FMO DATABASE

FMODB ID: ZYMVN

Calculation Name: 1I1R-B-Xray372

Preferred Name: Interleukin-6 receptor subunit beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1I1R

Chain ID: B

ChEMBL ID: CHEMBL3124734

UniProt ID: P40189

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	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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1787664.922212
FMO2-HF: Nuclear repulsion	1719775.708015
FMO2-HF: Total energy	-67889.214197
FMO2-MP2: Total energy	-68086.406911

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:6:GLU)

Summations of interaction energy for fragment #1(B:6: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.
8.961	7.501	13.336	-5.764	-6.113	0.069

Interaction energy analysis for fragmet #1(B:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.935 / q_NPA : -0.973

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	B	8	GLU	-1	-0.907	-0.960	3.817	26.395	28.108	-0.014	-0.618	-1.081	0.002
4	B	9	LYS	1	0.851	0.922	6.044	-30.860	-30.860	0.000	0.000	0.000	0.000
5	B	10	ASP	-1	-0.850	-0.921	9.029	20.915	20.915	0.000	0.000	0.000	0.000
6	B	11	LEU	0	0.007	0.008	8.418	-2.041	-2.041	0.000	0.000	0.000	0.000
7	B	12	LEU	0	-0.018	-0.018	8.688	-2.029	-2.029	0.000	0.000	0.000	0.000
8	B	13	ILE	0	0.058	0.018	11.729	-1.736	-1.736	0.000	0.000	0.000	0.000
9	B	14	GLN	0	-0.023	-0.005	13.430	-0.661	-0.661	0.000	0.000	0.000	0.000
10	B	15	ARG	1	0.801	0.896	8.657	-26.076	-26.076	0.000	0.000	0.000	0.000
11	B	16	LEU	0	0.000	0.009	15.591	-1.050	-1.050	0.000	0.000	0.000	0.000
12	B	17	ASN	0	-0.007	-0.015	17.890	-1.503	-1.503	0.000	0.000	0.000	0.000
13	B	18	TRP	0	-0.005	0.024	17.969	-0.493	-0.493	0.000	0.000	0.000	0.000
14	B	19	MET	0	0.000	-0.027	18.764	-0.685	-0.685	0.000	0.000	0.000	0.000
15	B	20	LEU	0	-0.038	-0.027	21.532	-0.650	-0.650	0.000	0.000	0.000	0.000
16	B	21	TRP	0	-0.005	0.014	23.654	-0.466	-0.466	0.000	0.000	0.000	0.000
17	B	22	VAL	0	0.020	-0.002	24.327	-0.482	-0.482	0.000	0.000	0.000	0.000
18	B	23	ILE	0	0.001	0.000	24.946	-0.460	-0.460	0.000	0.000	0.000	0.000
19	B	24	ASP	-1	-0.853	-0.928	27.433	9.283	9.283	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.849	-0.918	28.902	9.302	9.302	0.000	0.000	0.000	0.000
21	B	26	CYS	0	-0.065	-0.016	29.428	-0.319	-0.319	0.000	0.000	0.000	0.000
22	B	27	PHE	0	0.002	-0.002	30.473	-0.382	-0.382	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.787	0.885	31.413	-9.680	-9.680	0.000	0.000	0.000	0.000
24	B	29	ASP	-1	-0.752	-0.840	34.860	8.016	8.016	0.000	0.000	0.000	0.000
25	B	30	LEU	0	-0.061	-0.032	35.858	-0.271	-0.271	0.000	0.000	0.000	0.000
