FMO DATABASE

FMODB ID: 22ZMR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1203542.860546
FMO2-HF: Nuclear repulsion	1148382.385688
FMO2-HF: Total energy	-55160.474859
FMO2-MP2: Total energy	-55315.512245

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.
-4.904	-3.259	-0.019	-0.735	-0.891	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 : -0.082 / q_NPA : -0.050

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	-0.813	-0.914	3.845	-0.825	0.820	-0.019	-0.735	-0.891	0.003
4	A	326	LEU	0	-0.051	-0.030	6.694	0.076	0.076	0.000	0.000	0.000	0.000
5	A	327	ILE	0	-0.081	-0.058	9.300	0.388	0.388	0.000	0.000	0.000	0.000
6	A	328	ASP	-1	-0.857	-0.920	5.811	-5.005	-5.005	0.000	0.000	0.000	0.000
7	A	329	GLY	0	-0.089	-0.061	8.847	0.478	0.478	0.000	0.000	0.000	0.000
8	A	330	ILE	0	-0.011	0.005	6.753	-0.872	-0.872	0.000	0.000	0.000	0.000
9	A	331	ILE	0	-0.010	-0.026	8.513	0.372	0.372	0.000	0.000	0.000	0.000
10	A	332	PHE	0	0.015	0.000	10.672	0.037	0.037	0.000	0.000	0.000	0.000
11	A	333	ALA	0	0.078	0.061	13.615	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	334	ALA	0	-0.054	-0.024	16.263	0.057	0.057	0.000	0.000	0.000	0.000
13	A	335	ASN	0	0.054	0.032	19.646	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	336	TYR	0	-0.030	-0.052	22.981	0.014	0.014	0.000	0.000	0.000	0.000
15	A	337	LEU	0	-0.034	-0.004	24.556	0.027	0.027	0.000	0.000	0.000	0.000
16	A	338	GLY	0	0.075	0.030	28.121	0.019	0.019	0.000	0.000	0.000	0.000
17	A	339	SER	0	-0.029	-0.034	27.887	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	340	THR	0	-0.025	-0.008	30.296	0.028	0.028	0.000	0.000	0.000	0.000
19	A	341	GLN	0	-0.031	-0.014	32.753	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	342	LEU	0	0.028	0.018	34.802	0.016	0.016	0.000	0.000	0.000	0.000
21	A	343	LEU	0	-0.021	-0.019	37.066	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	344	SER	0	-0.018	-0.014	36.372	0.002	0.002	0.000	0.000	0.000	0.000
23	A	345	ASP	-1	-0.821	-0.896	38.350	-0.155	-0.155	0.000	0.000	0.000	0.000
24	A	346	LYS	1	0.857	0.895	37.592	0.154	0.154	0.000	0.000	0.000	0.000
25	A	347	THR	0	-0.012	-0.017	33.947	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	348	PRO	0	-0.015	0.021	35.295	0.012	0.012	0.000	0.000	0.000	0.000
27	A	349	SER	0	0.064	0.024	35.765	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	350	LYS	1	1.048	0.995	28.780	0.239	0.239	0.000	0.000	0.000	0.000
29	A	351	ASN	0	0.040	0.033	33.995	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	352	VAL	0	0.056	0.029	36.671	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	353	ARG	1	0.826	0.931	31.416	0.250	0.250	0.000	0.000	0.000	0.000
32	A	354	MET	0	0.018	0.009	29.903	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	355	MET	0	0.020	0.007	33.476	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	356	GLN	0	0.043	0.021	34.456	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	357	ALA	0	0.020	0.013	30.374	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	358	GLN	0	0.005	-0.013	32.248	0.001	0.001	0.000	0.000	0.000	0.000
37	A	359	GLU	-1	-0.873	-0.925	34.543	-0.182	-0.182	0.000	0.000	0.000	0.000
38	A	360	ALA	0	-0.014	-0.015	31.876	0.002	0.002	0.000	0.000	0.000	0.000
39	A	361	VAL	0	0.042	0.018	30.625	0.001	0.001	0.000	0.000	0.000	0.000
40	A	362	SER	0	-0.039	-0.007	33.082	0.005	0.005	0.000	0.000	0.000	0.000
41	A	363	ARG	1	0.820	0.891	35.877	0.205	0.205	0.000	0.000	0.000	0.000
42	A	364	ILE	0	-0.003	0.014	30.917	0.004	0.004	0.000	0.000	0.000	0.000
43	A	365	LYS	1	0.954	0.967	33.219	0.199	0.199	0.000	0.000	0.000	0.000
