FMO DATABASE

FMODB ID: R5388

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	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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1787500.656078
FMO2-HF: Nuclear repulsion	1719610.846236
FMO2-HF: Total energy	-67889.809842
FMO2-MP2: Total energy	-68086.87636

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.
5.734	1.872	16.146	-6.332	-5.952	0.07

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 : -0.916 / q_NPA : -0.964

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	-0.949	3.874	25.635	27.286	-0.008	-0.608	-1.035	0.002
4	B	9	LYS	1	0.837	0.911	5.946	-32.728	-32.728	0.000	0.000	0.000	0.000
5	B	10	ASP	-1	-0.853	-0.924	8.890	21.792	21.792	0.000	0.000	0.000	0.000
6	B	11	LEU	0	-0.004	0.012	8.487	-2.098	-2.098	0.000	0.000	0.000	0.000
7	B	12	LEU	0	-0.009	-0.011	8.660	-1.881	-1.881	0.000	0.000	0.000	0.000
8	B	13	ILE	0	0.046	0.021	11.838	-1.706	-1.706	0.000	0.000	0.000	0.000
9	B	14	GLN	0	-0.016	-0.004	13.483	-0.766	-0.766	0.000	0.000	0.000	0.000
10	B	15	ARG	1	0.790	0.870	8.291	-26.432	-26.432	0.000	0.000	0.000	0.000
11	B	16	LEU	0	0.005	0.002	15.449	-1.075	-1.075	0.000	0.000	0.000	0.000
12	B	17	ASN	0	-0.042	-0.029	17.815	-1.532	-1.532	0.000	0.000	0.000	0.000
13	B	18	TRP	0	-0.019	0.005	18.008	-0.523	-0.523	0.000	0.000	0.000	0.000
14	B	19	MET	0	-0.012	-0.014	18.846	-0.684	-0.684	0.000	0.000	0.000	0.000
15	B	20	LEU	0	-0.027	-0.022	21.493	-0.668	-0.668	0.000	0.000	0.000	0.000
16	B	21	TRP	0	-0.014	0.001	23.731	-0.424	-0.424	0.000	0.000	0.000	0.000
17	B	22	VAL	0	0.015	-0.001	24.338	-0.503	-0.503	0.000	0.000	0.000	0.000
18	B	23	ILE	0	-0.013	-0.009	24.980	-0.444	-0.444	0.000	0.000	0.000	0.000
19	B	24	ASP	-1	-0.831	-0.907	27.548	9.274	9.274	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.837	-0.893	28.921	9.290	9.290	0.000	0.000	0.000	0.000
21	B	26	CYS	0	-0.063	-0.020	29.315	-0.344	-0.344	0.000	0.000	0.000	0.000
22	B	27	PHE	0	-0.005	-0.020	30.303	-0.360	-0.360	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.766	0.862	30.979	-9.738	-9.738	0.000	0.000	0.000	0.000
24	B	29	ASP	-1	-0.746	-0.845	34.977	7.987	7.987	0.000	0.000	0.000	0.000
25	B	30	LEU	0	-0.065	-0.027	35.735	-0.263	-0.263	0.000	0.000	0.000	0.000
26	B	31	CYS	0	-0.030	-0.011	37.618	-0.095	-0.095	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.008	-0.006	39.392	-0.283	-0.283	0.000	0.000	0.000	0.000
28	B	33	ARG	1	0.758	0.858	36.677	-8.301	-8.301	0.000	0.000	0.000	0.000
