FMO DATABASE

FMODB ID: G6L31

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	OptHSide
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	-1550325.331077
FMO2-HF: Nuclear repulsion	1487475.848875
FMO2-HF: Total energy	-62849.482202
FMO2-MP2: Total energy	-63030.646269

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.
-26.063	-23.722	8.431	-4.087	-6.685	0.018

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 : 0.003 / q_NPA : -0.012

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	0.017	0.007	2.853	-3.406	-0.653	0.476	-1.351	-1.878	-0.006
4	A	22	SER	0	0.094	0.045	5.236	0.148	0.164	-0.001	-0.004	-0.011	0.000
5	A	23	GLU	-1	-0.834	-0.888	7.625	-0.943	-0.943	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.943	0.961	2.824	2.093	3.195	0.782	-0.408	-1.476	-0.003
7	A	25	ILE	0	0.026	0.023	7.529	0.156	0.156	0.000	0.000	0.000	0.000
8	A	26	ASP	-1	-0.824	-0.899	9.669	-0.137	-0.137	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.869	0.896	9.815	0.748	0.748	0.000	0.000	0.000	0.000
10	A	28	GLN	0	-0.012	-0.007	9.237	-0.119	-0.119	0.000	0.000	0.000	0.000
11	A	29	ILE	0	-0.003	-0.004	11.361	0.054	0.054	0.000	0.000	0.000	0.000
12	A	30	ARG	1	0.870	0.918	14.563	0.187	0.187	0.000	0.000	0.000	0.000
13	A	31	TYR	0	0.024	0.031	13.350	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	32	ILE	0	0.021	0.012	13.127	0.023	0.023	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.078	-0.040	16.757	0.010	0.010	0.000	0.000	0.000	0.000
16	A	34	ASP	-1	-0.897	-0.948	19.345	-0.109	-0.109	0.000	0.000	0.000	0.000
17	A	35	GLY	0	0.003	0.003	19.458	0.001	0.001	0.000	0.000	0.000	0.000
18	A	36	ILE	0	-0.018	-0.013	20.172	0.009	0.009	0.000	0.000	0.000	0.000
19	A	37	SER	0	-0.058	-0.021	22.742	0.004	0.004	0.000	0.000	0.000	0.000
20	A	38	ALA	0	-0.032	-0.019	23.620	0.003	0.003	0.000	0.000	0.000	0.000
21	A	39	LEU	0	0.052	0.031	22.651	0.001	0.001	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.937	0.962	26.076	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	41	LYS	1	0.942	0.961	27.795	0.044	0.044	0.000	0.000	0.000	0.000
24	A	42	GLU	-1	-0.852	-0.890	28.972	0.007	0.007	0.000	0.000	0.000	0.000
25	A	43	THR	0	0.046	0.024	30.124	0.007	0.007	0.000	0.000	0.000	0.000
26	A	44	CYS	0	-0.114	-0.053	32.105	0.003	0.003	0.000	0.000	0.000	0.000
27	A	45	ASN	0	-0.015	-0.005	34.541	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	46	LYS	1	0.899	0.941	33.166	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	47	SER	0	-0.009	0.019	36.045	0.000	0.000	0.000	0.000	0.000	0.000
30	A	48	ASN	0	-0.011	-0.003	37.721	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	61	ASN	0	0.008	0.000	34.979	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.051	-0.032	31.185	0.005	0.005	0.000	0.000	0.000	0.000
33	A	63	ASN	0	0.019	0.013	31.239	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	64	LEU	0	-0.019	0.000	26.664	0.013	0.013	0.000	0.000	0.000	0.000
35	A	65	PRO	0	0.029	0.034	23.261	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	66	LYS	1	0.949	0.968	25.799	-0.108	-0.108	0.000	0.000	0.000	0.000
