FMO DATABASE

FMODB ID: Z9RKN

Calculation Name: 1PVH-B-Xray547

Preferred Name: Interleukin-6 receptor subunit beta

Target Type: SINGLE PROTEIN

Ligand Name: iodide ion

Ligand 3-letter code: IOD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PVH

Chain ID: B

ChEMBL ID: CHEMBL3124734

UniProt ID: P40189

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1668386.927464
FMO2-HF: Nuclear repulsion	1602888.645115
FMO2-HF: Total energy	-65498.28235
FMO2-MP2: Total energy	-65688.431409

3D Structure Molmil

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:12:CYS)

Summations of interaction energy for fragment #1(B:12:CYS)

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.
33.332	52.513	29.589	-19.809	-28.961	-0.073

Interaction energy analysis for fragmet #1(B:12:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.766 / q_NPA : 0.896

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	14	ILE	0	0.006	-0.008	3.476	-0.266	1.478	0.001	-0.582	-1.163	0.002
7	B	18	CYS	0	-0.003	0.007	1.926	-22.840	-21.463	7.208	-3.826	-4.758	-0.051
69	B	80	LEU	0	0.015	-0.004	4.551	-0.864	-0.799	-0.002	-0.009	-0.055	0.000
119	B	130	LEU	0	0.019	0.010	2.895	-9.277	-9.851	5.827	-1.785	-3.468	-0.007
120	B	132	ARG	1	0.942	0.976	3.080	23.707	27.096	0.231	-1.930	-1.690	-0.010
123	B	136	LYS	1	0.802	0.912	3.802	22.472	24.821	-0.011	-1.188	-1.149	0.005
124	B	137	TYR	0	-0.046	-0.074	2.672	-0.913	0.967	1.133	-1.189	-1.825	0.021
125	B	138	HIS	1	0.850	0.936	2.558	25.246	26.036	3.409	-1.108	-3.091	0.011
126	B	139	VAL	0	0.021	0.011	2.102	-15.202	-11.737	4.952	-2.933	-5.483	0.024
127	B	140	GLY	0	0.077	0.060	3.043	-2.548	-1.384	1.389	-0.885	-1.668	-0.007
128	B	141	HIS	0	-0.096	-0.075	2.098	-49.027	-45.764	5.453	-4.317	-4.400	-0.061
129	B	142	VAL	0	0.017	0.007	3.972	6.790	7.059	-0.001	-0.057	-0.211	0.000
4	B	15	ARG	1	0.963	0.976	6.257	28.304	28.304	0.000	0.000	0.000	0.000
5	B	16	HIS	0	0.022	0.021	9.528	2.851	2.851	0.000	0.000	0.000	0.000
6	B	17	PRO	0	0.030	0.010	8.339	-2.986	-2.986	0.000	0.000	0.000	0.000
8	B	19	HIS	0	0.062	0.036	7.528	1.106	1.106	0.000	0.000	0.000	0.000
9	B	20	ASN	0	0.026	-0.002	9.654	-1.581	-1.581	0.000	0.000	0.000	0.000
10	B	21	ASN	0	0.028	0.025	12.084	0.202	0.202	0.000	0.000	0.000	0.000
11	B	22	LEU	0	-0.006	0.001	6.206	0.368	0.368	0.000	0.000	0.000	0.000
12	B	23	MET	0	0.019	0.012	8.304	-1.277	-1.277	0.000	0.000	0.000	0.000
13	B	24	ASN	0	0.026	0.005	10.802	0.981	0.981	0.000	0.000	0.000	0.000
14	B	25	GLN	0	-0.001	0.017	12.181	-0.350	-0.350	0.000	0.000	0.000	0.000
