FMO DATABASE

FMODB ID: 52YRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1049787.602528
FMO2-HF: Nuclear repulsion	995415.722672
FMO2-HF: Total energy	-54371.879856
FMO2-MP2: Total energy	-54518.930221

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.
-2.681	1.166	1.966	-2.273	-3.539	0.004

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 : -0.988 / q_NPA : -1.005

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

Sort

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	-0.074	-0.023	3.824	-5.711	-3.888	-0.027	-0.886	-0.909	0.000
4	D	4	ASP	-1	-0.775	-0.849	6.221	24.989	24.989	0.000	0.000	0.000	0.000
5	D	5	ASP	-1	-0.853	-0.921	9.742	19.420	19.420	0.000	0.000	0.000	0.000
6	D	6	ASP	-1	-0.897	-0.943	11.079	18.301	18.301	0.000	0.000	0.000	0.000
7	D	7	PRO	0	-0.065	-0.034	12.623	-0.566	-0.566	0.000	0.000	0.000	0.000
8	D	8	PRO	0	0.030	0.018	15.039	-0.611	-0.611	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.885	-0.921	18.534	12.207	12.207	0.000	0.000	0.000	0.000
10	D	10	ILE	0	-0.046	-0.025	21.657	-0.270	-0.270	0.000	0.000	0.000	0.000
11	D	11	PRO	0	0.017	-0.001	24.101	-0.129	-0.129	0.000	0.000	0.000	0.000
12	D	12	HIS	0	0.008	0.001	27.678	-0.059	-0.059	0.000	0.000	0.000	0.000
13	D	13	ALA	0	0.016	-0.007	24.859	-0.203	-0.203	0.000	0.000	0.000	0.000
14	D	14	THR	0	0.001	0.021	22.836	0.147	0.147	0.000	0.000	0.000	0.000
15	D	15	PHE	0	0.042	0.007	16.018	-0.108	-0.108	0.000	0.000	0.000	0.000
16	D	16	LYS	1	0.917	0.954	18.059	-12.632	-12.632	0.000	0.000	0.000	0.000
17	D	17	ALA	0	0.038	0.028	13.969	0.033	0.033	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.049	-0.022	15.918	-0.419	-0.419	0.000	0.000	0.000	0.000
19	D	19	ALA	0	-0.033	-0.028	14.702	-0.320	-0.320	0.000	0.000	0.000	0.000
20	D	20	TYR	0	-0.019	-0.017	11.198	0.606	0.606	0.000	0.000	0.000	0.000
21	D	21	LYS	1	0.940	0.976	6.812	-27.958	-27.958	0.000	0.000	0.000	0.000
22	D	22	GLU	-1	-0.900	-0.938	5.406	37.471	37.471	0.000	0.000	0.000	0.000
23	D	23	GLY	0	0.035	0.022	3.929	5.573	5.882	-0.001	-0.033	-0.275	0.000
24	D	24	THR	0	-0.129	-0.068	4.954	-2.770	-2.800	-0.001	-0.001	0.032	0.000
25	D	25	MET	0	-0.010	-0.020	7.897	-0.418	-0.418	0.000	0.000	0.000	0.000
26	D	26	LEU	0	-0.004	0.011	10.421	-0.927	-0.927	0.000	0.000	0.000	0.000
27	D	27	ASN	0	0.030	-0.003	14.152	1.037	1.037	0.000	0.000	0.000	0.000
28	D	28	CYS	0	-0.099	0.014	16.567	-0.521	-0.521	0.000	0.000	0.000	0.000
29	D	29	GLU	-1	-0.822	-0.896	19.755	14.173	14.173	0.000	0.000	0.000	0.000
30	D	30	CYS	0	-0.113	-0.056	22.340	0.001	0.001	0.000	0.000	0.000	0.000
31	D	31	LYS	1	0.901	0.973	25.998	-9.729	-9.729	0.000	0.000	0.000	0.000
32	D	32	ARG	1	1.005	0.980	28.950	-9.902	-9.902	0.000	0.000	0.000	0.000
33	D	33	GLY	0	0.036	0.021	31.768	-0.203	-0.203	0.000	0.000	0.000	0.000
34	D	34	PHE	0	-0.058	-0.033	29.856	-0.181	-0.181	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.888	0.946	27.751	-10.619	-10.619	0.000	0.000	0.000	0.000
36	D	36	ARG	1	1.011	0.989	21.903	-14.083	-14.083	0.000	0.000	0.000	0.000
37	D	37	ILE	0	0.001	0.014	25.786	-0.344	-0.344	0.000	0.000	0.000	0.000
38	D	38	LYS	1	0.923	0.951	26.077	-9.491	-9.491	0.000	0.000	0.000	0.000
