FMO DATABASE

FMODB ID: Z678N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1745884.364299
FMO2-HF: Nuclear repulsion	1679976.565375
FMO2-HF: Total energy	-65907.798924
FMO2-MP2: Total energy	-66102.081383

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.
-21.707	-22.222	22.429	-9.245	-12.669	-0.031

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 : -0.049 / q_NPA : -0.052

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	0.013	0.012	3.559	-4.175	-2.559	0.009	-0.737	-0.888	-0.001
4	A	628	LEU	0	-0.029	-0.022	5.521	1.320	1.320	0.000	0.000	0.000	0.000
5	A	629	GLU	-1	-0.857	-0.922	7.726	-3.805	-3.805	0.000	0.000	0.000	0.000
6	A	630	GLU	-1	-0.921	-0.934	9.486	-1.089	-1.089	0.000	0.000	0.000	0.000
7	A	631	LEU	0	-0.143	-0.081	8.566	0.338	0.338	0.000	0.000	0.000	0.000
8	A	632	GLN	0	0.022	0.003	11.685	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	633	ARG	1	0.883	0.939	14.411	0.644	0.644	0.000	0.000	0.000	0.000
10	A	634	ASN	0	0.040	0.016	13.803	-0.219	-0.219	0.000	0.000	0.000	0.000
11	A	635	LEU	0	-0.017	0.010	10.474	0.094	0.094	0.000	0.000	0.000	0.000
12	A	636	GLN	0	0.034	0.005	11.200	-0.049	-0.049	0.000	0.000	0.000	0.000
13	A	637	PHE	0	-0.044	-0.034	8.977	-0.194	-0.194	0.000	0.000	0.000	0.000
14	A	638	HIS	0	0.096	0.059	2.707	1.480	2.603	0.392	-0.448	-1.067	-0.003
15	A	639	ALA	0	-0.013	-0.023	6.657	0.759	0.759	0.000	0.000	0.000	0.000
16	A	640	PHE	0	0.002	0.019	9.545	-0.141	-0.141	0.000	0.000	0.000	0.000
17	A	641	ILE	0	-0.001	0.004	11.406	0.181	0.181	0.000	0.000	0.000	0.000
18	A	642	SER	0	-0.006	0.010	14.619	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	643	TYR	0	-0.069	-0.063	18.243	0.096	0.096	0.000	0.000	0.000	0.000
20	A	644	SER	0	0.095	0.071	20.472	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	645	GLY	0	-0.003	-0.009	23.425	0.009	0.009	0.000	0.000	0.000	0.000
22	A	646	HIS	0	0.005	-0.002	24.975	0.004	0.004	0.000	0.000	0.000	0.000
23	A	647	ASP	-1	-0.807	-0.903	21.903	0.110	0.110	0.000	0.000	0.000	0.000
24	A	648	SER	0	-0.045	-0.028	21.157	0.005	0.005	0.000	0.000	0.000	0.000
25	A	649	PHE	0	0.035	0.012	20.383	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	650	TRP	0	0.105	0.041	15.668	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	651	VAL	0	0.024	0.014	15.686	0.044	0.044	0.000	0.000	0.000	0.000
28	A	652	LYS	1	0.910	0.945	15.597	0.248	0.248	0.000	0.000	0.000	0.000
29	A	653	ASN	0	-0.073	-0.031	16.594	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	654	GLU	-1	-0.903	-0.937	15.573	0.514	0.514	0.000	0.000	0.000	0.000
31	A	655	LEU	0	-0.066	-0.048	11.653	0.087	0.087	0.000	0.000	0.000	0.000
32	A	656	LEU	0	0.021	0.009	11.074	0.104	0.104	0.000	0.000	0.000	0.000
33	A	657	PRO	0	0.011	0.013	9.990	-0.199	-0.199	0.000	0.000	0.000	0.000
34	A	658	ASN	0	-0.006	-0.014	9.616	-0.251	-0.251	0.000	0.000	0.000	0.000
35	A	659	LEU	0	-0.005	-0.019	6.594	0.819	0.819	0.000	0.000	0.000	0.000
36	A	660	GLU	-1	-0.862	-0.954	5.251	-1.973	-1.973	0.000	0.000	0.000	0.000
37	A	661	LYS	1	0.790	0.932	6.520	-0.411	-0.411	0.000	0.000	0.000	0.000
38	A	662	GLU	-1	-0.897	-0.950	3.651	7.080	7.499	0.001	-0.089	-0.332	0.000
