FMO DATABASE

FMODB ID: 496QN

Calculation Name: 2B5I-D-Xray372

Preferred Name: Interleukin-2 receptor alpha chain

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 2B5I

Chain ID: D

ChEMBL ID: CHEMBL1778

UniProt ID: P01589

Base Structure: X-ray

Registration Date: 2023-06-22

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1047623.15553
FMO2-HF: Nuclear repulsion	993252.201127
FMO2-HF: Total energy	-54370.954403
FMO2-MP2: Total energy	-54517.953791

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(D:1:GLU)

Summations of interaction energy for fragment #1(D:1:GLU)

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.
-1.825	2.145	2.346	-2.433	-3.88	0.006

Interaction energy analysis for fragmet #1(D:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.987 / q_NPA : -1.006

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	D	3	CYS	0	-0.092	-0.021	3.824	-5.661	-3.844	-0.028	-0.877	-0.912	0.000
4	D	4	ASP	-1	-0.881	-0.937	6.200	25.867	25.867	0.000	0.000	0.000	0.000
5	D	5	ASP	-1	-0.888	-0.936	9.719	19.705	19.705	0.000	0.000	0.000	0.000
6	D	6	ASP	-1	-0.901	-0.953	11.055	18.673	18.673	0.000	0.000	0.000	0.000
7	D	7	PRO	0	-0.071	-0.035	12.584	-0.607	-0.607	0.000	0.000	0.000	0.000
8	D	8	PRO	0	0.030	0.021	15.021	-0.613	-0.613	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.882	-0.924	18.516	12.444	12.444	0.000	0.000	0.000	0.000
10	D	10	ILE	0	-0.063	-0.025	21.638	-0.284	-0.284	0.000	0.000	0.000	0.000
11	D	11	PRO	0	0.026	0.002	24.085	-0.122	-0.122	0.000	0.000	0.000	0.000
12	D	12	HIS	0	-0.014	-0.013	27.661	-0.024	-0.024	0.000	0.000	0.000	0.000
13	D	13	ALA	0	0.015	-0.012	24.930	-0.207	-0.207	0.000	0.000	0.000	0.000
14	D	14	THR	0	-0.006	0.020	22.829	0.160	0.160	0.000	0.000	0.000	0.000
15	D	15	PHE	0	0.052	0.010	15.643	-0.129	-0.129	0.000	0.000	0.000	0.000
16	D	16	LYS	1	0.956	0.978	18.032	-12.600	-12.600	0.000	0.000	0.000	0.000
17	D	17	ALA	0	0.033	0.029	13.945	0.040	0.040	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.059	-0.027	15.909	-0.369	-0.369	0.000	0.000	0.000	0.000
19	D	19	ALA	0	-0.026	-0.023	14.675	-0.308	-0.308	0.000	0.000	0.000	0.000
20	D	20	TYR	0	-0.017	-0.011	11.179	0.619	0.619	0.000	0.000	0.000	0.000
21	D	21	LYS	1	0.953	0.978	6.872	-29.028	-29.028	0.000	0.000	0.000	0.000
22	D	22	GLU	-1	-0.890	-0.906	5.606	36.130	36.130	0.000	0.000	0.000	0.000
23	D	23	GLY	0	0.047	0.028	3.889	5.508	5.874	0.000	-0.038	-0.327	0.000
