FMO DATABASE

FMODB ID: 1721Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1548125.00375
FMO2-HF: Nuclear repulsion	1485276.457196
FMO2-HF: Total energy	-62848.546554
FMO2-MP2: Total energy	-63029.71472

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.
-23.998	-20.795	8.074	-4.49	-6.785	0.014

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 : 0.017 / q_NPA : -0.009

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	-0.001	0.002	3.070	-2.627	-0.110	0.118	-1.225	-1.409	-0.004
4	A	22	SER	0	0.062	0.026	5.590	0.097	0.097	0.000	0.000	0.000	0.000
5	A	23	GLU	-1	-0.835	-0.904	8.280	-0.714	-0.714	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.957	0.973	1.924	2.310	1.824	3.757	-0.991	-2.279	-0.005
7	A	25	ILE	0	0.024	0.019	7.776	0.110	0.110	0.000	0.000	0.000	0.000
8	A	26	ASP	-1	-0.886	-0.948	9.590	-0.125	-0.125	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.889	0.921	9.962	0.675	0.675	0.000	0.000	0.000	0.000
10	A	28	GLN	0	-0.024	-0.011	9.201	-0.154	-0.154	0.000	0.000	0.000	0.000
11	A	29	ILE	0	0.000	-0.003	11.307	0.060	0.060	0.000	0.000	0.000	0.000
12	A	30	ARG	1	0.892	0.942	14.492	0.173	0.173	0.000	0.000	0.000	0.000
13	A	31	TYR	0	0.030	0.035	13.735	0.001	0.001	0.000	0.000	0.000	0.000
14	A	32	ILE	0	0.019	0.008	12.985	0.026	0.026	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.079	-0.041	16.704	0.016	0.016	0.000	0.000	0.000	0.000
16	A	34	ASP	-1	-0.906	-0.952	19.312	-0.119	-0.119	0.000	0.000	0.000	0.000
17	A	35	GLY	0	0.006	0.006	19.415	0.003	0.003	0.000	0.000	0.000	0.000
18	A	36	ILE	0	-0.024	-0.013	20.051	0.011	0.011	0.000	0.000	0.000	0.000
19	A	37	SER	0	-0.059	-0.022	22.688	0.007	0.007	0.000	0.000	0.000	0.000
20	A	38	ALA	0	-0.017	-0.015	23.637	0.005	0.005	0.000	0.000	0.000	0.000
21	A	39	LEU	0	0.047	0.030	22.944	0.002	0.002	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.932	0.960	26.035	0.009	0.009	0.000	0.000	0.000	0.000
23	A	41	LYS	1	0.941	0.952	28.062	0.057	0.057	0.000	0.000	0.000	0.000
24	A	42	GLU	-1	-0.901	-0.895	28.774	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	43	THR	0	0.035	0.020	30.027	0.006	0.006	0.000	0.000	0.000	0.000
26	A	44	CYS	0	-0.091	-0.038	32.061	0.003	0.003	0.000	0.000	0.000	0.000
27	A	45	ASN	0	-0.020	-0.009	34.493	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	46	LYS	1	0.963	0.980	34.241	0.000	0.000	0.000	0.000	0.000	0.000
29	A	47	SER	0	0.015	0.032	36.052	0.000	0.000	0.000	0.000	0.000	0.000
30	A	48	ASN	0	-0.009	-0.005	37.669	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	61	ASN	0	0.005	-0.010	34.876	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.051	-0.023	30.540	0.005	0.005	0.000	0.000	0.000	0.000
33	A	63	ASN	0	0.016	0.014	31.052	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	64	LEU	0	-0.031	-0.008	26.567	0.011	0.011	0.000	0.000	0.000	0.000
35	A	65	PRO	0	0.016	0.027	23.186	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	66	LYS	1	0.955	0.975	25.692	-0.092	-0.092	0.000	0.000	0.000	0.000
37	A	67	MET	0	-0.049	-0.014	20.784	0.009	0.009	0.000	0.000	0.000	0.000
38	A	68	ALA	0	-0.028	-0.022	26.342	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.875	-0.956	28.197	0.079	0.079	0.000	0.000	0.000	0.000
40	A	70	LYS	1	0.960	0.980	29.199	-0.143	-0.143	0.000	0.000	0.000	0.000
41	A	71	ASP	-1	-0.817	-0.920	24.773	0.168	0.168	0.000	0.000	0.000	0.000
42	A	72	GLY	0	0.056	0.079	24.837	0.018	0.018	0.000	0.000	0.000	0.000
43	A	73	CYS	0	-0.072	-0.026	20.844	0.018	0.018	0.000	0.000	0.000	0.000
44	A	74	PHE	0	-0.054	-0.026	23.988	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	75	GLN	0	0.042	0.010	26.610	0.003	0.003	0.000	0.000	0.000	0.000
46	A	76	SER	0	-0.049	-0.021	27.898	0.000	0.000	0.000	0.000	0.000	0.000
47	A	77	GLY	0	0.065	0.025	29.867	0.005	0.005	0.000	0.000	0.000	0.000
48	A	78	PHE	0	-0.098	-0.036	20.343	0.013	0.013	0.000	0.000	0.000	0.000
49	A	79	ASN	0	0.011	-0.007	24.260	0.014	0.014	0.000	0.000	0.000	0.000
50	A	80	GLU	-1	-0.911	-0.961	18.291	0.172	0.172	0.000	0.000	0.000	0.000
51	A	81	GLU	-1	-0.881	-0.939	18.998	0.375	0.375	0.000	0.000	0.000	0.000
