FMO DATABASE

FMODB ID: 9G5R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1017819.16092
FMO2-HF: Nuclear repulsion	968116.583619
FMO2-HF: Total energy	-49702.577302
FMO2-MP2: Total energy	-49842.690768

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.
-8.499	-0.281	6.025	-4.671	-9.571	-0.025

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 : -0.037 / q_NPA : -0.024

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	0.013	0.018	2.481	-2.027	0.416	2.252	-1.552	-3.144	-0.009
4	B	333	ALA	0	0.084	0.058	5.389	0.008	0.021	-0.001	0.000	-0.011	0.000
5	B	334	ALA	0	-0.030	-0.011	9.114	-0.040	-0.040	0.000	0.000	0.000	0.000
6	B	335	ASN	0	-0.002	-0.010	11.317	0.056	0.056	0.000	0.000	0.000	0.000
7	B	336	TYR	0	-0.037	-0.022	14.889	-0.015	-0.015	0.000	0.000	0.000	0.000
8	B	337	LEU	0	-0.006	-0.006	16.109	0.040	0.040	0.000	0.000	0.000	0.000
9	B	338	GLY	0	0.044	0.023	18.591	0.027	0.027	0.000	0.000	0.000	0.000
10	B	339	SER	0	-0.017	-0.025	19.008	-0.022	-0.022	0.000	0.000	0.000	0.000
11	B	340	THR	0	-0.017	0.006	20.847	0.016	0.016	0.000	0.000	0.000	0.000
12	B	341	GLN	0	0.000	-0.012	22.478	-0.019	-0.019	0.000	0.000	0.000	0.000
13	B	342	LEU	0	-0.002	0.004	22.627	0.010	0.010	0.000	0.000	0.000	0.000
14	B	343	LEU	0	0.014	0.007	25.814	-0.005	-0.005	0.000	0.000	0.000	0.000
15	B	352	VAL	0	0.054	0.013	25.133	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	353	ARG	1	0.920	0.961	19.762	0.234	0.234	0.000	0.000	0.000	0.000
17	B	354	MET	0	0.089	0.049	18.114	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	355	MET	0	0.009	-0.002	21.359	0.004	0.004	0.000	0.000	0.000	0.000
19	B	356	GLN	0	0.005	-0.003	22.780	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	357	ALA	0	0.035	0.017	18.697	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	358	GLN	0	0.022	0.008	20.645	0.000	0.000	0.000	0.000	0.000	0.000
22	B	359	GLU	-1	-0.815	-0.895	22.910	-0.123	-0.123	0.000	0.000	0.000	0.000
23	B	360	ALA	0	-0.030	-0.012	20.742	0.008	0.008	0.000	0.000	0.000	0.000
24	B	361	VAL	0	0.046	0.010	19.182	0.004	0.004	0.000	0.000	0.000	0.000
25	B	362	SER	0	-0.017	-0.002	21.657	0.007	0.007	0.000	0.000	0.000	0.000
26	B	363	ARG	1	0.842	0.907	25.059	0.132	0.132	0.000	0.000	0.000	0.000
27	B	364	ILE	0	0.015	0.026	20.620	0.012	0.012	0.000	0.000	0.000	0.000
28	B	365	LYS	1	0.974	0.991	21.068	0.179	0.179	0.000	0.000	0.000	0.000
29	B	366	MET	0	-0.057	-0.026	25.146	0.013	0.013	0.000	0.000	0.000	0.000
30	B	367	ALA	0	0.034	0.022	26.330	0.009	0.009	0.000	0.000	0.000	0.000
31	B	368	GLN	0	0.005	-0.002	22.223	0.020	0.020	0.000	0.000	0.000	0.000
32	B	369	LYS	1	0.901	0.929	26.381	0.095	0.095	0.000	0.000	0.000	0.000
33	B	370	LEU	0	-0.061	-0.023	29.265	0.007	0.007	0.000	0.000	0.000	0.000
34	B	371	ALA	0	-0.022	-0.008	28.291	0.005	0.005	0.000	0.000	0.000	0.000
35	B	372	LYS	1	0.792	0.899	23.565	0.105	0.105	0.000	0.000	0.000	0.000
36	B	373	SER	0	0.027	0.020	29.973	0.004	0.004	0.000	0.000	0.000	0.000
37	B	385	MET	0	0.031	0.037	19.282	0.005	0.005	0.000	0.000	0.000	0.000
38	B	386	THR	0	-0.049	-0.034	18.334	0.014	0.014	0.000	0.000	0.000	0.000
