FMO DATABASE

FMODB ID: R9Q28

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1746335.626448
FMO2-HF: Nuclear repulsion	1680426.581443
FMO2-HF: Total energy	-65909.045005
FMO2-MP2: Total energy	-66103.227177

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.
-34.222	-31.994	20.524	-9.086	-13.665	0.013

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 : -0.024 / q_NPA : -0.016

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	0.024	0.029	3.668	-3.464	-2.042	0.007	-0.639	-0.790	0.000
4	A	628	LEU	0	-0.022	-0.031	5.621	1.349	1.349	0.000	0.000	0.000	0.000
5	A	629	GLU	-1	-0.881	-0.932	7.873	-3.471	-3.471	0.000	0.000	0.000	0.000
6	A	630	GLU	-1	-0.941	-0.943	9.649	-0.925	-0.925	0.000	0.000	0.000	0.000
7	A	631	LEU	0	-0.133	-0.069	8.925	0.372	0.372	0.000	0.000	0.000	0.000
8	A	632	GLN	0	0.035	0.013	11.926	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	633	ARG	1	0.895	0.939	14.498	0.362	0.362	0.000	0.000	0.000	0.000
10	A	634	ASN	0	0.038	0.017	14.070	-0.209	-0.209	0.000	0.000	0.000	0.000
11	A	635	LEU	0	-0.032	0.000	10.678	0.072	0.072	0.000	0.000	0.000	0.000
12	A	636	GLN	0	0.047	0.014	11.450	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	637	PHE	0	-0.031	-0.025	9.265	-0.211	-0.211	0.000	0.000	0.000	0.000
14	A	638	HIS	0	0.080	0.048	2.928	1.319	2.335	0.284	-0.308	-0.992	-0.002
15	A	639	ALA	0	-0.013	-0.024	6.570	0.749	0.749	0.000	0.000	0.000	0.000
16	A	640	PHE	0	0.003	0.024	9.277	-0.243	-0.243	0.000	0.000	0.000	0.000
17	A	641	ILE	0	0.005	0.010	11.180	0.201	0.201	0.000	0.000	0.000	0.000
18	A	642	SER	0	0.009	0.025	14.554	-0.116	-0.116	0.000	0.000	0.000	0.000
19	A	643	TYR	0	-0.071	-0.083	18.201	0.087	0.087	0.000	0.000	0.000	0.000
20	A	644	SER	0	0.092	0.068	20.527	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	645	GLY	0	0.004	-0.004	23.333	0.007	0.007	0.000	0.000	0.000	0.000
22	A	646	HIS	0	0.007	-0.006	24.958	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	647	ASP	-1	-0.787	-0.872	21.700	0.227	0.227	0.000	0.000	0.000	0.000
24	A	648	SER	0	-0.011	-0.013	20.976	0.004	0.004	0.000	0.000	0.000	0.000
25	A	649	PHE	0	0.013	0.006	20.250	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	650	TRP	0	0.083	0.035	15.194	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	651	VAL	0	0.016	0.010	15.716	0.034	0.034	0.000	0.000	0.000	0.000
28	A	652	LYS	1	0.875	0.929	15.417	0.132	0.132	0.000	0.000	0.000	0.000
29	A	653	ASN	0	-0.046	-0.018	16.483	-0.111	-0.111	0.000	0.000	0.000	0.000
30	A	654	GLU	-1	-0.853	-0.935	15.081	0.479	0.479	0.000	0.000	0.000	0.000
31	A	655	LEU	0	-0.032	-0.011	11.237	0.041	0.041	0.000	0.000	0.000	0.000
32	A	656	LEU	0	0.057	0.021	10.774	0.101	0.101	0.000	0.000	0.000	0.000
33	A	657	PRO	0	0.000	0.017	9.909	-0.245	-0.245	0.000	0.000	0.000	0.000
34	A	658	ASN	0	-0.064	-0.043	9.347	-0.232	-0.232	0.000	0.000	0.000	0.000
35	A	659	LEU	0	-0.002	-0.007	6.195	0.642	0.642	0.000	0.000	0.000	0.000
36	A	660	GLU	-1	-0.809	-0.901	5.176	-2.132	-2.110	-0.001	0.001	-0.022	0.000
37	A	661	LYS	1	0.829	0.930	6.755	-0.111	-0.111	0.000	0.000	0.000	0.000
38	A	662	GLU	-1	-0.858	-0.916	2.890	3.422	4.056	0.035	-0.146	-0.523	0.000