26	B	31	CYS	0	-0.045	-0.030	37.684	-0.103	-0.103	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.014	-0.004	39.371	-0.283	-0.283	0.000	0.000	0.000	0.000
28	B	33	ARG	1	0.809	0.899	36.825	-8.260	-8.260	0.000	0.000	0.000	0.000
29	B	34	THR	0	-0.061	-0.047	41.020	-0.228	-0.228	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.027	0.037	42.754	-0.154	-0.154	0.000	0.000	0.000	0.000
31	B	36	ILE	0	-0.067	-0.043	39.497	0.005	0.005	0.000	0.000	0.000	0.000
32	B	38	LYS	1	0.835	0.889	32.100	-9.669	-9.669	0.000	0.000	0.000	0.000
33	B	39	GLY	0	-0.028	-0.019	37.797	-0.065	-0.065	0.000	0.000	0.000	0.000
34	B	40	ILE	0	-0.078	-0.022	40.307	-0.154	-0.154	0.000	0.000	0.000	0.000
35	B	41	LEU	0	-0.034	-0.018	42.451	-0.214	-0.214	0.000	0.000	0.000	0.000
36	B	42	GLU	-1	-0.808	-0.890	38.472	8.366	8.366	0.000	0.000	0.000	0.000
37	B	43	PRO	0	-0.026	-0.018	39.708	-0.189	-0.189	0.000	0.000	0.000	0.000
38	B	44	ALA	0	0.007	0.023	42.844	0.041	0.041	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.042	-0.044	42.066	-0.109	-0.109	0.000	0.000	0.000	0.000
40	B	46	ILE	0	0.001	0.002	41.927	0.080	0.080	0.000	0.000	0.000	0.000
41	B	47	PHE	0	0.047	0.031	33.764	0.105	0.105	0.000	0.000	0.000	0.000
42	B	48	HIS	0	-0.040	-0.027	37.728	-0.217	-0.217	0.000	0.000	0.000	0.000
43	B	49	LEU	0	-0.036	-0.020	31.884	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	50	LYS	1	0.863	0.943	27.966	-11.065	-11.065	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.001	-0.017	28.761	0.097	0.097	0.000	0.000	0.000	0.000
46	B	52	PRO	0	-0.016	0.010	23.713	-0.117	-0.117	0.000	0.000	0.000	0.000
47	B	53	ALA	0	0.021	-0.001	25.778	-0.150	-0.150	0.000	0.000	0.000	0.000
48	B	54	ILE	0	-0.015	0.004	20.997	0.093	0.093	0.000	0.000	0.000	0.000
49	B	55	ASN	0	-0.041	-0.018	24.555	-0.645	-0.645	0.000	0.000	0.000	0.000
50	B	56	ASP	-1	-0.852	-0.940	25.322	11.248	11.248	0.000	0.000	0.000	0.000
51	B	57	THR	0	-0.036	-0.029	25.756	0.089	0.089	0.000	0.000	0.000	0.000
52	B	58	ASP	-1	-0.768	-0.859	21.505	13.612	13.612	0.000	0.000	0.000	0.000
53	B	59	HIS	0	-0.059	-0.021	21.086	0.742	0.742	0.000	0.000	0.000	0.000
54	B	60	CYS	0	-0.013	-0.003	17.152	0.594	0.594	0.000	0.000	0.000	0.000
55	B	61	GLY	0	0.030	0.028	20.819	0.191	0.191	0.000	0.000	0.000	0.000
56	B	62	LEU	0	0.035	-0.009	20.877	0.215	0.215	0.000	0.000	0.000	0.000
57	B	63	ILE	0	-0.027	-0.005	22.941	0.134	0.134	0.000	0.000	0.000	0.000
58	B	64	GLY	0	0.019	0.009	24.174	-0.213	-0.213	0.000	0.000	0.000	0.000
59	B	65	PHE	0	-0.004	0.014	15.341	0.203	0.203	0.000	0.000	0.000	0.000
60	B	66	ASN	0	0.007	-0.027	17.328	0.368	0.368	0.000	0.000	0.000	0.000
