FMO DATABASE

FMODB ID: YZ1N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1050025.134307
FMO2-HF: Nuclear repulsion	995652.261762
FMO2-HF: Total energy	-54372.872546
FMO2-MP2: Total energy	-54519.852085

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.
-6.324	-3.254	2.501	-2.114	-3.454	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 : -0.969 / q_NPA : -1.002

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	-0.040	0.010	3.871	-4.824	-3.478	-0.016	-0.626	-0.704	0.001
4	D	4	ASP	-1	-0.763	-0.841	6.518	26.310	26.310	0.000	0.000	0.000	0.000
5	D	5	ASP	-1	-0.835	-0.916	9.758	19.343	19.343	0.000	0.000	0.000	0.000
6	D	6	ASP	-1	-0.911	-0.944	10.948	18.455	18.455	0.000	0.000	0.000	0.000
7	D	7	PRO	0	-0.034	-0.018	12.846	-0.581	-0.581	0.000	0.000	0.000	0.000
8	D	8	PRO	0	0.018	0.012	15.157	-0.701	-0.701	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.891	-0.923	18.516	11.831	11.831	0.000	0.000	0.000	0.000
10	D	10	ILE	0	-0.046	-0.028	21.789	-0.164	-0.164	0.000	0.000	0.000	0.000
11	D	11	PRO	0	0.007	-0.004	24.410	-0.131	-0.131	0.000	0.000	0.000	0.000
12	D	12	HIS	0	0.011	0.006	28.072	-0.046	-0.046	0.000	0.000	0.000	0.000
13	D	13	ALA	0	0.009	0.004	25.007	-0.198	-0.198	0.000	0.000	0.000	0.000
14	D	14	THR	0	-0.005	0.010	23.040	0.121	0.121	0.000	0.000	0.000	0.000
15	D	15	PHE	0	0.041	0.010	16.380	-0.090	-0.090	0.000	0.000	0.000	0.000
16	D	16	LYS	1	0.916	0.952	17.999	-12.530	-12.530	0.000	0.000	0.000	0.000
17	D	17	ALA	0	0.047	0.043	13.783	0.101	0.101	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.026	-0.015	15.792	-0.789	-0.789	0.000	0.000	0.000	0.000
19	D	19	ALA	0	-0.028	-0.015	14.651	-0.554	-0.554	0.000	0.000	0.000	0.000
20	D	20	TYR	0	-0.025	-0.029	11.261	0.330	0.330	0.000	0.000	0.000	0.000
21	D	21	LYS	1	0.868	0.933	6.194	-27.114	-27.114	0.000	0.000	0.000	0.000
22	D	22	GLU	-1	-0.902	-0.960	5.270	36.470	36.470	0.000	0.000	0.000	0.000
23	D	23	GLY	0	0.020	0.015	3.880	4.230	4.471	0.000	-0.029	-0.212	0.000
24	D	24	THR	0	-0.097	-0.060	4.944	-3.039	-3.062	-0.001	-0.001	0.026	0.000
25	D	25	MET	0	0.005	-0.012	7.685	-1.000	-1.000	0.000	0.000	0.000	0.000
26	D	26	LEU	0	-0.015	-0.001	10.564	-0.763	-0.763	0.000	0.000	0.000	0.000
27	D	27	ASN	0	0.031	0.019	14.343	0.939	0.939	0.000	0.000	0.000	0.000
28	D	28	CYS	0	-0.111	-0.007	16.840	-0.444	-0.444	0.000	0.000	0.000	0.000
29	D	29	GLU	-1	-0.819	-0.908	19.956	13.720	13.720	0.000	0.000	0.000	0.000
30	D	30	CYS	0	-0.100	-0.054	22.366	0.090	0.090	0.000	0.000	0.000	0.000
31	D	31	LYS	1	0.884	0.960	26.063	-9.559	-9.559	0.000	0.000	0.000	0.000
32	D	32	ARG	1	0.969	0.968	29.184	-9.957	-9.957	0.000	0.000	0.000	0.000
33	D	33	GLY	0	0.042	0.025	31.786	-0.214	-0.214	0.000	0.000	0.000	0.000
34	D	34	PHE	0	-0.064	-0.029	30.126	-0.217	-0.217	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.885	0.943	27.691	-10.543	-10.543	0.000	0.000	0.000	0.000
36	D	36	ARG	1	0.988	0.980	21.843	-14.038	-14.038	0.000	0.000	0.000	0.000
37	D	37	ILE	0	0.006	0.013	25.651	-0.360	-0.360	0.000	0.000	0.000	0.000
38	D	38	LYS	1	0.927	0.955	26.052	-9.403	-9.403	0.000	0.000	0.000	0.000