37	A	67	MET	0	-0.040	0.005	20.872	0.008	0.008	0.000	0.000	0.000	0.000
38	A	68	ALA	0	0.001	-0.011	26.453	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.844	-0.916	28.310	0.082	0.082	0.000	0.000	0.000	0.000
40	A	70	LYS	1	0.906	0.945	27.946	-0.175	-0.175	0.000	0.000	0.000	0.000
41	A	71	ASP	-1	-0.785	-0.874	24.869	0.189	0.189	0.000	0.000	0.000	0.000
42	A	72	GLY	0	0.070	0.076	24.853	0.019	0.019	0.000	0.000	0.000	0.000
43	A	73	CYS	0	-0.084	-0.032	20.561	0.022	0.022	0.000	0.000	0.000	0.000
44	A	74	PHE	0	-0.057	-0.029	23.842	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	75	GLN	0	0.044	0.010	26.360	0.003	0.003	0.000	0.000	0.000	0.000
46	A	76	SER	0	-0.063	-0.045	27.668	0.000	0.000	0.000	0.000	0.000	0.000
47	A	77	GLY	0	0.064	0.021	29.596	0.006	0.006	0.000	0.000	0.000	0.000
48	A	78	PHE	0	-0.089	-0.034	19.971	0.014	0.014	0.000	0.000	0.000	0.000
49	A	79	ASN	0	0.011	-0.001	23.798	0.012	0.012	0.000	0.000	0.000	0.000
50	A	80	GLU	-1	-0.877	-0.953	17.625	0.177	0.177	0.000	0.000	0.000	0.000
51	A	81	GLU	-1	-0.861	-0.936	18.748	0.403	0.403	0.000	0.000	0.000	0.000
52	A	82	THR	0	-0.015	-0.026	20.436	0.030	0.030	0.000	0.000	0.000	0.000
53	A	84	LEU	0	0.046	0.003	13.716	0.019	0.019	0.000	0.000	0.000	0.000
54	A	85	VAL	0	0.053	0.038	17.427	0.063	0.063	0.000	0.000	0.000	0.000
55	A	86	LYS	1	0.831	0.914	19.584	-0.189	-0.189	0.000	0.000	0.000	0.000
56	A	87	ILE	0	-0.041	-0.033	15.729	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	88	ILE	0	0.009	0.001	13.993	0.006	0.006	0.000	0.000	0.000	0.000
58	A	89	THR	0	-0.006	-0.009	16.567	0.014	0.014	0.000	0.000	0.000	0.000
59	A	90	GLY	0	0.033	0.013	20.102	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	91	LEU	0	-0.058	-0.043	14.263	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	92	LEU	0	-0.004	-0.005	16.014	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	93	GLU	-1	-0.905	-0.955	18.680	0.241	0.241	0.000	0.000	0.000	0.000
63	A	94	PHE	0	-0.008	-0.033	20.137	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	95	GLU	-1	-0.850	-0.895	16.619	0.478	0.478	0.000	0.000	0.000	0.000
65	A	96	VAL	0	0.023	0.031	20.478	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	97	TYR	0	-0.004	-0.019	24.032	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	98	LEU	0	-0.030	-0.023	18.480	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	99	GLU	-1	-0.934	-0.965	22.409	0.196	0.196	0.000	0.000	0.000	0.000
69	A	100	TYR	0	-0.052	-0.042	23.651	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	101	LEU	0	-0.050	-0.032	23.465	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	102	GLN	0	0.048	0.016	21.319	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	103	ASN	0	0.001	-0.004	25.503	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	104	ARG	1	0.745	0.869	29.109	-0.071	-0.071	0.000	0.000	0.000	0.000
74	A	105	PHE	0	-0.014	-0.027	26.731	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	106	GLU	-1	-0.827	-0.894	27.910	0.075	0.075	0.000	0.000	0.000	0.000