29	B	34	THR	0	-0.053	-0.033	41.034	-0.231	-0.231	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.015	0.019	43.125	-0.110	-0.110	0.000	0.000	0.000	0.000
31	B	36	ILE	0	-0.059	-0.028	39.658	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	38	LYS	1	0.824	0.889	32.294	-9.585	-9.585	0.000	0.000	0.000	0.000
33	B	39	GLY	0	-0.040	-0.022	37.923	-0.060	-0.060	0.000	0.000	0.000	0.000
34	B	40	ILE	0	-0.070	-0.019	40.153	-0.170	-0.170	0.000	0.000	0.000	0.000
35	B	41	LEU	0	-0.045	-0.024	42.334	-0.208	-0.208	0.000	0.000	0.000	0.000
36	B	42	GLU	-1	-0.771	-0.884	38.036	8.435	8.435	0.000	0.000	0.000	0.000
37	B	43	PRO	0	-0.030	-0.014	39.180	-0.199	-0.199	0.000	0.000	0.000	0.000
38	B	44	ALA	0	0.025	0.011	42.251	0.092	0.092	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.046	-0.024	42.205	-0.152	-0.152	0.000	0.000	0.000	0.000
40	B	46	ILE	0	0.004	0.000	41.700	0.093	0.093	0.000	0.000	0.000	0.000
41	B	47	PHE	0	0.036	0.019	33.147	0.092	0.092	0.000	0.000	0.000	0.000
42	B	48	HIS	0	-0.030	-0.012	38.098	-0.148	-0.148	0.000	0.000	0.000	0.000
43	B	49	LEU	0	-0.032	-0.025	31.846	-0.015	-0.015	0.000	0.000	0.000	0.000
44	B	50	LYS	1	0.805	0.900	27.697	-11.099	-11.099	0.000	0.000	0.000	0.000
45	B	51	LEU	0	-0.012	-0.015	28.466	0.152	0.152	0.000	0.000	0.000	0.000
46	B	52	PRO	0	-0.019	0.002	23.308	-0.135	-0.135	0.000	0.000	0.000	0.000
47	B	53	ALA	0	0.024	0.013	25.443	-0.150	-0.150	0.000	0.000	0.000	0.000
48	B	54	ILE	0	-0.019	-0.007	20.650	0.210	0.210	0.000	0.000	0.000	0.000
49	B	55	ASN	0	-0.036	-0.023	24.448	-0.529	-0.529	0.000	0.000	0.000	0.000
50	B	56	ASP	-1	-0.856	-0.937	25.266	11.265	11.265	0.000	0.000	0.000	0.000
51	B	57	THR	0	-0.034	-0.029	26.068	0.106	0.106	0.000	0.000	0.000	0.000
52	B	58	ASP	-1	-0.755	-0.856	21.597	13.459	13.459	0.000	0.000	0.000	0.000
53	B	59	HIS	0	-0.043	-0.003	21.105	0.831	0.831	0.000	0.000	0.000	0.000
54	B	60	CYS	0	-0.012	0.003	16.808	0.523	0.523	0.000	0.000	0.000	0.000
55	B	61	GLY	0	0.054	0.035	21.071	0.068	0.068	0.000	0.000	0.000	0.000
56	B	62	LEU	0	0.010	-0.019	20.759	0.245	0.245	0.000	0.000	0.000	0.000
57	B	63	ILE	0	-0.022	-0.006	22.914	-0.019	-0.019	0.000	0.000	0.000	0.000
58	B	64	GLY	0	0.017	0.005	24.057	-0.206	-0.206	0.000	0.000	0.000	0.000
59	B	65	PHE	0	-0.036	-0.003	15.197	0.265	0.265	0.000	0.000	0.000	0.000
60	B	66	ASN	0	-0.011	-0.016	17.307	0.698	0.698	0.000	0.000	0.000	0.000
61	B	67	GLU	-1	-0.809	-0.922	10.524	27.359	27.359	0.000	0.000	0.000	0.000
62	B	68	THR	0	-0.002	0.002	14.504	-0.037	-0.037	0.000	0.000	0.000	0.000
63	B	69	SER	0	-0.036	-0.030	15.460	-0.362	-0.362	0.000	0.000	0.000	0.000
