FMO DATABASE

FMODB ID: 2GVKR

Calculation Name: 1MWP-A-Xray549

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MWP

Chain ID: A

ChEMBL ID: CHEMBL2487

UniProt ID: P05067

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-725366.087236
FMO2-HF: Nuclear repulsion	685056.446548
FMO2-HF: Total energy	-40309.640688
FMO2-MP2: Total energy	-40421.375993

3D Structure Molmil

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:28:LEU)

Summations of interaction energy for fragment #1(A:28:LEU)

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.
0.47200000000001	2.175	-0.01	-0.81	-0.883	-0.002

Interaction energy analysis for fragmet #1(A:28:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.913

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	30	ALA	0	-0.011	0.002	3.715	0.641	2.344	-0.010	-0.810	-0.883	-0.002
4	A	31	GLU	-1	-0.809	-0.890	6.268	-22.373	-22.373	0.000	0.000	0.000	0.000
5	A	32	PRO	0	0.007	0.013	8.892	1.034	1.034	0.000	0.000	0.000	0.000
6	A	33	GLN	0	0.002	-0.012	11.370	2.437	2.437	0.000	0.000	0.000	0.000
7	A	34	ILE	0	0.026	0.008	14.942	-0.355	-0.355	0.000	0.000	0.000	0.000
8	A	35	ALA	0	0.009	0.004	18.279	0.205	0.205	0.000	0.000	0.000	0.000
9	A	36	MET	0	-0.002	0.020	20.424	0.193	0.193	0.000	0.000	0.000	0.000
10	A	37	PHE	0	0.040	0.016	24.212	0.140	0.140	0.000	0.000	0.000	0.000
11	A	38	CYS	0	-0.012	-0.007	27.114	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	39	GLY	0	0.026	0.017	30.655	0.145	0.145	0.000	0.000	0.000	0.000
13	A	40	ARG	1	0.737	0.856	27.160	10.833	10.833	0.000	0.000	0.000	0.000
14	A	41	LEU	0	-0.067	-0.007	25.781	0.176	0.176	0.000	0.000	0.000	0.000
15	A	42	ASN	0	0.030	0.010	22.629	0.004	0.004	0.000	0.000	0.000	0.000
16	A	43	MET	0	-0.064	-0.011	19.240	0.087	0.087	0.000	0.000	0.000	0.000
17	A	44	HIS	1	0.923	0.960	15.700	18.667	18.667	0.000	0.000	0.000	0.000
18	A	45	MET	0	0.010	0.038	10.411	-0.798	-0.798	0.000	0.000	0.000	0.000
19	A	46	ASN	0	-0.028	-0.008	10.947	-2.883	-2.883	0.000	0.000	0.000	0.000
20	A	47	VAL	0	0.043	0.007	7.919	-1.911	-1.911	0.000	0.000	0.000	0.000
21	A	48	GLN	0	0.013	0.014	6.462	-5.025	-5.025	0.000	0.000	0.000	0.000
22	A	49	ASN	0	0.050	0.026	6.458	-4.122	-4.122	0.000	0.000	0.000	0.000
23	A	50	GLY	0	0.034	0.023	8.608	1.202	1.202	0.000	0.000	0.000	0.000
24	A	51	LYS	1	0.822	0.905	9.428	28.956	28.956	0.000	0.000	0.000	0.000
25	A	52	TRP	0	0.059	0.021	13.286	-0.482	-0.482	0.000	0.000	0.000	0.000
26	A	53	ASP	-1	-0.823	-0.894	15.675	-19.335	-19.335	0.000	0.000	0.000	0.000
