FMO DATABASE

FMODB ID: 5JQNZ

Calculation Name: 1PHT-A-Xray372

Preferred Name: PI3-kinase p85-alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1PHT

Chain ID: A

ChEMBL ID: CHEMBL2506

UniProt ID: P27986

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-560179.162971
FMO2-HF: Nuclear repulsion	527755.850192
FMO2-HF: Total energy	-32423.312779
FMO2-MP2: Total energy	-32520.254574

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:3:ALA)

Summations of interaction energy for fragment #1(A:3: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.
-3.598	2.652	0.811	-3.645	-3.416	-0.002

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / 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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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	5	GLY	0	-0.004	0.003	3.783	-1.819	1.605	-0.041	-1.959	-1.423	0.006
4	A	6	TYR	0	-0.009	-0.006	6.442	-0.167	-0.167	0.000	0.000	0.000	0.000
5	A	7	GLN	0	0.021	-0.010	10.148	-0.005	-0.005	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.023	-0.021	12.746	0.037	0.037	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.869	0.942	16.243	0.289	0.289	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.028	0.023	19.358	0.023	0.023	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.049	-0.034	22.035	0.002	0.002	0.000	0.000	0.000	0.000
10	A	12	TYR	0	-0.046	-0.017	25.303	0.018	0.018	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.866	-0.935	25.678	-0.163	-0.163	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.097	-0.059	24.218	0.010	0.010	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.956	0.988	26.375	0.073	0.073	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.931	0.970	23.697	0.103	0.103	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.994	-0.975	26.731	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.899	0.934	25.528	0.044	0.044	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.955	-0.990	25.540	-0.042	-0.042	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.941	-0.956	20.844	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.781	-0.878	20.516	-0.091	-0.091	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.102	-0.044	17.465	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.857	-0.939	21.647	-0.112	-0.112	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.090	-0.050	19.881	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	25	HIS	0	0.007	0.007	23.206	0.033	0.033	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.033	-0.014	23.736	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.061	-0.037	23.366	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.791	-0.892	19.781	-0.273	-0.273	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.039	-0.025	14.610	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.004	0.018	14.606	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.068	-0.074	8.129	-0.107	-0.107	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.041	0.034	9.974	0.066	0.066	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.014	-0.011	5.575	-0.263	-0.263	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.984	0.990	5.755	0.576	0.576	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.027	-0.011	6.376	0.088	0.088	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.003	-0.001	8.218	0.006	0.006	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.077	0.040	10.498	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.025	-0.019	9.601	0.026	0.026	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.043	-0.021	12.323	0.008	0.008	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.021	-0.005	14.237	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.024	-0.004	16.064	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	42	PHE	0	-0.021	-0.008	14.908	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.039	-0.013	14.423	0.009	0.009	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.949	-0.983	16.052	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.024	-0.003	15.434	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.011	0.000	16.600	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.887	-0.926	12.763	-0.294	-0.294	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.046	-0.030	15.535	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.859	0.939	17.906	0.155	0.155	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.034	0.024	17.992	0.017	0.017	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.878	-0.955	19.525	-0.152	-0.152	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.968	-0.985	22.208	-0.084	-0.084	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.057	-0.014	16.238	0.013	0.013	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.000	0.013	20.442	0.020	0.020	0.000	0.000	0.000	0.000
53	A	55	TRP	0	-0.025	-0.015	20.364	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	56	LEU	0	-0.009	0.004	14.772	0.007	0.007	0.000	0.000	0.000	0.000
55	A	57	ASN	0	0.019	0.002	13.691	0.001	0.001	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.052	-0.044	11.924	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	59	TYR	0	-0.104	-0.034	11.329	0.070	0.070	0.000	0.000	0.000	0.000
58	A	60	ASN	0	0.069	0.006	13.158	-0.100	-0.100	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.850	-0.910	11.055	-0.865	-0.865	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.027	-0.003	15.228	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	63	THR	0	0.000	-0.006	18.810	0.019	0.019	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.020	-0.004	16.561	0.022	0.022	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.926	-0.944	17.582	-0.117	-0.117	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.870	0.918	9.766	0.189	0.189	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.034	0.015	15.893	0.028	0.028	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.865	-0.927	16.729	-0.102	-0.102	0.000	0.000	0.000	0.000
67	A	69	PHE	0	-0.014	-0.015	15.071	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.002	0.008	19.865	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.051	0.013	20.278	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.013	-0.023	21.148	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.056	-0.021	23.403	0.005	0.005	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.006	0.006	18.552	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.835	-0.909	20.630	-0.256	-0.256	0.000	0.000	0.000	0.000
74	A	76	TYR	0	0.015	0.012	13.111	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.024	-0.021	15.643	0.021	0.021	0.000	0.000	0.000	0.000
76	A	78	GLY	0	-0.001	0.010	14.145	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.904	0.953	8.854	0.630	0.630	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.940	0.986	7.684	1.345	1.345	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.873	0.939	4.555	1.634	1.745	-0.001	-0.029	-0.080	0.000
80	A	82	ILE	0	-0.005	-0.006	2.313	0.112	1.493	0.767	-0.803	-1.346	0.000
81	A	83	SER	0	0.001	-0.009	2.996	-3.997	-2.663	0.086	-0.854	-0.567	-0.008
82	A	84	PRO	0	-0.034	-0.015	5.332	0.309	0.309	0.000	0.000	0.000	0.000
83	A	85	PRO	0	0.040	0.029	7.876	-0.063	-0.063	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)