39	A	663	GLY	0	0.033	0.020	2.195	-10.485	-8.952	1.813	-1.536	-1.811	-0.025
40	A	664	MET	0	-0.077	-0.012	2.465	-1.908	-1.154	3.074	-0.948	-2.880	0.005
41	A	665	GLN	0	-0.003	0.006	4.150	2.469	2.632	0.003	-0.057	-0.109	0.000
42	A	666	ILE	0	0.019	0.002	7.397	0.304	0.304	0.000	0.000	0.000	0.000
43	A	667	CYS	0	-0.088	-0.027	10.073	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	668	LEU	0	-0.018	-0.028	13.627	0.126	0.126	0.000	0.000	0.000	0.000
45	A	669	HIS	1	0.986	0.994	16.629	0.306	0.306	0.000	0.000	0.000	0.000
46	A	670	GLU	-1	-0.852	-0.943	19.653	-0.370	-0.370	0.000	0.000	0.000	0.000
47	A	671	ARG	1	0.944	0.967	12.762	0.977	0.977	0.000	0.000	0.000	0.000
48	A	672	ASN	0	-0.034	-0.020	14.681	0.011	0.011	0.000	0.000	0.000	0.000
49	A	673	PHE	0	-0.008	0.009	18.415	0.002	0.002	0.000	0.000	0.000	0.000
50	A	674	VAL	0	0.000	-0.010	21.871	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	675	PRO	0	-0.011	-0.005	24.595	0.036	0.036	0.000	0.000	0.000	0.000
52	A	676	GLY	0	0.027	0.015	28.271	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	677	LYS	1	0.904	0.968	23.532	0.472	0.472	0.000	0.000	0.000	0.000
54	A	678	SER	0	0.010	0.020	29.038	0.006	0.006	0.000	0.000	0.000	0.000
55	A	679	ILE	0	0.042	0.010	26.237	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	680	VAL	0	0.064	0.009	25.334	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	681	GLU	-1	-0.820	-0.929	24.789	-0.294	-0.294	0.000	0.000	0.000	0.000
58	A	682	ASN	0	-0.053	-0.008	22.702	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	683	ILE	0	-0.001	0.002	20.661	-0.062	-0.062	0.000	0.000	0.000	0.000
60	A	684	ILE	0	-0.033	0.000	19.872	-0.041	-0.041	0.000	0.000	0.000	0.000
61	A	685	THR	0	0.011	-0.010	19.518	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	687	ILE	0	-0.034	0.035	15.208	-0.097	-0.097	0.000	0.000	0.000	0.000
63	A	688	GLU	-1	-0.931	-0.960	15.360	-0.549	-0.549	0.000	0.000	0.000	0.000
64	A	689	LYS	1	0.892	0.962	14.811	0.922	0.922	0.000	0.000	0.000	0.000
65	A	690	SER	0	-0.021	-0.070	10.975	-0.234	-0.234	0.000	0.000	0.000	0.000
66	A	691	TYR	0	0.014	0.011	7.097	0.278	0.278	0.000	0.000	0.000	0.000
67	A	692	LYS	1	0.785	0.901	7.944	0.028	0.028	0.000	0.000	0.000	0.000
68	A	693	SER	0	0.039	0.015	10.797	-0.154	-0.154	0.000	0.000	0.000	0.000
69	A	694	ILE	0	0.008	-0.005	9.469	0.164	0.164	0.000	0.000	0.000	0.000
70	A	695	PHE	0	-0.004	-0.002	13.781	-0.098	-0.098	0.000	0.000	0.000	0.000
71	A	696	VAL	0	-0.005	-0.011	16.537	0.091	0.091	0.000	0.000	0.000	0.000
72	A	697	LEU	0	-0.019	-0.014	18.606	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	698	SER	0	0.066	0.012	21.729	0.032	0.032	0.000	0.000	0.000	0.000
74	A	699	PRO	0	0.061	0.014	24.890	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	700	ASN	0	0.041	0.026	26.625	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	701	PHE	0	0.004	0.038	21.240	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	702	VAL	0	-0.030	-0.014	25.361	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	703	GLN	0	-0.052	-0.037	27.790	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	704	SER	0	-0.040	-0.030	27.741	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	705	GLU	-1	-0.918	-0.969	23.309	-0.138	-0.138	0.000	0.000	0.000	0.000
