FMO DATABASE

FMODB ID: RQ328

Calculation Name: 2K89-A-Other547

Preferred Name: Phospholipase A-2-activating protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2K89

Chain ID: A

ChEMBL ID: CHEMBL6114

UniProt ID: Q9Y263

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-496403.242955
FMO2-HF: Nuclear repulsion	464812.40756
FMO2-HF: Total energy	-31590.835395
FMO2-MP2: Total energy	-31683.278381

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:49:ALA)

Summations of interaction energy for fragment #1(A:49:ALA)

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.
-108.188	-103.721	2.322	-3.026	-3.762	-0.029

Interaction energy analysis for fragmet #1(A:49:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.934

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	51	GLN	0	0.046	0.044	3.291	9.590	11.254	-0.003	-0.689	-0.972	-0.001
17	A	65	ASP	-1	-0.828	-0.880	4.829	-45.268	-45.162	-0.001	-0.002	-0.102	0.000
36	A	84	ASN	0	-0.022	-0.044	4.327	-6.706	-6.596	-0.001	-0.016	-0.093	0.000
37	A	85	THR	0	0.003	-0.020	4.156	-3.583	-3.368	0.000	-0.046	-0.169	0.000
38	A	86	SER	0	-0.107	-0.056	2.433	-24.912	-22.580	2.328	-2.255	-2.406	-0.028
39	A	87	ASP	-1	-0.811	-0.873	4.684	-26.202	-26.162	-0.001	-0.018	-0.020	0.000
4	A	52	GLN	0	0.056	0.024	5.537	-1.679	-1.679	0.000	0.000	0.000	0.000
5	A	53	THR	0	0.016	0.007	8.191	-2.422	-2.422	0.000	0.000	0.000	0.000
6	A	54	SER	0	-0.059	-0.035	7.553	2.396	2.396	0.000	0.000	0.000	0.000
7	A	55	GLY	0	0.040	0.008	10.241	1.963	1.963	0.000	0.000	0.000	0.000
8	A	56	LYS	1	0.802	0.932	5.880	35.391	35.391	0.000	0.000	0.000	0.000
9	A	57	VAL	0	0.026	0.017	11.224	1.904	1.904	0.000	0.000	0.000	0.000
10	A	58	LEU	0	0.020	0.014	13.623	-0.803	-0.803	0.000	0.000	0.000	0.000
11	A	59	TYR	0	0.000	-0.012	14.489	0.400	0.400	0.000	0.000	0.000	0.000
12	A	60	GLU	-1	-0.877	-0.947	17.851	-13.950	-13.950	0.000	0.000	0.000	0.000
13	A	61	GLY	0	-0.016	-0.008	19.626	0.630	0.630	0.000	0.000	0.000	0.000
14	A	62	LYS	1	0.857	0.931	13.945	19.671	19.671	0.000	0.000	0.000	0.000
15	A	63	GLU	-1	-0.905	-0.946	12.113	-20.733	-20.733	0.000	0.000	0.000	0.000
16	A	64	PHE	0	-0.043	-0.042	9.395	-1.183	-1.183	0.000	0.000	0.000	0.000
18	A	66	TYR	0	0.056	0.024	7.703	1.475	1.475	0.000	0.000	0.000	0.000
19	A	67	VAL	0	-0.038	-0.012	10.883	-0.409	-0.409	0.000	0.000	0.000	0.000
20	A	68	PHE	0	0.015	0.022	14.144	0.625	0.625	0.000	0.000	0.000	0.000
21	A	69	SER	0	-0.025	-0.030	17.092	0.067	0.067	0.000	0.000	0.000	0.000
22	A	70	ILE	0	-0.029	-0.010	20.016	0.104	0.104	0.000	0.000	0.000	0.000
23	A	71	ASP	-1	-0.834	-0.915	23.320	-11.340	-11.340	0.000	0.000	0.000	0.000
24	A	72	VAL	0	-0.029	-0.021	27.050	-0.072	-0.072	0.000	0.000	0.000	0.000
25	A	73	ASN	0	-0.055	-0.043	28.881	0.291	0.291	0.000	0.000	0.000	0.000
26	A	74	GLU	-1	-0.914	-0.941	31.748	-8.896	-8.896	0.000	0.000	0.000	0.000
27	A	75	GLY	0	0.000	0.010	31.253	-0.321	-0.321	0.000	0.000	0.000	0.000
28	A	76	GLY	0	-0.041	-0.021	30.930	0.101	0.101	0.000	0.000	0.000	0.000
29	A	77	PRO	0	-0.040	-0.009	28.074	0.234	0.234	0.000	0.000	0.000	0.000
30	A	78	SER	0	0.037	0.011	25.596	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	79	TYR	0	-0.023	-0.004	22.985	-0.253	-0.253	0.000	0.000	0.000	0.000
32	A	80	LYS	1	0.889	0.938	18.606	14.655	14.655	0.000	0.000	0.000	0.000