27	A	54	SER	0	0.008	-0.022	17.942	0.592	0.592	0.000	0.000	0.000	0.000
28	A	55	ASP	-1	-0.703	-0.844	21.057	-13.359	-13.359	0.000	0.000	0.000	0.000
29	A	56	PRO	0	-0.006	-0.001	19.891	0.434	0.434	0.000	0.000	0.000	0.000
30	A	57	SER	0	0.033	0.032	22.561	0.572	0.572	0.000	0.000	0.000	0.000
31	A	58	GLY	0	-0.004	-0.001	25.864	0.480	0.480	0.000	0.000	0.000	0.000
32	A	59	THR	0	-0.099	-0.079	27.678	0.678	0.678	0.000	0.000	0.000	0.000
33	A	60	LYS	1	0.846	0.921	25.877	11.999	11.999	0.000	0.000	0.000	0.000
34	A	61	THR	0	-0.020	-0.030	26.857	-0.215	-0.215	0.000	0.000	0.000	0.000
35	A	63	ILE	0	0.000	-0.006	25.785	0.279	0.279	0.000	0.000	0.000	0.000
36	A	64	ASP	-1	-0.867	-0.939	28.462	-9.735	-9.735	0.000	0.000	0.000	0.000
37	A	65	THR	0	0.007	0.021	30.278	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	66	LYS	1	0.912	0.958	24.600	11.682	11.682	0.000	0.000	0.000	0.000
39	A	67	GLU	-1	-0.862	-0.939	25.902	-10.922	-10.922	0.000	0.000	0.000	0.000
40	A	68	GLY	0	0.075	0.032	26.982	-0.328	-0.328	0.000	0.000	0.000	0.000
41	A	69	ILE	0	-0.014	-0.016	22.401	-0.457	-0.457	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.013	0.004	21.787	-0.711	-0.711	0.000	0.000	0.000	0.000
43	A	71	GLN	0	0.004	-0.002	22.689	-0.331	-0.331	0.000	0.000	0.000	0.000
44	A	72	TYR	0	-0.045	-0.053	21.395	-0.544	-0.544	0.000	0.000	0.000	0.000
45	A	73	CYS	0	-0.074	-0.044	15.197	0.367	0.367	0.000	0.000	0.000	0.000
46	A	74	GLN	0	-0.021	-0.023	18.771	-0.449	-0.449	0.000	0.000	0.000	0.000
47	A	75	GLU	-1	-0.846	-0.898	20.551	-12.577	-12.577	0.000	0.000	0.000	0.000
48	A	76	VAL	0	-0.101	-0.059	17.424	-0.127	-0.127	0.000	0.000	0.000	0.000
49	A	77	TYR	0	-0.057	-0.061	13.241	-1.217	-1.217	0.000	0.000	0.000	0.000
50	A	78	PRO	0	0.018	0.028	16.549	-0.225	-0.225	0.000	0.000	0.000	0.000
51	A	79	GLU	-1	-0.888	-0.952	15.155	-16.105	-16.105	0.000	0.000	0.000	0.000
52	A	80	LEU	0	-0.090	-0.044	11.441	-0.884	-0.884	0.000	0.000	0.000	0.000
53	A	81	GLN	0	0.035	0.014	14.715	0.306	0.306	0.000	0.000	0.000	0.000
54	A	82	ILE	0	-0.034	-0.004	14.936	0.191	0.191	0.000	0.000	0.000	0.000
55	A	83	THR	0	0.030	0.017	18.456	0.928	0.928	0.000	0.000	0.000	0.000
56	A	84	ASN	0	0.023	0.014	20.313	1.113	1.113	0.000	0.000	0.000	0.000
57	A	85	VAL	0	-0.004	-0.001	19.745	-0.761	-0.761	0.000	0.000	0.000	0.000
58	A	86	VAL	0	-0.019	-0.009	18.396	0.741	0.741	0.000	0.000	0.000	0.000
59	A	87	GLU	-1	-0.842	-0.906	19.304	-12.893	-12.893	0.000	0.000	0.000	0.000
