FMO DATABASE

FMODB ID: LJ5V9

Calculation Name: 1X11-B-Xray372

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1X11

Chain ID: B

ChEMBL ID: CHEMBL2487

UniProt ID: P05067

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:

Apendix: None

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1018482.831893
FMO2-HF: Nuclear repulsion	968781.338574
FMO2-HF: Total energy	-49701.493319
FMO2-MP2: Total energy	-49841.758892

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(B:330:ILE)

Summations of interaction energy for fragment #1(B:330:ILE)

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.
-8.584	-1.183	8.332	-5.167	-10.565	-0.029

Interaction energy analysis for fragmet #1(B:330:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.018

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	B	332	PHE	0	0.013	0.016	2.642	-2.380	0.732	1.316	-1.437	-2.991	-0.008
4	B	333	ALA	0	0.081	0.053	5.260	-0.017	-0.003	-0.001	0.000	-0.013	0.000
5	B	334	ALA	0	-0.012	0.005	8.953	-0.036	-0.036	0.000	0.000	0.000	0.000
6	B	335	ASN	0	-0.008	-0.004	11.142	0.067	0.067	0.000	0.000	0.000	0.000
7	B	336	TYR	0	-0.039	-0.016	14.685	-0.014	-0.014	0.000	0.000	0.000	0.000
8	B	337	LEU	0	-0.022	-0.023	15.858	0.047	0.047	0.000	0.000	0.000	0.000
9	B	338	GLY	0	0.044	0.033	18.343	0.030	0.030	0.000	0.000	0.000	0.000
10	B	339	SER	0	-0.046	-0.035	18.712	-0.031	-0.031	0.000	0.000	0.000	0.000
11	B	340	THR	0	-0.003	0.016	20.597	0.020	0.020	0.000	0.000	0.000	0.000
12	B	341	GLN	0	-0.006	-0.001	22.238	-0.024	-0.024	0.000	0.000	0.000	0.000
13	B	342	LEU	0	-0.004	0.003	22.255	0.012	0.012	0.000	0.000	0.000	0.000
14	B	343	LEU	0	0.009	0.004	25.506	-0.005	-0.005	0.000	0.000	0.000	0.000
15	B	352	VAL	0	0.040	0.015	25.054	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	353	ARG	1	0.960	0.976	19.607	0.265	0.265	0.000	0.000	0.000	0.000
17	B	354	MET	0	0.079	0.048	18.073	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	355	MET	0	0.012	-0.001	21.258	0.004	0.004	0.000	0.000	0.000	0.000
19	B	356	GLN	0	-0.016	-0.024	22.411	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	357	ALA	0	0.027	0.014	18.529	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	358	GLN	0	0.027	0.005	20.422	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	359	GLU	-1	-0.839	-0.922	22.713	-0.149	-0.149	0.000	0.000	0.000	0.000
23	B	360	ALA	0	-0.025	-0.013	20.561	0.008	0.008	0.000	0.000	0.000	0.000
24	B	361	VAL	0	0.048	0.012	19.161	0.003	0.003	0.000	0.000	0.000	0.000
25	B	362	SER	0	-0.009	-0.002	21.532	0.008	0.008	0.000	0.000	0.000	0.000
26	B	363	ARG	1	0.883	0.951	24.810	0.156	0.156	0.000	0.000	0.000	0.000
27	B	364	ILE	0	0.012	0.025	20.432	0.014	0.014	0.000	0.000	0.000	0.000
28	B	365	LYS	1	0.987	0.987	21.731	0.197	0.197	0.000	0.000	0.000	0.000
29	B	366	MET	0	-0.056	-0.023	24.998	0.016	0.016	0.000	0.000	0.000	0.000
30	B	367	ALA	0	0.046	0.025	26.111	0.010	0.010	0.000	0.000	0.000	0.000
31	B	368	GLN	0	0.021	0.007	22.340	0.009	0.009	0.000	0.000	0.000	0.000
32	B	369	LYS	1	0.891	0.929	26.194	0.111	0.111	0.000	0.000	0.000	0.000
33	B	370	LEU	0	-0.066	-0.029	29.105	0.008	0.008	0.000	0.000	0.000	0.000
34	B	371	ALA	0	-0.007	-0.001	28.080	0.006	0.006	0.000	0.000	0.000	0.000
