FMO DATABASE

FMODB ID: 66JYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1787304.845951
FMO2-HF: Nuclear repulsion	1719416.927315
FMO2-HF: Total energy	-67887.918636
FMO2-MP2: Total energy	-68085.185452

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.
36.96	42.312	2.474	-3.594	-4.233	0.039

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 : -0.966 / q_NPA : -0.995

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	-0.897	-0.956	3.750	27.544	29.316	-0.014	-0.653	-1.105	0.003
4	B	9	LYS	1	0.835	0.924	5.954	-30.101	-30.101	0.000	0.000	0.000	0.000
5	B	10	ASP	-1	-0.830	-0.910	9.014	19.706	19.706	0.000	0.000	0.000	0.000
6	B	11	LEU	0	-0.011	0.001	8.036	-2.056	-2.056	0.000	0.000	0.000	0.000
7	B	12	LEU	0	-0.036	-0.030	8.425	-2.151	-2.151	0.000	0.000	0.000	0.000
8	B	13	ILE	0	0.058	0.022	11.391	-1.701	-1.701	0.000	0.000	0.000	0.000
9	B	14	GLN	0	-0.040	-0.019	13.187	-0.304	-0.304	0.000	0.000	0.000	0.000
10	B	15	ARG	1	0.844	0.934	8.934	-25.766	-25.766	0.000	0.000	0.000	0.000
11	B	16	LEU	0	0.008	0.011	15.221	-1.053	-1.053	0.000	0.000	0.000	0.000
12	B	17	ASN	0	0.046	0.011	17.560	-1.194	-1.194	0.000	0.000	0.000	0.000
13	B	18	TRP	0	-0.026	0.016	17.913	-0.437	-0.437	0.000	0.000	0.000	0.000
14	B	19	MET	0	0.005	-0.025	18.433	-0.699	-0.699	0.000	0.000	0.000	0.000
15	B	20	LEU	0	-0.042	-0.025	21.210	-0.644	-0.644	0.000	0.000	0.000	0.000
16	B	21	TRP	0	-0.047	-0.023	23.315	-0.436	-0.436	0.000	0.000	0.000	0.000
17	B	22	VAL	0	0.018	0.004	24.039	-0.478	-0.478	0.000	0.000	0.000	0.000
18	B	23	ILE	0	-0.020	-0.011	24.363	-0.437	-0.437	0.000	0.000	0.000	0.000
19	B	24	ASP	-1	-0.894	-0.955	27.117	9.345	9.345	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.892	-0.948	28.949	9.645	9.645	0.000	0.000	0.000	0.000
21	B	26	CYS	0	-0.058	-0.008	29.098	-0.335	-0.335	0.000	0.000	0.000	0.000
22	B	27	PHE	0	0.018	0.014	29.989	-0.433	-0.433	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.945	0.982	32.449	-9.333	-9.333	0.000	0.000	0.000	0.000
24	B	29	ASP	-1	-0.772	-0.849	34.538	8.054	8.054	0.000	0.000	0.000	0.000
25	B	30	LEU	0	-0.050	-0.033	35.610	-0.277	-0.277	0.000	0.000	0.000	0.000
26	B	31	CYS	0	-0.039	-0.024	37.366	-0.110	-0.110	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.014	-0.011	39.050	-0.270	-0.270	0.000	0.000	0.000	0.000
28	B	33	ARG	1	0.840	0.910	36.939	-8.236	-8.236	0.000	0.000	0.000	0.000
29	B	34	THR	0	-0.039	-0.015	40.420	-0.244	-0.244	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.021	0.027	42.452	-0.154	-0.154	0.000	0.000	0.000	0.000
