FMO DATABASE

FMODB ID: QYK6Y

Calculation Name: 1FYV-A-Xray372

Preferred Name: Toll-like receptor 1/2

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 1FYV

Chain ID: A

ChEMBL ID: CHEMBL3885643

UniProt ID: Q15399

Base Structure: X-ray

Registration Date: 2023-06-22

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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1747707.701042
FMO2-HF: Nuclear repulsion	1681797.802247
FMO2-HF: Total energy	-65909.898796
FMO2-MP2: Total energy	-66103.973103

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:625:ASN)

Summations of interaction energy for fragment #1(A:625:ASN)

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.
-42.614	-38.445	23.648	-11.528	-16.286	-0.015

Interaction energy analysis for fragmet #1(A:625:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.040

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	627	PRO	0	0.042	0.042	3.904	-2.033	-0.931	-0.006	-0.435	-0.661	0.001
4	A	628	LEU	0	-0.030	-0.027	5.881	0.952	0.952	0.000	0.000	0.000	0.000
5	A	629	GLU	-1	-0.907	-0.963	8.223	-2.493	-2.493	0.000	0.000	0.000	0.000
6	A	630	GLU	-1	-0.935	-0.955	10.212	-0.449	-0.449	0.000	0.000	0.000	0.000
7	A	631	LEU	0	-0.065	-0.014	9.683	0.324	0.324	0.000	0.000	0.000	0.000
8	A	632	GLN	0	0.007	-0.014	12.258	-0.063	-0.063	0.000	0.000	0.000	0.000
9	A	633	ARG	1	0.894	0.944	14.356	-0.076	-0.076	0.000	0.000	0.000	0.000
10	A	634	ASN	0	0.029	0.022	13.664	-0.106	-0.106	0.000	0.000	0.000	0.000
11	A	635	LEU	0	-0.030	-0.003	11.096	0.047	0.047	0.000	0.000	0.000	0.000
12	A	636	GLN	0	0.025	0.002	11.545	-0.076	-0.076	0.000	0.000	0.000	0.000
13	A	637	PHE	0	-0.023	-0.014	9.021	-0.203	-0.203	0.000	0.000	0.000	0.000
14	A	638	HIS	0	0.082	0.040	3.110	0.246	1.271	0.230	-0.322	-0.933	-0.003
15	A	639	ALA	0	-0.020	-0.021	6.512	0.686	0.686	0.000	0.000	0.000	0.000
16	A	640	PHE	0	-0.006	0.008	9.485	-0.369	-0.369	0.000	0.000	0.000	0.000
17	A	641	ILE	0	-0.011	-0.008	11.045	0.207	0.207	0.000	0.000	0.000	0.000
18	A	642	SER	0	-0.028	0.003	14.782	-0.151	-0.151	0.000	0.000	0.000	0.000
19	A	643	TYR	0	-0.024	-0.051	18.530	0.073	0.073	0.000	0.000	0.000	0.000
20	A	644	SER	0	0.038	0.031	20.496	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	645	GLY	0	0.010	-0.005	23.397	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	646	HIS	0	-0.009	-0.018	25.172	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	647	ASP	-1	-0.741	-0.853	21.318	0.275	0.275	0.000	0.000	0.000	0.000
24	A	648	SER	0	0.013	0.005	20.810	0.000	0.000	0.000	0.000	0.000	0.000
25	A	649	PHE	0	0.004	0.014	20.418	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	650	TRP	0	0.072	0.025	15.142	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	651	VAL	0	0.008	-0.001	16.001	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	652	LYS	1	0.866	0.922	15.425	0.038	0.038	0.000	0.000	0.000	0.000
29	A	653	ASN	0	-0.029	-0.013	16.374	-0.136	-0.136	0.000	0.000	0.000	0.000
30	A	654	GLU	-1	-0.833	-0.918	14.779	0.186	0.186	0.000	0.000	0.000	0.000
31	A	655	LEU	0	-0.021	0.002	11.176	0.019	0.019	0.000	0.000	0.000	0.000
32	A	656	LEU	0	0.051	0.020	10.818	0.075	0.075	0.000	0.000	0.000	0.000
33	A	657	PRO	0	-0.049	-0.013	9.958	-0.285	-0.285	0.000	0.000	0.000	0.000