35	B	372	LYS	1	0.810	0.913	23.782	0.124	0.124	0.000	0.000	0.000	0.000
36	B	373	SER	0	0.028	0.015	29.790	0.005	0.005	0.000	0.000	0.000	0.000
37	B	385	MET	0	-0.007	0.003	19.204	0.009	0.009	0.000	0.000	0.000	0.000
38	B	386	THR	0	-0.001	0.003	18.239	0.011	0.011	0.000	0.000	0.000	0.000
39	B	387	GLU	-1	-0.799	-0.897	15.253	-0.145	-0.145	0.000	0.000	0.000	0.000
40	B	388	VAL	0	-0.083	-0.045	11.157	0.004	0.004	0.000	0.000	0.000	0.000
41	B	389	ASP	-1	-0.766	-0.875	8.456	-0.095	-0.095	0.000	0.000	0.000	0.000
42	B	390	LEU	0	-0.073	-0.051	5.767	-0.006	-0.006	0.000	0.000	0.000	0.000
43	B	391	PHE	0	0.037	0.005	3.769	-1.537	-1.162	0.002	-0.089	-0.288	0.000
44	B	392	ILE	0	-0.004	-0.027	2.179	-0.234	0.546	4.596	-1.543	-3.834	-0.001
45	B	393	LEU	0	-0.086	-0.007	2.432	-4.271	-2.486	1.799	-1.596	-1.988	-0.021
46	B	394	THR	0	0.058	0.013	4.965	0.179	0.287	-0.001	-0.007	-0.099	0.000
47	B	395	GLN	0	0.027	-0.003	7.499	0.206	0.206	0.000	0.000	0.000	0.000
48	B	396	ARG	1	0.853	0.899	8.414	0.695	0.695	0.000	0.000	0.000	0.000
49	B	397	ILE	0	0.030	0.026	6.602	-0.309	-0.309	0.000	0.000	0.000	0.000
50	B	398	LYS	1	0.860	0.949	7.981	0.623	0.623	0.000	0.000	0.000	0.000
51	B	399	VAL	0	0.020	0.020	8.699	-0.218	-0.218	0.000	0.000	0.000	0.000
52	B	400	LEU	0	0.006	-0.002	9.979	0.082	0.082	0.000	0.000	0.000	0.000
53	B	401	ASN	0	0.022	0.010	12.449	-0.019	-0.019	0.000	0.000	0.000	0.000
54	B	402	ALA	0	0.033	0.021	13.275	0.038	0.038	0.000	0.000	0.000	0.000
55	B	403	ASP	-1	-0.899	-0.921	14.166	0.046	0.046	0.000	0.000	0.000	0.000
56	B	404	THR	0	-0.060	-0.051	17.607	0.029	0.029	0.000	0.000	0.000	0.000
57	B	405	GLN	0	-0.082	-0.054	11.424	0.127	0.127	0.000	0.000	0.000	0.000
58	B	406	GLU	-1	-0.941	-0.957	13.993	-0.088	-0.088	0.000	0.000	0.000	0.000
59	B	407	THR	0	-0.072	-0.047	13.337	-0.055	-0.055	0.000	0.000	0.000	0.000
60	B	408	MET	0	0.012	0.008	14.737	0.009	0.009	0.000	0.000	0.000	0.000
61	B	409	MET	0	-0.046	-0.021	13.902	0.021	0.021	0.000	0.000	0.000	0.000
62	B	410	ASP	-1	-0.857	-0.932	12.640	-0.534	-0.534	0.000	0.000	0.000	0.000
63	B	411	HIS	0	0.006	0.003	12.280	0.093	0.093	0.000	0.000	0.000	0.000
64	B	412	PRO	0	0.012	0.005	11.866	-0.107	-0.107	0.000	0.000	0.000	0.000
65	B	413	LEU	0	0.119	0.065	7.843	0.082	0.082	0.000	0.000	0.000	0.000
66	B	414	ARG	1	0.974	1.010	12.009	0.331	0.331	0.000	0.000	0.000	0.000
67	B	415	THR	0	-0.163	-0.103	15.348	0.057	0.057	0.000	0.000	0.000	0.000
68	B	416	ILE	0	-0.009	-0.013	11.250	0.035	0.035	0.000	0.000	0.000	0.000
69	B	417	SER	0	-0.071	-0.038	14.697	0.022	0.022	0.000	0.000	0.000	0.000
70	B	418	TYR	0	0.022	-0.016	15.369	0.004	0.004	0.000	0.000	0.000	0.000
71	B	419	ILE	0	0.025	0.016	9.840	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	420	ALA	0	-0.026	-0.016	13.049	0.038	0.038	0.000	0.000	0.000	0.000
73	B	421	ASP	-1	-0.864	-0.915	11.980	-0.434	-0.434	0.000	0.000	0.000	0.000
74	B	422	ILE	0	-0.039	-0.028	14.046	0.045	0.045	0.000	0.000	0.000	0.000
75	B	423	GLY	0	-0.017	-0.009	17.581	0.011	0.011	0.000	0.000	0.000	0.000
76	B	424	ASN	0	0.039	0.016	15.395	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	425	ILE	0	-0.035	-0.011	15.266	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	426	VAL	0	0.022	0.005	9.937	-0.014	-0.014	0.000	0.000	0.000	0.000