31	B	36	ILE	0	-0.096	-0.059	39.096	0.005	0.005	0.000	0.000	0.000	0.000
32	B	38	LYS	1	0.936	0.948	32.331	-9.452	-9.452	0.000	0.000	0.000	0.000
33	B	39	GLY	0	-0.015	-0.009	37.485	-0.059	-0.059	0.000	0.000	0.000	0.000
34	B	40	ILE	0	-0.076	-0.021	40.001	-0.154	-0.154	0.000	0.000	0.000	0.000
35	B	41	LEU	0	-0.039	-0.027	42.142	-0.214	-0.214	0.000	0.000	0.000	0.000
36	B	42	GLU	-1	-0.829	-0.896	38.677	8.287	8.287	0.000	0.000	0.000	0.000
37	B	43	PRO	0	-0.039	-0.020	39.408	-0.187	-0.187	0.000	0.000	0.000	0.000
38	B	44	ALA	0	0.017	0.030	42.567	0.040	0.040	0.000	0.000	0.000	0.000
39	B	45	ALA	0	-0.040	-0.045	41.796	-0.105	-0.105	0.000	0.000	0.000	0.000
40	B	46	ILE	0	0.012	0.007	41.567	0.078	0.078	0.000	0.000	0.000	0.000
41	B	47	PHE	0	0.039	0.026	33.903	0.115	0.115	0.000	0.000	0.000	0.000
42	B	48	HIS	0	-0.034	-0.024	37.539	-0.205	-0.205	0.000	0.000	0.000	0.000
43	B	49	LEU	0	-0.048	-0.023	31.422	-0.017	-0.017	0.000	0.000	0.000	0.000
44	B	50	LYS	1	0.937	0.993	28.548	-10.742	-10.742	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.025	-0.009	28.547	0.078	0.078	0.000	0.000	0.000	0.000
46	B	52	PRO	0	-0.023	0.014	23.582	-0.153	-0.153	0.000	0.000	0.000	0.000
47	B	53	ALA	0	0.019	-0.014	25.641	-0.137	-0.137	0.000	0.000	0.000	0.000
48	B	54	ILE	0	-0.015	0.002	20.925	0.117	0.117	0.000	0.000	0.000	0.000
49	B	55	ASN	0	-0.045	-0.017	24.560	-0.796	-0.796	0.000	0.000	0.000	0.000
50	B	56	ASP	-1	-0.867	-0.950	25.333	11.121	11.121	0.000	0.000	0.000	0.000
51	B	57	THR	0	-0.035	-0.032	25.680	0.106	0.106	0.000	0.000	0.000	0.000
52	B	58	ASP	-1	-0.807	-0.901	21.533	13.632	13.632	0.000	0.000	0.000	0.000
53	B	59	HIS	0	-0.058	-0.025	21.100	0.701	0.701	0.000	0.000	0.000	0.000
54	B	60	CYS	0	-0.013	0.002	16.926	0.594	0.594	0.000	0.000	0.000	0.000
55	B	61	GLY	0	0.025	0.026	20.819	0.176	0.176	0.000	0.000	0.000	0.000
56	B	62	LEU	0	0.035	-0.009	20.963	0.207	0.207	0.000	0.000	0.000	0.000
57	B	63	ILE	0	-0.024	-0.003	22.939	0.125	0.125	0.000	0.000	0.000	0.000
58	B	64	GLY	0	0.017	0.008	24.174	-0.204	-0.204	0.000	0.000	0.000	0.000
59	B	65	PHE	0	-0.008	0.007	15.311	0.173	0.173	0.000	0.000	0.000	0.000
60	B	66	ASN	0	0.005	-0.022	17.350	0.404	0.404	0.000	0.000	0.000	0.000
61	B	67	GLU	-1	-0.818	-0.910	10.458	26.517	26.517	0.000	0.000	0.000	0.000
62	B	68	THR	0	-0.010	0.006	14.601	-0.073	-0.073	0.000	0.000	0.000	0.000
63	B	69	SER	0	-0.009	-0.003	15.770	-0.039	-0.039	0.000	0.000	0.000	0.000
64	B	71	LEU	0	0.063	0.016	10.620	-0.587	-0.587	0.000	0.000	0.000	0.000
