interaction energy for fragment #1(A:332:SER)

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.
-14.154	-7.419	3.708	-4.385	-6.058	0.013

Interaction energy analysis for fragmet #1(A:332:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.009

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	334	LEU	0	0.051	0.029	2.977	-3.627	-1.052	0.067	-1.188	-1.453	0.002
4	A	335	ARG	1	0.972	0.977	2.471	-0.605	1.202	2.171	-1.535	-2.443	-0.005
5	A	336	ARG	1	0.946	0.979	2.371	-9.489	-7.136	1.470	-1.662	-2.162	0.016
6	A	337	THR	0	-0.021	-0.007	5.552	-0.215	-0.215	0.000	0.000	0.000	0.000
7	A	338	MET	0	0.048	0.023	6.986	-0.094	-0.094	0.000	0.000	0.000	0.000
8	A	339	GLN	0	0.006	0.002	7.216	-0.125	-0.125	0.000	0.000	0.000	0.000
9	A	340	ASN	0	0.013	-0.005	9.445	-0.069	-0.069	0.000	0.000	0.000	0.000
10	A	341	LEU	0	0.006	0.013	11.489	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	342	GLU	-1	-0.941	-0.962	11.633	0.131	0.131	0.000	0.000	0.000	0.000
12	A	343	ILE	0	-0.038	-0.023	12.485	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	344	GLU	-1	-0.871	-0.934	15.467	0.195	0.195	0.000	0.000	0.000	0.000
14	A	345	LEU	0	-0.025	-0.018	17.011	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	346	GLN	0	0.036	0.008	17.951	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	347	SER	0	0.015	0.019	19.899	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	348	GLN	0	-0.025	-0.014	21.636	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	349	LEU	0	-0.031	-0.016	21.489	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	350	SER	0	-0.021	0.001	23.919	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	351	MET	0	-0.037	-0.034	25.642	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	352	LYS	1	0.936	0.977	27.284	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	353	ALA	0	0.050	0.036	28.643	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	354	SER	0	-0.067	-0.035	30.442	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	355	LEU	0	0.027	0.002	31.607	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	356	GLU	-1	-0.956	-0.980	31.935	0.049	0.049	0.000	0.000	0.000	0.000
26	A	357	ASN	0	0.027	0.004	34.121	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	358	SER	0	0.011	0.031	36.258	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	359	LEU	0	-0.013	0.010	37.756	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	360	GLU	-1	-0.946	-0.990	39.345	0.032	0.032	0.000	0.000	0.000	0.000
30	A	361	GLU	-1	-0.935	-0.961	40.558	0.044	0.044	0.000	0.000	0.000	0.000
31	A	362	THR	0	-0.100	-0.074	41.612	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	363	LYS	1	0.934	0.962	42.196	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	364	GLY	0	0.046	0.029	45.442	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	365	ARG	1	0.985	1.008	44.775	-0.041	-0.041	0.000	0.000	0.000	0.000
35	A	366	TYR	0	-0.026	-0.020	47.003	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	367	CYS	0	-0.038	-0.007	49.782	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	368	MET	0	0.058	0.014	51.265	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	369	GLN	0	-0.021	-0.018	51.200	0.001	0.001	0.000	0.000	0.000	0.000
39	A	370	LEU	0	-0.022	-0.006	54.261	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	371	ALA	0	0.017	-0.003	55.724	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	372	GLN	0	0.011	0.006	55.648	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	373	ILE	0	-0.033	-0.014	58.419	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	374	GLN	0	-0.002	-0.006	58.323	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	375	GLU	-1	-0.913	-0.942	61.734	0.016	0.016	0.000	0.000	0.000	0.000
