FMO DATABASE

FMODB ID: 66J4Z

Calculation Name: 1X11-A-Xray372

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1X11

Chain ID: A

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	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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204270.07948
FMO2-HF: Nuclear repulsion	1149108.942629
FMO2-HF: Total energy	-55161.136851
FMO2-MP2: Total energy	-55316.057809

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:323:MET)

Summations of interaction energy for fragment #1(A:323:MET)

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.
-4.343	-2.654	-0.018	-0.828	-0.843	0.003

Interaction energy analysis for fragmet #1(A:323:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.043

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	325	ASP	-1	-0.839	-0.930	3.870	-0.998	0.691	-0.018	-0.828	-0.843	0.003
4	A	326	LEU	0	-0.061	-0.037	6.883	0.135	0.135	0.000	0.000	0.000	0.000
5	A	327	ILE	0	-0.072	-0.060	9.641	0.378	0.378	0.000	0.000	0.000	0.000
6	A	328	ASP	-1	-0.842	-0.906	6.320	-4.599	-4.599	0.000	0.000	0.000	0.000
7	A	329	GLY	0	-0.099	-0.068	8.986	0.506	0.506	0.000	0.000	0.000	0.000
8	A	330	ILE	0	0.000	0.014	7.100	-0.664	-0.664	0.000	0.000	0.000	0.000
9	A	331	ILE	0	-0.005	-0.022	8.290	0.338	0.338	0.000	0.000	0.000	0.000
10	A	332	PHE	0	0.012	0.000	10.685	0.024	0.024	0.000	0.000	0.000	0.000
11	A	333	ALA	0	0.091	0.064	13.569	0.010	0.010	0.000	0.000	0.000	0.000
12	A	334	ALA	0	-0.053	-0.024	16.059	0.045	0.045	0.000	0.000	0.000	0.000
13	A	335	ASN	0	0.029	0.016	19.675	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	336	TYR	0	-0.029	-0.051	23.059	0.007	0.007	0.000	0.000	0.000	0.000
15	A	337	LEU	0	-0.011	0.008	24.576	0.024	0.024	0.000	0.000	0.000	0.000
16	A	338	GLY	0	0.052	0.027	27.917	0.022	0.022	0.000	0.000	0.000	0.000
17	A	339	SER	0	-0.006	-0.012	27.894	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	340	THR	0	-0.017	0.005	30.349	0.025	0.025	0.000	0.000	0.000	0.000
19	A	341	GLN	0	0.019	0.009	32.883	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	342	LEU	0	0.058	0.040	34.442	0.015	0.015	0.000	0.000	0.000	0.000
21	A	343	LEU	0	-0.026	-0.021	37.424	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	344	SER	0	-0.017	-0.029	36.097	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	345	ASP	-1	-0.782	-0.878	38.189	-0.147	-0.147	0.000	0.000	0.000	0.000
24	A	346	LYS	1	0.809	0.895	37.725	0.150	0.150	0.000	0.000	0.000	0.000
25	A	347	THR	0	-0.017	-0.018	34.485	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	348	PRO	0	-0.021	0.012	35.518	0.011	0.011	0.000	0.000	0.000	0.000
27	A	349	SER	0	0.055	0.015	35.540	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	350	LYS	1	1.023	0.990	28.537	0.243	0.243	0.000	0.000	0.000	0.000
29	A	351	ASN	0	0.040	0.032	33.866	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	352	VAL	0	0.062	0.029	36.453	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	353	ARG	1	0.823	0.915	31.494	0.242	0.242	0.000	0.000	0.000	0.000
32	A	354	MET	0	0.022	0.019	29.721	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	355	MET	0	0.009	0.008	33.243	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	356	GLN	0	0.029	0.022	34.243	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	357	ALA	0	0.024	0.013	30.285	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	358	GLN	0	0.027	-0.002	32.078	0.000	0.000	0.000	0.000	0.000	0.000
37	A	359	GLU	-1	-0.852	-0.910	34.551	-0.174	-0.174	0.000	0.000	0.000	0.000
38	A	360	ALA	0	-0.019	-0.018	31.861	0.003	0.003	0.000	0.000	0.000	0.000
39	A	361	VAL	0	0.047	0.015	30.320	0.001	0.001	0.000	0.000	0.000	0.000