15	B	26	ILE	0	0.025	0.009	8.551	0.538	0.538	0.000	0.000	0.000	0.000
16	B	27	ARG	1	0.827	0.883	11.974	16.236	16.236	0.000	0.000	0.000	0.000
17	B	28	SER	0	0.016	-0.003	14.748	1.016	1.016	0.000	0.000	0.000	0.000
18	B	29	GLN	0	-0.013	-0.006	12.775	-0.174	-0.174	0.000	0.000	0.000	0.000
19	B	30	LEU	0	-0.004	0.000	12.809	0.494	0.494	0.000	0.000	0.000	0.000
20	B	31	ALA	0	0.040	0.023	16.529	0.675	0.675	0.000	0.000	0.000	0.000
21	B	32	GLN	0	-0.011	0.001	19.369	0.065	0.065	0.000	0.000	0.000	0.000
22	B	33	LEU	0	-0.004	0.003	16.622	0.405	0.405	0.000	0.000	0.000	0.000
23	B	34	ASN	0	0.031	0.005	20.441	0.709	0.709	0.000	0.000	0.000	0.000
24	B	35	GLY	0	-0.019	-0.002	22.232	0.464	0.464	0.000	0.000	0.000	0.000
25	B	36	SER	0	-0.062	-0.040	23.434	0.339	0.339	0.000	0.000	0.000	0.000
26	B	37	ALA	0	0.003	-0.001	23.177	0.316	0.316	0.000	0.000	0.000	0.000
27	B	38	ASN	0	0.008	-0.008	25.237	0.314	0.314	0.000	0.000	0.000	0.000
28	B	39	ALA	0	0.058	0.030	28.639	0.228	0.228	0.000	0.000	0.000	0.000
29	B	40	LEU	0	-0.020	-0.008	25.227	0.219	0.219	0.000	0.000	0.000	0.000
30	B	41	PHE	0	0.049	0.018	28.836	0.171	0.171	0.000	0.000	0.000	0.000
31	B	42	ILE	0	0.020	0.012	30.324	0.191	0.191	0.000	0.000	0.000	0.000
32	B	43	LEU	0	-0.026	-0.008	31.275	0.211	0.211	0.000	0.000	0.000	0.000
33	B	44	TYR	0	-0.030	-0.028	30.893	0.063	0.063	0.000	0.000	0.000	0.000
34	B	45	TYR	0	0.115	0.033	33.060	0.097	0.097	0.000	0.000	0.000	0.000
35	B	46	THR	0	-0.041	-0.023	35.794	0.299	0.299	0.000	0.000	0.000	0.000
36	B	47	ALA	0	-0.037	-0.016	35.834	0.194	0.194	0.000	0.000	0.000	0.000
37	B	48	GLN	0	-0.088	-0.035	34.879	0.044	0.044	0.000	0.000	0.000	0.000
38	B	49	GLY	0	0.079	0.051	38.370	0.134	0.134	0.000	0.000	0.000	0.000
39	B	50	GLU	-1	-0.817	-0.911	41.130	-7.254	-7.254	0.000	0.000	0.000	0.000
40	B	51	PRO	0	-0.047	-0.018	41.676	-0.056	-0.056	0.000	0.000	0.000	0.000
41	B	52	PHE	0	-0.009	-0.020	36.264	-0.075	-0.075	0.000	0.000	0.000	0.000
42	B	53	PRO	0	-0.002	-0.014	39.204	-0.074	-0.074	0.000	0.000	0.000	0.000
43	B	54	ASN	0	0.005	0.004	40.415	-0.023	-0.023	0.000	0.000	0.000	0.000
44	B	55	ASN	0	-0.055	-0.027	40.722	0.155	0.155	0.000	0.000	0.000	0.000
45	B	56	LEU	0	0.032	0.008	35.590	-0.227	-0.227	0.000	0.000	0.000	0.000
46	B	57	ASP	-1	-0.895	-0.949	35.471	-8.176	-8.176	0.000	0.000	0.000	0.000
47	B	58	LYS	1	0.912	0.951	36.162	7.176	7.176	0.000	0.000	0.000	0.000
48	B	59	LEU	0	-0.055	-0.015	36.277	-0.093	-0.093	0.000	0.000	0.000	0.000
49	B	60	CYS	0	-0.070	-0.032	28.863	-0.418	-0.418	0.000	0.000	0.000	0.000
50	B	61	GLY	0	0.101	0.057	31.543	-0.139	-0.139	0.000	0.000	0.000	0.000
