FMO DATABASE

FMODB ID: 7G8KK

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1204170.033004
FMO2-HF: Nuclear repulsion	1149010.649187
FMO2-HF: Total energy	-55159.383818
FMO2-MP2: Total energy	-55314.577146

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.
-5.111	-3.556	-0.024	-0.637	-0.893	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 : -0.088 / q_NPA : -0.047

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	-0.806	-0.903	3.793	-1.421	0.134	-0.024	-0.637	-0.893	0.003
4	A	326	LEU	0	-0.052	-0.036	6.885	0.129	0.129	0.000	0.000	0.000	0.000
5	A	327	ILE	0	-0.072	-0.049	9.457	0.469	0.469	0.000	0.000	0.000	0.000
6	A	328	ASP	-1	-0.851	-0.924	5.890	-5.513	-5.513	0.000	0.000	0.000	0.000
7	A	329	GLY	0	-0.095	-0.064	8.512	0.546	0.546	0.000	0.000	0.000	0.000
8	A	330	ILE	0	-0.022	0.002	6.974	-0.869	-0.869	0.000	0.000	0.000	0.000
9	A	331	ILE	0	0.002	-0.021	8.513	0.361	0.361	0.000	0.000	0.000	0.000
10	A	332	PHE	0	0.019	-0.001	10.634	0.037	0.037	0.000	0.000	0.000	0.000
11	A	333	ALA	0	0.072	0.058	13.684	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	334	ALA	0	-0.043	-0.010	16.340	0.044	0.044	0.000	0.000	0.000	0.000
13	A	335	ASN	0	0.031	0.015	19.678	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	336	TYR	0	-0.043	-0.059	22.990	0.007	0.007	0.000	0.000	0.000	0.000
15	A	337	LEU	0	-0.027	-0.004	24.489	0.027	0.027	0.000	0.000	0.000	0.000
16	A	338	GLY	0	0.080	0.029	28.032	0.019	0.019	0.000	0.000	0.000	0.000
17	A	339	SER	0	-0.028	-0.057	27.772	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	340	THR	0	-0.043	-0.012	30.135	0.028	0.028	0.000	0.000	0.000	0.000
19	A	341	GLN	0	-0.031	-0.012	32.560	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	342	LEU	0	0.037	0.027	34.801	0.016	0.016	0.000	0.000	0.000	0.000
21	A	343	LEU	0	-0.046	-0.030	36.852	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	344	SER	0	-0.001	0.009	36.184	0.002	0.002	0.000	0.000	0.000	0.000
23	A	345	ASP	-1	-0.854	-0.919	38.159	-0.164	-0.164	0.000	0.000	0.000	0.000
24	A	346	LYS	1	0.840	0.880	37.383	0.167	0.167	0.000	0.000	0.000	0.000
25	A	347	THR	0	-0.018	-0.023	33.902	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	348	PRO	0	-0.023	0.022	35.291	0.011	0.011	0.000	0.000	0.000	0.000
27	A	349	SER	0	0.067	0.022	35.835	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	350	LYS	1	1.044	0.993	28.947	0.257	0.257	0.000	0.000	0.000	0.000
29	A	351	ASN	0	0.037	0.028	34.084	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	352	VAL	0	0.053	0.033	36.765	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	353	ARG	1	0.854	0.947	31.402	0.258	0.258	0.000	0.000	0.000	0.000
32	A	354	MET	0	0.022	0.018	30.138	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	355	MET	0	0.027	0.007	33.634	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	356	GLN	0	0.045	0.001	34.212	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	357	ALA	0	0.021	0.013	30.468	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	358	GLN	0	0.014	-0.012	32.232	0.002	0.002	0.000	0.000	0.000	0.000
37	A	359	GLU	-1	-0.959	-0.973	34.574	-0.174	-0.174	0.000	0.000	0.000	0.000
38	A	360	ALA	0	-0.025	-0.019	31.763	0.003	0.003	0.000	0.000	0.000	0.000
39	A	361	VAL	0	0.044	0.018	30.799	0.003	0.003	0.000	0.000	0.000	0.000
40	A	362	SER	0	-0.043	-0.010	33.060	0.007	0.007	0.000	0.000	0.000	0.000
41	A	363	ARG	1	0.913	0.945	35.727	0.203	0.203	0.000	0.000	0.000	0.000
42	A	364	ILE	0	0.002	0.015	30.856	0.004	0.004	0.000	0.000	0.000	0.000
43	A	365	LYS	1	0.948	0.962	33.286	0.192	0.192	0.000	0.000	0.000	0.000