39	D	39	SER	0	0.005	-0.016	24.541	-0.110	-0.110	0.000	0.000	0.000	0.000
40	D	40	GLY	0	0.033	0.046	23.082	0.349	0.349	0.000	0.000	0.000	0.000
41	D	41	SER	0	0.029	-0.001	17.793	-0.221	-0.221	0.000	0.000	0.000	0.000
42	D	42	LEU	0	-0.013	-0.010	16.759	-0.797	-0.797	0.000	0.000	0.000	0.000
43	D	43	TYR	0	0.039	0.008	11.135	-0.878	-0.878	0.000	0.000	0.000	0.000
44	D	44	MET	0	-0.029	0.003	14.662	-0.451	-0.451	0.000	0.000	0.000	0.000
45	D	45	LEU	0	0.039	0.004	7.328	0.083	0.083	0.000	0.000	0.000	0.000
46	D	46	CYS	0	-0.058	0.012	9.105	-2.845	-2.845	0.000	0.000	0.000	0.000
47	D	47	THR	0	0.033	-0.018	8.264	5.140	5.140	0.000	0.000	0.000	0.000
48	D	48	GLY	0	-0.023	-0.035	9.059	-2.591	-2.591	0.000	0.000	0.000	0.000
49	D	49	ASN	0	0.064	0.025	10.401	2.666	2.666	0.000	0.000	0.000	0.000
50	D	50	SER	0	0.062	0.034	11.334	-1.245	-1.245	0.000	0.000	0.000	0.000
51	D	51	SER	0	-0.123	-0.071	13.303	-1.578	-1.578	0.000	0.000	0.000	0.000
52	D	52	HIS	0	-0.056	-0.013	15.020	-0.744	-0.744	0.000	0.000	0.000	0.000
53	D	53	SER	0	0.023	-0.002	13.237	1.843	1.843	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.050	-0.017	13.427	-1.628	-1.628	0.000	0.000	0.000	0.000
55	D	55	TRP	0	-0.018	-0.024	11.891	1.834	1.834	0.000	0.000	0.000	0.000
56	D	56	ASP	-1	-0.787	-0.852	11.708	23.028	23.028	0.000	0.000	0.000	0.000
57	D	57	ASN	0	-0.053	-0.013	14.533	-1.140	-1.140	0.000	0.000	0.000	0.000
58	D	58	GLN	0	0.002	-0.010	16.708	-0.362	-0.362	0.000	0.000	0.000	0.000
59	D	60	GLN	0	0.071	0.023	21.317	-0.236	-0.236	0.000	0.000	0.000	0.000
60	D	62	THR	0	0.013	0.003	27.721	-0.222	-0.222	0.000	0.000	0.000	0.000
61	D	63	SER	0	0.018	0.006	31.243	0.104	0.104	0.000	0.000	0.000	0.000
62	D	64	SER	0	-0.052	-0.021	32.575	0.088	0.088	0.000	0.000	0.000	0.000
63	D	103	HIS	0	0.076	0.048	10.431	0.432	0.432	0.000	0.000	0.000	0.000
64	D	105	ARG	1	0.891	0.927	13.901	-14.525	-14.525	0.000	0.000	0.000	0.000
65	D	106	GLU	-1	-0.733	-0.828	16.782	15.908	15.908	0.000	0.000	0.000	0.000
66	D	107	PRO	0	0.004	0.016	16.642	-0.644	-0.644	0.000	0.000	0.000	0.000
67	D	108	PRO	0	0.044	0.018	19.397	-0.428	-0.428	0.000	0.000	0.000	0.000
68	D	109	PRO	0	-0.002	0.004	22.593	0.334	0.334	0.000	0.000	0.000	0.000
69	D	110	TRP	0	-0.002	-0.004	19.104	-0.290	-0.290	0.000	0.000	0.000	0.000
70	D	111	GLU	-1	-0.909	-0.966	25.481	9.621	9.621	0.000	0.000	0.000	0.000
71	D	112	ASN	0	-0.046	-0.032	27.969	-0.455	-0.455	0.000	0.000	0.000	0.000
72	D	113	GLU	-1	-0.687	-0.794	22.530	13.121	13.121	0.000	0.000	0.000	0.000
73	D	114	ALA	0	-0.062	-0.019	23.732	-0.531	-0.531	0.000	0.000	0.000	0.000
74	D	115	THR	0	-0.045	-0.041	25.037	0.004	0.004	0.000	0.000	0.000	0.000
75	D	116	GLU	-1	-0.879	-0.929	21.889	11.880	11.880	0.000	0.000	0.000	0.000
76	D	117	ARG	1	0.693	0.785	18.242	-13.776	-13.776	0.000	0.000	0.000	0.000
77	D	118	ILE	0	0.011	0.007	15.948	0.408	0.408	0.000	0.000	0.000	0.000
78	D	119	TYR	0	-0.026	-0.037	12.467	0.659	0.659	0.000	0.000	0.000	0.000
79	D	120	HIS	0	-0.010	0.004	9.542	0.402	0.402	0.000	0.000	0.000	0.000
80	D	121	PHE	0	-0.009	0.013	8.100	1.527	1.527	0.000	0.000	0.000	0.000
81	D	122	VAL	0	0.090	0.044	2.505	0.448	0.955	0.569	-0.403	-0.672	0.001