40	A	362	SER	0	-0.042	-0.012	32.891	0.007	0.007	0.000	0.000	0.000	0.000
41	A	363	ARG	1	0.784	0.861	35.805	0.196	0.196	0.000	0.000	0.000	0.000
42	A	364	ILE	0	0.028	0.021	30.783	0.006	0.006	0.000	0.000	0.000	0.000
43	A	365	LYS	1	0.914	0.973	32.462	0.187	0.187	0.000	0.000	0.000	0.000
44	A	366	MET	0	-0.051	-0.025	35.588	0.007	0.007	0.000	0.000	0.000	0.000
45	A	367	ALA	0	-0.027	-0.003	36.139	0.007	0.007	0.000	0.000	0.000	0.000
46	A	368	GLN	0	-0.027	-0.016	31.729	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	385	MET	0	-0.041	-0.035	27.408	0.005	0.005	0.000	0.000	0.000	0.000
48	A	386	THR	0	-0.040	-0.029	23.140	0.006	0.006	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.903	-0.921	20.612	-0.327	-0.327	0.000	0.000	0.000	0.000
50	A	388	VAL	0	-0.062	-0.050	18.930	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	389	ASP	-1	-0.794	-0.877	13.414	-0.865	-0.865	0.000	0.000	0.000	0.000
52	A	390	LEU	0	-0.061	-0.038	15.473	0.006	0.006	0.000	0.000	0.000	0.000
53	A	391	PHE	0	0.030	0.015	9.615	0.003	0.003	0.000	0.000	0.000	0.000
54	A	392	ILE	0	-0.032	-0.029	12.513	0.235	0.235	0.000	0.000	0.000	0.000
55	A	393	LEU	0	0.037	0.037	12.118	-0.147	-0.147	0.000	0.000	0.000	0.000
56	A	394	THR	0	-0.001	-0.005	14.033	0.166	0.166	0.000	0.000	0.000	0.000
57	A	395	GLN	0	0.039	0.012	16.257	0.146	0.146	0.000	0.000	0.000	0.000
58	A	396	ARG	1	0.823	0.900	15.044	1.146	1.146	0.000	0.000	0.000	0.000
59	A	397	ILE	0	0.006	0.024	16.477	-0.072	-0.072	0.000	0.000	0.000	0.000
60	A	398	LYS	1	0.801	0.897	15.382	0.997	0.997	0.000	0.000	0.000	0.000
61	A	399	VAL	0	0.002	0.010	17.159	-0.031	-0.031	0.000	0.000	0.000	0.000
62	A	400	LEU	0	0.006	0.007	13.474	0.029	0.029	0.000	0.000	0.000	0.000
63	A	401	ASN	0	0.036	-0.009	17.677	0.028	0.028	0.000	0.000	0.000	0.000
64	A	402	ALA	0	0.015	0.015	16.821	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.945	-0.963	17.113	-0.356	-0.356	0.000	0.000	0.000	0.000
66	A	404	THR	0	-0.034	-0.046	19.327	0.006	0.006	0.000	0.000	0.000	0.000
67	A	405	GLN	0	-0.094	-0.056	13.669	-0.155	-0.155	0.000	0.000	0.000	0.000
68	A	406	GLU	-1	-0.866	-0.891	16.757	-0.525	-0.525	0.000	0.000	0.000	0.000
69	A	407	THR	0	-0.072	-0.052	18.072	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	408	MET	0	0.005	0.022	19.794	0.047	0.047	0.000	0.000	0.000	0.000
71	A	409	MET	0	-0.058	-0.032	21.152	0.037	0.037	0.000	0.000	0.000	0.000
72	A	410	ASP	-1	-0.813	-0.916	19.263	-0.883	-0.883	0.000	0.000	0.000	0.000
73	A	411	HIS	0	-0.001	0.014	20.544	0.089	0.089	0.000	0.000	0.000	0.000
74	A	412	PRO	0	0.014	0.003	20.896	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	413	LEU	0	0.052	0.051	19.346	0.084	0.084	0.000	0.000	0.000	0.000
76	A	414	ARG	1	0.967	0.973	21.619	0.515	0.515	0.000	0.000	0.000	0.000
77	A	415	THR	0	-0.132	-0.081	24.661	0.052	0.052	0.000	0.000	0.000	0.000
78	A	416	ILE	0	0.018	0.020	22.599	0.039	0.039	0.000	0.000	0.000	0.000
79	A	417	SER	0	-0.095	-0.045	25.906	0.023	0.023	0.000	0.000	0.000	0.000
80	A	418	TYR	0	-0.027	-0.041	27.547	0.025	0.025	0.000	0.000	0.000	0.000
81	A	419	ILE	0	0.027	0.020	21.825	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	420	ALA	0	-0.035	-0.013	25.301	0.026	0.026	0.000	0.000	0.000	0.000
83	A	421	ASP	-1	-0.820	-0.885	23.521	-0.311	-0.311	0.000	0.000	0.000	0.000
84	A	422	ILE	0	-0.046	-0.045	25.627	0.027	0.027	0.000	0.000	0.000	0.000
85	A	423	GLY	0	0.025	0.022	27.412	0.009	0.009	0.000	0.000	0.000	0.000
86	A	424	ASN	0	0.047	0.031	24.656	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	425	ILE	0	-0.005	-0.004	25.405	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	426	VAL	0	0.036	0.029	21.293	0.003	0.003	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.042	-0.019	24.678	0.011	0.011	0.000	0.000	0.000	0.000
