FMO DATABASE

FMODB ID: 858YY

Calculation Name: 4O9H-A-Xray372

Preferred Name: Interleukin-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4O9H

Chain ID: A

ChEMBL ID: CHEMBL1795129

UniProt ID: P05231

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1559581.207577
FMO2-HF: Nuclear repulsion	1496731.026781
FMO2-HF: Total energy	-62850.180796
FMO2-MP2: Total energy	-63031.346714

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(A:19:LEU)

Summations of interaction energy for fragment #1(A:19:LEU)

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.
-31.037	-34.822	17.533	-6.57	-7.178	0.043

Interaction energy analysis for fragmet #1(A:19:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.024

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	A	21	SER	0	0.004	-0.003	2.738	-3.916	-1.308	0.711	-1.361	-1.958	-0.007
4	A	22	SER	0	0.078	0.037	5.210	0.162	0.194	-0.001	-0.004	-0.027	0.000
5	A	23	GLU	-1	-0.825	-0.889	7.089	-0.995	-0.995	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.940	0.967	2.910	1.871	2.922	0.618	-0.343	-1.326	-0.002
7	A	25	ILE	0	0.019	0.013	7.414	0.167	0.167	0.000	0.000	0.000	0.000
8	A	26	ASP	-1	-0.830	-0.886	9.990	-0.123	-0.123	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.886	0.909	9.717	0.678	0.678	0.000	0.000	0.000	0.000
10	A	28	GLN	0	-0.016	-0.003	9.947	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	29	ILE	0	0.001	-0.007	12.077	0.042	0.042	0.000	0.000	0.000	0.000
12	A	30	ARG	1	0.857	0.912	15.263	0.140	0.140	0.000	0.000	0.000	0.000
13	A	31	TYR	0	0.041	0.031	13.532	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	32	ILE	0	0.002	0.006	13.500	0.017	0.017	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.049	-0.021	17.262	0.004	0.004	0.000	0.000	0.000	0.000
16	A	34	ASP	-1	-0.909	-0.950	19.884	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	35	GLY	0	0.009	0.002	19.860	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	36	ILE	0	-0.008	-0.007	20.544	0.003	0.003	0.000	0.000	0.000	0.000
19	A	37	SER	0	-0.053	-0.025	23.184	0.000	0.000	0.000	0.000	0.000	0.000
20	A	38	ALA	0	-0.046	-0.018	24.037	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	39	LEU	0	0.042	0.018	22.919	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.920	0.947	26.584	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	41	LYS	1	0.943	0.963	27.986	0.012	0.012	0.000	0.000	0.000	0.000
24	A	42	GLU	-1	-0.853	-0.895	28.991	0.031	0.031	0.000	0.000	0.000	0.000
25	A	43	THR	0	0.031	0.014	30.681	0.005	0.005	0.000	0.000	0.000	0.000
26	A	44	CYS	0	-0.009	-0.002	32.628	0.001	0.001	0.000	0.000	0.000	0.000
27	A	45	ASN	0	-0.023	0.000	34.887	0.000	0.000	0.000	0.000	0.000	0.000
28	A	46	LYS	1	0.867	0.932	33.386	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	47	SER	0	0.016	0.024	36.689	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	48	ASN	0	-0.076	-0.035	38.582	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	61	ASN	0	-0.001	-0.007	35.229	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.027	-0.017	31.748	0.005	0.005	0.000	0.000	0.000	0.000