81	A	706	TRP	0	-0.052	-0.034	22.354	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	707	CYS	0	-0.009	0.011	26.553	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	708	HIS	0	0.062	0.015	25.953	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	709	TYR	0	0.009	0.005	20.847	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	710	GLU	-1	-0.821	-0.897	25.803	0.018	0.018	0.000	0.000	0.000	0.000
86	A	711	LEU	0	0.007	-0.004	28.695	0.000	0.000	0.000	0.000	0.000	0.000
87	A	712	TYR	0	0.016	0.004	24.214	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	713	PHE	0	-0.052	-0.065	21.474	0.000	0.000	0.000	0.000	0.000	0.000
89	A	714	ALA	0	0.012	0.034	27.172	0.010	0.010	0.000	0.000	0.000	0.000
90	A	715	HIS	0	-0.054	-0.027	30.817	0.001	0.001	0.000	0.000	0.000	0.000
91	A	716	HIS	1	0.889	0.943	26.612	0.146	0.146	0.000	0.000	0.000	0.000
92	A	717	ASN	0	-0.004	0.007	24.909	0.008	0.008	0.000	0.000	0.000	0.000
93	A	718	LEU	0	0.014	0.010	19.017	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	719	PHE	0	-0.003	-0.010	17.056	0.002	0.002	0.000	0.000	0.000	0.000
95	A	720	HIS	0	0.037	0.022	20.551	0.046	0.046	0.000	0.000	0.000	0.000
96	A	721	GLU	-1	-0.905	-0.970	20.981	0.144	0.144	0.000	0.000	0.000	0.000
97	A	722	GLY	0	0.040	0.004	20.331	0.004	0.004	0.000	0.000	0.000	0.000
98	A	723	SER	0	-0.095	-0.027	17.494	0.026	0.026	0.000	0.000	0.000	0.000
99	A	724	ASN	0	0.041	-0.004	12.333	0.062	0.062	0.000	0.000	0.000	0.000
100	A	725	SER	0	-0.030	-0.015	12.615	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	726	LEU	0	-0.019	-0.001	13.404	-0.053	-0.053	0.000	0.000	0.000	0.000
102	A	727	ILE	0	0.011	0.016	10.504	0.122	0.122	0.000	0.000	0.000	0.000
103	A	728	LEU	0	-0.020	-0.014	13.945	-0.088	-0.088	0.000	0.000	0.000	0.000
104	A	729	ILE	0	0.017	0.010	13.145	0.110	0.110	0.000	0.000	0.000	0.000
105	A	730	LEU	0	-0.022	-0.011	17.155	-0.090	-0.090	0.000	0.000	0.000	0.000
106	A	731	LEU	0	-0.012	-0.012	19.365	0.057	0.057	0.000	0.000	0.000	0.000
107	A	732	GLU	-1	-0.913	-0.969	21.320	0.190	0.190	0.000	0.000	0.000	0.000
108	A	733	PRO	0	-0.029	-0.019	25.090	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	734	ILE	0	0.025	0.012	25.097	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	735	PRO	0	-0.019	0.017	28.906	0.005	0.005	0.000	0.000	0.000	0.000
111	A	736	GLN	0	0.075	-0.004	32.119	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	737	TYR	0	0.005	0.001	33.832	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	738	SER	0	-0.044	-0.012	32.036	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	739	ILE	0	0.007	0.007	29.567	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	740	PRO	0	0.073	0.054	32.533	0.002	0.002	0.000	0.000	0.000	0.000
116	A	741	SER	0	-0.003	-0.018	34.095	0.001	0.001	0.000	0.000	0.000	0.000
117	A	742	SER	0	0.042	0.012	35.377	0.005	0.005	0.000	0.000	0.000	0.000
118	A	743	TYR	0	0.000	-0.003	30.043	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	744	HIS	0	0.071	0.031	31.187	0.025	0.025	0.000	0.000	0.000	0.000