90	A	428	LEU	0	0.039	0.036	21.762	0.004	0.004	0.000	0.000	0.000	0.000
91	A	429	MET	0	-0.028	-0.024	25.078	0.029	0.029	0.000	0.000	0.000	0.000
92	A	430	ALA	0	0.060	0.044	26.504	0.001	0.001	0.000	0.000	0.000	0.000
93	A	431	ARG	1	0.934	0.965	28.070	0.343	0.343	0.000	0.000	0.000	0.000
94	A	451	ASP	-1	-0.788	-0.885	37.907	-0.165	-0.165	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.015	0.013	35.934	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	453	LYS	1	0.942	0.957	29.853	0.303	0.303	0.000	0.000	0.000	0.000
97	A	454	ARG	1	0.973	0.986	36.397	0.182	0.182	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.049	-0.033	33.864	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	456	TYR	0	0.032	0.015	37.833	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	457	LYS	1	0.836	0.918	36.174	0.198	0.198	0.000	0.000	0.000	0.000
101	A	458	MET	0	0.001	0.012	32.592	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	459	ILE	0	-0.010	-0.023	30.183	0.018	0.018	0.000	0.000	0.000	0.000
103	A	460	CYS	0	-0.053	-0.007	29.330	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.043	0.029	25.341	0.010	0.010	0.000	0.000	0.000	0.000
105	A	462	VAL	0	0.000	0.005	26.147	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	463	PHE	0	0.014	0.002	22.355	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	464	GLU	-1	-0.894	-0.940	23.690	-0.233	-0.233	0.000	0.000	0.000	0.000
108	A	465	SER	0	0.019	-0.020	18.620	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	466	GLU	-1	-0.877	-0.936	20.570	-0.176	-0.176	0.000	0.000	0.000	0.000
110	A	467	ASP	-1	-0.904	-0.939	15.874	-0.516	-0.516	0.000	0.000	0.000	0.000
111	A	468	ALA	0	-0.059	-0.032	18.333	-0.051	-0.051	0.000	0.000	0.000	0.000
112	A	469	GLN	0	-0.035	-0.050	20.784	-0.029	-0.029	0.000	0.000	0.000	0.000
113	A	470	LEU	0	0.053	0.024	13.749	0.000	0.000	0.000	0.000	0.000	0.000
114	A	471	ILE	0	0.015	0.035	16.269	-0.086	-0.086	0.000	0.000	0.000	0.000
115	A	472	ALA	0	-0.012	-0.010	17.519	-0.037	-0.037	0.000	0.000	0.000	0.000
116	A	473	GLN	0	-0.048	-0.023	17.678	0.000	0.000	0.000	0.000	0.000	0.000
117	A	474	SER	0	0.033	0.012	14.154	-0.043	-0.043	0.000	0.000	0.000	0.000
118	A	475	ILE	0	-0.003	-0.004	15.853	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	476	GLY	0	-0.010	0.002	18.572	0.025	0.025	0.000	0.000	0.000	0.000
120	A	477	GLN	0	0.014	0.012	14.429	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	478	ALA	0	0.038	0.013	16.311	0.019	0.019	0.000	0.000	0.000	0.000
122	A	479	PHE	0	-0.060	-0.048	17.748	0.045	0.045	0.000	0.000	0.000	0.000
123	A	480	SER	0	-0.051	-0.026	19.921	0.054	0.054	0.000	0.000	0.000	0.000
124	A	481	VAL	0	0.016	0.013	15.689	0.052	0.052	0.000	0.000	0.000	0.000
125	A	482	ALA	0	0.042	0.022	19.093	0.037	0.037	0.000	0.000	0.000	0.000
126	A	483	TYR	0	-0.062	-0.032	20.858	0.043	0.043	0.000	0.000	0.000	0.000
127	A	484	GLN	0	0.016	-0.005	21.586	0.038	0.038	0.000	0.000	0.000	0.000
128	A	485	GLU	-1	-0.897	-0.926	18.764	-0.526	-0.526	0.000	0.000	0.000	0.000
129	A	486	PHE	0	-0.025	-0.016	22.267	0.025	0.025	0.000	0.000	0.000	0.000
130	A	487	LEU	0	-0.044	-0.011	25.515	0.023	0.023	0.000	0.000	0.000	0.000
131	A	488	ARG	1	0.878	0.924	19.471	0.368	0.368	0.000	0.000	0.000	0.000
132	A	489	ALA	0	-0.029	-0.005	24.607	0.017	0.017	0.000	0.000	0.000	0.000
133	A	490	ASN	0	-0.096	-0.060	26.382	0.022	0.022	0.000	0.000	0.000	0.000
134	A	491	GLY	0	0.014	0.033	29.630	0.013	0.013	0.000	0.000	0.000	0.000
135	A	492	ILE	0	-0.022	-0.016	30.799	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:323:MET)