64	B	71	LEU	0	0.050	0.015	10.323	-0.647	-0.647	0.000	0.000	0.000	0.000
65	B	72	LYS	1	0.814	0.900	14.612	-16.200	-16.200	0.000	0.000	0.000	0.000
66	B	73	LYS	1	0.799	0.900	16.983	-13.415	-13.415	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.027	0.004	15.320	-0.517	-0.517	0.000	0.000	0.000	0.000
68	B	75	ALA	0	0.025	0.020	14.115	-0.420	-0.420	0.000	0.000	0.000	0.000
69	B	76	ASP	-1	-0.821	-0.901	15.817	15.296	15.296	0.000	0.000	0.000	0.000
70	B	77	GLY	0	-0.017	-0.018	19.419	-0.698	-0.698	0.000	0.000	0.000	0.000
71	B	78	PHE	0	0.047	0.015	15.834	-0.807	-0.807	0.000	0.000	0.000	0.000
72	B	79	PHE	0	0.041	0.043	14.355	-0.345	-0.345	0.000	0.000	0.000	0.000
73	B	80	GLU	-1	-0.856	-0.917	19.547	11.129	11.129	0.000	0.000	0.000	0.000
74	B	81	PHE	0	0.022	-0.005	21.226	-0.731	-0.731	0.000	0.000	0.000	0.000
75	B	82	GLU	-1	-0.789	-0.867	20.655	13.853	13.853	0.000	0.000	0.000	0.000
76	B	83	VAL	0	-0.079	-0.040	23.065	-0.476	-0.476	0.000	0.000	0.000	0.000
77	B	84	LEU	0	-0.012	-0.008	26.179	-0.486	-0.486	0.000	0.000	0.000	0.000
78	B	85	PHE	0	0.084	0.018	21.853	-0.383	-0.383	0.000	0.000	0.000	0.000
79	B	86	LYS	1	0.866	0.938	24.820	-12.099	-12.099	0.000	0.000	0.000	0.000
80	B	87	PHE	0	-0.040	-0.007	28.327	-0.388	-0.388	0.000	0.000	0.000	0.000
81	B	88	LEU	0	0.037	0.015	28.045	-0.300	-0.300	0.000	0.000	0.000	0.000
82	B	89	THR	0	0.022	-0.017	27.361	-0.221	-0.221	0.000	0.000	0.000	0.000
83	B	90	THR	0	-0.069	-0.020	30.104	-0.323	-0.323	0.000	0.000	0.000	0.000
84	B	91	GLU	-1	-0.796	-0.873	33.454	7.956	7.956	0.000	0.000	0.000	0.000
85	B	92	PHE	0	0.015	-0.002	31.566	-0.219	-0.219	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.035	0.033	31.373	0.024	0.024	0.000	0.000	0.000	0.000
87	B	94	LYS	1	0.803	0.891	32.233	-8.318	-8.318	0.000	0.000	0.000	0.000
88	B	95	SER	0	-0.077	-0.064	34.526	-0.151	-0.151	0.000	0.000	0.000	0.000
89	B	96	VAL	0	0.006	0.006	29.439	-0.038	-0.038	0.000	0.000	0.000	0.000
90	B	97	ILE	0	0.018	0.006	27.480	0.097	0.097	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.010	-0.013	24.062	0.298	0.298	0.000	0.000	0.000	0.000
92	B	99	VAL	0	0.020	0.009	24.672	0.479	0.479	0.000	0.000	0.000	0.000
93	B	100	ASP	-1	-0.857	-0.938	25.614	11.341	11.341	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.007	0.014	21.248	0.226	0.226	0.000	0.000	0.000	0.000
95	B	102	MET	0	-0.004	0.031	20.530	0.816	0.816	0.000	0.000	0.000	0.000
96	B	103	GLU	-1	-0.817	-0.893	20.726	12.020	12.020	0.000	0.000	0.000	0.000
97	B	104	LEU	0	-0.039	-0.022	18.795	0.322	0.322	0.000	0.000	0.000	0.000