44	A	366	MET	0	-0.049	-0.016	35.768	0.006	0.006	0.000	0.000	0.000	0.000
45	A	367	ALA	0	-0.038	-0.008	36.283	0.007	0.007	0.000	0.000	0.000	0.000
46	A	368	GLN	0	-0.045	-0.011	32.057	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	385	MET	0	-0.035	-0.034	27.463	0.006	0.006	0.000	0.000	0.000	0.000
48	A	386	THR	0	-0.047	-0.032	22.868	0.005	0.005	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.910	-0.914	20.620	-0.309	-0.309	0.000	0.000	0.000	0.000
50	A	388	VAL	0	-0.093	-0.072	18.733	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	389	ASP	-1	-0.787	-0.869	13.230	-0.817	-0.817	0.000	0.000	0.000	0.000
52	A	390	LEU	0	-0.078	-0.048	15.289	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	391	PHE	0	0.012	0.015	8.989	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	392	ILE	0	-0.004	-0.016	12.461	0.217	0.217	0.000	0.000	0.000	0.000
55	A	393	LEU	0	0.054	0.037	11.440	-0.169	-0.169	0.000	0.000	0.000	0.000
56	A	394	THR	0	-0.064	-0.028	13.663	0.199	0.199	0.000	0.000	0.000	0.000
57	A	395	GLN	0	0.035	0.002	15.501	0.215	0.215	0.000	0.000	0.000	0.000
58	A	396	ARG	1	0.856	0.922	13.639	1.346	1.346	0.000	0.000	0.000	0.000
59	A	397	ILE	0	0.031	0.030	16.044	-0.080	-0.080	0.000	0.000	0.000	0.000
60	A	398	LYS	1	0.923	0.968	13.840	1.262	1.262	0.000	0.000	0.000	0.000
61	A	399	VAL	0	0.000	0.007	16.517	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	400	LEU	0	-0.017	-0.003	13.306	0.028	0.028	0.000	0.000	0.000	0.000
63	A	401	ASN	0	0.052	0.015	17.285	0.038	0.038	0.000	0.000	0.000	0.000
64	A	402	ALA	0	0.042	0.024	16.451	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.962	-0.963	16.851	-0.321	-0.321	0.000	0.000	0.000	0.000
66	A	404	THR	0	0.045	0.007	19.164	0.000	0.000	0.000	0.000	0.000	0.000
67	A	405	GLN	0	-0.067	-0.053	13.357	-0.093	-0.093	0.000	0.000	0.000	0.000
68	A	406	GLU	-1	-0.937	-0.956	16.474	-0.529	-0.529	0.000	0.000	0.000	0.000
69	A	407	THR	0	-0.108	-0.070	17.669	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	408	MET	0	-0.010	0.015	19.455	0.053	0.053	0.000	0.000	0.000	0.000
71	A	409	MET	0	-0.065	-0.036	20.944	0.037	0.037	0.000	0.000	0.000	0.000
72	A	410	ASP	-1	-0.891	-0.946	19.368	-0.885	-0.885	0.000	0.000	0.000	0.000
73	A	411	HIS	0	-0.004	0.005	20.260	0.074	0.074	0.000	0.000	0.000	0.000
74	A	412	PRO	0	0.002	-0.002	20.356	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	413	LEU	0	0.100	0.072	19.127	0.083	0.083	0.000	0.000	0.000	0.000
76	A	414	ARG	1	0.960	0.985	21.384	0.554	0.554	0.000	0.000	0.000	0.000
77	A	415	THR	0	-0.160	-0.124	24.338	0.057	0.057	0.000	0.000	0.000	0.000
78	A	416	ILE	0	0.056	0.040	22.250	0.040	0.040	0.000	0.000	0.000	0.000
79	A	417	SER	0	-0.083	-0.042	25.536	0.002	0.002	0.000	0.000	0.000	0.000
80	A	418	TYR	0	-0.014	-0.031	27.213	0.016	0.016	0.000	0.000	0.000	0.000
81	A	419	ILE	0	0.055	0.031	21.800	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	420	ALA	0	-0.050	-0.025	25.165	0.026	0.026	0.000	0.000	0.000	0.000
83	A	421	ASP	-1	-0.841	-0.904	23.609	-0.323	-0.323	0.000	0.000	0.000	0.000
84	A	422	ILE	0	-0.046	-0.032	25.714	0.030	0.030	0.000	0.000	0.000	0.000
85	A	423	GLY	0	0.015	0.014	27.833	0.006	0.006	0.000	0.000	0.000	0.000
86	A	424	ASN	0	0.077	0.039	24.969	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	425	ILE	0	-0.042	-0.014	25.125	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	426	VAL	0	0.069	0.052	21.293	0.000	0.000	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.046	-0.026	24.559	0.011	0.011	0.000	0.000	0.000	0.000