24	D	24	THR	0	-0.117	-0.042	4.912	-2.537	-2.564	-0.001	-0.001	0.031	0.000
25	D	25	MET	0	-0.006	-0.013	7.814	-0.545	-0.545	0.000	0.000	0.000	0.000
26	D	26	LEU	0	-0.005	0.007	10.312	-1.068	-1.068	0.000	0.000	0.000	0.000
27	D	27	ASN	0	0.055	0.034	14.045	1.099	1.099	0.000	0.000	0.000	0.000
28	D	28	CYS	0	-0.085	0.020	16.443	-0.489	-0.489	0.000	0.000	0.000	0.000
29	D	29	GLU	-1	-0.847	-0.926	19.639	14.302	14.302	0.000	0.000	0.000	0.000
30	D	30	CYS	0	-0.110	-0.049	22.213	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	31	LYS	1	0.947	0.991	25.875	-9.786	-9.786	0.000	0.000	0.000	0.000
32	D	32	ARG	1	0.996	0.975	28.826	-10.033	-10.033	0.000	0.000	0.000	0.000
33	D	33	GLY	0	0.028	0.017	31.636	-0.212	-0.212	0.000	0.000	0.000	0.000
34	D	34	PHE	0	-0.053	-0.027	29.724	-0.179	-0.179	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.945	0.981	27.137	-10.783	-10.783	0.000	0.000	0.000	0.000
36	D	36	ARG	1	1.044	1.017	21.690	-14.063	-14.063	0.000	0.000	0.000	0.000
37	D	37	ILE	0	-0.023	-0.004	25.556	-0.322	-0.322	0.000	0.000	0.000	0.000
38	D	38	LYS	1	0.918	0.948	25.599	-9.612	-9.612	0.000	0.000	0.000	0.000
39	D	39	SER	0	0.005	-0.015	24.179	-0.114	-0.114	0.000	0.000	0.000	0.000
40	D	40	GLY	0	-0.001	0.021	22.531	0.309	0.309	0.000	0.000	0.000	0.000
41	D	41	SER	0	0.042	0.023	16.930	0.426	0.426	0.000	0.000	0.000	0.000
42	D	42	LEU	0	-0.004	-0.022	16.392	-0.638	-0.638	0.000	0.000	0.000	0.000
43	D	43	TYR	0	0.025	0.010	10.478	-0.618	-0.618	0.000	0.000	0.000	0.000
44	D	44	MET	0	-0.041	-0.017	14.140	-0.701	-0.701	0.000	0.000	0.000	0.000
45	D	45	LEU	0	0.032	0.003	6.442	-0.105	-0.105	0.000	0.000	0.000	0.000
46	D	46	CYS	0	-0.085	-0.003	8.837	-2.610	-2.610	0.000	0.000	0.000	0.000
47	D	47	THR	0	0.037	-0.030	7.994	5.603	5.603	0.000	0.000	0.000	0.000
48	D	48	GLY	0	0.033	0.060	9.349	-2.771	-2.771	0.000	0.000	0.000	0.000
49	D	49	ASN	0	0.084	0.020	9.969	1.613	1.613	0.000	0.000	0.000	0.000
50	D	50	SER	0	0.039	0.017	11.531	-1.204	-1.204	0.000	0.000	0.000	0.000
51	D	51	SER	0	-0.103	-0.057	13.905	-1.513	-1.513	0.000	0.000	0.000	0.000
52	D	52	HIS	0	-0.056	-0.023	14.727	-0.603	-0.603	0.000	0.000	0.000	0.000
53	D	53	SER	0	0.044	-0.008	11.278	1.450	1.450	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.074	-0.043	13.021	-1.286	-1.286	0.000	0.000	0.000	0.000
55	D	55	TRP	0	0.000	-0.011	11.761	1.980	1.980	0.000	0.000	0.000	0.000
56	D	56	ASP	-1	-0.863	-0.940	11.907	23.544	23.544	0.000	0.000	0.000	0.000