65	B	72	LYS	1	0.844	0.929	14.681	-15.773	-15.773	0.000	0.000	0.000	0.000
66	B	73	LYS	1	0.891	0.972	16.795	-13.474	-13.474	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.000	-0.011	15.102	-0.485	-0.485	0.000	0.000	0.000	0.000
68	B	75	ALA	0	0.035	0.016	13.756	-0.347	-0.347	0.000	0.000	0.000	0.000
69	B	76	ASP	-1	-0.868	-0.934	15.738	15.780	15.780	0.000	0.000	0.000	0.000
70	B	77	GLY	0	0.001	-0.012	19.050	-0.658	-0.658	0.000	0.000	0.000	0.000
71	B	78	PHE	0	0.032	0.005	15.647	-0.744	-0.744	0.000	0.000	0.000	0.000
72	B	79	PHE	0	0.014	0.023	13.964	-0.299	-0.299	0.000	0.000	0.000	0.000
73	B	80	GLU	-1	-1.001	-1.006	19.249	12.050	12.050	0.000	0.000	0.000	0.000
74	B	81	PHE	0	-0.004	-0.009	20.689	-0.801	-0.801	0.000	0.000	0.000	0.000
75	B	82	GLU	-1	-0.897	-0.934	20.690	13.987	13.987	0.000	0.000	0.000	0.000
76	B	83	VAL	0	-0.038	-0.027	22.765	-0.516	-0.516	0.000	0.000	0.000	0.000
77	B	84	LEU	0	-0.020	-0.012	25.853	-0.538	-0.538	0.000	0.000	0.000	0.000
78	B	85	PHE	0	0.114	0.021	21.432	-0.429	-0.429	0.000	0.000	0.000	0.000
79	B	86	LYS	1	0.859	0.955	25.138	-11.945	-11.945	0.000	0.000	0.000	0.000
80	B	87	PHE	0	-0.086	-0.046	27.944	-0.381	-0.381	0.000	0.000	0.000	0.000
81	B	88	LEU	0	0.048	0.010	27.345	-0.305	-0.305	0.000	0.000	0.000	0.000
82	B	89	THR	0	0.031	0.025	27.105	-0.255	-0.255	0.000	0.000	0.000	0.000
83	B	90	THR	0	-0.102	-0.042	29.880	-0.301	-0.301	0.000	0.000	0.000	0.000
84	B	91	GLU	-1	-0.880	-0.919	33.113	8.069	8.069	0.000	0.000	0.000	0.000
85	B	92	PHE	0	0.012	-0.008	31.264	-0.224	-0.224	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.007	0.022	30.982	0.004	0.004	0.000	0.000	0.000	0.000
87	B	94	LYS	1	0.871	0.921	31.982	-8.075	-8.075	0.000	0.000	0.000	0.000
88	B	95	SER	0	-0.078	-0.067	34.377	-0.118	-0.118	0.000	0.000	0.000	0.000
89	B	96	VAL	0	0.012	0.020	29.039	-0.048	-0.048	0.000	0.000	0.000	0.000
90	B	97	ILE	0	0.025	0.004	27.311	0.139	0.139	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.002	-0.011	23.936	0.266	0.266	0.000	0.000	0.000	0.000
92	B	99	VAL	0	0.033	0.021	24.542	0.443	0.443	0.000	0.000	0.000	0.000
93	B	100	ASP	-1	-0.900	-0.964	25.386	11.513	11.513	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.005	0.023	20.976	0.278	0.278	0.000	0.000	0.000	0.000
95	B	102	MET	0	0.001	0.015	20.129	0.860	0.860	0.000	0.000	0.000	0.000
96	B	103	GLU	-1	-0.868	-0.944	20.328	12.458	12.458	0.000	0.000	0.000	0.000
97	B	104	LEU	0	-0.014	-0.011	18.111	0.488	0.488	0.000	0.000	0.000	0.000
98	B	105	LEU	0	-0.002	-0.003	15.134	1.166	1.166	0.000	0.000	0.000	0.000
