FMO DATABASE

FMODB ID: MNQ3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-778229.796472
FMO2-HF: Nuclear repulsion	735055.22833
FMO2-HF: Total energy	-43174.568142
FMO2-MP2: Total energy	-43294.46291

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.
1.749	2.992	-0.011	-0.428	-0.805	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 : -0.024 / q_NPA : -0.031

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	0.013	0.009	3.732	0.994	2.237	-0.011	-0.428	-0.805	0.001
4	A	25	ASN	0	0.009	-0.016	6.328	0.789	0.789	0.000	0.000	0.000	0.000
5	A	26	ALA	0	0.032	0.014	9.551	0.104	0.104	0.000	0.000	0.000	0.000
6	A	27	GLY	0	0.025	0.020	11.658	0.123	0.123	0.000	0.000	0.000	0.000
7	A	28	LEU	0	-0.064	-0.028	9.665	0.106	0.106	0.000	0.000	0.000	0.000
8	A	29	LEU	0	-0.057	-0.010	12.737	0.067	0.067	0.000	0.000	0.000	0.000
9	A	30	ALA	0	-0.006	0.000	15.524	0.013	0.013	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.825	-0.910	19.244	-0.273	-0.273	0.000	0.000	0.000	0.000
11	A	32	PRO	0	0.007	0.014	20.858	0.023	0.023	0.000	0.000	0.000	0.000
12	A	33	GLN	0	-0.034	-0.032	23.611	0.024	0.024	0.000	0.000	0.000	0.000
13	A	34	ILE	0	0.032	0.016	27.196	0.002	0.002	0.000	0.000	0.000	0.000
14	A	35	ALA	0	-0.001	-0.001	30.432	0.002	0.002	0.000	0.000	0.000	0.000
15	A	36	MET	0	-0.003	0.023	33.245	0.003	0.003	0.000	0.000	0.000	0.000
16	A	37	PHE	0	0.047	0.021	36.848	0.002	0.002	0.000	0.000	0.000	0.000
17	A	38	CYS	0	-0.038	-0.012	39.247	0.000	0.000	0.000	0.000	0.000	0.000
18	A	39	GLY	0	0.036	0.026	42.940	0.002	0.002	0.000	0.000	0.000	0.000
19	A	40	ARG	1	0.792	0.891	39.125	0.064	0.064	0.000	0.000	0.000	0.000
20	A	41	LEU	0	-0.055	0.004	36.420	0.000	0.000	0.000	0.000	0.000	0.000
21	A	42	ASN	0	0.010	-0.006	34.313	0.002	0.002	0.000	0.000	0.000	0.000
22	A	43	MET	0	-0.067	-0.016	31.257	0.002	0.002	0.000	0.000	0.000	0.000
23	A	44	HIS	0	0.002	-0.003	25.902	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	45	MET	0	-0.017	0.029	22.600	0.003	0.003	0.000	0.000	0.000	0.000
25	A	46	ASN	0	0.009	0.011	21.102	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.033	0.004	17.140	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	48	GLN	0	0.015	0.019	15.563	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	49	ASN	0	-0.002	-0.012	16.916	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	50	GLY	0	0.042	0.021	19.413	0.017	0.017	0.000	0.000	0.000	0.000
30	A	51	LYS	1	0.884	0.946	21.314	0.165	0.165	0.000	0.000	0.000	0.000
31	A	52	TRP	0	0.037	0.010	24.696	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	53	ASP	-1	-0.826	-0.897	25.749	-0.134	-0.134	0.000	0.000	0.000	0.000
33	A	54	SER	0	-0.015	-0.038	28.813	0.003	0.003	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.654	-0.798	30.946	-0.101	-0.101	0.000	0.000	0.000	0.000
35	A	56	PRO	0	0.082	0.046	29.006	0.009	0.009	0.000	0.000	0.000	0.000
36	A	57	SER	0	-0.010	-0.003	31.528	0.008	0.008	0.000	0.000	0.000	0.000
37	A	58	GLY	0	-0.007	-0.002	34.944	0.006	0.006	0.000	0.000	0.000	0.000
38	A	59	THR	0	-0.121	-0.093	36.761	0.007	0.007	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.815	0.906	36.032	0.093	0.093	0.000	0.000	0.000	0.000
40	A	61	THR	0	-0.019	-0.031	37.701	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	63	ILE	0	-0.007	-0.014	36.580	0.003	0.003	0.000	0.000	0.000	0.000
42	A	64	ASP	-1	-0.897	-0.949	40.350	-0.071	-0.071	0.000	0.000	0.000	0.000
43	A	65	THR	0	0.032	0.025	41.255	0.000	0.000	0.000	0.000	0.000	0.000
44	A	66	LYS	1	0.921	0.957	35.290	0.109	0.109	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.876	-0.951	36.989	-0.093	-0.093	0.000	0.000	0.000	0.000
46	A	68	GLY	0	0.044	0.019	37.219	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	69	ILE	0	-0.012	-0.011	33.697	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	70	LEU	0	-0.013	0.002	31.412	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	71	GLN	0	0.006	0.004	32.306	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	72	TYR	0	-0.032	-0.051	32.556	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	73	CYS	0	-0.067	-0.034	26.033	0.008	0.008	0.000	0.000	0.000	0.000