57	D	57	ASN	0	-0.082	-0.028	13.704	-1.898	-1.898	0.000	0.000	0.000	0.000
58	D	58	GLN	0	0.002	-0.025	16.349	-0.397	-0.397	0.000	0.000	0.000	0.000
59	D	60	GLN	0	0.077	0.025	21.021	-0.323	-0.323	0.000	0.000	0.000	0.000
60	D	62	THR	0	-0.007	-0.004	27.494	-0.284	-0.284	0.000	0.000	0.000	0.000
61	D	63	SER	0	0.028	0.014	30.931	0.169	0.169	0.000	0.000	0.000	0.000
62	D	64	SER	0	-0.038	-0.006	32.073	0.043	0.043	0.000	0.000	0.000	0.000
63	D	103	HIS	0	0.013	0.003	10.992	0.356	0.356	0.000	0.000	0.000	0.000
64	D	105	ARG	1	0.938	0.964	13.902	-14.500	-14.500	0.000	0.000	0.000	0.000
65	D	106	GLU	-1	-0.758	-0.879	16.609	16.385	16.385	0.000	0.000	0.000	0.000
66	D	107	PRO	0	-0.017	0.005	16.373	-0.759	-0.759	0.000	0.000	0.000	0.000
67	D	108	PRO	0	0.032	-0.001	19.148	-0.423	-0.423	0.000	0.000	0.000	0.000
68	D	109	PRO	0	-0.026	-0.014	22.523	0.371	0.371	0.000	0.000	0.000	0.000
69	D	110	TRP	0	0.007	0.014	19.481	-0.320	-0.320	0.000	0.000	0.000	0.000
70	D	111	GLU	-1	-0.957	-0.983	25.436	9.808	9.808	0.000	0.000	0.000	0.000
71	D	112	ASN	0	-0.072	-0.033	28.105	-0.442	-0.442	0.000	0.000	0.000	0.000
72	D	113	GLU	-1	-0.710	-0.876	23.140	13.437	13.437	0.000	0.000	0.000	0.000
73	D	114	ALA	0	-0.066	-0.033	23.466	-0.604	-0.604	0.000	0.000	0.000	0.000
74	D	115	THR	0	-0.036	-0.033	24.686	0.101	0.101	0.000	0.000	0.000	0.000
75	D	116	GLU	-1	-0.919	-0.949	21.757	12.473	12.473	0.000	0.000	0.000	0.000
76	D	117	ARG	1	0.763	0.894	18.315	-14.281	-14.281	0.000	0.000	0.000	0.000
77	D	118	ILE	0	0.000	0.008	15.551	0.212	0.212	0.000	0.000	0.000	0.000
78	D	119	TYR	0	-0.033	-0.038	12.224	0.288	0.288	0.000	0.000	0.000	0.000
79	D	120	HIS	0	0.009	0.006	9.188	0.290	0.290	0.000	0.000	0.000	0.000
80	D	121	PHE	0	-0.014	-0.013	7.808	1.398	1.398	0.000	0.000	0.000	0.000
81	D	122	VAL	0	0.086	0.045	2.374	0.376	1.087	0.890	-0.659	-0.942	0.000
82	D	123	VAL	0	0.032	-0.017	2.606	-6.192	-5.268	1.487	-0.853	-1.558	0.006
83	D	124	GLY	0	-0.082	-0.047	4.824	0.536	0.659	-0.001	-0.003	-0.119	0.000
84	D	125	GLN	0	-0.065	-0.026	7.192	-0.850	-0.850	0.000	0.000	0.000	0.000
85	D	126	MET	0	-0.006	0.003	9.019	-1.102	-1.102	0.000	0.000	0.000	0.000
86	D	127	VAL	0	-0.013	-0.001	12.742	0.162	0.162	0.000	0.000	0.000	0.000
87	D	128	TYR	0	0.026	0.010	15.090	-0.717	-0.717	0.000	0.000	0.000	0.000
88	D	129	TYR	0	0.009	-0.027	17.362	0.159	0.159	0.000	0.000	0.000	0.000
89	D	130	GLN	0	-0.044	-0.033	21.524	-0.159	-0.159	0.000	0.000	0.000	0.000