98	B	105	LEU	0	0.020	0.008	15.543	1.114	1.114	0.000	0.000	0.000	0.000
99	B	106	THR	0	-0.023	-0.026	15.877	0.835	0.835	0.000	0.000	0.000	0.000
100	B	107	LYS	1	0.839	0.905	16.205	-14.480	-14.480	0.000	0.000	0.000	0.000
101	B	108	THR	0	-0.080	-0.040	11.575	1.243	1.243	0.000	0.000	0.000	0.000
102	B	109	LEU	0	0.010	0.023	12.328	0.596	0.596	0.000	0.000	0.000	0.000
103	B	110	GLY	0	0.016	0.001	12.342	1.149	1.149	0.000	0.000	0.000	0.000
104	B	111	TRP	0	-0.003	-0.024	10.582	0.228	0.228	0.000	0.000	0.000	0.000
105	B	112	ASP	-1	-0.743	-0.853	7.155	29.980	29.980	0.000	0.000	0.000	0.000
106	B	113	ILE	0	0.007	0.010	7.872	3.170	3.170	0.000	0.000	0.000	0.000
107	B	114	GLN	0	-0.040	-0.038	10.469	-0.792	-0.792	0.000	0.000	0.000	0.000
108	B	115	GLU	-1	-0.999	-0.987	5.193	41.921	42.015	-0.001	0.000	-0.092	0.000
109	B	116	GLU	-1	-0.771	-0.887	4.054	68.517	68.789	0.001	-0.109	-0.164	0.000
110	B	117	LEU	0	-0.041	-0.007	7.302	-1.745	-1.745	0.000	0.000	0.000	0.000
111	B	118	ASN	0	-0.017	-0.007	9.488	-3.251	-3.251	0.000	0.000	0.000	0.000
112	B	119	LYS	1	0.797	0.904	1.721	-114.653	-120.532	16.154	-5.615	-4.661	0.068
113	B	120	LEU	0	-0.035	-0.011	7.983	-1.677	-1.677	0.000	0.000	0.000	0.000
114	B	121	THR	0	-0.077	-0.048	10.860	-3.746	-3.746	0.000	0.000	0.000	0.000
115	B	122	LYS	1	0.956	0.965	12.748	-18.950	-18.950	0.000	0.000	0.000	0.000
116	B	123	THR	0	-0.042	-0.017	15.417	-0.708	-0.708	0.000	0.000	0.000	0.000
117	B	124	HIS	0	0.034	0.031	12.434	1.301	1.301	0.000	0.000	0.000	0.000
118	B	125	TYR	0	-0.010	-0.023	14.221	-2.597	-2.597	0.000	0.000	0.000	0.000
119	B	126	SER	0	0.007	0.010	14.739	0.992	0.992	0.000	0.000	0.000	0.000
120	B	127	PRO	0	0.015	0.009	15.718	-0.322	-0.322	0.000	0.000	0.000	0.000
121	B	128	PRO	0	-0.019	-0.002	17.890	-0.792	-0.792	0.000	0.000	0.000	0.000
122	B	129	LYS	1	0.864	0.914	21.570	-11.584	-11.584	0.000	0.000	0.000	0.000
123	B	130	PHE	0	0.053	0.014	23.702	-0.378	-0.378	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.805	-0.878	25.056	10.001	10.001	0.000	0.000	0.000	0.000
125	B	132	ARG	1	0.998	0.984	28.281	-10.766	-10.766	0.000	0.000	0.000	0.000
126	B	133	GLY	0	0.023	0.028	30.839	-0.294	-0.294	0.000	0.000	0.000	0.000
127	B	134	LEU	0	-0.024	-0.020	29.049	-0.333	-0.333	0.000	0.000	0.000	0.000
128	B	135	LEU	0	0.025	0.012	29.045	-0.194	-0.194	0.000	0.000	0.000	0.000
129	B	136	GLY	0	-0.004	-0.001	31.853	-0.207	-0.207	0.000	0.000	0.000	0.000
130	B	137	ARG	1	0.910	0.943	35.003	-9.015	-9.015	0.000	0.000	0.000	0.000
131	B	138	LEU	0	-0.013	0.005	31.215	-0.210	-0.210	0.000	0.000	0.000	0.000