61	B	67	GLU	-1	-0.845	-0.928	10.559	27.083	27.083	0.000	0.000	0.000	0.000
62	B	68	THR	0	-0.009	0.001	14.601	-0.041	-0.041	0.000	0.000	0.000	0.000
63	B	69	SER	0	-0.001	-0.004	15.746	-0.070	-0.070	0.000	0.000	0.000	0.000
64	B	71	LEU	0	0.049	0.022	10.508	-0.615	-0.615	0.000	0.000	0.000	0.000
65	B	72	LYS	1	0.795	0.890	14.670	-16.240	-16.240	0.000	0.000	0.000	0.000
66	B	73	LYS	1	0.818	0.902	16.775	-13.582	-13.582	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.017	0.001	14.952	-0.507	-0.507	0.000	0.000	0.000	0.000
68	B	75	ALA	0	0.025	0.012	13.911	-0.409	-0.409	0.000	0.000	0.000	0.000
69	B	76	ASP	-1	-0.826	-0.899	15.839	15.481	15.481	0.000	0.000	0.000	0.000
70	B	77	GLY	0	-0.004	-0.017	19.162	-0.678	-0.678	0.000	0.000	0.000	0.000
71	B	78	PHE	0	0.024	0.003	15.907	-0.755	-0.755	0.000	0.000	0.000	0.000
72	B	79	PHE	0	0.024	0.023	14.241	-0.408	-0.408	0.000	0.000	0.000	0.000
73	B	80	GLU	-1	-0.913	-0.951	19.416	11.596	11.596	0.000	0.000	0.000	0.000
74	B	81	PHE	0	-0.001	-0.008	21.176	-0.775	-0.775	0.000	0.000	0.000	0.000
75	B	82	GLU	-1	-0.804	-0.871	20.601	14.007	14.007	0.000	0.000	0.000	0.000
76	B	83	VAL	0	-0.044	-0.028	22.969	-0.487	-0.487	0.000	0.000	0.000	0.000
77	B	84	LEU	0	-0.008	-0.006	26.071	-0.526	-0.526	0.000	0.000	0.000	0.000
78	B	85	PHE	0	0.102	0.021	21.690	-0.409	-0.409	0.000	0.000	0.000	0.000
79	B	86	LYS	1	0.849	0.936	25.009	-12.038	-12.038	0.000	0.000	0.000	0.000
80	B	87	PHE	0	-0.061	-0.030	28.164	-0.382	-0.382	0.000	0.000	0.000	0.000
81	B	88	LEU	0	0.051	0.009	28.053	-0.315	-0.315	0.000	0.000	0.000	0.000
82	B	89	THR	0	0.035	0.029	27.346	-0.274	-0.274	0.000	0.000	0.000	0.000
83	B	90	THR	0	-0.073	-0.020	30.134	-0.316	-0.316	0.000	0.000	0.000	0.000
84	B	91	GLU	-1	-0.821	-0.897	33.360	8.010	8.010	0.000	0.000	0.000	0.000
85	B	92	PHE	0	-0.003	-0.017	31.539	-0.221	-0.221	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.004	0.022	31.257	-0.002	-0.002	0.000	0.000	0.000	0.000
87	B	94	LYS	1	0.819	0.894	32.254	-8.337	-8.337	0.000	0.000	0.000	0.000
88	B	95	SER	0	-0.069	-0.066	34.669	-0.129	-0.129	0.000	0.000	0.000	0.000
89	B	96	VAL	0	0.002	0.007	29.470	-0.033	-0.033	0.000	0.000	0.000	0.000
90	B	97	ILE	0	0.021	0.007	27.697	0.154	0.154	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.008	-0.011	24.186	0.257	0.257	0.000	0.000	0.000	0.000
92	B	99	VAL	0	0.053	0.024	24.833	0.441	0.441	0.000	0.000	0.000	0.000
93	B	100	ASP	-1	-0.910	-0.964	25.657	11.414	11.414	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.008	0.017	21.299	0.262	0.262	0.000	0.000	0.000	0.000
95	B	102	MET	0	0.000	0.026	20.605	0.833	0.833	0.000	0.000	0.000	0.000
