FMO DATABASE

FMODB ID: M3KLZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1017209.954619
FMO2-HF: Nuclear repulsion	967506.757881
FMO2-HF: Total energy	-49703.196737
FMO2-MP2: Total energy	-49843.197885

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.
-8.85	-1.268	6.103	-4.43	-9.256	-0.024

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 : -0.020

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

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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	0.006	0.012	2.511	-1.756	0.118	2.442	-1.413	-2.903	-0.007
4	B	333	ALA	0	0.100	0.062	5.650	0.032	0.032	0.000	0.000	0.000	0.000
5	B	334	ALA	0	-0.032	-0.021	9.406	-0.080	-0.080	0.000	0.000	0.000	0.000
6	B	335	ASN	0	0.010	-0.001	11.640	0.070	0.070	0.000	0.000	0.000	0.000
7	B	336	TYR	0	-0.021	-0.019	14.870	-0.021	-0.021	0.000	0.000	0.000	0.000
8	B	337	LEU	0	-0.022	-0.018	15.904	0.043	0.043	0.000	0.000	0.000	0.000
9	B	338	GLY	0	0.037	0.025	18.480	0.032	0.032	0.000	0.000	0.000	0.000
10	B	339	SER	0	-0.009	-0.009	18.806	-0.025	-0.025	0.000	0.000	0.000	0.000
11	B	340	THR	0	-0.016	0.003	20.713	0.018	0.018	0.000	0.000	0.000	0.000
12	B	341	GLN	0	0.012	-0.007	22.400	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	342	LEU	0	-0.017	-0.008	23.340	0.009	0.009	0.000	0.000	0.000	0.000
14	B	343	LEU	0	0.022	0.011	26.205	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	352	VAL	0	0.056	0.014	25.217	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	353	ARG	1	0.896	0.937	19.867	0.235	0.235	0.000	0.000	0.000	0.000
17	B	354	MET	0	0.077	0.049	18.143	-0.006	-0.006	0.000	0.000	0.000	0.000
18	B	355	MET	0	0.001	0.000	21.510	0.003	0.003	0.000	0.000	0.000	0.000
19	B	356	GLN	0	0.026	0.010	22.886	-0.007	-0.007	0.000	0.000	0.000	0.000
20	B	357	ALA	0	0.021	0.014	18.700	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	358	GLN	0	0.038	0.013	20.625	0.000	0.000	0.000	0.000	0.000	0.000
22	B	359	GLU	-1	-0.793	-0.865	22.973	-0.127	-0.127	0.000	0.000	0.000	0.000
23	B	360	ALA	0	-0.040	-0.019	20.577	0.008	0.008	0.000	0.000	0.000	0.000
24	B	361	VAL	0	0.047	0.016	19.603	0.004	0.004	0.000	0.000	0.000	0.000
25	B	362	SER	0	-0.041	-0.031	21.962	0.011	0.011	0.000	0.000	0.000	0.000
26	B	363	ARG	1	0.857	0.907	25.312	0.135	0.135	0.000	0.000	0.000	0.000
27	B	364	ILE	0	0.026	0.026	20.622	0.013	0.013	0.000	0.000	0.000	0.000
28	B	365	LYS	1	0.880	0.929	20.702	0.198	0.198	0.000	0.000	0.000	0.000
29	B	366	MET	0	-0.039	-0.010	24.971	0.014	0.014	0.000	0.000	0.000	0.000
30	B	367	ALA	0	0.008	0.004	26.142	0.009	0.009	0.000	0.000	0.000	0.000
31	B	368	GLN	0	0.019	-0.028	22.243	0.019	0.019	0.000	0.000	0.000	0.000
32	B	369	LYS	1	0.886	0.936	26.188	0.103	0.103	0.000	0.000	0.000	0.000
33	B	370	LEU	0	-0.040	-0.023	29.134	0.007	0.007	0.000	0.000	0.000	0.000
34	B	371	ALA	0	-0.032	0.003	27.931	0.006	0.006	0.000	0.000	0.000	0.000
35	B	372	LYS	1	0.845	0.921	24.092	0.113	0.113	0.000	0.000	0.000	0.000
36	B	373	SER	0	0.004	0.011	30.281	0.004	0.004	0.000	0.000	0.000	0.000
37	B	385	MET	0	-0.010	0.020	19.632	0.006	0.006	0.000	0.000	0.000	0.000
38	B	386	THR	0	-0.049	-0.024	18.388	0.018	0.018	0.000	0.000	0.000	0.000