45	A	376	MET	0	-0.063	-0.029	62.836	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	377	ILE	0	-0.023	-0.016	63.957	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	378	GLY	0	0.069	0.054	66.155	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	379	SER	0	0.030	0.011	67.845	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	380	VAL	0	-0.038	-0.021	69.286	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	381	GLU	-1	-0.950	-0.973	69.244	0.015	0.015	0.000	0.000	0.000	0.000
51	A	382	GLU	-1	-0.922	-0.959	71.429	0.013	0.013	0.000	0.000	0.000	0.000
52	A	383	GLN	0	-0.012	0.003	73.733	0.000	0.000	0.000	0.000	0.000	0.000
53	A	384	LEU	0	-0.083	-0.056	75.168	0.000	0.000	0.000	0.000	0.000	0.000
54	A	385	ALA	0	-0.029	-0.028	76.379	0.000	0.000	0.000	0.000	0.000	0.000
55	A	386	GLN	0	0.012	0.009	77.933	0.000	0.000	0.000	0.000	0.000	0.000
56	A	387	LEU	0	0.008	0.010	79.724	0.000	0.000	0.000	0.000	0.000	0.000
57	A	388	ARG	1	0.923	0.952	77.589	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	389	CYS	0	-0.013	0.001	82.347	0.000	0.000	0.000	0.000	0.000	0.000
59	A	390	GLU	-1	-0.885	-0.954	83.508	0.010	0.010	0.000	0.000	0.000	0.000
60	A	391	MET	0	-0.095	-0.048	84.950	0.000	0.000	0.000	0.000	0.000	0.000
61	A	392	GLU	-1	-0.906	-0.941	86.924	0.009	0.009	0.000	0.000	0.000	0.000
62	A	393	GLN	0	0.011	-0.010	88.529	0.000	0.000	0.000	0.000	0.000	0.000
63	A	394	GLN	0	-0.016	0.005	90.097	0.000	0.000	0.000	0.000	0.000	0.000
64	A	395	ASN	0	0.000	-0.005	90.054	0.000	0.000	0.000	0.000	0.000	0.000
65	A	396	GLN	0	-0.030	-0.010	91.252	0.000	0.000	0.000	0.000	0.000	0.000
66	A	397	GLU	-1	-0.910	-0.954	93.540	0.008	0.008	0.000	0.000	0.000	0.000
67	A	398	TYR	0	-0.019	-0.011	96.042	0.000	0.000	0.000	0.000	0.000	0.000
68	A	399	LYS	1	0.841	0.933	97.536	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	400	ILE	0	0.015	0.011	98.068	0.000	0.000	0.000	0.000	0.000	0.000
70	A	401	LEU	0	-0.003	0.001	100.759	0.000	0.000	0.000	0.000	0.000	0.000
71	A	402	LEU	0	-0.022	-0.022	101.592	0.000	0.000	0.000	0.000	0.000	0.000
72	A	403	ASP	-1	-0.808	-0.923	103.475	0.007	0.007	0.000	0.000	0.000	0.000
73	A	404	VAL	0	-0.071	-0.034	105.501	0.000	0.000	0.000	0.000	0.000	0.000
74	A	405	LYS	1	0.919	0.971	106.402	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	406	THR	0	-0.027	-0.021	106.775	0.000	0.000	0.000	0.000	0.000	0.000
76	A	407	ARG	1	0.997	1.016	108.826	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	408	LEU	0	-0.013	-0.011	110.383	0.000	0.000	0.000	0.000	0.000	0.000
78	A	409	GLU	-1	-0.911	-0.963	110.992	0.007	0.007	0.000	0.000	0.000	0.000
79	A	410	GLN	0	-0.007	-0.022	113.511	0.000	0.000	0.000	0.000	0.000	0.000
80	A	411	GLU	-1	-0.936	-0.945	115.259	0.005	0.005	0.000	0.000	0.000	0.000
81	A	412	ILE	0	0.012	-0.004	115.568	0.000	0.000	0.000	0.000	0.000	0.000
82	A	413	ALA	0	-0.015	0.000	118.394	0.000	0.000	0.000	0.000	0.000	0.000
83	A	414	THR	0	-0.061	-0.034	120.136	0.000	0.000	0.000	0.000	0.000	0.000
84	A	415	TYR	0	0.070	0.023	119.553	0.000	0.000	0.000	0.000	0.000	0.000
85	A	416	ARG	1	0.876	0.938	118.279	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	417	ARG	1	0.930	0.983	124.339	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	418	LEU	0	-0.049	-0.047	125.753	0.000	0.000	0.000	0.000	0.000	0.000
88	A	419	LEU	0	-0.059	-0.012	126.709	0.000	0.000	0.000	0.000	0.000	0.000
89	A	420	GLU	-1	-0.923	-0.956	129.639	0.005	0.005	0.000	0.000	0.000	0.000
90	A	421	GLY	0	-0.056	-0.010	130.783	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:332:SER)