79	B	427	VAL	0	-0.037	-0.016	13.173	0.028	0.028	0.000	0.000	0.000	0.000
80	B	428	LEU	0	0.013	0.020	10.350	-0.020	-0.020	0.000	0.000	0.000	0.000
81	B	429	MET	0	-0.036	-0.001	13.872	0.065	0.065	0.000	0.000	0.000	0.000
82	B	430	ALA	0	0.067	0.050	15.655	-0.014	-0.014	0.000	0.000	0.000	0.000
83	B	431	ARG	1	0.958	0.979	17.419	0.300	0.300	0.000	0.000	0.000	0.000
84	B	456	TYR	0	0.060	0.000	25.639	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	457	LYS	1	0.884	0.938	25.339	0.176	0.176	0.000	0.000	0.000	0.000
86	B	458	MET	0	-0.070	-0.015	19.650	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	459	ILE	0	0.008	0.008	18.312	0.023	0.023	0.000	0.000	0.000	0.000
88	B	460	CYS	0	-0.068	-0.028	18.304	-0.033	-0.033	0.000	0.000	0.000	0.000
89	B	461	HIS	0	0.089	0.031	14.652	0.038	0.038	0.000	0.000	0.000	0.000
90	B	462	VAL	0	0.001	0.002	15.418	-0.033	-0.033	0.000	0.000	0.000	0.000
91	B	463	PHE	0	0.009	0.005	12.187	0.005	0.005	0.000	0.000	0.000	0.000
92	B	464	GLU	-1	-0.928	-0.974	14.219	-0.208	-0.208	0.000	0.000	0.000	0.000
93	B	465	SER	0	-0.031	-0.028	10.392	-0.042	-0.042	0.000	0.000	0.000	0.000
94	B	466	GLU	-1	-0.796	-0.896	10.833	-0.339	-0.339	0.000	0.000	0.000	0.000
95	B	467	ASP	-1	-0.912	-0.945	7.913	-0.314	-0.314	0.000	0.000	0.000	0.000
96	B	468	ALA	0	-0.044	-0.036	8.748	-0.161	-0.161	0.000	0.000	0.000	0.000
97	B	469	GLN	0	0.073	0.035	10.440	-0.099	-0.099	0.000	0.000	0.000	0.000
98	B	470	LEU	0	0.016	0.016	5.260	-0.021	-0.021	0.000	0.000	0.000	0.000
99	B	471	ILE	0	0.040	0.041	5.085	-0.333	-0.333	0.000	0.000	0.000	0.000
100	B	472	ALA	0	0.020	0.012	5.915	-0.179	-0.179	0.000	0.000	0.000	0.000
101	B	473	GLN	0	-0.036	-0.019	7.512	0.018	0.018	0.000	0.000	0.000	0.000
102	B	474	SER	0	-0.018	-0.030	2.455	-1.157	-0.180	0.623	-0.477	-1.123	0.001
103	B	475	ILE	0	-0.012	-0.005	4.386	-0.096	0.083	-0.001	-0.012	-0.166	0.000
104	B	476	GLY	0	-0.001	0.007	6.360	0.134	0.134	0.000	0.000	0.000	0.000
105	B	477	GLN	0	-0.019	-0.017	5.280	0.126	0.126	0.000	0.000	0.000	0.000
106	B	478	ALA	0	0.001	0.004	4.402	0.050	0.121	-0.001	-0.006	-0.063	0.000
107	B	479	PHE	0	-0.044	-0.026	5.972	0.111	0.111	0.000	0.000	0.000	0.000
108	B	480	SER	0	0.000	-0.004	9.646	0.087	0.087	0.000	0.000	0.000	0.000
109	B	481	VAL	0	-0.001	0.009	7.199	0.059	0.059	0.000	0.000	0.000	0.000
110	B	482	ALA	0	0.051	0.025	9.399	0.057	0.057	0.000	0.000	0.000	0.000
111	B	483	TYR	0	-0.035	-0.014	11.044	0.065	0.065	0.000	0.000	0.000	0.000
112	B	484	GLN	0	0.017	0.007	12.636	0.047	0.047	0.000	0.000	0.000	0.000
113	B	485	GLU	-1	-0.910	-0.969	11.235	-0.287	-0.287	0.000	0.000	0.000	0.000
114	B	486	PHE	0	-0.034	-0.015	15.020	0.029	0.029	0.000	0.000	0.000	0.000
115	B	487	LEU	0	-0.044	-0.024	17.052	0.025	0.025	0.000	0.000	0.000	0.000
116	B	488	ARG	1	1.003	0.999	14.149	0.142	0.142	0.000	0.000	0.000	0.000
117	B	489	ALA	0	-0.058	-0.026	19.102	0.016	0.016	0.000	0.000	0.000	0.000
118	B	490	ASN	0	-0.094	-0.052	20.912	0.015	0.015	0.000	0.000	0.000	0.000
119	B	491	GLY	0	0.005	0.016	23.466	0.006	0.006	0.000	0.000	0.000	0.000
120	B	492	ILE	0	-0.034	-0.004	22.436	0.007	0.007	0.000	0.000	0.000	0.000
121	B	493	ASN	0	0.006	-0.012	21.816	-0.003	-0.003	0.000	0.000	0.000	0.000
122	B	494	PRO	0	-0.064	-0.011	17.136	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:330:ILE)