76	A	107	SER	0	-0.129	-0.065	29.156	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	108	SER	0	-0.038	-0.044	26.642	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	109	GLU	-1	-0.788	-0.883	25.512	0.020	0.020	0.000	0.000	0.000	0.000
79	A	110	GLU	-1	-0.857	-0.926	20.498	0.044	0.044	0.000	0.000	0.000	0.000
80	A	111	GLN	0	-0.059	-0.023	20.819	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	112	ALA	0	0.020	-0.001	20.903	0.008	0.008	0.000	0.000	0.000	0.000
82	A	113	ARG	1	0.893	0.944	18.391	-0.065	-0.065	0.000	0.000	0.000	0.000
83	A	114	ALA	0	-0.004	0.000	16.954	0.036	0.036	0.000	0.000	0.000	0.000
84	A	115	VAL	0	0.003	0.018	16.085	0.014	0.014	0.000	0.000	0.000	0.000
85	A	116	GLN	0	0.012	0.025	16.549	0.054	0.054	0.000	0.000	0.000	0.000
86	A	117	MET	0	-0.012	-0.021	14.005	0.095	0.095	0.000	0.000	0.000	0.000
87	A	118	SER	0	-0.022	-0.028	11.917	0.060	0.060	0.000	0.000	0.000	0.000
88	A	119	THR	0	0.007	-0.013	11.580	0.033	0.033	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.896	0.933	12.383	-0.392	-0.392	0.000	0.000	0.000	0.000
90	A	121	VAL	0	0.005	0.021	6.321	0.242	0.242	0.000	0.000	0.000	0.000
91	A	122	LEU	0	-0.052	-0.021	7.753	0.354	0.354	0.000	0.000	0.000	0.000
92	A	123	ILE	0	0.023	0.010	10.052	0.141	0.141	0.000	0.000	0.000	0.000
93	A	124	GLN	0	0.036	0.019	7.041	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	125	PHE	0	-0.071	-0.041	2.575	-0.081	0.610	0.155	-0.211	-0.635	0.000
95	A	126	LEU	0	0.018	-0.009	6.933	0.017	0.017	0.000	0.000	0.000	0.000
96	A	127	GLN	0	0.076	0.034	10.333	0.024	0.024	0.000	0.000	0.000	0.000
97	A	128	LYS	1	0.912	0.966	2.224	-25.392	-27.613	7.019	-2.113	-2.685	0.027
98	A	129	LYS	1	0.805	0.896	8.065	-0.615	-0.615	0.000	0.000	0.000	0.000
99	A	130	ALA	0	0.053	0.016	9.481	-0.184	-0.184	0.000	0.000	0.000	0.000
100	A	131	LYS	1	0.888	0.961	8.274	-1.324	-1.324	0.000	0.000	0.000	0.000
101	A	132	ASN	0	-0.060	-0.013	12.028	-0.077	-0.077	0.000	0.000	0.000	0.000
102	A	133	LEU	0	-0.015	-0.022	15.238	-0.067	-0.067	0.000	0.000	0.000	0.000
103	A	134	ASP	-1	-0.927	-0.951	15.245	0.979	0.979	0.000	0.000	0.000	0.000
104	A	135	ALA	0	-0.062	-0.042	18.163	-0.040	-0.040	0.000	0.000	0.000	0.000
105	A	136	ILE	0	-0.030	-0.005	18.472	-0.035	-0.035	0.000	0.000	0.000	0.000
106	A	137	THR	0	0.042	0.032	21.543	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	138	THR	0	0.007	-0.013	19.366	0.011	0.011	0.000	0.000	0.000	0.000
108	A	139	PRO	0	-0.007	-0.004	21.185	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	140	ASP	-1	-0.802	-0.876	24.139	0.249	0.249	0.000	0.000	0.000	0.000
110	A	141	PRO	0	0.020	0.001	24.420	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	142	THR	0	0.042	0.015	26.575	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	143	THR	0	-0.044	-0.040	29.602	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	144	ASN	0	-0.013	-0.011	24.350	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	145	ALA	0	0.038	0.016	28.349	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	146	SER	0	-0.001	0.006	29.926	-0.016	-0.016	0.000	0.000	0.000	0.000