51	B	62	PRO	0	-0.026	-0.026	26.873	-0.250	-0.250	0.000	0.000	0.000	0.000
52	B	63	ASN	0	-0.020	-0.017	27.068	0.137	0.137	0.000	0.000	0.000	0.000
53	B	64	VAL	0	-0.022	-0.022	22.670	-0.407	-0.407	0.000	0.000	0.000	0.000
54	B	65	THR	0	-0.019	-0.007	25.160	0.010	0.010	0.000	0.000	0.000	0.000
55	B	66	ASP	-1	-0.760	-0.863	23.229	-13.131	-13.131	0.000	0.000	0.000	0.000
56	B	67	PHE	0	-0.045	-0.021	18.519	-0.727	-0.727	0.000	0.000	0.000	0.000
57	B	68	PRO	0	-0.007	-0.005	15.878	0.242	0.242	0.000	0.000	0.000	0.000
58	B	69	PRO	0	0.010	0.010	16.241	0.326	0.326	0.000	0.000	0.000	0.000
59	B	70	PHE	0	-0.001	-0.015	12.459	-0.944	-0.944	0.000	0.000	0.000	0.000
60	B	71	HIS	0	-0.056	-0.038	15.174	1.467	1.467	0.000	0.000	0.000	0.000
61	B	72	ALA	0	0.007	-0.005	15.386	-0.393	-0.393	0.000	0.000	0.000	0.000
62	B	73	ASN	0	-0.003	-0.006	16.791	-0.372	-0.372	0.000	0.000	0.000	0.000
63	B	74	GLY	0	0.067	0.046	14.286	0.178	0.178	0.000	0.000	0.000	0.000
64	B	75	THR	0	0.038	0.002	11.029	-0.498	-0.498	0.000	0.000	0.000	0.000
65	B	76	GLU	-1	-0.801	-0.869	7.233	-21.308	-21.308	0.000	0.000	0.000	0.000
66	B	77	LYS	1	0.969	0.985	5.431	18.879	18.879	0.000	0.000	0.000	0.000
67	B	78	ALA	0	-0.001	0.001	6.981	-1.510	-1.510	0.000	0.000	0.000	0.000
68	B	79	LYS	1	0.927	0.984	9.777	15.312	15.312	0.000	0.000	0.000	0.000
70	B	81	VAL	0	-0.027	-0.017	5.934	-1.779	-1.779	0.000	0.000	0.000	0.000
71	B	82	GLU	-1	-0.810	-0.875	7.574	-16.801	-16.801	0.000	0.000	0.000	0.000
72	B	83	LEU	0	0.011	0.015	9.318	0.108	0.108	0.000	0.000	0.000	0.000
73	B	84	TYR	0	0.000	-0.011	7.230	-0.073	-0.073	0.000	0.000	0.000	0.000
74	B	85	ARG	1	0.892	0.932	9.371	23.156	23.156	0.000	0.000	0.000	0.000
75	B	86	ILE	0	0.013	0.015	12.438	0.892	0.892	0.000	0.000	0.000	0.000
76	B	87	VAL	0	0.005	-0.001	12.053	1.041	1.041	0.000	0.000	0.000	0.000
77	B	88	VAL	0	-0.030	-0.003	11.283	0.543	0.543	0.000	0.000	0.000	0.000
78	B	89	TYR	0	-0.013	-0.011	14.525	0.889	0.889	0.000	0.000	0.000	0.000
79	B	90	LEU	0	-0.020	0.002	16.910	1.062	1.062	0.000	0.000	0.000	0.000
80	B	91	GLY	0	0.020	0.010	17.329	0.820	0.820	0.000	0.000	0.000	0.000
81	B	92	THR	0	-0.059	-0.049	16.170	0.983	0.983	0.000	0.000	0.000	0.000
82	B	93	SER	0	0.014	-0.008	18.820	0.982	0.982	0.000	0.000	0.000	0.000
83	B	94	LEU	0	-0.004	0.002	21.658	0.750	0.750	0.000	0.000	0.000	0.000
84	B	95	GLY	0	0.016	0.020	21.459	0.585	0.585	0.000	0.000	0.000	0.000
85	B	96	ASN	0	-0.003	0.006	22.478	0.526	0.526	0.000	0.000	0.000	0.000
86	B	97	ILE	0	0.029	0.025	24.929	0.577	0.577	0.000	0.000	0.000	0.000