96	B	103	GLU	-1	-0.852	-0.922	20.585	12.278	12.278	0.000	0.000	0.000	0.000
97	B	104	LEU	0	-0.017	-0.008	18.399	0.443	0.443	0.000	0.000	0.000	0.000
98	B	105	LEU	0	0.036	0.023	15.427	1.166	1.166	0.000	0.000	0.000	0.000
99	B	106	THR	0	-0.004	-0.023	15.582	1.067	1.067	0.000	0.000	0.000	0.000
100	B	107	LYS	1	0.817	0.907	16.227	-14.858	-14.858	0.000	0.000	0.000	0.000
101	B	108	THR	0	-0.047	-0.035	11.079	1.060	1.060	0.000	0.000	0.000	0.000
102	B	109	LEU	0	-0.026	0.008	11.336	1.815	1.815	0.000	0.000	0.000	0.000
103	B	110	GLY	0	0.027	0.013	12.177	1.227	1.227	0.000	0.000	0.000	0.000
104	B	111	TRP	0	-0.010	-0.029	10.667	0.486	0.486	0.000	0.000	0.000	0.000
105	B	112	ASP	-1	-0.690	-0.835	7.395	31.280	31.280	0.000	0.000	0.000	0.000
106	B	113	ILE	0	-0.018	-0.004	7.832	3.250	3.250	0.000	0.000	0.000	0.000
107	B	114	GLN	0	-0.110	-0.076	10.148	-0.405	-0.405	0.000	0.000	0.000	0.000
108	B	115	GLU	-1	-0.993	-0.988	4.650	47.883	48.026	-0.001	-0.005	-0.137	0.000
109	B	116	GLU	-1	-0.806	-0.905	4.423	64.012	64.205	-0.001	-0.034	-0.159	0.000
110	B	117	LEU	0	-0.005	0.004	7.566	-1.399	-1.399	0.000	0.000	0.000	0.000
111	B	118	ASN	0	-0.005	0.003	9.320	-2.907	-2.907	0.000	0.000	0.000	0.000
112	B	119	LYS	1	0.832	0.925	1.789	-116.256	-119.765	13.352	-5.107	-4.736	0.067
113	B	120	LEU	0	-0.039	-0.004	8.265	-1.802	-1.802	0.000	0.000	0.000	0.000
114	B	121	THR	0	-0.074	-0.054	10.850	-3.608	-3.608	0.000	0.000	0.000	0.000
115	B	122	LYS	1	0.958	0.979	12.815	-18.787	-18.787	0.000	0.000	0.000	0.000
116	B	123	THR	0	-0.055	-0.020	15.271	-0.516	-0.516	0.000	0.000	0.000	0.000
117	B	124	HIS	0	0.038	0.026	12.413	1.132	1.132	0.000	0.000	0.000	0.000
118	B	125	TYR	0	-0.006	-0.018	14.063	-2.483	-2.483	0.000	0.000	0.000	0.000
119	B	126	SER	0	-0.014	-0.012	14.847	0.670	0.670	0.000	0.000	0.000	0.000
120	B	127	PRO	0	0.001	0.014	15.211	-0.671	-0.671	0.000	0.000	0.000	0.000
121	B	128	PRO	0	-0.008	-0.012	17.527	-0.828	-0.828	0.000	0.000	0.000	0.000
122	B	129	LYS	1	0.960	0.993	21.285	-11.944	-11.944	0.000	0.000	0.000	0.000
123	B	130	PHE	0	0.035	0.008	23.803	-0.392	-0.392	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.848	-0.933	25.141	9.938	9.938	0.000	0.000	0.000	0.000
125	B	132	ARG	1	0.993	0.983	28.239	-10.829	-10.829	0.000	0.000	0.000	0.000
126	B	133	GLY	0	0.030	0.029	30.959	-0.303	-0.303	0.000	0.000	0.000	0.000
127	B	134	LEU	0	-0.032	-0.014	29.038	-0.326	-0.326	0.000	0.000	0.000	0.000
128	B	135	LEU	0	0.034	0.025	29.349	-0.245	-0.245	0.000	0.000	0.000	0.000
129	B	136	GLY	0	-0.016	-0.005	32.042	-0.228	-0.228	0.000	0.000	0.000	0.000
130	B	137	ARG	1	0.922	0.958	34.954	-9.116	-9.116	0.000	0.000	0.000	0.000