33	A	63	ASN	0	0.006	0.007	31.713	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	64	LEU	0	-0.004	0.013	27.528	0.015	0.015	0.000	0.000	0.000	0.000
35	A	65	PRO	0	0.042	0.040	23.815	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	66	LYS	1	0.948	0.966	26.177	-0.124	-0.124	0.000	0.000	0.000	0.000
37	A	67	MET	0	-0.027	0.001	21.438	0.008	0.008	0.000	0.000	0.000	0.000
38	A	68	ALA	0	-0.008	-0.016	26.890	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.844	-0.897	28.454	0.092	0.092	0.000	0.000	0.000	0.000
40	A	70	LYS	1	0.919	0.946	28.313	-0.184	-0.184	0.000	0.000	0.000	0.000
41	A	71	ASP	-1	-0.782	-0.885	25.099	0.205	0.205	0.000	0.000	0.000	0.000
42	A	72	GLY	0	0.051	0.057	24.756	0.021	0.021	0.000	0.000	0.000	0.000
43	A	73	CYS	0	-0.062	-0.013	20.671	0.020	0.020	0.000	0.000	0.000	0.000
44	A	74	PHE	0	-0.057	-0.029	23.839	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	75	GLN	0	0.045	0.011	26.373	0.003	0.003	0.000	0.000	0.000	0.000
46	A	76	SER	0	-0.052	-0.044	27.497	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	77	GLY	0	0.053	0.010	29.216	0.008	0.008	0.000	0.000	0.000	0.000
48	A	78	PHE	0	-0.075	-0.019	19.875	0.014	0.014	0.000	0.000	0.000	0.000
49	A	79	ASN	0	0.028	-0.004	23.476	0.010	0.010	0.000	0.000	0.000	0.000
50	A	80	GLU	-1	-0.794	-0.901	15.720	0.218	0.218	0.000	0.000	0.000	0.000
51	A	81	GLU	-1	-0.840	-0.920	18.572	0.412	0.412	0.000	0.000	0.000	0.000
52	A	82	THR	0	0.004	-0.026	20.191	0.034	0.034	0.000	0.000	0.000	0.000
53	A	84	LEU	0	0.020	-0.003	13.630	0.025	0.025	0.000	0.000	0.000	0.000
54	A	85	VAL	0	0.056	0.036	17.422	0.069	0.069	0.000	0.000	0.000	0.000
55	A	86	LYS	1	0.836	0.939	19.418	-0.209	-0.209	0.000	0.000	0.000	0.000
56	A	87	ILE	0	-0.051	-0.042	16.399	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	88	ILE	0	0.015	0.002	13.942	0.018	0.018	0.000	0.000	0.000	0.000
58	A	89	THR	0	-0.006	-0.015	16.903	0.012	0.012	0.000	0.000	0.000	0.000
59	A	90	GLY	0	0.032	0.007	20.442	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	91	LEU	0	-0.067	-0.039	14.695	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	92	LEU	0	0.006	-0.005	16.501	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	93	GLU	-1	-0.924	-0.961	19.297	0.256	0.256	0.000	0.000	0.000	0.000
63	A	94	PHE	0	-0.006	-0.024	20.548	-0.040	-0.040	0.000	0.000	0.000	0.000
64	A	95	GLU	-1	-0.834	-0.883	17.570	0.500	0.500	0.000	0.000	0.000	0.000
65	A	96	VAL	0	0.033	0.027	20.817	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	97	TYR	0	-0.016	-0.029	24.468	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	98	LEU	0	-0.035	-0.031	19.046	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	99	GLU	-1	-0.937	-0.965	22.781	0.236	0.236	0.000	0.000	0.000	0.000
69	A	100	TYR	0	-0.038	-0.042	23.888	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	101	LEU	0	-0.042	-0.022	23.537	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	102	GLN	0	0.018	0.005	21.834	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	103	ASN	0	0.005	-0.011	26.045	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	104	ARG	1	0.741	0.854	29.275	-0.089	-0.089	0.000	0.000	0.000	0.000