39	B	387	GLU	-1	-0.783	-0.876	15.596	-0.155	-0.155	0.000	0.000	0.000	0.000
40	B	388	VAL	0	-0.074	-0.049	11.581	0.013	0.013	0.000	0.000	0.000	0.000
41	B	389	ASP	-1	-0.801	-0.885	8.691	-0.093	-0.093	0.000	0.000	0.000	0.000
42	B	390	LEU	0	-0.050	-0.036	6.260	0.046	0.046	0.000	0.000	0.000	0.000
43	B	391	PHE	0	0.000	0.001	3.128	-1.716	-0.999	0.031	-0.225	-0.523	0.000
44	B	392	ILE	0	-0.012	-0.019	2.311	-0.719	0.970	1.807	-0.829	-2.668	0.002
45	B	393	LEU	0	-0.007	-0.003	2.553	-4.278	-2.112	1.224	-1.502	-1.889	-0.020
46	B	394	THR	0	-0.011	-0.026	5.145	0.183	0.256	-0.001	-0.003	-0.069	0.000
47	B	395	GLN	0	0.009	0.003	7.632	0.124	0.124	0.000	0.000	0.000	0.000
48	B	396	ARG	1	0.798	0.860	8.587	0.460	0.460	0.000	0.000	0.000	0.000
49	B	397	ILE	0	0.024	0.031	6.636	-0.257	-0.257	0.000	0.000	0.000	0.000
50	B	398	LYS	1	0.784	0.892	8.090	0.433	0.433	0.000	0.000	0.000	0.000
51	B	399	VAL	0	0.021	0.017	8.847	-0.201	-0.201	0.000	0.000	0.000	0.000
52	B	400	LEU	0	-0.011	-0.011	9.625	0.076	0.076	0.000	0.000	0.000	0.000
53	B	401	ASN	0	0.010	-0.003	12.687	-0.045	-0.045	0.000	0.000	0.000	0.000
54	B	402	ALA	0	0.045	0.024	13.712	0.044	0.044	0.000	0.000	0.000	0.000
55	B	403	ASP	-1	-0.904	-0.934	14.660	0.074	0.074	0.000	0.000	0.000	0.000
56	B	404	THR	0	-0.072	-0.059	17.497	0.027	0.027	0.000	0.000	0.000	0.000
57	B	405	GLN	0	-0.115	-0.061	11.375	0.109	0.109	0.000	0.000	0.000	0.000
58	B	406	GLU	-1	-0.869	-0.911	13.781	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	407	THR	0	-0.062	-0.047	13.670	-0.046	-0.046	0.000	0.000	0.000	0.000
60	B	408	MET	0	0.034	0.031	14.892	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	409	MET	0	-0.053	-0.024	14.269	0.012	0.012	0.000	0.000	0.000	0.000
62	B	410	ASP	-1	-0.782	-0.875	12.753	-0.326	-0.326	0.000	0.000	0.000	0.000
63	B	411	HIS	0	0.042	0.028	12.410	0.067	0.067	0.000	0.000	0.000	0.000
64	B	412	PRO	0	0.045	0.014	11.966	-0.095	-0.095	0.000	0.000	0.000	0.000
65	B	413	LEU	0	0.040	0.053	7.915	0.064	0.064	0.000	0.000	0.000	0.000
66	B	414	ARG	1	0.997	1.005	12.355	0.236	0.236	0.000	0.000	0.000	0.000
67	B	415	THR	0	-0.094	-0.075	15.405	0.044	0.044	0.000	0.000	0.000	0.000
68	B	416	ILE	0	-0.004	0.003	11.462	0.034	0.034	0.000	0.000	0.000	0.000
69	B	417	SER	0	-0.060	-0.024	15.607	0.034	0.034	0.000	0.000	0.000	0.000
70	B	418	TYR	0	0.016	-0.018	15.803	0.024	0.024	0.000	0.000	0.000	0.000
71	B	419	ILE	0	0.006	0.015	10.025	-0.011	-0.011	0.000	0.000	0.000	0.000
72	B	420	ALA	0	-0.011	0.001	13.363	0.034	0.034	0.000	0.000	0.000	0.000
73	B	421	ASP	-1	-0.814	-0.894	12.467	-0.442	-0.442	0.000	0.000	0.000	0.000
74	B	422	ILE	0	-0.039	-0.031	14.488	0.040	0.040	0.000	0.000	0.000	0.000
75	B	423	GLY	0	0.011	0.011	17.883	0.014	0.014	0.000	0.000	0.000	0.000
76	B	424	ASN	0	-0.016	-0.025	15.774	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	425	ILE	0	-0.040	-0.010	15.402	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	426	VAL	0	0.029	0.025	10.091	-0.012	-0.012	0.000	0.000	0.000	0.000
79	B	427	VAL	0	-0.030	-0.018	13.346	0.038	0.038	0.000	0.000	0.000	0.000
80	B	428	LEU	0	0.014	0.012	10.456	-0.028	-0.028	0.000	0.000	0.000	0.000