44	A	366	MET	0	-0.041	-0.014	35.767	0.006	0.006	0.000	0.000	0.000	0.000
45	A	367	ALA	0	-0.045	-0.014	36.486	0.007	0.007	0.000	0.000	0.000	0.000
46	A	368	GLN	0	-0.028	-0.004	31.777	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	385	MET	0	-0.047	-0.039	27.460	0.007	0.007	0.000	0.000	0.000	0.000
48	A	386	THR	0	-0.040	-0.030	23.068	0.006	0.006	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.913	-0.916	20.693	-0.365	-0.365	0.000	0.000	0.000	0.000
50	A	388	VAL	0	-0.088	-0.070	18.850	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	389	ASP	-1	-0.780	-0.878	13.341	-0.946	-0.946	0.000	0.000	0.000	0.000
52	A	390	LEU	0	-0.082	-0.047	15.358	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	391	PHE	0	0.033	0.017	9.366	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	392	ILE	0	-0.017	-0.014	12.639	0.236	0.236	0.000	0.000	0.000	0.000
55	A	393	LEU	0	0.045	0.029	11.828	-0.157	-0.157	0.000	0.000	0.000	0.000
56	A	394	THR	0	-0.034	-0.012	13.696	0.186	0.186	0.000	0.000	0.000	0.000
57	A	395	GLN	0	0.029	-0.004	15.867	0.148	0.148	0.000	0.000	0.000	0.000
58	A	396	ARG	1	0.845	0.920	14.659	1.252	1.252	0.000	0.000	0.000	0.000
59	A	397	ILE	0	0.027	0.028	16.343	-0.074	-0.074	0.000	0.000	0.000	0.000
60	A	398	LYS	1	0.819	0.912	15.092	1.106	1.106	0.000	0.000	0.000	0.000
61	A	399	VAL	0	-0.008	0.007	16.748	-0.055	-0.055	0.000	0.000	0.000	0.000
62	A	400	LEU	0	0.005	0.002	13.349	0.051	0.051	0.000	0.000	0.000	0.000
63	A	401	ASN	0	0.049	0.009	17.508	0.032	0.032	0.000	0.000	0.000	0.000
64	A	402	ALA	0	0.032	0.023	16.540	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.938	-0.955	16.929	-0.411	-0.411	0.000	0.000	0.000	0.000
66	A	404	THR	0	-0.008	-0.041	19.279	0.003	0.003	0.000	0.000	0.000	0.000
67	A	405	GLN	0	-0.112	-0.065	13.842	-0.138	-0.138	0.000	0.000	0.000	0.000
68	A	406	GLU	-1	-0.864	-0.887	16.740	-0.576	-0.576	0.000	0.000	0.000	0.000
69	A	407	THR	0	-0.100	-0.070	17.947	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	408	MET	0	0.014	0.028	19.782	0.052	0.052	0.000	0.000	0.000	0.000
71	A	409	MET	0	-0.058	-0.032	21.225	0.040	0.040	0.000	0.000	0.000	0.000
72	A	410	ASP	-1	-0.817	-0.910	19.163	-0.946	-0.946	0.000	0.000	0.000	0.000
73	A	411	HIS	0	-0.001	0.007	20.596	0.083	0.083	0.000	0.000	0.000	0.000
74	A	412	PRO	0	-0.003	-0.006	20.695	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	413	LEU	0	0.072	0.058	19.323	0.079	0.079	0.000	0.000	0.000	0.000
76	A	414	ARG	1	0.969	0.984	21.696	0.530	0.530	0.000	0.000	0.000	0.000
77	A	415	THR	0	-0.142	-0.102	24.646	0.055	0.055	0.000	0.000	0.000	0.000
78	A	416	ILE	0	0.027	0.029	22.560	0.040	0.040	0.000	0.000	0.000	0.000
79	A	417	SER	0	-0.088	-0.037	25.785	0.018	0.018	0.000	0.000	0.000	0.000
80	A	418	TYR	0	-0.020	-0.030	27.144	0.018	0.018	0.000	0.000	0.000	0.000
81	A	419	ILE	0	0.045	0.029	21.622	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	420	ALA	0	-0.049	-0.025	25.130	0.030	0.030	0.000	0.000	0.000	0.000
83	A	421	ASP	-1	-0.819	-0.886	23.534	-0.322	-0.322	0.000	0.000	0.000	0.000
84	A	422	ILE	0	-0.053	-0.036	25.642	0.032	0.032	0.000	0.000	0.000	0.000
85	A	423	GLY	0	0.017	0.014	27.740	0.004	0.004	0.000	0.000	0.000	0.000
86	A	424	ASN	0	0.070	0.039	24.959	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	425	ILE	0	-0.035	-0.013	25.105	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	426	VAL	0	0.072	0.056	21.258	0.003	0.003	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.053	-0.026	24.554	0.010	0.010	0.000	0.000	0.000	0.000