90	D	131	CYS	0	-0.054	0.018	25.159	0.005	0.005	0.000	0.000	0.000	0.000
91	D	132	VAL	0	0.003	0.016	28.280	-0.082	-0.082	0.000	0.000	0.000	0.000
92	D	133	GLN	0	0.039	-0.006	29.506	-0.177	-0.177	0.000	0.000	0.000	0.000
93	D	134	GLY	0	0.002	0.005	32.700	-0.148	-0.148	0.000	0.000	0.000	0.000
94	D	135	TYR	0	-0.058	-0.017	31.792	-0.226	-0.226	0.000	0.000	0.000	0.000
95	D	136	ARG	1	0.925	0.960	32.812	-7.572	-7.572	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.047	0.002	29.262	0.091	0.091	0.000	0.000	0.000	0.000
97	D	138	LEU	0	-0.037	-0.012	30.700	-0.214	-0.214	0.000	0.000	0.000	0.000
98	D	139	HIS	0	0.051	0.020	26.237	0.383	0.383	0.000	0.000	0.000	0.000
99	D	140	ARG	1	0.961	0.982	26.781	-10.429	-10.429	0.000	0.000	0.000	0.000
100	D	141	GLY	0	-0.034	-0.038	25.223	0.211	0.211	0.000	0.000	0.000	0.000
101	D	142	PRO	0	0.034	0.029	20.282	-0.264	-0.264	0.000	0.000	0.000	0.000
102	D	143	ALA	0	0.039	0.026	22.205	-0.080	-0.080	0.000	0.000	0.000	0.000
103	D	144	GLU	-1	-0.911	-0.968	16.864	13.861	13.861	0.000	0.000	0.000	0.000
104	D	145	SER	0	-0.054	-0.037	14.967	0.143	0.143	0.000	0.000	0.000	0.000
105	D	146	VAL	0	-0.001	-0.028	10.771	0.567	0.567	0.000	0.000	0.000	0.000
106	D	148	LYS	1	0.914	0.956	8.281	-17.463	-17.463	0.000	0.000	0.000	0.000
107	D	149	MET	0	0.050	0.012	5.217	-0.542	-0.486	-0.001	-0.002	-0.053	0.000
108	D	150	THR	0	-0.101	-0.049	8.238	-1.695	-1.695	0.000	0.000	0.000	0.000
109	D	151	HIS	0	0.037	0.022	10.080	1.080	1.080	0.000	0.000	0.000	0.000
110	D	152	GLY	0	0.006	-0.010	8.610	-0.980	-0.980	0.000	0.000	0.000	0.000
111	D	153	LYS	1	0.960	0.986	9.280	-20.305	-20.305	0.000	0.000	0.000	0.000
112	D	154	THR	0	0.047	0.046	5.870	0.080	0.080	0.000	0.000	0.000	0.000
113	D	155	ARG	1	0.972	0.995	9.043	-19.181	-19.181	0.000	0.000	0.000	0.000
114	D	156	TRP	0	0.043	0.027	9.688	1.274	1.274	0.000	0.000	0.000	0.000
115	D	157	THR	0	-0.110	-0.047	13.125	-0.789	-0.789	0.000	0.000	0.000	0.000
116	D	158	GLN	0	0.054	0.032	15.881	0.530	0.530	0.000	0.000	0.000	0.000
117	D	159	PRO	0	0.013	0.025	18.290	-0.317	-0.317	0.000	0.000	0.000	0.000
118	D	160	GLN	0	-0.062	-0.024	20.780	-0.169	-0.169	0.000	0.000	0.000	0.000
119	D	161	LEU	0	-0.018	-0.016	24.277	-0.411	-0.411	0.000	0.000	0.000	0.000
120	D	162	ILE	0	0.014	0.008	26.204	0.091	0.091	0.000	0.000	0.000	0.000
121	D	164	THR	0	0.024	0.010	30.621	-0.130	-0.130	0.000	0.000	0.000	0.000
122	D	165	GLY	0	0.012	0.017	34.363	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:GLU)