52	A	82	THR	0	-0.015	-0.038	20.422	0.027	0.027	0.000	0.000	0.000	0.000
53	A	84	LEU	0	0.041	0.004	13.688	0.014	0.014	0.000	0.000	0.000	0.000
54	A	85	VAL	0	0.046	0.033	17.307	0.055	0.055	0.000	0.000	0.000	0.000
55	A	86	LYS	1	0.906	0.985	19.573	-0.173	-0.173	0.000	0.000	0.000	0.000
56	A	87	ILE	0	-0.039	-0.032	15.727	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	88	ILE	0	0.009	-0.004	13.849	0.004	0.004	0.000	0.000	0.000	0.000
58	A	89	THR	0	-0.004	-0.009	16.450	0.012	0.012	0.000	0.000	0.000	0.000
59	A	90	GLY	0	0.033	0.013	19.986	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	91	LEU	0	-0.052	-0.043	14.229	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	92	LEU	0	0.002	0.006	15.898	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	93	GLU	-1	-0.943	-0.969	18.576	0.206	0.206	0.000	0.000	0.000	0.000
63	A	94	PHE	0	-0.020	-0.037	20.083	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	95	GLU	-1	-0.857	-0.935	16.453	0.429	0.429	0.000	0.000	0.000	0.000
65	A	96	VAL	0	0.006	0.026	20.393	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	97	TYR	0	-0.002	-0.018	23.945	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	98	LEU	0	-0.026	-0.026	18.501	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	99	GLU	-1	-0.922	-0.956	22.339	0.151	0.151	0.000	0.000	0.000	0.000
69	A	100	TYR	0	-0.043	-0.029	23.588	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	101	LEU	0	-0.057	-0.041	23.421	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	102	GLN	0	0.065	0.019	21.023	0.001	0.001	0.000	0.000	0.000	0.000
72	A	103	ASN	0	0.045	0.025	25.459	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	104	ARG	1	0.784	0.900	29.044	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	105	PHE	0	-0.005	-0.017	26.622	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	106	GLU	-1	-0.889	-0.928	27.879	0.045	0.045	0.000	0.000	0.000	0.000
76	A	107	SER	0	-0.130	-0.070	29.038	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	108	SER	0	-0.069	-0.076	26.646	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	109	GLU	-1	-0.783	-0.880	25.491	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	110	GLU	-1	-0.954	-0.990	20.469	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	111	GLN	0	-0.049	-0.026	20.806	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	112	ALA	0	0.027	0.003	20.874	0.004	0.004	0.000	0.000	0.000	0.000
82	A	113	ARG	1	0.953	0.995	17.907	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	114	ALA	0	-0.001	0.002	16.933	0.027	0.027	0.000	0.000	0.000	0.000
84	A	115	VAL	0	0.004	0.013	16.050	0.003	0.003	0.000	0.000	0.000	0.000
85	A	116	GLN	0	0.037	0.054	16.492	0.039	0.039	0.000	0.000	0.000	0.000
86	A	117	MET	0	-0.036	-0.038	13.965	0.081	0.081	0.000	0.000	0.000	0.000
87	A	118	SER	0	-0.015	-0.017	11.876	0.033	0.033	0.000	0.000	0.000	0.000
88	A	119	THR	0	0.002	-0.028	11.517	0.009	0.009	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.944	0.982	12.244	-0.334	-0.334	0.000	0.000	0.000	0.000
90	A	121	VAL	0	0.000	0.017	6.283	0.219	0.219	0.000	0.000	0.000	0.000
91	A	122	LEU	0	-0.046	-0.015	7.660	0.269	0.269	0.000	0.000	0.000	0.000
92	A	123	ILE	0	0.010	0.004	9.943	0.128	0.128	0.000	0.000	0.000	0.000
93	A	124	GLN	0	0.036	0.024	6.874	-0.183	-0.183	0.000	0.000	0.000	0.000
94	A	125	PHE	0	-0.076	-0.046	2.561	-0.160	0.466	0.165	-0.216	-0.576	-0.001
95	A	126	LEU	0	0.026	-0.009	6.815	0.082	0.082	0.000	0.000	0.000	0.000
96	A	127	GLN	0	0.092	0.039	10.279	0.103	0.103	0.000	0.000	0.000	0.000
97	A	128	LYS	1	0.918	0.969	2.318	-24.044	-23.498	4.034	-2.058	-2.521	0.024
98	A	129	LYS	1	0.792	0.898	8.061	-0.548	-0.548	0.000	0.000	0.000	0.000
99	A	130	ALA	0	0.072	0.022	9.467	-0.161	-0.161	0.000	0.000	0.000	0.000
100	A	131	LYS	1	0.890	0.973	8.295	-1.235	-1.235	0.000	0.000	0.000	0.000
101	A	132	ASN	0	-0.052	-0.016	12.023	-0.077	-0.077	0.000	0.000	0.000	0.000
102	A	133	LEU	0	-0.016	-0.016	15.230	-0.064	-0.064	0.000	0.000	0.000	0.000
103	A	134	ASP	-1	-0.927	-0.957	15.264	0.933	0.933	0.000	0.000	0.000	0.000