39	A	663	GLY	0	0.033	0.015	2.337	-10.416	-9.191	1.832	-1.347	-1.711	-0.019
40	A	664	MET	0	-0.069	-0.003	2.620	-0.225	1.384	2.705	-1.112	-3.202	0.010
41	A	665	GLN	0	-0.011	-0.008	4.573	1.963	2.075	-0.001	-0.021	-0.090	0.000
42	A	666	ILE	0	0.029	0.003	7.578	0.416	0.416	0.000	0.000	0.000	0.000
43	A	667	CYS	0	-0.095	-0.044	10.569	-0.137	-0.137	0.000	0.000	0.000	0.000
44	A	668	LEU	0	-0.005	-0.014	13.916	0.148	0.148	0.000	0.000	0.000	0.000
45	A	669	HIS	1	0.969	0.988	16.978	0.100	0.100	0.000	0.000	0.000	0.000
46	A	670	GLU	-1	-0.822	-0.904	19.872	-0.198	-0.198	0.000	0.000	0.000	0.000
47	A	671	ARG	1	0.851	0.906	12.636	0.847	0.847	0.000	0.000	0.000	0.000
48	A	672	ASN	0	-0.033	-0.034	15.207	0.015	0.015	0.000	0.000	0.000	0.000
49	A	673	PHE	0	-0.002	0.018	19.092	0.015	0.015	0.000	0.000	0.000	0.000
50	A	674	VAL	0	0.003	-0.009	22.359	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	675	PRO	0	0.007	0.000	25.110	0.036	0.036	0.000	0.000	0.000	0.000
52	A	676	GLY	0	0.013	0.009	28.843	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	677	LYS	1	0.865	0.943	23.479	0.320	0.320	0.000	0.000	0.000	0.000
54	A	678	SER	0	-0.019	-0.042	29.076	0.010	0.010	0.000	0.000	0.000	0.000
55	A	679	ILE	0	0.036	0.005	25.552	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	680	VAL	0	0.055	0.008	25.173	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	681	GLU	-1	-0.785	-0.851	24.596	-0.162	-0.162	0.000	0.000	0.000	0.000
58	A	682	ASN	0	-0.043	-0.022	22.803	-0.065	-0.065	0.000	0.000	0.000	0.000
59	A	683	ILE	0	-0.002	0.004	20.432	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	684	ILE	0	-0.022	-0.001	19.678	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	685	THR	0	0.037	0.018	19.560	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	687	ILE	0	-0.030	0.006	15.081	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	688	GLU	-1	-0.935	-0.959	15.138	-0.274	-0.274	0.000	0.000	0.000	0.000
64	A	689	LYS	1	0.879	0.950	14.941	0.690	0.690	0.000	0.000	0.000	0.000
65	A	690	SER	0	-0.041	-0.033	10.745	-0.189	-0.189	0.000	0.000	0.000	0.000
66	A	691	TYR	0	0.045	0.019	6.818	0.233	0.233	0.000	0.000	0.000	0.000
67	A	692	LYS	1	0.768	0.890	8.085	-1.257	-1.257	0.000	0.000	0.000	0.000
68	A	693	SER	0	0.017	0.006	10.651	-0.198	-0.198	0.000	0.000	0.000	0.000
69	A	694	ILE	0	0.016	-0.004	9.545	0.151	0.151	0.000	0.000	0.000	0.000
70	A	695	PHE	0	-0.013	-0.008	13.899	-0.156	-0.156	0.000	0.000	0.000	0.000
71	A	696	VAL	0	-0.012	-0.011	16.281	0.100	0.100	0.000	0.000	0.000	0.000
72	A	697	LEU	0	-0.007	-0.006	18.588	-0.075	-0.075	0.000	0.000	0.000	0.000
73	A	698	SER	0	0.034	-0.006	21.729	0.025	0.025	0.000	0.000	0.000	0.000
74	A	699	PRO	0	0.066	0.019	24.706	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	700	ASN	0	0.005	-0.003	26.222	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	701	PHE	0	-0.004	0.026	21.039	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	702	VAL	0	-0.027	-0.013	25.475	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	703	GLN	0	-0.036	-0.031	27.976	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	704	SER	0	-0.041	-0.026	27.645	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	705	GLU	-1	-0.903	-0.966	23.424	0.014	0.014	0.000	0.000	0.000	0.000