90	A	428	LEU	0	0.041	0.031	20.881	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	429	MET	0	-0.057	-0.021	24.961	0.028	0.028	0.000	0.000	0.000	0.000
92	A	430	ALA	0	0.057	0.029	26.187	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	431	ARG	1	0.920	0.969	27.896	0.381	0.381	0.000	0.000	0.000	0.000
94	A	451	ASP	-1	-0.842	-0.903	37.857	-0.185	-0.185	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.033	0.020	35.972	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	453	LYS	1	0.934	0.944	30.114	0.324	0.324	0.000	0.000	0.000	0.000
97	A	454	ARG	1	0.980	1.005	36.435	0.203	0.203	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.035	-0.018	34.151	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	456	TYR	0	0.072	0.023	38.002	0.000	0.000	0.000	0.000	0.000	0.000
100	A	457	LYS	1	0.898	0.961	35.911	0.200	0.200	0.000	0.000	0.000	0.000
101	A	458	MET	0	-0.029	-0.004	32.235	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	459	ILE	0	0.019	-0.007	29.055	0.021	0.021	0.000	0.000	0.000	0.000
103	A	460	CYS	0	-0.073	-0.027	29.057	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.091	0.096	25.001	0.026	0.026	0.000	0.000	0.000	0.000
105	A	462	VAL	0	0.007	0.009	26.191	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	463	PHE	0	0.034	0.010	22.004	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	464	GLU	-1	-0.914	-0.948	24.107	-0.239	-0.239	0.000	0.000	0.000	0.000
108	A	465	SER	0	-0.022	-0.066	19.105	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	466	GLU	-1	-0.907	-0.943	20.392	-0.204	-0.204	0.000	0.000	0.000	0.000
110	A	467	ASP	-1	-0.857	-0.919	16.158	-0.467	-0.467	0.000	0.000	0.000	0.000
111	A	468	ALA	0	-0.067	-0.035	18.531	-0.064	-0.064	0.000	0.000	0.000	0.000
112	A	469	GLN	0	-0.036	-0.044	20.947	-0.030	-0.030	0.000	0.000	0.000	0.000
113	A	470	LEU	0	0.067	0.028	13.307	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	471	ILE	0	0.043	0.049	16.334	-0.085	-0.085	0.000	0.000	0.000	0.000
115	A	472	ALA	0	-0.010	-0.016	17.344	-0.053	-0.053	0.000	0.000	0.000	0.000
116	A	473	GLN	0	-0.054	-0.014	17.676	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	474	SER	0	0.022	-0.006	14.046	-0.029	-0.029	0.000	0.000	0.000	0.000
118	A	475	ILE	0	-0.010	-0.004	15.932	-0.057	-0.057	0.000	0.000	0.000	0.000
119	A	476	GLY	0	-0.002	0.013	18.193	0.033	0.033	0.000	0.000	0.000	0.000
120	A	477	GLN	0	0.014	-0.002	13.829	-0.064	-0.064	0.000	0.000	0.000	0.000
121	A	478	ALA	0	0.003	0.004	16.521	0.014	0.014	0.000	0.000	0.000	0.000
122	A	479	PHE	0	-0.053	-0.040	17.634	0.043	0.043	0.000	0.000	0.000	0.000
123	A	480	SER	0	-0.050	-0.026	19.221	0.062	0.062	0.000	0.000	0.000	0.000
124	A	481	VAL	0	0.000	-0.002	15.384	0.061	0.061	0.000	0.000	0.000	0.000
125	A	482	ALA	0	0.056	0.035	18.726	0.049	0.049	0.000	0.000	0.000	0.000
126	A	483	TYR	0	-0.043	-0.011	20.559	0.052	0.052	0.000	0.000	0.000	0.000
127	A	484	GLN	0	0.010	-0.010	21.451	0.042	0.042	0.000	0.000	0.000	0.000
128	A	485	GLU	-1	-0.991	-0.990	19.449	-0.620	-0.620	0.000	0.000	0.000	0.000
129	A	486	PHE	0	-0.063	-0.038	22.121	0.034	0.034	0.000	0.000	0.000	0.000
130	A	487	LEU	0	-0.041	-0.016	25.375	0.025	0.025	0.000	0.000	0.000	0.000
131	A	488	ARG	1	0.973	0.980	19.532	0.392	0.392	0.000	0.000	0.000	0.000
132	A	489	ALA	0	-0.029	0.004	24.672	0.018	0.018	0.000	0.000	0.000	0.000
133	A	490	ASN	0	-0.054	-0.023	26.327	0.030	0.030	0.000	0.000	0.000	0.000
134	A	491	GLY	0	0.025	0.027	29.948	0.013	0.013	0.000	0.000	0.000	0.000
135	A	492	ILE	0	-0.049	-0.026	30.645	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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