33	A	81	LEU	0	0.007	0.019	15.098	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	82	PRO	0	-0.041	-0.031	13.002	-0.570	-0.570	0.000	0.000	0.000	0.000
35	A	83	TYR	0	0.034	0.018	9.156	-0.246	-0.246	0.000	0.000	0.000	0.000
40	A	88	ASP	-1	-0.877	-0.937	8.369	-23.997	-23.997	0.000	0.000	0.000	0.000
41	A	89	PRO	0	-0.020	-0.011	11.710	0.735	0.735	0.000	0.000	0.000	0.000
42	A	90	TRP	0	0.023	-0.009	14.322	0.764	0.764	0.000	0.000	0.000	0.000
43	A	91	LEU	0	0.023	0.022	12.609	1.295	1.295	0.000	0.000	0.000	0.000
44	A	92	THR	0	-0.003	-0.030	11.569	0.478	0.478	0.000	0.000	0.000	0.000
45	A	93	ALA	0	-0.032	-0.006	14.013	1.015	1.015	0.000	0.000	0.000	0.000
46	A	94	TYR	0	0.020	0.006	17.584	1.091	1.091	0.000	0.000	0.000	0.000
47	A	95	ASN	0	-0.032	-0.013	14.329	1.756	1.756	0.000	0.000	0.000	0.000
48	A	96	PHE	0	-0.003	-0.017	17.445	0.582	0.582	0.000	0.000	0.000	0.000
49	A	97	LEU	0	0.001	-0.002	18.987	0.695	0.695	0.000	0.000	0.000	0.000
50	A	98	GLN	0	0.006	0.004	18.916	1.074	1.074	0.000	0.000	0.000	0.000
51	A	99	LYS	1	0.871	0.952	19.544	14.634	14.634	0.000	0.000	0.000	0.000
52	A	100	ASN	0	-0.096	-0.087	22.001	0.488	0.488	0.000	0.000	0.000	0.000
53	A	101	ASP	-1	-0.886	-0.910	24.605	-10.521	-10.521	0.000	0.000	0.000	0.000
54	A	102	LEU	0	-0.032	0.007	23.147	0.341	0.341	0.000	0.000	0.000	0.000
55	A	103	ASN	0	0.038	0.005	26.702	-0.173	-0.173	0.000	0.000	0.000	0.000
56	A	104	PRO	0	0.048	0.006	25.802	-0.285	-0.285	0.000	0.000	0.000	0.000
57	A	105	MET	0	-0.024	0.001	26.170	-0.169	-0.169	0.000	0.000	0.000	0.000
58	A	106	PHE	0	0.004	-0.006	24.578	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	107	LEU	0	0.007	0.007	20.127	-0.488	-0.488	0.000	0.000	0.000	0.000
60	A	108	ASP	-1	-0.820	-0.901	21.216	-14.096	-14.096	0.000	0.000	0.000	0.000
61	A	109	GLN	0	0.042	0.016	21.627	-0.258	-0.258	0.000	0.000	0.000	0.000
62	A	110	VAL	0	-0.012	-0.007	18.843	-0.405	-0.405	0.000	0.000	0.000	0.000
63	A	111	ALA	0	0.018	0.013	17.109	-0.992	-0.992	0.000	0.000	0.000	0.000
64	A	112	LYS	1	0.818	0.889	17.000	12.846	12.846	0.000	0.000	0.000	0.000
65	A	113	PHE	0	0.053	0.029	16.946	-0.382	-0.382	0.000	0.000	0.000	0.000
66	A	114	ILE	0	-0.034	0.001	12.097	-0.644	-0.644	0.000	0.000	0.000	0.000
67	A	115	ILE	0	-0.001	-0.007	13.210	-1.158	-1.158	0.000	0.000	0.000	0.000
68	A	116	ASP	-1	-0.843	-0.930	14.718	-15.808	-15.808	0.000	0.000	0.000	0.000
69	A	117	ASN	0	-0.062	-0.029	10.779	-1.703	-1.703	0.000	0.000	0.000	0.000
70	A	118	THR	0	-0.011	-0.011	9.064	-1.211	-1.211	0.000	0.000	0.000	0.000
71	A	119	LYS	1	0.800	0.910	11.786	15.875	15.875	0.000	0.000	0.000	0.000
72	A	120	GLY	0	0.027	0.017	15.227	0.067	0.067	0.000	0.000	0.000	0.000
73	A	121	GLN	0	-0.058	-0.035	18.170	-0.434	-0.434	0.000	0.000	0.000	0.000
74	A	122	MET	0	0.027	0.022	16.999	0.345	0.345	0.000	0.000	0.000	0.000
75	A	123	LEU	0	-0.025	0.006	12.067	-0.028	-0.028	0.000	0.000	0.000	0.000
76	A	124	GLY	0	-0.021	-0.030	15.624	0.176	0.176	0.000	0.000	0.000	0.000
77	A	125	LEU	0	-0.021	-0.010	16.496	0.670	0.670	0.000	0.000	0.000	0.000
78	A	126	GLY	0	0.008	0.010	20.243	0.197	0.197	0.000	0.000	0.000	0.000
79	A	127	ASN	0	-0.078	-0.047	22.174	0.061	0.061	0.000	0.000	0.000	0.000
80	A	128	PRO	-1	-0.927	-0.945	25.400	-10.483	-10.483	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:49:ALA)