132	B	139	GLN	0	0.034	0.003	33.998	-0.313	-0.313	0.000	0.000	0.000	0.000
133	B	140	GLY	0	0.004	0.011	36.078	-0.198	-0.198	0.000	0.000	0.000	0.000
134	B	141	LEU	0	-0.028	0.004	37.114	-0.270	-0.270	0.000	0.000	0.000	0.000
135	B	142	LYS	1	0.943	0.970	40.325	-6.679	-6.679	0.000	0.000	0.000	0.000
136	B	143	TYR	0	0.032	-0.003	43.149	-0.069	-0.069	0.000	0.000	0.000	0.000
137	B	144	TRP	0	0.089	0.046	42.708	0.190	0.190	0.000	0.000	0.000	0.000
138	B	145	VAL	0	0.030	0.020	40.730	0.121	0.121	0.000	0.000	0.000	0.000
139	B	146	ARG	1	0.718	0.827	36.783	-7.984	-7.984	0.000	0.000	0.000	0.000
140	B	147	HIS	0	0.056	0.037	37.337	0.354	0.354	0.000	0.000	0.000	0.000
141	B	148	PHE	0	0.009	0.002	37.800	0.137	0.137	0.000	0.000	0.000	0.000
142	B	149	ALA	0	0.005	0.005	35.395	0.188	0.188	0.000	0.000	0.000	0.000
143	B	150	SER	0	0.011	-0.002	33.343	0.354	0.354	0.000	0.000	0.000	0.000
144	B	151	PHE	0	0.004	0.019	32.895	0.307	0.307	0.000	0.000	0.000	0.000
145	B	152	TYR	0	-0.005	-0.005	33.595	0.195	0.195	0.000	0.000	0.000	0.000
146	B	153	VAL	0	-0.009	-0.012	28.554	0.287	0.287	0.000	0.000	0.000	0.000
147	B	154	LEU	0	0.045	0.023	28.762	0.437	0.437	0.000	0.000	0.000	0.000
148	B	155	SER	0	-0.014	-0.013	28.789	0.240	0.240	0.000	0.000	0.000	0.000
149	B	156	ALA	0	-0.045	-0.010	27.557	0.081	0.081	0.000	0.000	0.000	0.000
150	B	157	MET	0	-0.017	-0.012	24.516	0.301	0.301	0.000	0.000	0.000	0.000
151	B	158	GLU	-1	-0.801	-0.885	24.136	10.502	10.502	0.000	0.000	0.000	0.000
152	B	159	LYS	1	0.917	0.966	25.252	-9.586	-9.586	0.000	0.000	0.000	0.000
153	B	160	PHE	0	0.018	0.022	19.334	0.215	0.215	0.000	0.000	0.000	0.000
154	B	161	ALA	0	0.051	0.020	20.132	0.712	0.712	0.000	0.000	0.000	0.000
155	B	162	GLY	0	0.024	0.018	20.335	0.478	0.478	0.000	0.000	0.000	0.000
156	B	163	GLN	0	-0.059	-0.035	21.803	0.158	0.158	0.000	0.000	0.000	0.000
157	B	164	ALA	0	0.044	0.010	16.947	0.437	0.437	0.000	0.000	0.000	0.000
158	B	165	VAL	0	-0.001	0.009	16.373	0.990	0.990	0.000	0.000	0.000	0.000
159	B	166	ARG	1	0.935	0.963	16.623	-12.334	-12.334	0.000	0.000	0.000	0.000
160	B	167	VAL	0	-0.006	0.000	15.044	0.217	0.217	0.000	0.000	0.000	0.000
161	B	168	LEU	0	-0.012	-0.009	10.838	0.904	0.904	0.000	0.000	0.000	0.000
162	B	169	ASP	-1	-0.889	-0.945	12.520	17.910	17.910	0.000	0.000	0.000	0.000
163	B	170	SER	0	-0.138	-0.068	14.951	-0.161	-0.161	0.000	0.000	0.000	0.000
164	B	171	ILE	0	-0.007	0.014	10.548	-0.193	-0.193	0.000	0.000	0.000	0.000
165	B	172	PRO	0	-0.002	0.010	10.202	3.182	3.182	0.000	0.000	0.000	0.000

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