FMO DATABASE

FMODB ID: J4ZL9

Calculation Name: 2EOB-A-Other547

Preferred Name: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EOB

Chain ID: A

ChEMBL ID: CHEMBL5230

UniProt ID: P24135

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1036296.108283
FMO2-HF: Nuclear repulsion	986281.553024
FMO2-HF: Total energy	-50014.555258
FMO2-MP2: Total energy	-50160.35287

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:1:GLY)

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

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.
21.15	22.152	-0.015	-0.391	-0.596	-0.001

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.918

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	3	SER	0	-0.021	-0.006	3.836	4.813	5.815	-0.015	-0.391	-0.596	-0.001
4	A	4	GLY	0	0.070	0.022	7.089	0.078	0.078	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.016	0.011	10.873	0.919	0.919	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.034	-0.032	12.061	-0.374	-0.374	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.042	0.011	14.184	0.518	0.518	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.943	-0.948	17.472	-14.478	-14.478	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.028	-0.005	16.213	-0.072	-0.072	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.018	0.000	18.267	0.753	0.753	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.015	0.017	20.989	-0.201	-0.201	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.052	0.011	21.744	0.362	0.362	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.011	0.000	23.784	0.235	0.235	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.015	-0.006	24.801	0.841	0.841	0.000	0.000	0.000	0.000
15	A	15	PRO	0	0.051	0.029	25.474	-0.423	-0.423	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.038	0.002	26.320	-0.142	-0.142	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.809	-0.894	23.855	-12.240	-12.240	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.020	0.001	21.895	-0.654	-0.654	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.827	0.918	22.897	11.515	11.515	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.055	0.028	23.636	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	21	TRP	0	0.052	0.009	24.607	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.115	-0.072	24.669	0.746	0.746	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.030	0.004	25.112	-0.407	-0.407	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.808	-0.897	22.898	-12.760	-12.760	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.913	0.929	21.323	13.473	13.473	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.025	0.046	24.710	0.168	0.168	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.083	0.034	27.742	0.454	0.454	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.868	0.933	30.926	8.377	8.377	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.018	0.009	34.298	0.114	0.114	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.837	-0.905	28.071	-11.246	-11.246	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.026	-0.023	32.008	0.057	0.057	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.848	-0.940	32.946	-8.030	-8.030	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.829	-0.917	33.822	-9.062	-9.062	0.000	0.000	0.000	0.000
34	A	34	MET	0	0.002	-0.004	28.965	-0.057	-0.057	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.052	-0.030	33.171	0.130	0.130	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.077	-0.044	36.148	0.242	0.242	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.954	0.997	29.980	10.224	10.224	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.006	0.015	32.309	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.004	0.014	36.246	0.247	0.247	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.916	0.953	37.080	8.317	8.317	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.961	-0.996	39.885	-7.292	-7.292	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.009	-0.014	40.308	0.178	0.178	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.004	0.026	35.731	-0.143	-0.143	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.010	-0.016	33.499	0.230	0.230	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.066	0.054	30.726	-0.240	-0.240	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.001	-0.009	30.972	0.355	0.355	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.903	0.951	29.682	9.442	9.442	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.885	0.949	25.294	12.371	12.371	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.768	0.863	30.437	8.816	8.816	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.890	-0.931	29.644	-10.503	-10.503	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.027	0.021	31.900	0.274	0.274	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.030	-0.038	34.891	0.296	0.296	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.811	-0.869	34.285	-9.307	-9.307	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.032	-0.013	35.444	0.154	0.154	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.048	0.028	29.751	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.020	-0.023	34.305	0.329	0.329	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.005	0.023	34.363	-0.288	-0.288	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.009	-0.023	34.944	0.194	0.194	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.033	-0.008	36.027	-0.120	-0.120	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.949	1.000	38.566	7.754	7.754	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.011	-0.011	40.696	0.099	0.099	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.890	0.927	44.408	6.406	6.406	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.034	0.013	44.128	0.114	0.114	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.961	1.005	43.045	6.438	6.438	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.038	0.025	38.207	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.874	0.939	41.212	7.056	7.056	0.000	0.000	0.000	0.000