81	B	429	MET	0	-0.026	-0.011	14.246	0.054	0.054	0.000	0.000	0.000	0.000
82	B	430	ALA	0	0.041	0.019	15.952	-0.013	-0.013	0.000	0.000	0.000	0.000
83	B	431	ARG	1	0.856	0.915	17.988	0.243	0.243	0.000	0.000	0.000	0.000
84	B	456	TYR	0	0.053	0.013	26.031	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	457	LYS	1	0.905	0.952	26.306	0.130	0.130	0.000	0.000	0.000	0.000
86	B	458	MET	0	-0.062	0.008	19.874	-0.006	-0.006	0.000	0.000	0.000	0.000
87	B	459	ILE	0	0.022	0.017	18.861	0.018	0.018	0.000	0.000	0.000	0.000
88	B	460	CYS	0	-0.040	-0.019	18.513	-0.028	-0.028	0.000	0.000	0.000	0.000
89	B	461	HIS	0	0.072	0.040	14.945	0.038	0.038	0.000	0.000	0.000	0.000
90	B	462	VAL	0	-0.006	-0.004	15.922	-0.030	-0.030	0.000	0.000	0.000	0.000
91	B	463	PHE	0	0.015	0.003	12.547	0.008	0.008	0.000	0.000	0.000	0.000
92	B	464	GLU	-1	-0.807	-0.896	14.578	-0.197	-0.197	0.000	0.000	0.000	0.000
93	B	465	SER	0	0.003	-0.002	10.684	-0.023	-0.023	0.000	0.000	0.000	0.000
94	B	466	GLU	-1	-0.863	-0.939	12.696	-0.287	-0.287	0.000	0.000	0.000	0.000
95	B	467	ASP	-1	-0.827	-0.920	8.056	-0.543	-0.543	0.000	0.000	0.000	0.000
96	B	468	ALA	0	-0.075	-0.031	9.037	-0.133	-0.133	0.000	0.000	0.000	0.000
97	B	469	GLN	0	0.020	-0.001	10.176	-0.073	-0.073	0.000	0.000	0.000	0.000
98	B	470	LEU	0	0.029	0.028	5.588	-0.032	-0.032	0.000	0.000	0.000	0.000
99	B	471	ILE	0	0.021	0.027	5.385	-0.289	-0.289	0.000	0.000	0.000	0.000
100	B	472	ALA	0	-0.002	-0.012	6.169	-0.136	-0.136	0.000	0.000	0.000	0.000
101	B	473	GLN	0	-0.052	-0.031	7.606	-0.035	-0.035	0.000	0.000	0.000	0.000
102	B	474	SER	0	-0.009	-0.010	2.388	-1.084	-0.227	0.602	-0.446	-1.014	0.001
103	B	475	ILE	0	-0.009	-0.008	4.470	-0.055	0.089	-0.001	-0.007	-0.135	0.000
104	B	476	GLY	0	0.012	0.014	6.737	0.139	0.139	0.000	0.000	0.000	0.000
105	B	477	GLN	0	0.003	0.001	5.388	0.148	0.148	0.000	0.000	0.000	0.000
106	B	478	ALA	0	0.006	0.011	4.524	0.061	0.123	-0.001	-0.005	-0.055	0.000
107	B	479	PHE	0	-0.012	-0.029	6.166	0.108	0.108	0.000	0.000	0.000	0.000
108	B	480	SER	0	-0.023	-0.017	9.625	0.095	0.095	0.000	0.000	0.000	0.000
109	B	481	VAL	0	-0.016	-0.005	7.585	0.064	0.064	0.000	0.000	0.000	0.000
110	B	482	ALA	0	0.049	0.029	9.522	0.058	0.058	0.000	0.000	0.000	0.000
111	B	483	TYR	0	-0.048	-0.016	11.202	0.058	0.058	0.000	0.000	0.000	0.000
112	B	484	GLN	0	0.030	0.015	12.712	0.057	0.057	0.000	0.000	0.000	0.000
113	B	485	GLU	-1	-0.881	-0.943	10.737	-0.238	-0.238	0.000	0.000	0.000	0.000
114	B	486	PHE	0	-0.011	-0.005	14.700	0.029	0.029	0.000	0.000	0.000	0.000
115	B	487	LEU	0	-0.025	-0.002	17.128	0.022	0.022	0.000	0.000	0.000	0.000
116	B	488	ARG	1	0.933	0.950	13.746	0.138	0.138	0.000	0.000	0.000	0.000
117	B	489	ALA	0	-0.033	-0.010	18.822	0.016	0.016	0.000	0.000	0.000	0.000
118	B	490	ASN	0	-0.102	-0.056	20.541	0.016	0.016	0.000	0.000	0.000	0.000
119	B	491	GLY	0	0.017	0.017	22.903	0.006	0.006	0.000	0.000	0.000	0.000
120	B	492	ILE	0	-0.042	-0.015	22.294	0.005	0.005	0.000	0.000	0.000	0.000
121	B	493	ASN	0	-0.001	-0.013	21.355	-0.004	-0.004	0.000	0.000	0.000	0.000
122	B	494	PRO	0	-0.021	0.013	17.275	-0.001	-0.001	0.000	0.000	0.000	0.000

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