FMO DATABASE

FMODB ID: 981G2

Calculation Name: 4PQD-A-Xray372

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4PQD

Chain ID: A

ChEMBL ID: CHEMBL2487

UniProt ID: P05067

Base Structure: X-ray

Registration Date: 2023-09-23

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-778231.043188
FMO2-HF: Nuclear repulsion	735056.804497
FMO2-HF: Total energy	-43174.238691
FMO2-MP2: Total energy	-43294.147635

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:22:THR)

Summations of interaction energy for fragment #1(A:22:THR)

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.
2.036	3.255	-0.009	-0.356	-0.853	0.001

Interaction energy analysis for fragmet #1(A:22:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.028

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	A	24	GLY	0	0.008	0.007	3.408	1.176	2.395	-0.009	-0.356	-0.853	0.001
4	A	25	ASN	0	0.009	-0.013	5.811	0.832	0.832	0.000	0.000	0.000	0.000
5	A	26	ALA	0	0.036	0.013	9.457	0.094	0.094	0.000	0.000	0.000	0.000
6	A	27	GLY	0	0.025	0.020	11.647	0.116	0.116	0.000	0.000	0.000	0.000
7	A	28	LEU	0	-0.068	-0.030	9.638	0.096	0.096	0.000	0.000	0.000	0.000
8	A	29	LEU	0	-0.053	-0.007	12.791	0.059	0.059	0.000	0.000	0.000	0.000
9	A	30	ALA	0	-0.008	-0.003	15.618	0.016	0.016	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.932	-0.980	19.346	-0.248	-0.248	0.000	0.000	0.000	0.000
11	A	32	PRO	0	0.003	0.013	20.986	0.020	0.020	0.000	0.000	0.000	0.000
12	A	33	GLN	0	-0.021	-0.026	23.726	0.025	0.025	0.000	0.000	0.000	0.000
13	A	34	ILE	0	0.025	0.014	27.310	0.001	0.001	0.000	0.000	0.000	0.000
14	A	35	ALA	0	0.004	-0.003	30.531	0.003	0.003	0.000	0.000	0.000	0.000
15	A	36	MET	0	-0.003	0.018	33.338	0.003	0.003	0.000	0.000	0.000	0.000
16	A	37	PHE	0	0.045	0.022	36.935	0.002	0.002	0.000	0.000	0.000	0.000
17	A	38	CYS	0	-0.040	-0.024	39.333	0.000	0.000	0.000	0.000	0.000	0.000
18	A	39	GLY	0	0.019	0.016	43.015	0.002	0.002	0.000	0.000	0.000	0.000
19	A	40	ARG	1	0.814	0.901	39.215	0.060	0.060	0.000	0.000	0.000	0.000
20	A	41	LEU	0	-0.065	-0.013	36.503	0.000	0.000	0.000	0.000	0.000	0.000
21	A	42	ASN	0	0.026	0.007	34.317	0.002	0.002	0.000	0.000	0.000	0.000
22	A	43	MET	0	-0.079	-0.024	31.246	0.000	0.000	0.000	0.000	0.000	0.000
23	A	44	HIS	0	0.008	0.003	25.757	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	45	MET	0	-0.020	0.028	22.669	0.001	0.001	0.000	0.000	0.000	0.000
25	A	46	ASN	0	0.008	0.019	21.019	-0.035	-0.035	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.032	0.005	17.196	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	48	GLN	0	0.022	0.025	15.504	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	49	ASN	0	-0.008	-0.018	16.913	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	50	GLY	0	0.041	0.021	19.401	0.015	0.015	0.000	0.000	0.000	0.000
30	A	51	LYS	1	0.883	0.944	21.305	0.164	0.164	0.000	0.000	0.000	0.000
31	A	52	TRP	0	0.026	0.006	24.686	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	53	ASP	-1	-0.826	-0.898	25.865	-0.138	-0.138	0.000	0.000	0.000	0.000
33	A	54	SER	0	-0.010	-0.039	28.836	0.005	0.005	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.676	-0.814	30.969	-0.096	-0.096	0.000	0.000	0.000	0.000
35	A	56	PRO	0	0.078	0.042	29.081	0.008	0.008	0.000	0.000	0.000	0.000
36	A	57	SER	0	0.013	0.016	31.544	0.007	0.007	0.000	0.000	0.000	0.000
37	A	58	GLY	0	-0.015	-0.006	34.959	0.006	0.006	0.000	0.000	0.000	0.000
38	A	59	THR	0	-0.129	-0.096	36.771	0.007	0.007	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.937	0.990	36.086	0.079	0.079	0.000	0.000	0.000	0.000
40	A	61	THR	0	-0.013	-0.006	37.754	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	63	ILE	0	-0.015	-0.013	36.626	0.003	0.003	0.000	0.000	0.000	0.000
42	A	64	ASP	-1	-0.914	-0.959	40.462	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	65	THR	0	0.041	0.034	41.374	0.000	0.000	0.000	0.000	0.000	0.000
44	A	66	LYS	1	0.974	0.983	35.678	0.087	0.087	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.891	-0.955	37.127	-0.076	-0.076	0.000	0.000	0.000	0.000