39	D	39	SER	0	0.005	-0.016	24.601	-0.111	-0.111	0.000	0.000	0.000	0.000
40	D	40	GLY	0	0.030	0.041	22.977	0.302	0.302	0.000	0.000	0.000	0.000
41	D	41	SER	0	0.049	0.013	17.369	-0.194	-0.194	0.000	0.000	0.000	0.000
42	D	42	LEU	0	-0.029	-0.029	16.838	-0.612	-0.612	0.000	0.000	0.000	0.000
43	D	43	TYR	0	0.023	0.007	10.815	-0.893	-0.893	0.000	0.000	0.000	0.000
44	D	44	MET	0	-0.046	-0.011	14.349	-0.822	-0.822	0.000	0.000	0.000	0.000
45	D	45	LEU	0	0.049	0.011	6.896	-0.093	-0.093	0.000	0.000	0.000	0.000
46	D	46	CYS	0	-0.076	0.009	8.945	-2.307	-2.307	0.000	0.000	0.000	0.000
47	D	47	THR	0	0.133	0.028	8.187	5.140	5.140	0.000	0.000	0.000	0.000
48	D	48	GLY	0	-0.107	-0.123	8.934	-1.309	-1.309	0.000	0.000	0.000	0.000
49	D	49	ASN	0	0.111	0.060	9.303	1.187	1.187	0.000	0.000	0.000	0.000
50	D	50	SER	0	0.007	0.017	10.469	-1.264	-1.264	0.000	0.000	0.000	0.000
51	D	51	SER	0	-0.098	-0.052	12.841	-1.765	-1.765	0.000	0.000	0.000	0.000
52	D	52	HIS	0	-0.074	-0.026	14.386	-0.767	-0.767	0.000	0.000	0.000	0.000
53	D	53	SER	0	0.043	-0.001	12.171	1.794	1.794	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.003	-0.009	13.072	-1.685	-1.685	0.000	0.000	0.000	0.000
55	D	55	TRP	0	-0.023	-0.024	11.895	2.024	2.024	0.000	0.000	0.000	0.000
56	D	56	ASP	-1	-0.813	-0.888	11.123	24.467	24.467	0.000	0.000	0.000	0.000
57	D	57	ASN	0	-0.068	-0.012	14.124	-1.824	-1.824	0.000	0.000	0.000	0.000
58	D	58	GLN	0	0.020	-0.016	16.675	-0.588	-0.588	0.000	0.000	0.000	0.000
59	D	60	GLN	0	0.066	0.022	21.215	-0.311	-0.311	0.000	0.000	0.000	0.000
60	D	62	THR	0	0.001	0.001	27.602	-0.267	-0.267	0.000	0.000	0.000	0.000
61	D	63	SER	0	0.047	0.025	31.123	0.103	0.103	0.000	0.000	0.000	0.000
62	D	64	SER	0	-0.064	-0.019	32.335	0.032	0.032	0.000	0.000	0.000	0.000
63	D	103	HIS	0	-0.010	0.024	10.352	-0.007	-0.007	0.000	0.000	0.000	0.000
64	D	105	ARG	1	0.938	0.966	13.893	-14.575	-14.575	0.000	0.000	0.000	0.000
65	D	106	GLU	-1	-0.748	-0.856	16.635	16.212	16.212	0.000	0.000	0.000	0.000
66	D	107	PRO	0	-0.009	0.009	16.488	-0.712	-0.712	0.000	0.000	0.000	0.000
67	D	108	PRO	0	0.024	0.005	19.195	-0.406	-0.406	0.000	0.000	0.000	0.000
68	D	109	PRO	0	-0.016	-0.007	22.586	0.319	0.319	0.000	0.000	0.000	0.000
69	D	110	TRP	0	0.029	0.021	19.203	-0.320	-0.320	0.000	0.000	0.000	0.000
70	D	111	GLU	-1	-0.952	-0.979	25.513	9.638	9.638	0.000	0.000	0.000	0.000
71	D	112	ASN	0	-0.040	-0.023	28.252	-0.399	-0.399	0.000	0.000	0.000	0.000
72	D	113	GLU	-1	-0.693	-0.830	22.873	13.440	13.440	0.000	0.000	0.000	0.000
73	D	114	ALA	0	-0.068	-0.031	23.589	-0.574	-0.574	0.000	0.000	0.000	0.000
74	D	115	THR	0	-0.035	-0.029	24.752	0.071	0.071	0.000	0.000	0.000	0.000
75	D	116	GLU	-1	-0.907	-0.946	21.820	12.141	12.141	0.000	0.000	0.000	0.000
76	D	117	ARG	1	0.727	0.821	18.375	-13.980	-13.980	0.000	0.000	0.000	0.000
77	D	118	ILE	0	0.002	0.005	15.602	0.210	0.210	0.000	0.000	0.000	0.000
78	D	119	TYR	0	-0.024	-0.040	12.283	0.433	0.433	0.000	0.000	0.000	0.000
79	D	120	HIS	0	0.011	0.022	9.180	0.546	0.546	0.000	0.000	0.000	0.000
80	D	121	PHE	0	-0.008	0.011	7.828	1.359	1.359	0.000	0.000	0.000	0.000