81	A	706	TRP	0	-0.062	-0.046	22.278	0.001	0.001	0.000	0.000	0.000	0.000
82	A	707	CYS	0	-0.010	0.014	26.606	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	708	HIS	0	0.058	0.013	25.747	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	709	TYR	0	0.008	-0.009	20.532	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	710	GLU	-1	-0.782	-0.859	25.733	0.162	0.162	0.000	0.000	0.000	0.000
86	A	711	LEU	0	0.004	-0.010	28.689	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	712	TYR	0	0.011	0.007	23.987	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	713	PHE	0	-0.041	-0.051	21.276	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	714	ALA	0	0.014	0.039	27.077	0.007	0.007	0.000	0.000	0.000	0.000
90	A	715	HIS	0	-0.059	-0.031	30.669	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	716	HIS	1	0.873	0.930	26.431	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	717	ASN	0	-0.019	-0.001	25.072	0.017	0.017	0.000	0.000	0.000	0.000
93	A	718	LEU	0	0.019	0.010	19.398	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	719	PHE	0	0.011	-0.004	16.834	0.028	0.028	0.000	0.000	0.000	0.000
95	A	720	HIS	0	0.025	0.015	20.529	0.031	0.031	0.000	0.000	0.000	0.000
96	A	721	GLU	-1	-0.812	-0.878	21.122	0.328	0.328	0.000	0.000	0.000	0.000
97	A	722	GLY	0	0.038	0.011	20.672	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	723	SER	0	-0.074	-0.022	17.735	0.071	0.071	0.000	0.000	0.000	0.000
99	A	724	ASN	0	0.036	0.000	12.516	0.081	0.081	0.000	0.000	0.000	0.000
100	A	725	SER	0	-0.005	-0.003	12.775	0.073	0.073	0.000	0.000	0.000	0.000
101	A	726	LEU	0	-0.056	-0.015	13.419	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	727	ILE	0	0.009	0.010	10.720	0.117	0.117	0.000	0.000	0.000	0.000
103	A	728	LEU	0	-0.005	-0.001	14.249	-0.119	-0.119	0.000	0.000	0.000	0.000
104	A	729	ILE	0	0.018	0.006	12.777	0.114	0.114	0.000	0.000	0.000	0.000
105	A	730	LEU	0	-0.027	-0.013	17.030	-0.109	-0.109	0.000	0.000	0.000	0.000
106	A	731	LEU	0	-0.011	-0.013	18.938	0.045	0.045	0.000	0.000	0.000	0.000
107	A	732	GLU	-1	-0.892	-0.954	20.804	0.250	0.250	0.000	0.000	0.000	0.000
108	A	733	PRO	0	-0.020	-0.015	24.571	0.000	0.000	0.000	0.000	0.000	0.000
109	A	734	ILE	0	0.022	0.007	25.057	-0.029	-0.029	0.000	0.000	0.000	0.000
110	A	735	PRO	0	0.002	0.022	28.726	0.005	0.005	0.000	0.000	0.000	0.000
111	A	736	GLN	0	0.032	-0.025	32.447	0.002	0.002	0.000	0.000	0.000	0.000
112	A	737	TYR	0	0.026	0.017	33.857	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	738	SER	0	-0.049	-0.015	32.015	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	739	ILE	0	0.001	0.003	29.757	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	740	PRO	0	0.070	0.056	32.744	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	741	SER	0	0.034	0.014	34.295	0.008	0.008	0.000	0.000	0.000	0.000
117	A	742	SER	0	0.021	0.002	35.690	0.009	0.009	0.000	0.000	0.000	0.000
118	A	743	TYR	0	-0.011	-0.011	30.190	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	744	HIS	0	0.059	0.039	31.388	0.031	0.031	0.000	0.000	0.000	0.000