116	A	147	LEU	0	-0.030	-0.014	28.865	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	148	LEU	0	0.016	0.003	27.423	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	149	THR	0	0.038	0.014	30.740	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	150	LYS	1	0.858	0.940	34.157	-0.112	-0.112	0.000	0.000	0.000	0.000
120	A	151	LEU	0	-0.068	-0.052	30.177	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	152	GLN	0	0.010	0.002	30.230	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	153	ALA	0	0.004	0.025	34.633	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	154	GLN	0	-0.060	-0.010	34.918	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	155	ASN	0	0.055	0.028	38.869	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	156	GLN	0	0.125	0.038	37.600	0.002	0.002	0.000	0.000	0.000	0.000
126	A	157	TRP	0	0.069	0.051	37.845	0.000	0.000	0.000	0.000	0.000	0.000
127	A	158	LEU	0	0.001	-0.014	38.103	0.001	0.001	0.000	0.000	0.000	0.000
128	A	159	GLN	0	0.020	0.033	34.379	0.007	0.007	0.000	0.000	0.000	0.000
129	A	160	ASP	-1	-0.778	-0.864	33.371	0.052	0.052	0.000	0.000	0.000	0.000
130	A	161	MET	0	-0.056	-0.027	33.837	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	162	THR	0	-0.031	-0.029	30.892	0.005	0.005	0.000	0.000	0.000	0.000
132	A	163	THR	0	0.046	0.019	28.712	0.010	0.010	0.000	0.000	0.000	0.000
133	A	164	HIS	0	-0.027	-0.007	28.974	0.001	0.001	0.000	0.000	0.000	0.000
134	A	165	LEU	0	-0.047	-0.033	30.068	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	166	ILE	0	0.011	0.010	25.198	0.005	0.005	0.000	0.000	0.000	0.000
136	A	167	LEU	0	0.021	0.009	24.337	0.008	0.008	0.000	0.000	0.000	0.000
137	A	168	ARG	1	0.912	0.967	25.408	-0.053	-0.053	0.000	0.000	0.000	0.000
138	A	169	SER	0	0.016	0.009	26.718	0.002	0.002	0.000	0.000	0.000	0.000
139	A	170	PHE	0	0.064	0.024	17.499	0.003	0.003	0.000	0.000	0.000	0.000
140	A	171	LYS	1	0.850	0.915	21.833	-0.036	-0.036	0.000	0.000	0.000	0.000
141	A	172	GLU	-1	-0.870	-0.937	22.988	0.055	0.055	0.000	0.000	0.000	0.000
142	A	173	PHE	0	0.011	0.018	18.674	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	174	LEU	0	0.043	0.025	16.461	0.010	0.010	0.000	0.000	0.000	0.000
144	A	175	GLN	0	0.004	-0.005	19.120	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	176	SER	0	-0.078	-0.033	21.780	-0.018	-0.018	0.000	0.000	0.000	0.000
146	A	177	SER	0	0.027	-0.004	17.195	0.011	0.011	0.000	0.000	0.000	0.000
147	A	178	LEU	0	-0.052	-0.004	16.030	0.000	0.000	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.934	0.955	17.787	-0.046	-0.046	0.000	0.000	0.000	0.000
149	A	180	ALA	0	0.039	0.024	19.740	-0.016	-0.016	0.000	0.000	0.000	0.000
150	A	181	LEU	0	0.015	-0.013	13.438	0.000	0.000	0.000	0.000	0.000	0.000
151	A	182	ARG	1	0.799	0.902	14.672	0.166	0.166	0.000	0.000	0.000	0.000
152	A	183	GLN	0	-0.032	-0.011	16.838	-0.031	-0.031	0.000	0.000	0.000	0.000
153	A	184	MET	0	-0.003	0.049	14.435	0.071	0.071	0.000	0.000	0.000	0.000

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