87	B	98	THR	0	-0.020	-0.028	25.247	0.574	0.574	0.000	0.000	0.000	0.000
88	B	99	ARG	1	0.911	0.950	21.790	13.855	13.855	0.000	0.000	0.000	0.000
89	B	100	ASP	0	-0.030	-0.026	28.105	0.544	0.544	0.000	0.000	0.000	0.000
90	B	101	GLN	0	0.036	0.017	30.529	0.591	0.591	0.000	0.000	0.000	0.000
91	B	102	LYS	1	0.882	0.951	29.638	10.255	10.255	0.000	0.000	0.000	0.000
92	B	103	ILE	0	-0.001	0.003	32.084	0.225	0.225	0.000	0.000	0.000	0.000
93	B	104	LEU	0	-0.044	-0.026	34.252	0.284	0.284	0.000	0.000	0.000	0.000
94	B	105	ASN	0	-0.002	-0.014	35.760	0.483	0.483	0.000	0.000	0.000	0.000
95	B	106	PRO	0	0.025	0.018	36.223	-0.187	-0.187	0.000	0.000	0.000	0.000
96	B	107	SER	0	0.045	0.014	37.310	-0.148	-0.148	0.000	0.000	0.000	0.000
97	B	108	ALA	0	0.010	0.017	35.603	0.056	0.056	0.000	0.000	0.000	0.000
98	B	109	LEU	0	0.035	0.006	34.786	-0.357	-0.357	0.000	0.000	0.000	0.000
99	B	110	SER	0	0.005	0.001	33.672	-0.356	-0.356	0.000	0.000	0.000	0.000
100	B	111	LEU	0	0.033	0.022	30.566	-0.359	-0.359	0.000	0.000	0.000	0.000
101	B	112	HIS	0	0.005	-0.005	30.147	-0.548	-0.548	0.000	0.000	0.000	0.000
102	B	113	SER	0	-0.023	0.005	28.840	-0.483	-0.483	0.000	0.000	0.000	0.000
103	B	114	LYS	1	0.913	0.945	27.547	10.378	10.378	0.000	0.000	0.000	0.000
104	B	115	LEU	0	0.016	0.021	25.858	-0.430	-0.430	0.000	0.000	0.000	0.000
105	B	116	ASN	0	0.005	0.003	24.180	-0.909	-0.909	0.000	0.000	0.000	0.000
106	B	117	ALA	0	0.048	0.029	22.997	-0.638	-0.638	0.000	0.000	0.000	0.000
107	B	118	THR	0	0.000	-0.008	21.129	-0.504	-0.504	0.000	0.000	0.000	0.000
108	B	119	ALA	0	0.014	0.000	19.830	-0.853	-0.853	0.000	0.000	0.000	0.000
109	B	120	ASP	-1	-0.897	-0.947	18.416	-16.350	-16.350	0.000	0.000	0.000	0.000
110	B	121	ILE	0	-0.015	-0.001	17.222	-1.175	-1.175	0.000	0.000	0.000	0.000
111	B	122	LEU	0	0.006	0.004	15.468	-1.186	-1.186	0.000	0.000	0.000	0.000
112	B	123	ARG	1	0.893	0.942	13.920	16.016	16.016	0.000	0.000	0.000	0.000
113	B	124	GLY	0	0.029	0.014	12.615	-2.059	-2.059	0.000	0.000	0.000	0.000
114	B	125	LEU	0	-0.025	-0.006	10.940	-1.370	-1.370	0.000	0.000	0.000	0.000
115	B	126	LEU	0	0.007	-0.001	9.612	-2.085	-2.085	0.000	0.000	0.000	0.000
116	B	127	SER	0	-0.025	0.001	7.763	-5.035	-5.035	0.000	0.000	0.000	0.000
117	B	128	ASN	0	0.016	-0.012	6.790	-4.913	-4.913	0.000	0.000	0.000	0.000
118	B	129	VAL	0	0.034	0.021	5.744	-2.947	-2.947	0.000	0.000	0.000	0.000
130	B	143	ASP	-1	-0.814	-0.881	7.286	-27.135	-27.135	0.000	0.000	0.000	0.000
131	B	144	VAL	0	0.032	0.012	10.386	0.489	0.489	0.000	0.000	0.000	0.000
132	B	145	THR	0	0.004	-0.021	12.544	1.397	1.397	0.000	0.000	0.000	0.000