34	A	658	ASN	0	-0.057	-0.040	9.038	-0.400	-0.400	0.000	0.000	0.000	0.000
35	A	659	LEU	0	-0.011	-0.009	5.678	0.223	0.223	0.000	0.000	0.000	0.000
36	A	660	GLU	-1	-0.760	-0.864	5.349	-2.177	-2.177	0.000	0.000	0.000	0.000
37	A	661	LYS	1	0.857	0.932	7.115	0.581	0.581	0.000	0.000	0.000	0.000
38	A	662	GLU	-1	-0.798	-0.856	2.155	-12.256	-9.874	3.685	-2.854	-3.213	-0.037
39	A	663	GLY	0	0.021	0.016	2.105	-12.329	-12.284	3.584	-1.561	-2.068	-0.023
40	A	664	MET	0	-0.076	-0.007	2.538	2.327	4.661	3.398	-1.567	-4.165	0.020
41	A	665	GLN	0	0.004	-0.001	4.736	1.069	1.164	-0.001	-0.013	-0.081	0.000
42	A	666	ILE	0	0.008	-0.008	7.541	0.615	0.615	0.000	0.000	0.000	0.000
43	A	667	CYS	0	-0.088	-0.029	10.223	-0.223	-0.223	0.000	0.000	0.000	0.000
44	A	668	LEU	0	0.009	-0.002	13.636	0.150	0.150	0.000	0.000	0.000	0.000
45	A	669	HIS	1	0.975	0.987	16.680	-0.149	-0.149	0.000	0.000	0.000	0.000
46	A	670	GLU	-1	-0.839	-0.912	19.836	0.010	0.010	0.000	0.000	0.000	0.000
47	A	671	ARG	1	0.797	0.867	12.738	0.517	0.517	0.000	0.000	0.000	0.000
48	A	672	ASN	0	0.018	-0.002	15.067	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	673	PHE	0	-0.018	0.004	18.745	0.031	0.031	0.000	0.000	0.000	0.000
50	A	674	VAL	0	0.019	0.008	22.141	-0.039	-0.039	0.000	0.000	0.000	0.000
51	A	675	PRO	0	0.016	0.001	24.788	0.030	0.030	0.000	0.000	0.000	0.000
52	A	676	GLY	0	0.007	0.008	28.567	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	677	LYS	1	0.848	0.930	23.507	0.071	0.071	0.000	0.000	0.000	0.000
54	A	678	SER	0	-0.028	-0.060	29.306	0.002	0.002	0.000	0.000	0.000	0.000
55	A	679	ILE	0	0.024	-0.006	25.085	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	680	VAL	0	0.044	0.022	25.123	0.014	0.014	0.000	0.000	0.000	0.000
57	A	681	GLU	-1	-0.770	-0.840	24.742	0.038	0.038	0.000	0.000	0.000	0.000
58	A	682	ASN	0	-0.032	-0.018	22.835	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	683	ILE	0	-0.013	0.009	20.699	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	684	ILE	0	0.000	0.005	19.777	0.031	0.031	0.000	0.000	0.000	0.000
61	A	685	THR	0	0.036	0.014	19.502	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	687	ILE	0	-0.027	0.017	15.184	0.048	0.048	0.000	0.000	0.000	0.000
63	A	688	GLU	-1	-0.920	-0.971	15.800	0.132	0.132	0.000	0.000	0.000	0.000
64	A	689	LYS	1	0.884	0.950	15.074	0.241	0.241	0.000	0.000	0.000	0.000
65	A	690	SER	0	-0.036	-0.037	11.103	-0.095	-0.095	0.000	0.000	0.000	0.000
66	A	691	TYR	0	0.020	0.016	7.305	-0.199	-0.199	0.000	0.000	0.000	0.000
67	A	692	LYS	1	0.773	0.887	8.564	-2.616	-2.616	0.000	0.000	0.000	0.000
68	A	693	SER	0	0.018	0.016	11.313	-0.264	-0.264	0.000	0.000	0.000	0.000
69	A	694	ILE	0	0.013	0.003	9.583	0.155	0.155	0.000	0.000	0.000	0.000
70	A	695	PHE	0	-0.015	-0.006	14.230	-0.168	-0.168	0.000	0.000	0.000	0.000
71	A	696	VAL	0	-0.009	-0.016	16.367	0.080	0.080	0.000	0.000	0.000	0.000
72	A	697	LEU	0	0.000	0.003	18.589	-0.086	-0.086	0.000	0.000	0.000	0.000
73	A	698	SER	0	0.053	0.016	21.613	0.015	0.015	0.000	0.000	0.000	0.000
