FMO DATABASE

FMODB ID: 761GK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-778577.867586
FMO2-HF: Nuclear repulsion	735403.174652
FMO2-HF: Total energy	-43174.692934
FMO2-MP2: Total energy	-43294.589994

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.
2.309	3.316	-0.009	-0.358	-0.641	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 : -0.019 / q_NPA : -0.030

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	0.012	0.008	3.853	1.724	2.731	-0.009	-0.358	-0.641	0.001
4	A	25	ASN	0	-0.004	-0.019	6.160	0.695	0.695	0.000	0.000	0.000	0.000
5	A	26	ALA	0	0.041	0.012	9.712	0.121	0.121	0.000	0.000	0.000	0.000
6	A	27	GLY	0	0.023	0.018	12.177	0.115	0.115	0.000	0.000	0.000	0.000
7	A	28	LEU	0	-0.081	-0.038	9.518	0.113	0.113	0.000	0.000	0.000	0.000
8	A	29	LEU	0	-0.036	-0.003	13.056	0.056	0.056	0.000	0.000	0.000	0.000
9	A	30	ALA	0	-0.022	-0.006	16.007	0.008	0.008	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.805	-0.884	19.729	-0.276	-0.276	0.000	0.000	0.000	0.000
11	A	32	PRO	0	0.025	0.026	21.111	0.025	0.025	0.000	0.000	0.000	0.000
12	A	33	GLN	0	-0.028	-0.032	23.891	0.023	0.023	0.000	0.000	0.000	0.000
13	A	34	ILE	0	0.020	0.008	27.525	0.004	0.004	0.000	0.000	0.000	0.000
14	A	35	ALA	0	0.004	0.001	30.793	0.002	0.002	0.000	0.000	0.000	0.000
15	A	36	MET	0	-0.009	0.012	33.682	0.003	0.003	0.000	0.000	0.000	0.000
16	A	37	PHE	0	0.038	0.016	37.266	0.002	0.002	0.000	0.000	0.000	0.000
17	A	38	CYS	0	-0.025	-0.014	39.647	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	39	GLY	0	0.044	0.030	43.533	0.003	0.003	0.000	0.000	0.000	0.000
19	A	40	ARG	1	0.777	0.896	39.267	0.061	0.061	0.000	0.000	0.000	0.000
20	A	41	LEU	0	-0.047	0.003	36.877	0.000	0.000	0.000	0.000	0.000	0.000
21	A	42	ASN	0	0.015	0.004	34.642	0.003	0.003	0.000	0.000	0.000	0.000
22	A	43	MET	0	-0.067	-0.008	31.651	0.005	0.005	0.000	0.000	0.000	0.000
23	A	44	HIS	0	-0.011	-0.016	26.292	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	45	MET	0	0.010	0.034	22.973	0.006	0.006	0.000	0.000	0.000	0.000
25	A	46	ASN	0	-0.002	0.002	21.596	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.041	0.007	17.614	0.000	0.000	0.000	0.000	0.000	0.000
27	A	48	GLN	0	0.023	0.025	15.993	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	49	ASN	0	0.007	-0.002	16.975	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	50	GLY	0	0.052	0.039	19.399	0.023	0.023	0.000	0.000	0.000	0.000
30	A	51	LYS	1	0.807	0.892	21.334	0.170	0.170	0.000	0.000	0.000	0.000
31	A	52	TRP	0	0.055	0.024	24.813	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	53	ASP	-1	-0.806	-0.884	25.816	-0.116	-0.116	0.000	0.000	0.000	0.000
33	A	54	SER	0	-0.034	-0.044	28.859	0.000	0.000	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.671	-0.807	31.505	-0.099	-0.099	0.000	0.000	0.000	0.000
35	A	56	PRO	0	0.082	0.053	29.269	0.010	0.010	0.000	0.000	0.000	0.000
36	A	57	SER	0	-0.014	-0.007	31.793	0.008	0.008	0.000	0.000	0.000	0.000
37	A	58	GLY	0	0.005	0.007	35.263	0.007	0.007	0.000	0.000	0.000	0.000
38	A	59	THR	0	-0.130	-0.096	37.192	0.008	0.008	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.811	0.897	36.540	0.095	0.095	0.000	0.000	0.000	0.000
40	A	61	THR	0	-0.014	-0.033	38.344	0.000	0.000	0.000	0.000	0.000	0.000
41	A	63	ILE	0	0.013	0.004	37.209	0.003	0.003	0.000	0.000	0.000	0.000
42	A	64	ASP	-1	-0.870	-0.931	40.976	-0.075	-0.075	0.000	0.000	0.000	0.000
43	A	65	THR	0	0.009	0.003	41.792	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	66	LYS	1	0.905	0.959	35.672	0.118	0.118	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.858	-0.942	36.977	-0.104	-0.104	0.000	0.000	0.000	0.000
46	A	68	GLY	0	0.060	0.030	37.396	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	69	ILE	0	-0.012	-0.013	34.128	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	70	LEU	0	-0.024	-0.004	31.641	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	71	GLN	0	0.015	0.012	32.581	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	72	TYR	0	-0.042	-0.055	33.000	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	73	CYS	0	-0.064	-0.036	26.307	0.007	0.007	0.000	0.000	0.000	0.000