99	B	106	THR	0	0.010	-0.031	15.321	1.111	1.111	0.000	0.000	0.000	0.000
100	B	107	LYS	1	0.876	0.959	16.075	-15.943	-15.943	0.000	0.000	0.000	0.000
101	B	108	THR	0	-0.024	-0.010	11.194	1.475	1.475	0.000	0.000	0.000	0.000
102	B	109	LEU	0	-0.023	0.006	11.108	1.793	1.793	0.000	0.000	0.000	0.000
103	B	110	GLY	0	0.029	0.016	11.959	1.161	1.161	0.000	0.000	0.000	0.000
104	B	111	TRP	0	-0.030	-0.047	10.466	0.055	0.055	0.000	0.000	0.000	0.000
105	B	112	ASP	-1	-0.731	-0.867	7.202	32.799	32.799	0.000	0.000	0.000	0.000
106	B	113	ILE	0	-0.043	-0.014	7.680	3.021	3.021	0.000	0.000	0.000	0.000
107	B	114	GLN	0	-0.088	-0.059	10.158	1.673	1.673	0.000	0.000	0.000	0.000
108	B	115	GLU	-1	-0.947	-0.968	4.060	56.801	57.053	0.003	-0.043	-0.212	0.000
109	B	116	GLU	-1	-0.811	-0.920	5.126	53.825	53.932	-0.001	-0.005	-0.101	0.000
110	B	117	LEU	0	-0.033	-0.008	7.590	-1.499	-1.499	0.000	0.000	0.000	0.000
111	B	118	ASN	0	-0.021	-0.005	9.382	-3.135	-3.135	0.000	0.000	0.000	0.000
112	B	119	LYS	1	0.877	0.970	2.219	-94.207	-90.986	2.486	-2.893	-2.815	0.036
113	B	120	LEU	0	-0.048	-0.009	8.603	-1.755	-1.755	0.000	0.000	0.000	0.000
114	B	121	THR	0	-0.054	-0.030	10.883	-3.358	-3.358	0.000	0.000	0.000	0.000
115	B	122	LYS	1	0.955	0.966	13.150	-18.015	-18.015	0.000	0.000	0.000	0.000
116	B	123	THR	0	-0.078	-0.024	15.553	-0.548	-0.548	0.000	0.000	0.000	0.000
117	B	124	HIS	0	0.051	0.022	12.559	1.132	1.132	0.000	0.000	0.000	0.000
118	B	125	TYR	0	-0.014	-0.022	14.147	-1.970	-1.970	0.000	0.000	0.000	0.000
119	B	126	SER	0	-0.025	-0.013	14.728	0.757	0.757	0.000	0.000	0.000	0.000
120	B	127	PRO	0	-0.012	0.009	14.880	-0.662	-0.662	0.000	0.000	0.000	0.000
121	B	128	PRO	0	-0.001	-0.013	17.283	-0.884	-0.884	0.000	0.000	0.000	0.000
122	B	129	LYS	1	0.947	0.991	21.058	-12.395	-12.395	0.000	0.000	0.000	0.000
123	B	130	PHE	0	0.068	0.022	23.601	-0.427	-0.427	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.850	-0.939	24.828	9.943	9.943	0.000	0.000	0.000	0.000
125	B	132	ARG	1	0.995	0.982	28.053	-10.837	-10.837	0.000	0.000	0.000	0.000
126	B	133	GLY	0	0.030	0.030	30.749	-0.305	-0.305	0.000	0.000	0.000	0.000
127	B	134	LEU	0	-0.043	-0.014	28.938	-0.323	-0.323	0.000	0.000	0.000	0.000
128	B	135	LEU	0	0.032	0.028	29.566	-0.248	-0.248	0.000	0.000	0.000	0.000
129	B	136	GLY	0	-0.017	-0.007	31.872	-0.229	-0.229	0.000	0.000	0.000	0.000
130	B	137	ARG	1	0.929	0.962	34.366	-9.152	-9.152	0.000	0.000	0.000	0.000
131	B	138	LEU	0	0.008	-0.003	31.070	-0.216	-0.216	0.000	0.000	0.000	0.000
132	B	139	GLN	0	-0.001	-0.002	32.834	-0.381	-0.381	0.000	0.000	0.000	0.000