104	A	135	ALA	0	-0.056	-0.040	18.160	-0.036	-0.036	0.000	0.000	0.000	0.000
105	A	136	ILE	0	-0.026	0.008	18.399	-0.031	-0.031	0.000	0.000	0.000	0.000
106	A	137	THR	0	0.048	0.019	21.543	-0.029	-0.029	0.000	0.000	0.000	0.000
107	A	138	THR	0	0.003	-0.010	19.692	0.006	0.006	0.000	0.000	0.000	0.000
108	A	139	PRO	0	-0.012	0.000	21.081	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	140	ASP	-1	-0.846	-0.916	24.043	0.222	0.222	0.000	0.000	0.000	0.000
110	A	141	PRO	0	0.040	0.002	24.375	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	142	THR	0	0.040	0.013	26.490	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	143	THR	0	-0.029	-0.010	29.489	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	144	ASN	0	0.006	-0.004	24.262	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	145	ALA	0	0.036	0.017	28.262	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	146	SER	0	0.004	0.011	29.850	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	147	LEU	0	-0.030	-0.016	28.558	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	148	LEU	0	0.013	0.000	27.219	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	149	THR	0	0.022	0.009	30.664	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	150	LYS	1	0.920	0.965	34.086	-0.104	-0.104	0.000	0.000	0.000	0.000
120	A	151	LEU	0	-0.072	-0.039	29.962	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	152	GLN	0	0.027	0.001	29.838	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	153	ALA	0	-0.002	0.023	34.567	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	154	GLN	0	-0.096	-0.034	34.957	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	155	ASN	0	0.050	0.017	38.805	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	156	GLN	0	0.102	0.032	37.026	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	157	TRP	0	0.079	0.058	37.785	0.000	0.000	0.000	0.000	0.000	0.000
127	A	158	LEU	0	0.003	-0.013	38.037	0.000	0.000	0.000	0.000	0.000	0.000
128	A	159	GLN	0	0.003	0.019	34.159	0.007	0.007	0.000	0.000	0.000	0.000
129	A	160	ASP	-1	-0.826	-0.904	33.306	0.035	0.035	0.000	0.000	0.000	0.000
130	A	161	MET	0	-0.064	-0.030	33.771	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	162	THR	0	-0.021	-0.022	30.820	0.004	0.004	0.000	0.000	0.000	0.000
132	A	163	THR	0	0.047	0.022	28.555	0.008	0.008	0.000	0.000	0.000	0.000
133	A	164	HIS	0	-0.019	0.000	28.904	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	165	LEU	0	-0.057	-0.041	29.993	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	166	ILE	0	0.006	0.008	25.079	0.005	0.005	0.000	0.000	0.000	0.000
136	A	167	LEU	0	0.025	0.012	24.384	0.006	0.006	0.000	0.000	0.000	0.000
137	A	168	ARG	1	0.907	0.960	25.332	-0.041	-0.041	0.000	0.000	0.000	0.000
138	A	169	SER	0	0.036	0.015	26.633	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	170	PHE	0	0.060	0.029	17.365	0.004	0.004	0.000	0.000	0.000	0.000
140	A	171	LYS	1	0.945	0.976	21.745	-0.015	-0.015	0.000	0.000	0.000	0.000
141	A	172	GLU	-1	-0.964	-0.996	22.904	0.045	0.045	0.000	0.000	0.000	0.000
142	A	173	PHE	0	0.014	0.014	18.863	-0.010	-0.010	0.000	0.000	0.000	0.000
143	A	174	LEU	0	0.035	0.028	16.439	0.009	0.009	0.000	0.000	0.000	0.000
144	A	175	GLN	0	-0.007	-0.009	19.031	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	176	SER	0	-0.056	-0.023	21.695	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	177	SER	0	0.031	-0.009	17.117	0.012	0.012	0.000	0.000	0.000	0.000
147	A	178	LEU	0	-0.062	-0.010	16.143	0.002	0.002	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.923	0.955	18.070	-0.033	-0.033	0.000	0.000	0.000	0.000
149	A	180	ALA	0	0.047	0.023	19.724	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	181	LEU	0	0.027	-0.014	13.531	0.004	0.004	0.000	0.000	0.000	0.000
151	A	182	ARG	1	0.853	0.932	15.378	0.126	0.126	0.000	0.000	0.000	0.000
152	A	183	GLN	0	-0.036	-0.011	17.095	-0.023	-0.023	0.000	0.000	0.000	0.000
153	A	184	MET	0	0.020	0.053	14.329	0.061	0.061	0.000	0.000	0.000	0.000

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