52	A	74	GLN	0	-0.028	-0.027	28.624	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	75	GLU	-1	-0.841	-0.893	29.413	-0.103	-0.103	0.000	0.000	0.000	0.000
54	A	76	VAL	0	-0.074	-0.036	27.010	0.001	0.001	0.000	0.000	0.000	0.000
55	A	77	TYR	0	-0.033	-0.050	23.643	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	78	PRO	0	0.020	0.019	25.473	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	79	GLU	-1	-0.930	-0.967	21.347	-0.225	-0.225	0.000	0.000	0.000	0.000
58	A	80	LEU	0	-0.068	-0.030	19.621	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	81	GLN	0	0.018	-0.002	22.449	0.002	0.002	0.000	0.000	0.000	0.000
60	A	82	ILE	0	-0.028	0.001	24.585	0.003	0.003	0.000	0.000	0.000	0.000
61	A	83	THR	0	0.010	0.006	27.188	0.016	0.016	0.000	0.000	0.000	0.000
62	A	84	ASN	0	0.018	0.013	29.796	0.021	0.021	0.000	0.000	0.000	0.000
63	A	85	VAL	0	-0.007	0.001	30.285	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	86	VAL	0	-0.016	-0.006	30.606	0.009	0.009	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.831	-0.881	31.957	-0.110	-0.110	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.008	-0.007	30.099	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	89	ASN	0	-0.019	-0.014	30.473	0.005	0.005	0.000	0.000	0.000	0.000
68	A	90	GLN	0	-0.027	-0.016	30.882	0.012	0.012	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.020	0.021	32.872	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	92	VAL	0	0.002	0.000	29.554	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	93	THR	0	-0.005	-0.014	32.576	0.009	0.009	0.000	0.000	0.000	0.000
72	A	94	ILE	0	-0.019	0.000	31.418	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	95	GLN	0	0.003	-0.004	32.773	0.007	0.007	0.000	0.000	0.000	0.000
74	A	96	ASN	0	0.017	-0.008	31.154	0.000	0.000	0.000	0.000	0.000	0.000
75	A	97	TRP	0	0.047	0.034	34.781	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	98	CYS	0	-0.016	0.017	36.171	0.006	0.006	0.000	0.000	0.000	0.000
77	A	99	LYS	1	0.934	0.956	38.491	0.044	0.044	0.000	0.000	0.000	0.000
78	A	100	ARG	1	1.019	0.996	40.131	0.056	0.056	0.000	0.000	0.000	0.000
79	A	101	GLY	0	-0.037	-0.025	39.468	0.004	0.004	0.000	0.000	0.000	0.000
80	A	102	ARG	1	0.878	0.922	33.330	0.085	0.085	0.000	0.000	0.000	0.000
81	A	103	LYS	1	0.966	0.998	37.472	0.048	0.048	0.000	0.000	0.000	0.000
82	A	104	GLN	0	0.001	-0.018	40.359	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.926	0.962	38.565	0.044	0.044	0.000	0.000	0.000	0.000
84	A	107	THR	0	0.067	0.031	35.408	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	108	HIS	0	-0.035	-0.018	37.298	0.002	0.002	0.000	0.000	0.000	0.000
86	A	109	PRO	0	-0.001	0.010	36.936	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	110	HIS	0	-0.017	-0.010	37.275	0.008	0.008	0.000	0.000	0.000	0.000
88	A	111	PHE	0	-0.007	0.000	36.510	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.004	0.002	35.146	0.004	0.004	0.000	0.000	0.000	0.000
90	A	113	ILE	0	0.048	0.028	35.051	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	114	PRO	0	-0.049	-0.004	30.764	0.003	0.003	0.000	0.000	0.000	0.000
92	A	115	TYR	0	-0.013	-0.051	32.249	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	116	ARG	1	0.843	0.887	24.689	0.223	0.223	0.000	0.000	0.000	0.000
94	A	118	LEU	0	-0.014	-0.011	25.736	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	119	VAL	0	0.039	0.012	21.050	0.014	0.014	0.000	0.000	0.000	0.000
96	A	120	GLY	0	-0.031	0.002	24.405	0.004	0.004	0.000	0.000	0.000	0.000
97	A	121	GLU	-1	-0.959	-0.980	22.878	-0.301	-0.301	0.000	0.000	0.000	0.000
98	A	122	PHE	0	-0.040	-0.025	24.892	0.019	0.019	0.000	0.000	0.000	0.000
99	A	123	VAL	0	0.057	0.031	26.184	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	124	SER	0	-0.084	-0.054	28.840	0.006	0.006	0.000	0.000	0.000	0.000
101	A	125	ASP	-1	-0.901	-0.932	31.940	-0.122	-0.122	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.051	-0.027	35.607	0.004	0.004	0.000	0.000	0.000	0.000

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