133	B	140	GLY	0	0.007	0.011	36.053	-0.192	-0.192	0.000	0.000	0.000	0.000
134	B	141	LEU	0	-0.040	-0.002	37.066	-0.279	-0.279	0.000	0.000	0.000	0.000
135	B	142	LYS	1	0.996	0.987	40.418	-6.804	-6.804	0.000	0.000	0.000	0.000
136	B	143	TYR	0	-0.015	-0.015	43.088	-0.081	-0.081	0.000	0.000	0.000	0.000
137	B	144	TRP	0	0.101	0.053	42.438	0.175	0.175	0.000	0.000	0.000	0.000
138	B	145	VAL	0	0.037	0.021	40.764	0.139	0.139	0.000	0.000	0.000	0.000
139	B	146	ARG	1	0.740	0.842	36.052	-8.110	-8.110	0.000	0.000	0.000	0.000
140	B	147	HIS	0	0.067	0.022	37.155	0.347	0.347	0.000	0.000	0.000	0.000
141	B	148	PHE	0	0.002	0.009	37.346	0.159	0.159	0.000	0.000	0.000	0.000
142	B	149	ALA	0	-0.002	0.009	34.856	0.192	0.192	0.000	0.000	0.000	0.000
143	B	150	SER	0	0.027	0.004	33.136	0.349	0.349	0.000	0.000	0.000	0.000
144	B	151	PHE	0	0.023	0.022	32.704	0.314	0.314	0.000	0.000	0.000	0.000
145	B	152	TYR	0	0.012	-0.005	33.316	0.191	0.191	0.000	0.000	0.000	0.000
146	B	153	VAL	0	-0.013	-0.006	28.423	0.282	0.282	0.000	0.000	0.000	0.000
147	B	154	LEU	0	0.051	0.030	28.545	0.425	0.425	0.000	0.000	0.000	0.000
148	B	155	SER	0	-0.068	-0.035	28.651	0.208	0.208	0.000	0.000	0.000	0.000
149	B	156	ALA	0	-0.043	-0.024	27.964	0.179	0.179	0.000	0.000	0.000	0.000
150	B	157	MET	0	-0.010	-0.008	23.792	0.282	0.282	0.000	0.000	0.000	0.000
151	B	158	GLU	-1	-0.908	-0.946	24.141	10.817	10.817	0.000	0.000	0.000	0.000
152	B	159	LYS	1	0.911	0.951	25.042	-9.622	-9.622	0.000	0.000	0.000	0.000
153	B	160	PHE	0	0.015	0.025	19.221	0.169	0.169	0.000	0.000	0.000	0.000
154	B	161	ALA	0	0.051	0.026	20.023	0.616	0.616	0.000	0.000	0.000	0.000
155	B	162	GLY	0	0.031	0.020	20.203	0.499	0.499	0.000	0.000	0.000	0.000
156	B	163	GLN	0	-0.065	-0.049	21.563	0.177	0.177	0.000	0.000	0.000	0.000
157	B	164	ALA	0	0.016	0.012	16.680	0.476	0.476	0.000	0.000	0.000	0.000
158	B	165	VAL	0	0.028	0.018	16.607	0.918	0.918	0.000	0.000	0.000	0.000
159	B	166	ARG	1	0.938	0.970	17.082	-12.227	-12.227	0.000	0.000	0.000	0.000
160	B	167	VAL	0	-0.002	-0.012	15.311	0.252	0.252	0.000	0.000	0.000	0.000
161	B	168	LEU	0	-0.031	-0.025	11.334	0.852	0.852	0.000	0.000	0.000	0.000
162	B	169	ASP	-1	-0.873	-0.940	12.809	17.951	17.951	0.000	0.000	0.000	0.000
163	B	170	SER	0	-0.152	-0.054	15.138	-0.410	-0.410	0.000	0.000	0.000	0.000
164	B	171	ILE	0	-0.021	0.000	10.871	-0.027	-0.027	0.000	0.000	0.000	0.000
165	B	172	PRO	0	0.009	0.009	9.193	1.104	1.104	0.000	0.000	0.000	0.000

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