74	A	105	PHE	0	-0.022	-0.020	27.121	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	106	GLU	-1	-0.781	-0.877	28.637	0.103	0.103	0.000	0.000	0.000	0.000
76	A	107	SER	0	-0.126	-0.071	30.101	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	108	SER	0	-0.078	-0.056	27.554	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	109	GLU	-1	-0.794	-0.877	25.642	0.053	0.053	0.000	0.000	0.000	0.000
79	A	110	GLU	-1	-0.834	-0.918	20.459	0.108	0.108	0.000	0.000	0.000	0.000
80	A	111	GLN	0	-0.041	-0.017	21.032	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	112	ALA	0	0.010	0.001	21.419	0.011	0.011	0.000	0.000	0.000	0.000
82	A	113	ARG	1	0.891	0.935	19.058	-0.111	-0.111	0.000	0.000	0.000	0.000
83	A	114	ALA	0	0.010	0.010	17.091	0.043	0.043	0.000	0.000	0.000	0.000
84	A	115	VAL	0	0.008	0.020	16.312	0.032	0.032	0.000	0.000	0.000	0.000
85	A	116	GLN	0	0.036	0.034	17.038	0.075	0.075	0.000	0.000	0.000	0.000
86	A	117	MET	0	-0.002	-0.012	14.062	0.103	0.103	0.000	0.000	0.000	0.000
87	A	118	SER	0	-0.029	-0.034	12.204	0.094	0.094	0.000	0.000	0.000	0.000
88	A	119	THR	0	0.015	-0.005	12.097	0.070	0.070	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.820	0.897	12.884	-0.392	-0.392	0.000	0.000	0.000	0.000
90	A	121	VAL	0	0.005	0.013	6.837	0.235	0.235	0.000	0.000	0.000	0.000
91	A	122	LEU	0	-0.039	-0.017	8.297	0.372	0.372	0.000	0.000	0.000	0.000
92	A	123	ILE	0	0.034	0.016	10.546	0.133	0.133	0.000	0.000	0.000	0.000
93	A	124	GLN	0	0.026	0.015	7.250	0.169	0.169	0.000	0.000	0.000	0.000
94	A	125	PHE	0	-0.077	-0.046	3.188	0.319	0.805	0.011	-0.110	-0.387	0.000
95	A	126	LEU	0	0.025	0.005	7.238	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	127	GLN	0	0.038	0.012	10.592	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	128	LYS	1	0.874	0.928	1.887	-30.239	-38.201	16.194	-4.752	-3.480	0.052
98	A	129	LYS	1	0.752	0.880	7.979	-0.624	-0.624	0.000	0.000	0.000	0.000
99	A	130	ALA	0	0.039	-0.005	9.650	-0.139	-0.139	0.000	0.000	0.000	0.000
100	A	131	LYS	1	0.862	0.935	8.502	-1.314	-1.314	0.000	0.000	0.000	0.000
101	A	132	ASN	0	-0.082	-0.017	12.602	-0.063	-0.063	0.000	0.000	0.000	0.000
102	A	133	LEU	0	0.002	-0.016	15.646	-0.058	-0.058	0.000	0.000	0.000	0.000
103	A	134	ASP	-1	-0.888	-0.921	15.120	1.029	1.029	0.000	0.000	0.000	0.000
104	A	135	ALA	0	-0.038	-0.032	18.107	-0.045	-0.045	0.000	0.000	0.000	0.000
105	A	136	ILE	0	-0.050	-0.006	18.605	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	137	THR	0	0.034	0.021	21.546	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	138	THR	0	0.009	-0.014	19.755	0.009	0.009	0.000	0.000	0.000	0.000
108	A	139	PRO	0	-0.003	0.005	21.905	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	140	ASP	-1	-0.732	-0.833	24.595	0.260	0.260	0.000	0.000	0.000	0.000
110	A	141	PRO	0	0.020	0.000	24.408	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	142	THR	0	-0.012	-0.012	26.745	-0.015	-0.015	0.000	0.000	0.000	0.000