133	B	146	TYR	0	-0.015	-0.004	13.029	-1.098	-1.098	0.000	0.000	0.000	0.000
134	B	147	GLY	0	0.062	0.043	17.918	0.604	0.604	0.000	0.000	0.000	0.000
135	B	148	PRO	0	-0.037	-0.017	21.447	-0.023	-0.023	0.000	0.000	0.000	0.000
136	B	149	ASP	-1	-0.864	-0.928	23.935	-11.074	-11.074	0.000	0.000	0.000	0.000
137	B	150	THR	0	0.002	0.012	26.391	0.562	0.562	0.000	0.000	0.000	0.000
138	B	151	SER	0	-0.002	-0.013	28.144	0.204	0.204	0.000	0.000	0.000	0.000
139	B	152	GLY	0	0.003	0.021	30.949	0.375	0.375	0.000	0.000	0.000	0.000
140	B	153	LYS	0	-0.006	-0.022	29.988	0.035	0.035	0.000	0.000	0.000	0.000
141	B	154	ASP	0	0.032	0.024	34.753	0.013	0.013	0.000	0.000	0.000	0.000
142	B	155	VAL	0	0.053	0.012	36.646	-0.193	-0.193	0.000	0.000	0.000	0.000
143	B	156	PHE	0	0.049	0.028	36.806	-0.216	-0.216	0.000	0.000	0.000	0.000
144	B	157	GLN	0	0.026	0.001	33.819	-0.149	-0.149	0.000	0.000	0.000	0.000
145	B	158	LYS	1	0.921	0.957	31.563	9.782	9.782	0.000	0.000	0.000	0.000
146	B	159	LYS	1	0.864	0.947	32.643	8.065	8.065	0.000	0.000	0.000	0.000
147	B	160	LYS	1	0.976	1.002	33.773	8.662	8.662	0.000	0.000	0.000	0.000
148	B	161	LEU	0	-0.004	0.009	29.514	-0.121	-0.121	0.000	0.000	0.000	0.000
149	B	162	GLY	0	0.054	0.019	28.691	-0.368	-0.368	0.000	0.000	0.000	0.000
150	B	164	GLN	0	-0.020	0.001	29.719	0.200	0.200	0.000	0.000	0.000	0.000
151	B	165	LEU	0	-0.014	0.014	22.669	-0.255	-0.255	0.000	0.000	0.000	0.000
152	B	166	LEU	0	-0.006	-0.012	24.885	-0.397	-0.397	0.000	0.000	0.000	0.000
153	B	167	GLY	0	0.023	0.013	26.418	-0.035	-0.035	0.000	0.000	0.000	0.000
154	B	168	LYS	1	0.859	0.940	21.452	12.458	12.458	0.000	0.000	0.000	0.000
155	B	169	TYR	0	0.002	-0.007	19.526	-0.465	-0.465	0.000	0.000	0.000	0.000
156	B	170	LYS	1	0.903	0.958	22.145	9.571	9.571	0.000	0.000	0.000	0.000
157	B	171	GLN	0	0.012	0.021	23.887	-0.312	-0.312	0.000	0.000	0.000	0.000
158	B	172	ILE	0	-0.018	-0.014	17.577	-0.053	-0.053	0.000	0.000	0.000	0.000
159	B	173	ILE	0	-0.001	-0.004	17.477	-0.467	-0.467	0.000	0.000	0.000	0.000
160	B	174	ALA	0	0.011	0.009	19.450	-0.247	-0.247	0.000	0.000	0.000	0.000
161	B	175	VAL	0	-0.044	-0.013	19.110	0.167	0.167	0.000	0.000	0.000	0.000
162	B	176	LEU	0	-0.014	-0.007	13.873	-0.470	-0.470	0.000	0.000	0.000	0.000
163	B	177	ALA	0	-0.041	-0.035	15.998	-0.386	-0.386	0.000	0.000	0.000	0.000
164	B	178	GLN	0	-0.006	0.004	17.948	-0.262	-0.262	0.000	0.000	0.000	0.000
165	B	179	ALA	0	0.006	0.015	16.005	0.377	0.377	0.000	0.000	0.000	0.000
166	B	180	PHE	-1	-0.837	-0.893	9.435	-16.484	-16.484	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:12:CYS)