39	B	387	GLU	-1	-0.771	-0.869	15.479	-0.115	-0.115	0.000	0.000	0.000	0.000
40	B	388	VAL	0	-0.079	-0.047	11.572	0.005	0.005	0.000	0.000	0.000	0.000
41	B	389	ASP	-1	-0.763	-0.873	8.757	-0.003	-0.003	0.000	0.000	0.000	0.000
42	B	390	LEU	0	-0.081	-0.052	6.064	0.013	0.013	0.000	0.000	0.000	0.000
43	B	391	PHE	0	0.022	0.006	3.339	-1.261	-0.784	0.010	-0.111	-0.375	0.000
44	B	392	ILE	0	-0.027	-0.036	2.312	-1.021	0.894	2.003	-1.044	-2.875	0.002
45	B	393	LEU	0	-0.029	-0.007	2.562	-4.148	-2.061	1.152	-1.441	-1.798	-0.018
46	B	394	THR	0	0.043	0.013	5.050	0.159	0.250	-0.001	-0.005	-0.086	0.000
47	B	395	GLN	0	0.003	-0.007	7.436	0.179	0.179	0.000	0.000	0.000	0.000
48	B	396	ARG	1	0.804	0.855	8.523	0.534	0.534	0.000	0.000	0.000	0.000
49	B	397	ILE	0	0.035	0.035	6.586	-0.267	-0.267	0.000	0.000	0.000	0.000
50	B	398	LYS	1	0.801	0.911	8.133	0.457	0.457	0.000	0.000	0.000	0.000
51	B	399	VAL	0	0.016	0.017	9.058	-0.174	-0.174	0.000	0.000	0.000	0.000
52	B	400	LEU	0	0.011	0.001	9.858	0.068	0.068	0.000	0.000	0.000	0.000
53	B	401	ASN	0	0.038	0.022	12.766	-0.025	-0.025	0.000	0.000	0.000	0.000
54	B	402	ALA	0	0.039	0.015	13.519	0.042	0.042	0.000	0.000	0.000	0.000
55	B	403	ASP	-1	-0.916	-0.930	14.436	0.080	0.080	0.000	0.000	0.000	0.000
56	B	404	THR	0	-0.071	-0.076	17.753	0.030	0.030	0.000	0.000	0.000	0.000
57	B	405	GLN	0	-0.096	-0.052	11.686	0.127	0.127	0.000	0.000	0.000	0.000
58	B	406	GLU	-1	-0.922	-0.930	14.098	-0.019	-0.019	0.000	0.000	0.000	0.000
59	B	407	THR	0	-0.047	-0.043	13.873	-0.047	-0.047	0.000	0.000	0.000	0.000
60	B	408	MET	0	0.013	0.011	14.949	0.000	0.000	0.000	0.000	0.000	0.000
61	B	409	MET	0	-0.045	-0.018	14.161	0.010	0.010	0.000	0.000	0.000	0.000
62	B	410	ASP	-1	-0.784	-0.875	12.793	-0.369	-0.369	0.000	0.000	0.000	0.000
63	B	411	HIS	0	0.016	0.010	12.419	0.075	0.075	0.000	0.000	0.000	0.000
64	B	412	PRO	0	0.040	0.016	11.984	-0.091	-0.091	0.000	0.000	0.000	0.000
65	B	413	LEU	0	0.101	0.059	7.856	0.074	0.074	0.000	0.000	0.000	0.000
66	B	414	ARG	1	0.986	1.013	12.154	0.273	0.273	0.000	0.000	0.000	0.000
67	B	415	THR	0	-0.129	-0.091	15.486	0.050	0.050	0.000	0.000	0.000	0.000
68	B	416	ILE	0	-0.016	-0.016	11.235	0.033	0.033	0.000	0.000	0.000	0.000
69	B	417	SER	0	-0.066	-0.026	14.905	0.017	0.017	0.000	0.000	0.000	0.000
70	B	418	TYR	0	0.019	-0.010	15.551	0.003	0.003	0.000	0.000	0.000	0.000
71	B	419	ILE	0	0.022	0.014	9.935	-0.005	-0.005	0.000	0.000	0.000	0.000
72	B	420	ALA	0	-0.022	-0.010	13.249	0.029	0.029	0.000	0.000	0.000	0.000
73	B	421	ASP	-1	-0.814	-0.886	12.098	-0.391	-0.391	0.000	0.000	0.000	0.000
74	B	422	ILE	0	-0.035	-0.023	14.160	0.037	0.037	0.000	0.000	0.000	0.000
75	B	423	GLY	0	-0.013	-0.007	17.675	0.011	0.011	0.000	0.000	0.000	0.000
76	B	424	ASN	0	0.002	-0.007	15.391	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	425	ILE	0	-0.009	-0.004	15.314	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	426	VAL	0	0.007	0.006	9.999	-0.014	-0.014	0.000	0.000	0.000	0.000
79	B	427	VAL	0	-0.024	-0.015	13.271	0.028	0.028	0.000	0.000	0.000	0.000
80	B	428	LEU	0	0.008	0.017	10.500	-0.021	-0.021	0.000	0.000	0.000	0.000
81	B	429	MET	0	-0.027	-0.005	14.153	0.056	0.056	0.000	0.000	0.000	0.000