60	A	88	ALA	0	-0.018	-0.021	16.298	-0.439	-0.439	0.000	0.000	0.000	0.000
61	A	89	ASN	0	-0.036	-0.026	16.826	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	90	GLN	0	0.026	0.013	16.836	0.781	0.781	0.000	0.000	0.000	0.000
63	A	91	PRO	0	-0.006	0.016	18.808	-0.355	-0.355	0.000	0.000	0.000	0.000
64	A	92	VAL	0	0.010	-0.001	15.686	-0.457	-0.457	0.000	0.000	0.000	0.000
65	A	93	THR	0	-0.005	-0.013	18.680	0.892	0.892	0.000	0.000	0.000	0.000
66	A	94	ILE	0	-0.038	-0.007	18.165	-0.830	-0.830	0.000	0.000	0.000	0.000
67	A	95	GLN	0	0.020	0.007	20.387	0.654	0.654	0.000	0.000	0.000	0.000
68	A	96	ASN	0	0.021	-0.007	20.235	0.141	0.141	0.000	0.000	0.000	0.000
69	A	97	TRP	0	0.067	0.045	22.637	0.048	0.048	0.000	0.000	0.000	0.000
70	A	98	CYS	0	-0.043	0.015	25.138	0.643	0.643	0.000	0.000	0.000	0.000
71	A	99	LYS	1	0.933	0.968	27.381	9.462	9.462	0.000	0.000	0.000	0.000
72	A	100	ARG	1	1.022	1.004	30.013	9.465	9.465	0.000	0.000	0.000	0.000
73	A	101	GLY	0	-0.008	-0.010	30.243	0.304	0.304	0.000	0.000	0.000	0.000
74	A	102	ARG	1	0.914	0.967	20.726	14.258	14.258	0.000	0.000	0.000	0.000
75	A	103	LYS	1	0.947	0.981	27.674	9.553	9.553	0.000	0.000	0.000	0.000
76	A	104	GLN	0	0.007	-0.026	30.254	0.040	0.040	0.000	0.000	0.000	0.000
77	A	106	LYS	1	0.971	0.990	27.763	9.722	9.722	0.000	0.000	0.000	0.000
78	A	107	THR	0	0.065	0.025	25.088	-0.181	-0.181	0.000	0.000	0.000	0.000
79	A	108	HIS	0	-0.032	-0.013	25.618	0.019	0.019	0.000	0.000	0.000	0.000
80	A	109	PRO	0	-0.003	0.003	24.125	-0.300	-0.300	0.000	0.000	0.000	0.000
81	A	110	HIS	0	-0.005	-0.001	24.225	0.604	0.604	0.000	0.000	0.000	0.000
82	A	111	PHE	0	-0.008	0.001	22.674	-0.644	-0.644	0.000	0.000	0.000	0.000
83	A	112	VAL	0	0.006	0.005	21.317	0.556	0.556	0.000	0.000	0.000	0.000
84	A	113	ILE	0	0.060	0.032	20.945	-0.620	-0.620	0.000	0.000	0.000	0.000
85	A	114	PRO	0	-0.062	-0.027	16.584	0.245	0.245	0.000	0.000	0.000	0.000
86	A	115	TYR	0	0.008	-0.003	18.946	0.196	0.196	0.000	0.000	0.000	0.000
87	A	116	ARG	1	0.837	0.893	13.255	18.726	18.726	0.000	0.000	0.000	0.000
88	A	118	LEU	0	-0.015	-0.012	14.874	-1.258	-1.258	0.000	0.000	0.000	0.000
89	A	119	VAL	0	0.026	0.005	12.205	0.752	0.752	0.000	0.000	0.000	0.000
90	A	120	GLY	0	-0.033	-0.001	15.633	0.298	0.298	0.000	0.000	0.000	0.000
91	A	121	GLU	-1	-0.969	-0.983	17.711	-16.490	-16.490	0.000	0.000	0.000	0.000
92	A	122	PHE	0	-0.073	-0.048	19.208	0.614	0.614	0.000	0.000	0.000	0.000
93	A	123	VAL	-1	-0.914	-0.944	22.407	-11.776	-11.776	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:LEU)