112	A	143	THR	0	-0.035	-0.036	29.955	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	144	ASN	0	-0.007	-0.008	24.403	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	145	ALA	0	0.054	0.027	28.425	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	146	SER	0	-0.017	-0.014	30.146	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	147	LEU	0	-0.042	-0.016	29.032	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	148	LEU	0	0.009	0.005	27.592	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	149	THR	0	0.014	-0.004	30.756	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	150	LYS	1	0.866	0.941	34.175	-0.128	-0.128	0.000	0.000	0.000	0.000
120	A	151	LEU	0	-0.060	-0.048	30.387	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	152	GLN	0	0.000	-0.008	30.800	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	153	ALA	0	-0.015	0.006	34.824	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	154	GLN	0	-0.045	0.004	35.166	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	155	ASN	0	0.044	0.018	39.009	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	156	GLN	0	0.119	0.048	38.111	0.004	0.004	0.000	0.000	0.000	0.000
126	A	157	TRP	0	0.083	0.053	38.132	0.002	0.002	0.000	0.000	0.000	0.000
127	A	158	LEU	0	0.006	-0.007	38.571	0.001	0.001	0.000	0.000	0.000	0.000
128	A	159	GLN	0	0.031	0.046	34.601	0.009	0.009	0.000	0.000	0.000	0.000
129	A	160	ASP	-1	-0.793	-0.863	33.762	0.071	0.071	0.000	0.000	0.000	0.000
130	A	161	MET	0	-0.040	-0.026	34.125	0.000	0.000	0.000	0.000	0.000	0.000
131	A	162	THR	0	-0.026	-0.026	31.349	0.005	0.005	0.000	0.000	0.000	0.000
132	A	163	THR	0	0.022	0.002	29.198	0.012	0.012	0.000	0.000	0.000	0.000
133	A	164	HIS	0	-0.020	-0.008	29.423	0.005	0.005	0.000	0.000	0.000	0.000
134	A	165	LEU	0	-0.031	-0.016	30.414	0.001	0.001	0.000	0.000	0.000	0.000
135	A	166	ILE	0	0.009	0.012	25.604	0.006	0.006	0.000	0.000	0.000	0.000
136	A	167	LEU	0	0.003	0.009	24.732	0.010	0.010	0.000	0.000	0.000	0.000
137	A	168	ARG	1	0.884	0.935	25.848	-0.072	-0.072	0.000	0.000	0.000	0.000
138	A	169	SER	0	0.014	0.002	27.162	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	170	PHE	0	0.049	0.020	17.877	0.004	0.004	0.000	0.000	0.000	0.000
140	A	171	LYS	1	0.880	0.931	22.396	-0.061	-0.061	0.000	0.000	0.000	0.000
141	A	172	GLU	-1	-0.844	-0.917	23.701	0.073	0.073	0.000	0.000	0.000	0.000
142	A	173	PHE	0	-0.003	0.022	19.251	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	174	LEU	0	0.033	0.031	17.215	0.010	0.010	0.000	0.000	0.000	0.000
144	A	175	GLN	0	-0.004	-0.017	20.096	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	176	SER	0	-0.092	-0.046	22.287	-0.021	-0.021	0.000	0.000	0.000	0.000
146	A	177	SER	0	0.025	-0.010	18.061	0.008	0.008	0.000	0.000	0.000	0.000
147	A	178	LEU	0	-0.039	-0.002	15.826	0.003	0.003	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.938	0.957	17.843	-0.074	-0.074	0.000	0.000	0.000	0.000
149	A	180	ALA	0	0.043	0.034	19.740	-0.016	-0.016	0.000	0.000	0.000	0.000
150	A	181	LEU	0	0.034	-0.006	13.236	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	182	ARG	1	0.778	0.884	14.557	0.138	0.138	0.000	0.000	0.000	0.000
152	A	183	GLN	0	0.005	0.019	16.805	-0.041	-0.041	0.000	0.000	0.000	0.000
153	A	184	MET	0	-0.087	-0.007	13.589	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:LEU)