82	B	430	ALA	0	0.061	0.039	15.825	-0.008	-0.008	0.000	0.000	0.000	0.000
83	B	431	ARG	1	0.930	0.974	17.734	0.265	0.265	0.000	0.000	0.000	0.000
84	B	456	TYR	0	0.063	0.011	25.903	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	457	LYS	1	0.882	0.936	25.593	0.143	0.143	0.000	0.000	0.000	0.000
86	B	458	MET	0	-0.082	-0.019	19.690	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	459	ILE	0	-0.004	0.000	18.781	0.018	0.018	0.000	0.000	0.000	0.000
88	B	460	CYS	0	-0.050	-0.017	18.520	-0.031	-0.031	0.000	0.000	0.000	0.000
89	B	461	HIS	0	0.063	0.031	14.895	0.035	0.035	0.000	0.000	0.000	0.000
90	B	462	VAL	0	-0.001	-0.001	15.620	-0.031	-0.031	0.000	0.000	0.000	0.000
91	B	463	PHE	0	0.009	0.002	12.356	0.007	0.007	0.000	0.000	0.000	0.000
92	B	464	GLU	-1	-0.897	-0.957	14.408	-0.181	-0.181	0.000	0.000	0.000	0.000
93	B	465	SER	0	-0.015	-0.016	10.407	-0.037	-0.037	0.000	0.000	0.000	0.000
94	B	466	GLU	-1	-0.829	-0.918	12.028	-0.232	-0.232	0.000	0.000	0.000	0.000
95	B	467	ASP	-1	-0.880	-0.930	7.862	-0.314	-0.314	0.000	0.000	0.000	0.000
96	B	468	ALA	0	-0.057	-0.037	8.670	-0.139	-0.139	0.000	0.000	0.000	0.000
97	B	469	GLN	0	-0.005	-0.018	10.532	-0.048	-0.048	0.000	0.000	0.000	0.000
98	B	470	LEU	0	0.050	0.029	5.262	-0.039	-0.039	0.000	0.000	0.000	0.000
99	B	471	ILE	0	0.025	0.034	5.221	-0.289	-0.289	0.000	0.000	0.000	0.000
100	B	472	ALA	0	0.017	0.003	6.066	-0.153	-0.153	0.000	0.000	0.000	0.000
101	B	473	GLN	0	-0.028	-0.010	7.612	-0.056	-0.056	0.000	0.000	0.000	0.000
102	B	474	SER	0	-0.001	-0.018	2.404	-1.174	-0.206	0.612	-0.503	-1.076	0.000
103	B	475	ILE	0	-0.025	-0.012	4.497	-0.109	0.048	-0.001	-0.008	-0.147	0.000
104	B	476	GLY	0	0.007	0.009	6.503	0.122	0.122	0.000	0.000	0.000	0.000
105	B	477	GLN	0	-0.020	-0.014	5.283	0.126	0.126	0.000	0.000	0.000	0.000
106	B	478	ALA	0	0.002	0.003	4.443	0.056	0.123	-0.001	-0.007	-0.059	0.000
107	B	479	PHE	0	-0.042	-0.024	6.018	0.117	0.117	0.000	0.000	0.000	0.000
108	B	480	SER	0	0.004	-0.004	9.698	0.086	0.086	0.000	0.000	0.000	0.000
109	B	481	VAL	0	0.004	0.007	7.076	0.062	0.062	0.000	0.000	0.000	0.000
110	B	482	ALA	0	0.055	0.028	9.326	0.059	0.059	0.000	0.000	0.000	0.000
111	B	483	TYR	0	-0.043	-0.015	10.967	0.064	0.064	0.000	0.000	0.000	0.000
112	B	484	GLN	0	0.007	0.002	12.431	0.055	0.055	0.000	0.000	0.000	0.000
113	B	485	GLU	-1	-0.909	-0.969	11.125	-0.270	-0.270	0.000	0.000	0.000	0.000
114	B	486	PHE	0	-0.028	-0.013	14.847	0.029	0.029	0.000	0.000	0.000	0.000
115	B	487	LEU	0	-0.033	-0.012	16.952	0.024	0.024	0.000	0.000	0.000	0.000
116	B	488	ARG	1	0.968	0.984	13.856	0.159	0.159	0.000	0.000	0.000	0.000
117	B	489	ALA	0	-0.048	-0.020	18.936	0.016	0.016	0.000	0.000	0.000	0.000
118	B	490	ASN	0	-0.103	-0.061	20.744	0.017	0.017	0.000	0.000	0.000	0.000
119	B	491	GLY	0	0.006	0.016	23.298	0.006	0.006	0.000	0.000	0.000	0.000
120	B	492	ILE	0	-0.041	-0.008	22.322	0.006	0.006	0.000	0.000	0.000	0.000
121	B	493	ASN	0	0.003	-0.009	21.719	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	494	PRO	0	-0.029	0.000	17.072	-0.004	-0.004	0.000	0.000	0.000	0.000

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