82	D	123	VAL	0	0.024	-0.007	2.356	-6.389	-5.503	1.950	-1.052	-1.784	0.004
83	D	124	GLY	0	-0.038	-0.021	4.736	-0.030	0.083	-0.001	-0.003	-0.108	0.000
84	D	125	GLN	0	-0.065	-0.030	7.090	-0.818	-0.818	0.000	0.000	0.000	0.000
85	D	126	MET	0	-0.022	-0.010	8.873	-0.843	-0.843	0.000	0.000	0.000	0.000
86	D	127	VAL	0	0.005	0.008	12.466	0.003	0.003	0.000	0.000	0.000	0.000
87	D	128	TYR	0	0.029	0.011	15.106	-0.332	-0.332	0.000	0.000	0.000	0.000
88	D	129	TYR	0	-0.012	-0.035	17.241	0.207	0.207	0.000	0.000	0.000	0.000
89	D	130	GLN	0	-0.027	-0.007	21.599	0.026	0.026	0.000	0.000	0.000	0.000
90	D	131	CYS	0	0.013	0.032	25.290	0.062	0.062	0.000	0.000	0.000	0.000
91	D	132	VAL	0	0.007	0.014	28.388	0.008	0.008	0.000	0.000	0.000	0.000
92	D	133	GLN	0	0.032	-0.006	29.757	-0.095	-0.095	0.000	0.000	0.000	0.000
93	D	134	GLY	0	0.019	0.010	32.818	-0.147	-0.147	0.000	0.000	0.000	0.000
94	D	135	TYR	0	-0.110	-0.047	32.029	-0.295	-0.295	0.000	0.000	0.000	0.000
95	D	136	ARG	1	0.909	0.949	32.904	-7.446	-7.446	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.045	0.003	29.467	0.126	0.126	0.000	0.000	0.000	0.000
97	D	138	LEU	0	-0.032	-0.005	30.557	-0.248	-0.248	0.000	0.000	0.000	0.000
98	D	139	HIS	0	0.067	0.028	26.372	0.414	0.414	0.000	0.000	0.000	0.000
99	D	140	ARG	1	0.938	0.955	27.306	-10.282	-10.282	0.000	0.000	0.000	0.000
100	D	141	GLY	0	-0.028	-0.011	24.807	0.121	0.121	0.000	0.000	0.000	0.000
101	D	142	PRO	0	0.026	0.035	20.045	-0.327	-0.327	0.000	0.000	0.000	0.000
102	D	143	ALA	0	0.021	0.013	21.874	-0.195	-0.195	0.000	0.000	0.000	0.000
103	D	144	GLU	-1	-0.901	-0.970	17.022	13.833	13.833	0.000	0.000	0.000	0.000
104	D	145	SER	0	-0.039	-0.022	15.225	0.148	0.148	0.000	0.000	0.000	0.000
105	D	146	VAL	0	-0.011	-0.032	10.885	0.452	0.452	0.000	0.000	0.000	0.000
106	D	148	LYS	1	0.898	0.944	8.407	-18.256	-18.256	0.000	0.000	0.000	0.000
107	D	149	MET	0	0.041	0.025	5.353	0.028	0.028	0.000	0.000	0.000	0.000
108	D	150	THR	0	-0.053	-0.043	8.133	-2.459	-2.459	0.000	0.000	0.000	0.000
109	D	151	HIS	0	0.021	0.010	9.797	1.548	1.548	0.000	0.000	0.000	0.000
110	D	152	GLY	0	0.013	0.001	8.940	-1.158	-1.158	0.000	0.000	0.000	0.000
111	D	153	LYS	1	0.804	0.887	9.511	-24.192	-24.192	0.000	0.000	0.000	0.000
112	D	154	THR	0	-0.017	-0.017	5.646	0.404	0.404	0.000	0.000	0.000	0.000
113	D	155	ARG	1	0.949	0.986	8.897	-19.079	-19.079	0.000	0.000	0.000	0.000
114	D	156	TRP	0	0.018	0.005	10.031	1.138	1.138	0.000	0.000	0.000	0.000
115	D	157	THR	0	-0.076	-0.037	13.133	-0.562	-0.562	0.000	0.000	0.000	0.000
116	D	158	GLN	0	0.048	0.033	15.873	0.469	0.469	0.000	0.000	0.000	0.000
117	D	159	PRO	0	0.016	0.031	18.331	-0.227	-0.227	0.000	0.000	0.000	0.000
118	D	160	GLN	0	-0.078	-0.055	20.697	-0.211	-0.211	0.000	0.000	0.000	0.000
119	D	161	LEU	0	-0.017	-0.012	24.250	-0.422	-0.422	0.000	0.000	0.000	0.000
120	D	162	ILE	0	0.012	0.009	26.180	0.092	0.092	0.000	0.000	0.000	0.000
121	D	164	THR	0	-0.016	-0.024	30.820	-0.164	-0.164	0.000	0.000	0.000	0.000
122	D	165	GLY	0	0.041	0.047	34.554	-0.089	-0.089	0.000	0.000	0.000	0.000

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