46	A	68	GLY	0	0.041	0.017	37.345	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	69	ILE	0	-0.013	-0.011	33.752	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	70	LEU	0	-0.013	0.000	31.550	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	71	GLN	0	0.001	0.004	32.425	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	72	TYR	0	-0.035	-0.056	32.376	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	73	CYS	0	-0.063	-0.033	26.167	0.007	0.007	0.000	0.000	0.000	0.000
52	A	74	GLN	0	-0.032	-0.028	28.388	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	75	GLU	-1	-0.933	-0.958	28.997	-0.094	-0.094	0.000	0.000	0.000	0.000
54	A	76	VAL	0	-0.066	-0.039	26.722	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	77	TYR	0	-0.038	-0.051	23.267	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	78	PRO	0	0.021	0.016	25.311	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	79	GLU	-1	-0.963	-0.981	21.060	-0.180	-0.180	0.000	0.000	0.000	0.000
58	A	80	LEU	0	-0.033	-0.018	19.607	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	81	GLN	0	-0.019	0.001	22.610	0.002	0.002	0.000	0.000	0.000	0.000
60	A	82	ILE	0	-0.007	0.003	24.594	0.000	0.000	0.000	0.000	0.000	0.000
61	A	83	THR	0	-0.002	-0.004	27.136	0.014	0.014	0.000	0.000	0.000	0.000
62	A	84	ASN	0	0.018	0.005	29.577	0.015	0.015	0.000	0.000	0.000	0.000
63	A	85	VAL	0	-0.003	0.006	29.975	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	86	VAL	0	-0.036	-0.021	30.145	0.007	0.007	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.917	-0.943	31.763	-0.092	-0.092	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.038	-0.027	29.873	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	89	ASN	0	0.005	-0.006	29.123	0.011	0.011	0.000	0.000	0.000	0.000
68	A	90	GLN	0	-0.015	-0.002	30.192	0.011	0.011	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.016	0.023	32.533	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	92	VAL	0	0.008	0.000	29.656	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	93	THR	0	0.000	-0.013	32.602	0.008	0.008	0.000	0.000	0.000	0.000
72	A	94	ILE	0	-0.014	0.008	31.119	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	95	GLN	0	0.007	-0.010	32.590	0.008	0.008	0.000	0.000	0.000	0.000
74	A	96	ASN	0	0.009	-0.013	31.350	0.001	0.001	0.000	0.000	0.000	0.000
75	A	97	TRP	0	0.065	0.047	34.883	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	98	CYS	0	-0.005	0.023	36.130	0.004	0.004	0.000	0.000	0.000	0.000
77	A	99	LYS	1	0.918	0.955	38.402	0.048	0.048	0.000	0.000	0.000	0.000
78	A	100	ARG	1	1.044	1.004	39.831	0.053	0.053	0.000	0.000	0.000	0.000
79	A	101	GLY	0	-0.052	-0.032	39.255	0.003	0.003	0.000	0.000	0.000	0.000
80	A	102	ARG	1	0.907	0.950	33.186	0.088	0.088	0.000	0.000	0.000	0.000
81	A	103	LYS	1	0.976	1.004	37.293	0.051	0.051	0.000	0.000	0.000	0.000
82	A	104	GLN	0	-0.023	-0.035	40.216	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.940	0.971	38.539	0.050	0.050	0.000	0.000	0.000	0.000
84	A	107	THR	0	0.062	0.030	35.644	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	108	HIS	0	-0.038	-0.017	37.279	0.001	0.001	0.000	0.000	0.000	0.000
86	A	109	PRO	0	0.006	0.010	36.578	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	110	HIS	0	-0.042	-0.013	37.113	0.007	0.007	0.000	0.000	0.000	0.000
88	A	111	PHE	0	-0.009	0.000	36.376	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.007	-0.004	34.819	0.004	0.004	0.000	0.000	0.000	0.000
90	A	113	ILE	0	0.053	0.020	34.832	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	114	PRO	0	-0.036	0.006	30.596	0.002	0.002	0.000	0.000	0.000	0.000
92	A	115	TYR	0	0.059	0.015	32.016	0.001	0.001	0.000	0.000	0.000	0.000
93	A	116	ARG	1	0.958	0.976	24.682	0.169	0.169	0.000	0.000	0.000	0.000
94	A	118	LEU	0	-0.030	-0.023	25.571	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	119	VAL	0	0.049	0.015	21.151	0.012	0.012	0.000	0.000	0.000	0.000
96	A	120	GLY	0	-0.037	-0.002	24.310	0.004	0.004	0.000	0.000	0.000	0.000
97	A	121	GLU	-1	-0.945	-0.974	23.135	-0.183	-0.183	0.000	0.000	0.000	0.000
98	A	122	PHE	0	-0.044	-0.030	24.699	0.012	0.012	0.000	0.000	0.000	0.000
99	A	123	VAL	0	0.040	0.022	26.053	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	124	SER	0	-0.077	-0.041	28.597	0.005	0.005	0.000	0.000	0.000	0.000
101	A	125	ASP	-1	-0.877	-0.923	31.423	-0.073	-0.073	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.063	-0.038	35.066	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:THR)