81	D	122	VAL	0	0.085	0.047	2.375	0.375	1.025	0.884	-0.647	-0.887	0.001
82	D	123	VAL	0	0.024	-0.016	2.479	-6.057	-5.089	1.112	-0.703	-1.377	0.003
83	D	124	GLY	0	-0.064	-0.035	4.824	0.595	0.722	-0.001	-0.003	-0.123	0.000
84	D	125	GLN	0	-0.068	-0.031	7.194	-0.949	-0.949	0.000	0.000	0.000	0.000
85	D	126	MET	0	-0.007	0.006	9.022	-1.004	-1.004	0.000	0.000	0.000	0.000
86	D	127	VAL	0	0.000	0.006	12.503	0.150	0.150	0.000	0.000	0.000	0.000
87	D	128	TYR	0	0.022	0.007	15.099	-0.358	-0.358	0.000	0.000	0.000	0.000
88	D	129	TYR	0	0.001	-0.025	17.213	0.111	0.111	0.000	0.000	0.000	0.000
89	D	130	GLN	0	-0.017	-0.010	21.534	0.014	0.014	0.000	0.000	0.000	0.000
90	D	131	CYS	0	-0.043	0.016	25.170	-0.003	-0.003	0.000	0.000	0.000	0.000
91	D	132	VAL	0	0.003	0.017	28.293	-0.080	-0.080	0.000	0.000	0.000	0.000
92	D	133	GLN	0	0.038	-0.004	29.521	-0.115	-0.115	0.000	0.000	0.000	0.000
93	D	134	GLY	0	0.008	0.006	32.714	-0.147	-0.147	0.000	0.000	0.000	0.000
94	D	135	TYR	0	-0.080	-0.032	31.817	-0.278	-0.278	0.000	0.000	0.000	0.000
95	D	136	ARG	1	0.899	0.945	32.823	-7.524	-7.524	0.000	0.000	0.000	0.000
96	D	137	ALA	0	0.029	-0.005	29.311	0.090	0.090	0.000	0.000	0.000	0.000
97	D	138	LEU	0	-0.041	-0.013	30.714	-0.202	-0.202	0.000	0.000	0.000	0.000
98	D	139	HIS	0	0.062	0.022	26.511	0.421	0.421	0.000	0.000	0.000	0.000
99	D	140	ARG	1	0.951	0.981	26.684	-10.432	-10.432	0.000	0.000	0.000	0.000
100	D	141	GLY	0	-0.014	-0.018	25.222	0.213	0.213	0.000	0.000	0.000	0.000
101	D	142	PRO	0	0.030	0.025	20.283	-0.272	-0.272	0.000	0.000	0.000	0.000
102	D	143	ALA	0	0.029	0.024	22.147	-0.099	-0.099	0.000	0.000	0.000	0.000
103	D	144	GLU	-1	-0.901	-0.971	16.976	13.848	13.848	0.000	0.000	0.000	0.000
104	D	145	SER	0	-0.054	-0.034	14.964	0.155	0.155	0.000	0.000	0.000	0.000
105	D	146	VAL	0	-0.010	-0.032	10.923	0.549	0.549	0.000	0.000	0.000	0.000
106	D	148	LYS	1	0.905	0.952	8.280	-17.734	-17.734	0.000	0.000	0.000	0.000
107	D	149	MET	0	0.056	0.024	5.066	-0.302	-0.302	0.000	0.000	0.000	0.000
108	D	150	THR	0	-0.083	-0.049	8.238	-1.619	-1.619	0.000	0.000	0.000	0.000
109	D	151	HIS	0	0.028	0.017	10.080	1.230	1.230	0.000	0.000	0.000	0.000
110	D	152	GLY	0	0.010	-0.007	8.591	-1.038	-1.038	0.000	0.000	0.000	0.000
111	D	153	LYS	1	0.825	0.902	9.252	-22.622	-22.622	0.000	0.000	0.000	0.000
112	D	154	THR	0	-0.015	-0.010	5.775	-0.120	-0.120	0.000	0.000	0.000	0.000
113	D	155	ARG	1	0.992	1.005	9.043	-18.957	-18.957	0.000	0.000	0.000	0.000
114	D	156	TRP	0	0.042	0.028	9.664	1.414	1.414	0.000	0.000	0.000	0.000
115	D	157	THR	0	-0.090	-0.042	13.136	-0.763	-0.763	0.000	0.000	0.000	0.000
116	D	158	GLN	0	0.052	0.035	15.887	0.473	0.473	0.000	0.000	0.000	0.000
117	D	159	PRO	0	0.012	0.023	18.362	-0.303	-0.303	0.000	0.000	0.000	0.000
118	D	160	GLN	0	-0.091	-0.054	20.788	-0.304	-0.304	0.000	0.000	0.000	0.000
119	D	161	LEU	0	-0.017	-0.011	24.255	-0.396	-0.396	0.000	0.000	0.000	0.000
120	D	162	ILE	0	0.014	0.010	26.212	0.088	0.088	0.000	0.000	0.000	0.000
121	D	164	THR	0	0.019	0.011	30.634	-0.147	-0.147	0.000	0.000	0.000	0.000
122	D	165	GLY	0	0.050	0.035	34.376	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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