67	A	67	HIS	0	0.020	0.004	37.363	-0.319	-0.319	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.044	-0.011	39.641	0.300	0.300	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.929	0.969	39.207	7.443	7.443	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.004	0.011	35.437	0.096	0.096	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.011	-0.014	38.611	-0.225	-0.225	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.845	0.903	33.982	8.895	8.895	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.861	-0.915	39.910	-7.028	-7.028	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.003	-0.005	42.145	0.011	0.011	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.884	0.931	37.373	7.898	7.898	0.000	0.000	0.000	0.000
76	A	76	HIS	0	0.058	0.054	37.351	-0.248	-0.248	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.013	-0.021	32.443	0.023	0.023	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.034	0.019	38.390	0.114	0.114	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.049	-0.024	40.027	-0.085	-0.085	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.025	-0.006	41.696	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.030	0.000	45.317	0.107	0.107	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.038	0.008	46.200	-0.149	-0.149	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.026	-0.012	44.169	0.070	0.070	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.013	0.008	42.411	-0.129	-0.129	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.012	-0.003	37.885	0.043	0.043	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.909	-0.937	34.256	-9.140	-9.140	0.000	0.000	0.000	0.000
87	A	87	SER	0	0.062	0.025	31.855	-0.267	-0.267	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.028	-0.027	31.607	0.167	0.167	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.007	-0.009	29.768	0.042	0.042	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.868	-0.933	32.855	-8.206	-8.206	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.055	-0.007	36.426	0.198	0.198	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.008	-0.024	33.348	0.213	0.213	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.024	0.012	35.973	0.230	0.230	0.000	0.000	0.000	0.000
94	A	94	TYR	0	0.001	0.004	37.698	0.247	0.247	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.003	-0.026	39.894	0.223	0.223	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.915	-0.944	36.439	-8.472	-8.472	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.866	0.948	40.542	7.154	7.154	0.000	0.000	0.000	0.000
98	A	98	HIS	0	0.041	0.024	44.141	0.139	0.139	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.025	-0.022	44.907	-0.101	-0.101	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.004	0.005	40.467	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.037	-0.015	44.407	0.034	0.034	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.963	0.962	47.055	6.060	6.060	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.976	0.987	48.718	6.200	6.200	0.000	0.000	0.000	0.000
104	A	104	MET	0	-0.010	0.018	41.213	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.924	0.961	42.182	7.204	7.204	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.013	0.012	36.797	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.954	0.977	38.213	7.396	7.396	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.008	-0.001	34.944	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.021	0.015	30.713	0.036	0.036	0.000	0.000	0.000	0.000
110	A	110	VAL	0	-0.009	-0.013	29.965	-0.180	-0.180	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.011	-0.004	26.049	-0.197	-0.197	0.000	0.000	0.000	0.000
112	A	112	PRO	0	0.007	-0.003	22.387	0.257	0.257	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.891	-0.936	22.979	-12.875	-12.875	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.060	-0.024	24.643	0.308	0.308	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.014	-0.028	27.364	0.339	0.339	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.810	-0.867	23.327	-12.377	-12.377	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.949	0.978	26.715	10.841	10.841	0.000	0.000	0.000	0.000
118	A	118	TYR	0	-0.103	-0.060	28.605	0.602	0.602	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.050	-0.021	29.204	0.490	0.490	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.049	0.038	29.089	-0.304	-0.304	0.000	0.000	0.000	0.000
121	A	121	PRO	0	-0.044	-0.029	29.406	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.042	-0.033	24.351	-0.193	-0.193	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.060	-0.055	22.701	0.072	0.072	0.000	0.000	0.000	0.000
124	A	124	GLY	-1	-0.935	-0.947	18.843	-16.617	-16.617	0.000	0.000	0.000	0.000

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