131	B	138	LEU	0	-0.007	-0.005	31.373	-0.211	-0.211	0.000	0.000	0.000	0.000
132	B	139	GLN	0	-0.015	-0.017	33.691	-0.292	-0.292	0.000	0.000	0.000	0.000
133	B	140	GLY	0	0.016	0.011	36.254	-0.194	-0.194	0.000	0.000	0.000	0.000
134	B	141	LEU	0	-0.043	-0.002	37.407	-0.275	-0.275	0.000	0.000	0.000	0.000
135	B	142	LYS	1	0.958	0.975	40.632	-6.731	-6.731	0.000	0.000	0.000	0.000
136	B	143	TYR	0	0.016	-0.014	43.313	-0.069	-0.069	0.000	0.000	0.000	0.000
137	B	144	TRP	0	0.097	0.054	42.690	0.187	0.187	0.000	0.000	0.000	0.000
138	B	145	VAL	0	0.036	0.019	41.095	0.139	0.139	0.000	0.000	0.000	0.000
139	B	146	ARG	1	0.742	0.851	36.526	-8.058	-8.058	0.000	0.000	0.000	0.000
140	B	147	HIS	0	0.053	0.016	37.413	0.342	0.342	0.000	0.000	0.000	0.000
141	B	148	PHE	0	0.005	0.011	37.621	0.158	0.158	0.000	0.000	0.000	0.000
142	B	149	ALA	0	0.001	0.011	35.155	0.198	0.198	0.000	0.000	0.000	0.000
143	B	150	SER	0	0.017	0.000	33.400	0.345	0.345	0.000	0.000	0.000	0.000
144	B	151	PHE	0	-0.006	0.013	32.982	0.312	0.312	0.000	0.000	0.000	0.000
145	B	152	TYR	0	0.013	-0.008	33.598	0.193	0.193	0.000	0.000	0.000	0.000
146	B	153	VAL	0	-0.010	-0.006	28.618	0.291	0.291	0.000	0.000	0.000	0.000
147	B	154	LEU	0	0.041	0.026	28.839	0.436	0.436	0.000	0.000	0.000	0.000
148	B	155	SER	0	-0.035	-0.016	28.942	0.255	0.255	0.000	0.000	0.000	0.000
149	B	156	ALA	0	-0.049	-0.025	28.255	0.197	0.197	0.000	0.000	0.000	0.000
150	B	157	MET	0	-0.009	-0.009	24.329	0.310	0.310	0.000	0.000	0.000	0.000
151	B	158	GLU	-1	-0.816	-0.886	24.429	10.581	10.581	0.000	0.000	0.000	0.000
152	B	159	LYS	1	0.937	0.962	25.342	-9.581	-9.581	0.000	0.000	0.000	0.000
153	B	160	PHE	0	0.015	0.028	19.376	0.194	0.194	0.000	0.000	0.000	0.000
154	B	161	ALA	0	0.054	0.025	20.318	0.626	0.626	0.000	0.000	0.000	0.000
155	B	162	GLY	0	0.027	0.018	20.377	0.499	0.499	0.000	0.000	0.000	0.000
156	B	163	GLN	0	-0.056	-0.045	21.563	0.238	0.238	0.000	0.000	0.000	0.000
157	B	164	ALA	0	0.018	0.010	16.919	0.507	0.507	0.000	0.000	0.000	0.000
158	B	165	VAL	0	0.018	0.012	16.607	0.926	0.926	0.000	0.000	0.000	0.000
159	B	166	ARG	1	0.933	0.972	17.093	-12.345	-12.345	0.000	0.000	0.000	0.000
160	B	167	VAL	0	0.010	-0.008	15.315	0.291	0.291	0.000	0.000	0.000	0.000
161	B	168	LEU	0	-0.032	-0.021	11.192	0.849	0.849	0.000	0.000	0.000	0.000
162	B	169	ASP	-1	-0.878	-0.941	12.818	17.952	17.952	0.000	0.000	0.000	0.000
163	B	170	SER	0	-0.150	-0.065	15.148	-0.426	-0.426	0.000	0.000	0.000	0.000
164	B	171	ILE	0	-0.005	0.016	10.788	-0.132	-0.132	0.000	0.000	0.000	0.000
165	B	172	PRO	0	0.012	0.018	9.340	1.063	1.063	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:GLU)