90	A	428	LEU	0	0.045	0.040	21.580	0.003	0.003	0.000	0.000	0.000	0.000
91	A	429	MET	0	-0.033	-0.025	25.097	0.027	0.027	0.000	0.000	0.000	0.000
92	A	430	ALA	0	0.048	0.025	26.488	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	431	ARG	1	0.938	0.978	28.144	0.358	0.358	0.000	0.000	0.000	0.000
94	A	451	ASP	-1	-0.842	-0.912	37.657	-0.166	-0.166	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.028	0.025	35.753	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	453	LYS	1	0.939	0.948	30.080	0.304	0.304	0.000	0.000	0.000	0.000
97	A	454	ARG	1	0.969	0.993	36.646	0.187	0.187	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.046	-0.022	34.080	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	456	TYR	0	0.039	-0.004	38.286	0.000	0.000	0.000	0.000	0.000	0.000
100	A	457	LYS	1	0.887	0.964	36.124	0.205	0.205	0.000	0.000	0.000	0.000
101	A	458	MET	0	-0.020	-0.002	32.390	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	459	ILE	0	0.023	-0.009	29.771	0.019	0.019	0.000	0.000	0.000	0.000
103	A	460	CYS	0	-0.062	-0.020	29.251	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.069	0.057	25.148	0.016	0.016	0.000	0.000	0.000	0.000
105	A	462	VAL	0	0.013	0.011	26.300	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	463	PHE	0	0.027	0.004	22.288	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	464	GLU	-1	-0.919	-0.949	24.080	-0.260	-0.260	0.000	0.000	0.000	0.000
108	A	465	SER	0	-0.009	-0.049	19.003	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	466	GLU	-1	-0.897	-0.940	20.445	-0.213	-0.213	0.000	0.000	0.000	0.000
110	A	467	ASP	-1	-0.886	-0.935	16.425	-0.514	-0.514	0.000	0.000	0.000	0.000
111	A	468	ALA	0	-0.062	-0.037	18.466	-0.059	-0.059	0.000	0.000	0.000	0.000
112	A	469	GLN	0	-0.043	-0.057	20.870	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	470	LEU	0	0.061	0.027	13.541	0.000	0.000	0.000	0.000	0.000	0.000
114	A	471	ILE	0	0.028	0.042	16.280	-0.077	-0.077	0.000	0.000	0.000	0.000
115	A	472	ALA	0	-0.009	-0.011	17.287	-0.046	-0.046	0.000	0.000	0.000	0.000
116	A	473	GLN	0	-0.040	-0.011	17.694	0.006	0.006	0.000	0.000	0.000	0.000
117	A	474	SER	0	0.024	-0.001	14.005	-0.024	-0.024	0.000	0.000	0.000	0.000
118	A	475	ILE	0	-0.002	-0.004	15.825	-0.048	-0.048	0.000	0.000	0.000	0.000
119	A	476	GLY	0	-0.008	0.012	18.137	0.035	0.035	0.000	0.000	0.000	0.000
120	A	477	GLN	0	0.004	-0.010	14.002	-0.040	-0.040	0.000	0.000	0.000	0.000
121	A	478	ALA	0	0.011	0.009	16.302	0.026	0.026	0.000	0.000	0.000	0.000
122	A	479	PHE	0	-0.060	-0.043	17.428	0.051	0.051	0.000	0.000	0.000	0.000
123	A	480	SER	0	-0.046	-0.022	19.141	0.061	0.061	0.000	0.000	0.000	0.000
124	A	481	VAL	0	0.023	0.008	15.053	0.059	0.059	0.000	0.000	0.000	0.000
125	A	482	ALA	0	0.053	0.034	18.484	0.048	0.048	0.000	0.000	0.000	0.000
126	A	483	TYR	0	-0.044	-0.016	20.326	0.047	0.047	0.000	0.000	0.000	0.000
127	A	484	GLN	0	-0.005	-0.011	21.186	0.043	0.043	0.000	0.000	0.000	0.000
128	A	485	GLU	-1	-0.979	-0.991	18.786	-0.543	-0.543	0.000	0.000	0.000	0.000
129	A	486	PHE	0	-0.049	-0.028	21.872	0.027	0.027	0.000	0.000	0.000	0.000
130	A	487	LEU	0	-0.054	-0.026	25.133	0.022	0.022	0.000	0.000	0.000	0.000
131	A	488	ARG	1	0.969	0.984	19.172	0.325	0.325	0.000	0.000	0.000	0.000
132	A	489	ALA	0	-0.024	0.004	24.373	0.017	0.017	0.000	0.000	0.000	0.000
133	A	490	ASN	0	-0.067	-0.031	26.082	0.031	0.031	0.000	0.000	0.000	0.000
134	A	491	GLY	0	0.027	0.027	29.722	0.009	0.009	0.000	0.000	0.000	0.000
135	A	492	ILE	0	-0.039	-0.018	30.391	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)