120	A	745	LYS	1	0.818	0.893	25.498	-0.202	-0.202	0.000	0.000	0.000	0.000
121	A	746	LEU	0	0.024	0.025	25.149	0.031	0.031	0.000	0.000	0.000	0.000
122	A	747	LYS	1	0.796	0.876	26.723	-0.150	-0.150	0.000	0.000	0.000	0.000
123	A	748	SER	0	-0.036	-0.057	26.928	0.018	0.018	0.000	0.000	0.000	0.000
124	A	749	LEU	0	0.020	0.013	21.443	0.036	0.036	0.000	0.000	0.000	0.000
125	A	750	MET	0	-0.028	-0.018	23.576	0.047	0.047	0.000	0.000	0.000	0.000
126	A	751	ALA	0	-0.013	0.006	25.349	0.027	0.027	0.000	0.000	0.000	0.000
127	A	752	ARG	1	0.837	0.925	18.056	-0.585	-0.585	0.000	0.000	0.000	0.000
128	A	753	ARG	1	0.935	0.969	23.834	-0.394	-0.394	0.000	0.000	0.000	0.000
129	A	754	THR	0	0.014	0.006	18.747	0.027	0.027	0.000	0.000	0.000	0.000
130	A	755	TYR	0	-0.058	-0.008	17.998	0.091	0.091	0.000	0.000	0.000	0.000
131	A	756	LEU	0	0.009	0.014	12.567	0.020	0.020	0.000	0.000	0.000	0.000
132	A	757	GLU	-1	-0.849	-0.927	16.840	0.510	0.510	0.000	0.000	0.000	0.000
133	A	758	TRP	0	-0.035	-0.001	15.148	0.109	0.109	0.000	0.000	0.000	0.000
134	A	759	PRO	0	-0.041	-0.009	17.754	-0.081	-0.081	0.000	0.000	0.000	0.000
135	A	760	LYS	1	0.912	0.938	20.682	-0.591	-0.591	0.000	0.000	0.000	0.000
136	A	761	GLU	-1	-0.878	-0.941	23.092	0.531	0.531	0.000	0.000	0.000	0.000
137	A	762	LYS	1	0.990	0.980	21.320	-0.311	-0.311	0.000	0.000	0.000	0.000
138	A	763	SER	0	-0.008	-0.005	20.058	0.051	0.051	0.000	0.000	0.000	0.000
139	A	764	LYS	1	0.927	0.975	19.466	-0.609	-0.609	0.000	0.000	0.000	0.000
140	A	765	ARG	1	0.938	0.981	16.187	-0.441	-0.441	0.000	0.000	0.000	0.000
141	A	766	GLY	0	-0.016	0.005	12.938	-0.031	-0.031	0.000	0.000	0.000	0.000
142	A	767	LEU	0	0.015	-0.013	12.449	0.316	0.316	0.000	0.000	0.000	0.000
143	A	768	PHE	0	0.007	0.006	13.201	0.225	0.225	0.000	0.000	0.000	0.000
144	A	769	TRP	0	0.071	0.018	9.487	0.260	0.260	0.000	0.000	0.000	0.000
145	A	770	ALA	0	-0.009	0.020	8.475	0.898	0.898	0.000	0.000	0.000	0.000
146	A	771	ASN	0	0.031	0.000	8.587	0.914	0.914	0.000	0.000	0.000	0.000
147	A	772	LEU	0	-0.002	0.006	8.727	0.035	0.035	0.000	0.000	0.000	0.000
148	A	773	ARG	1	0.900	0.929	3.812	-5.798	-5.187	0.005	-0.177	-0.438	0.001
149	A	774	ALA	0	-0.021	0.000	5.449	1.075	1.170	-0.001	0.000	-0.093	0.000
150	A	775	ALA	0	0.002	-0.008	7.573	-0.467	-0.467	0.000	0.000	0.000	0.000
151	A	776	ILE	0	-0.008	-0.007	4.483	-0.896	-0.801	-0.001	-0.005	-0.089	0.000
152	A	777	ASN	0	0.012	-0.004	1.827	-17.543	-22.207	15.661	-5.325	-5.672	0.023
153	A	778	ILE	0	-0.015	0.024	5.101	-1.074	-1.023	-0.001	-0.007	-0.043	0.000
154	A	779	LYS	1	0.885	0.912	8.339	-0.807	-0.807	0.000	0.000	0.000	0.000
155	A	780	LEU	0	-0.011	0.009	10.275	0.100	0.100	0.000	0.000	0.000	0.000
156	A	781	THR	0	0.009	0.006	13.053	-0.009	-0.009	0.000	0.000	0.000	0.000
157	A	782	GLU	-1	-0.818	-0.886	16.616	0.233	0.233	0.000	0.000	0.000	0.000
158	A	783	GLN	0	-0.009	-0.014	19.158	0.001	0.001	0.000	0.000	0.000	0.000
159	A	784	ALA	0	-0.035	-0.017	22.349	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	785	LYS	1	1.008	1.020	24.522	-0.141	-0.141	0.000	0.000	0.000	0.000

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