74	A	699	PRO	0	0.036	0.001	24.262	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	700	ASN	0	-0.027	-0.020	25.559	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	701	PHE	0	0.006	0.012	21.434	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	702	VAL	0	-0.020	-0.017	25.154	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	703	GLN	0	-0.024	-0.019	27.719	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	704	SER	0	-0.037	-0.028	27.136	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	705	GLU	-1	-0.848	-0.904	23.758	0.144	0.144	0.000	0.000	0.000	0.000
81	A	706	TRP	0	-0.062	-0.045	22.609	0.024	0.024	0.000	0.000	0.000	0.000
82	A	707	CYS	0	-0.018	0.004	26.905	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	708	HIS	0	0.023	-0.001	25.478	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	709	TYR	0	-0.005	-0.020	20.687	0.005	0.005	0.000	0.000	0.000	0.000
85	A	710	GLU	-1	-0.794	-0.873	26.072	0.309	0.309	0.000	0.000	0.000	0.000
86	A	711	LEU	0	0.013	0.007	29.240	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	712	TYR	0	0.018	0.015	24.220	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	713	PHE	0	0.015	-0.016	21.760	0.000	0.000	0.000	0.000	0.000	0.000
89	A	714	ALA	0	-0.003	0.019	27.712	0.002	0.002	0.000	0.000	0.000	0.000
90	A	715	HIS	0	-0.075	-0.036	30.680	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	716	HIS	1	0.847	0.916	26.727	-0.200	-0.200	0.000	0.000	0.000	0.000
92	A	717	ASN	0	-0.009	0.002	25.784	0.029	0.029	0.000	0.000	0.000	0.000
93	A	718	LEU	0	0.020	0.009	20.318	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	719	PHE	0	0.006	-0.003	17.317	0.055	0.055	0.000	0.000	0.000	0.000
95	A	720	HIS	0	0.058	0.028	21.223	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	721	GLU	-1	-0.776	-0.857	21.455	0.525	0.525	0.000	0.000	0.000	0.000
97	A	722	GLY	0	0.018	-0.003	20.866	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	723	SER	0	-0.050	0.001	18.083	0.070	0.070	0.000	0.000	0.000	0.000
99	A	724	ASN	0	-0.018	-0.025	12.718	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	725	SER	0	0.005	-0.004	13.214	0.161	0.161	0.000	0.000	0.000	0.000
101	A	726	LEU	0	-0.055	-0.009	14.521	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	727	ILE	0	0.009	0.007	10.993	0.022	0.022	0.000	0.000	0.000	0.000
103	A	728	LEU	0	0.010	0.002	14.447	-0.168	-0.168	0.000	0.000	0.000	0.000
104	A	729	ILE	0	0.002	-0.002	12.598	0.110	0.110	0.000	0.000	0.000	0.000
105	A	730	LEU	0	-0.018	0.004	16.853	-0.104	-0.104	0.000	0.000	0.000	0.000
106	A	731	LEU	0	-0.013	-0.011	18.836	0.015	0.015	0.000	0.000	0.000	0.000
107	A	732	GLU	-1	-0.866	-0.950	20.653	0.227	0.227	0.000	0.000	0.000	0.000
108	A	733	PRO	0	-0.021	-0.020	24.462	0.023	0.023	0.000	0.000	0.000	0.000
109	A	734	ILE	0	0.027	0.016	24.668	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	735	PRO	0	0.007	0.033	28.285	0.008	0.008	0.000	0.000	0.000	0.000
111	A	736	GLN	0	0.025	-0.018	32.030	0.007	0.007	0.000	0.000	0.000	0.000
112	A	737	TYR	0	0.033	0.022	33.469	0.001	0.001	0.000	0.000	0.000	0.000
113	A	738	SER	0	-0.053	-0.036	31.533	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	739	ILE	0	-0.007	0.000	29.330	0.005	0.005	0.000	0.000	0.000	0.000
115	A	740	PRO	0	0.045	0.034	32.699	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	741	SER	0	0.049	0.025	34.447	0.017	0.017	0.000	0.000	0.000	0.000
117	A	742	SER	0	0.016	0.002	35.812	0.015	0.015	0.000	0.000	0.000	0.000