120	A	745	LYS	1	0.888	0.946	25.018	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	746	LEU	0	0.037	0.028	24.963	0.017	0.017	0.000	0.000	0.000	0.000
122	A	747	LYS	1	0.817	0.919	26.441	-0.048	-0.048	0.000	0.000	0.000	0.000
123	A	748	SER	0	-0.041	-0.025	27.024	0.019	0.019	0.000	0.000	0.000	0.000
124	A	749	LEU	0	0.019	0.011	20.996	0.027	0.027	0.000	0.000	0.000	0.000
125	A	750	MET	0	-0.029	-0.021	23.213	0.035	0.035	0.000	0.000	0.000	0.000
126	A	751	ALA	0	-0.012	0.010	24.944	0.029	0.029	0.000	0.000	0.000	0.000
127	A	752	ARG	1	0.828	0.953	18.217	-0.257	-0.257	0.000	0.000	0.000	0.000
128	A	753	ARG	1	0.923	0.963	23.597	-0.285	-0.285	0.000	0.000	0.000	0.000
129	A	754	THR	0	0.042	-0.006	18.445	0.013	0.013	0.000	0.000	0.000	0.000
130	A	755	TYR	0	-0.095	-0.017	17.838	0.054	0.054	0.000	0.000	0.000	0.000
131	A	756	LEU	0	0.003	0.009	12.729	0.037	0.037	0.000	0.000	0.000	0.000
132	A	757	GLU	-1	-0.892	-0.961	17.155	0.400	0.400	0.000	0.000	0.000	0.000
133	A	758	TRP	0	-0.015	0.006	15.561	0.119	0.119	0.000	0.000	0.000	0.000
134	A	759	PRO	0	-0.048	-0.010	18.097	-0.071	-0.071	0.000	0.000	0.000	0.000
135	A	760	LYS	1	0.999	0.985	21.072	-0.484	-0.484	0.000	0.000	0.000	0.000
136	A	761	GLU	-1	-0.914	-0.958	23.308	0.516	0.516	0.000	0.000	0.000	0.000
137	A	762	LYS	1	0.984	0.973	21.515	-0.380	-0.380	0.000	0.000	0.000	0.000
138	A	763	SER	0	-0.003	-0.003	20.196	0.060	0.060	0.000	0.000	0.000	0.000
139	A	764	LYS	1	0.955	0.985	19.687	-0.633	-0.633	0.000	0.000	0.000	0.000
140	A	765	ARG	1	1.000	1.019	16.430	-0.497	-0.497	0.000	0.000	0.000	0.000
141	A	766	GLY	0	-0.017	0.007	13.044	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	767	LEU	0	0.009	-0.014	12.627	0.302	0.302	0.000	0.000	0.000	0.000
143	A	768	PHE	0	0.023	0.008	13.726	0.165	0.165	0.000	0.000	0.000	0.000
144	A	769	TRP	0	0.063	0.018	9.740	0.182	0.182	0.000	0.000	0.000	0.000
145	A	770	ALA	0	0.004	0.026	8.870	0.670	0.670	0.000	0.000	0.000	0.000
146	A	771	ASN	0	0.033	0.004	9.048	0.667	0.667	0.000	0.000	0.000	0.000
147	A	772	LEU	0	-0.013	0.005	9.151	-0.067	-0.067	0.000	0.000	0.000	0.000
148	A	773	ARG	1	0.938	0.962	4.076	-6.671	-6.305	0.000	-0.063	-0.303	0.000
149	A	774	ALA	0	-0.029	0.000	5.443	0.265	0.265	0.000	0.000	0.000	0.000
150	A	775	ALA	0	-0.002	-0.011	7.749	-0.466	-0.466	0.000	0.000	0.000	0.000
151	A	776	ILE	0	-0.010	-0.005	4.429	-0.708	-0.580	-0.001	-0.006	-0.120	0.000
152	A	777	ASN	0	0.040	-0.002	1.780	-6.881	-13.624	17.139	-5.323	-5.073	-0.007
153	A	778	ILE	0	0.000	0.036	4.790	-0.657	-0.531	-0.001	-0.038	-0.086	0.000
154	A	779	LYS	1	0.956	0.980	8.367	-0.511	-0.511	0.000	0.000	0.000	0.000
155	A	780	LEU	0	-0.029	-0.001	10.261	0.145	0.145	0.000	0.000	0.000	0.000
156	A	781	THR	0	0.010	0.010	13.062	0.038	0.038	0.000	0.000	0.000	0.000
157	A	782	GLU	-1	-0.864	-0.936	16.616	-0.017	-0.017	0.000	0.000	0.000	0.000
158	A	783	GLN	0	-0.007	-0.016	19.140	0.010	0.010	0.000	0.000	0.000	0.000
159	A	784	ALA	0	-0.027	-0.009	22.476	0.009	0.009	0.000	0.000	0.000	0.000
160	A	785	LYS	1	1.000	1.011	24.502	-0.026	-0.026	0.000	0.000	0.000	0.000

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