52	A	74	GLN	0	-0.028	-0.025	28.289	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	75	GLU	-1	-0.846	-0.892	28.912	-0.100	-0.100	0.000	0.000	0.000	0.000
54	A	76	VAL	0	-0.071	-0.037	26.680	0.001	0.001	0.000	0.000	0.000	0.000
55	A	77	TYR	0	-0.030	-0.049	23.264	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	78	PRO	0	0.023	0.018	25.165	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	79	GLU	-1	-0.960	-0.978	21.201	-0.199	-0.199	0.000	0.000	0.000	0.000
58	A	80	LEU	0	-0.040	-0.025	19.525	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	81	GLN	0	0.004	0.009	22.493	0.002	0.002	0.000	0.000	0.000	0.000
60	A	82	ILE	0	-0.012	0.002	24.330	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	83	THR	0	0.007	0.004	26.994	0.016	0.016	0.000	0.000	0.000	0.000
62	A	84	ASN	0	0.031	0.019	29.484	0.020	0.020	0.000	0.000	0.000	0.000
63	A	85	VAL	0	0.003	0.004	29.868	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	86	VAL	0	-0.023	-0.012	30.266	0.008	0.008	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.851	-0.887	31.755	-0.106	-0.106	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.034	-0.026	29.896	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	89	ASN	0	0.006	-0.006	30.143	0.009	0.009	0.000	0.000	0.000	0.000
68	A	90	GLN	0	-0.013	-0.002	30.398	0.014	0.014	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.016	0.022	32.494	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	92	VAL	0	0.001	-0.004	29.551	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	93	THR	0	-0.005	-0.012	32.619	0.009	0.009	0.000	0.000	0.000	0.000
72	A	94	ILE	0	-0.012	0.009	31.151	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	95	GLN	0	0.002	-0.008	32.598	0.008	0.008	0.000	0.000	0.000	0.000
74	A	96	ASN	0	0.006	-0.014	31.370	0.001	0.001	0.000	0.000	0.000	0.000
75	A	97	TRP	0	0.053	0.039	34.895	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	98	CYS	0	-0.012	0.018	36.058	0.005	0.005	0.000	0.000	0.000	0.000
77	A	99	LYS	1	0.924	0.951	38.388	0.048	0.048	0.000	0.000	0.000	0.000
78	A	100	ARG	1	1.038	1.001	39.824	0.056	0.056	0.000	0.000	0.000	0.000
79	A	101	GLY	0	-0.048	-0.029	39.265	0.004	0.004	0.000	0.000	0.000	0.000
80	A	102	ARG	1	0.886	0.931	33.135	0.088	0.088	0.000	0.000	0.000	0.000
81	A	103	LYS	1	0.972	1.002	37.300	0.051	0.051	0.000	0.000	0.000	0.000
82	A	104	GLN	0	-0.008	-0.019	40.233	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.944	0.974	38.551	0.049	0.049	0.000	0.000	0.000	0.000
84	A	107	THR	0	0.067	0.029	35.633	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	108	HIS	0	-0.055	-0.029	37.284	0.001	0.001	0.000	0.000	0.000	0.000
86	A	109	PRO	0	0.007	0.013	36.616	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	110	HIS	0	-0.022	-0.007	37.127	0.008	0.008	0.000	0.000	0.000	0.000
88	A	111	PHE	0	-0.006	0.002	36.377	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.012	-0.007	34.725	0.005	0.005	0.000	0.000	0.000	0.000
90	A	113	ILE	0	0.054	0.024	34.798	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	114	PRO	0	-0.041	0.001	30.503	0.003	0.003	0.000	0.000	0.000	0.000
92	A	115	TYR	0	-0.007	-0.039	31.881	0.000	0.000	0.000	0.000	0.000	0.000
93	A	116	ARG	1	0.857	0.908	24.381	0.212	0.212	0.000	0.000	0.000	0.000
94	A	118	LEU	0	-0.020	-0.017	25.421	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	119	VAL	0	0.041	0.012	21.062	0.014	0.014	0.000	0.000	0.000	0.000
96	A	120	GLY	0	-0.037	-0.004	24.284	0.003	0.003	0.000	0.000	0.000	0.000
97	A	121	GLU	-1	-0.960	-0.981	22.970	-0.253	-0.253	0.000	0.000	0.000	0.000
98	A	122	PHE	0	-0.041	-0.027	25.026	0.015	0.015	0.000	0.000	0.000	0.000
99	A	123	VAL	0	0.043	0.021	26.302	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	124	SER	0	-0.063	-0.032	28.834	0.008	0.008	0.000	0.000	0.000	0.000
101	A	125	ASP	-1	-0.897	-0.935	31.621	-0.102	-0.102	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.057	-0.033	35.271	0.003	0.003	0.000	0.000	0.000	0.000

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