118	A	743	TYR	0	-0.001	0.008	30.368	0.002	0.002	0.000	0.000	0.000	0.000
119	A	744	HIS	0	0.038	0.020	31.222	0.030	0.030	0.000	0.000	0.000	0.000
120	A	745	LYS	1	0.801	0.878	26.092	-0.375	-0.375	0.000	0.000	0.000	0.000
121	A	746	LEU	0	0.025	0.021	24.975	0.041	0.041	0.000	0.000	0.000	0.000
122	A	747	LYS	1	0.803	0.879	26.612	-0.238	-0.238	0.000	0.000	0.000	0.000
123	A	748	SER	0	-0.034	-0.045	27.315	0.009	0.009	0.000	0.000	0.000	0.000
124	A	749	LEU	0	0.001	-0.004	21.992	0.042	0.042	0.000	0.000	0.000	0.000
125	A	750	MET	0	-0.021	-0.010	23.154	0.054	0.054	0.000	0.000	0.000	0.000
126	A	751	ALA	0	-0.014	-0.005	24.916	0.023	0.023	0.000	0.000	0.000	0.000
127	A	752	ARG	1	0.859	0.939	17.979	-0.898	-0.898	0.000	0.000	0.000	0.000
128	A	753	ARG	1	0.904	0.951	23.220	-0.441	-0.441	0.000	0.000	0.000	0.000
129	A	754	THR	0	0.033	0.021	18.261	0.032	0.032	0.000	0.000	0.000	0.000
130	A	755	TYR	0	-0.053	-0.008	17.474	0.126	0.126	0.000	0.000	0.000	0.000
131	A	756	LEU	0	-0.015	-0.007	12.115	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	757	GLU	-1	-0.853	-0.933	16.619	0.501	0.501	0.000	0.000	0.000	0.000
133	A	758	TRP	0	-0.020	0.009	14.681	0.085	0.085	0.000	0.000	0.000	0.000
134	A	759	PRO	0	-0.079	-0.027	17.185	-0.072	-0.072	0.000	0.000	0.000	0.000
135	A	760	LYS	1	0.933	0.946	20.204	-0.558	-0.558	0.000	0.000	0.000	0.000
136	A	761	GLU	-1	-0.851	-0.930	22.816	0.371	0.371	0.000	0.000	0.000	0.000
137	A	762	LYS	1	0.989	0.974	20.385	-0.086	-0.086	0.000	0.000	0.000	0.000
138	A	763	SER	0	-0.011	-0.005	19.264	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	764	LYS	1	0.914	0.975	18.553	-0.443	-0.443	0.000	0.000	0.000	0.000
140	A	765	ARG	1	0.874	0.933	15.278	-0.195	-0.195	0.000	0.000	0.000	0.000
141	A	766	GLY	0	0.009	0.015	11.922	-0.059	-0.059	0.000	0.000	0.000	0.000
142	A	767	LEU	0	0.019	0.007	11.589	0.272	0.272	0.000	0.000	0.000	0.000
143	A	768	PHE	0	-0.003	-0.002	12.694	0.306	0.306	0.000	0.000	0.000	0.000
144	A	769	TRP	0	0.059	0.012	8.799	0.309	0.309	0.000	0.000	0.000	0.000
145	A	770	ALA	0	0.014	0.027	8.022	0.855	0.855	0.000	0.000	0.000	0.000
146	A	771	ASN	0	0.018	0.002	8.366	1.016	1.016	0.000	0.000	0.000	0.000
147	A	772	LEU	0	0.000	0.002	8.473	0.256	0.256	0.000	0.000	0.000	0.000
148	A	773	ARG	1	0.864	0.897	3.792	-1.140	-0.520	0.004	-0.153	-0.471	0.001
149	A	774	ALA	0	0.019	0.017	5.135	2.295	2.407	-0.001	0.000	-0.110	0.000
150	A	775	ALA	0	-0.001	-0.003	7.581	-0.189	-0.189	0.000	0.000	0.000	0.000
151	A	776	ILE	0	0.003	-0.004	4.890	-0.775	-0.775	0.000	0.000	0.000	0.000
152	A	777	ASN	0	-0.004	-0.015	1.840	-14.369	-17.910	12.756	-4.621	-4.593	0.026
153	A	778	ILE	0	-0.030	0.008	5.193	-1.309	-1.314	-0.001	-0.002	0.009	0.000
154	A	779	LYS	1	0.855	0.902	8.546	-1.247	-1.247	0.000	0.000	0.000	0.000
155	A	780	LEU	0	0.027	0.028	10.596	-0.029	-0.029	0.000	0.000	0.000	0.000
156	A	781	THR	0	0.000	-0.003	13.155	-0.036	-0.036	0.000	0.000	0.000	0.000
157	A	782	GLU	-1	-0.784	-0.872	16.759	0.671	0.671	0.000	0.000	0.000	0.000
158	A	783	GLN	0	-0.006	-0.010	19.429	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	784	ALA	0	-0.012	0.005	22.546	-0.031	-0.031	0.000	0.000	0.000	0.000
160	A	785	LYS	1	0.973	0.994	24.533	-0.301	-0.301	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:625:ASN)