FMO DATABASE

FMODB ID: YVMV2

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	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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-561202.382851
FMO2-HF: Nuclear repulsion	528778.624728
FMO2-HF: Total energy	-32423.758124
FMO2-MP2: Total energy	-32520.751913

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.
-3.69	2.481	0.569	-3.47	-3.269	-0.003

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 : 0.041 / q_NPA : 0.026

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	0.003	0.004	3.783	-1.693	1.633	-0.040	-1.883	-1.403	0.005
4	A	6	TYR	0	-0.015	-0.014	6.549	-0.126	-0.126	0.000	0.000	0.000	0.000
5	A	7	GLN	0	0.031	-0.006	10.249	0.000	0.000	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.026	-0.031	12.862	0.043	0.043	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.813	0.889	16.355	0.288	0.288	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.031	0.024	19.477	0.023	0.023	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.024	-0.025	22.147	0.003	0.003	0.000	0.000	0.000	0.000
10	A	12	TYR	0	-0.055	-0.024	25.410	0.019	0.019	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.853	-0.922	25.782	-0.167	-0.167	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.113	-0.080	24.269	0.011	0.011	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.950	0.983	26.462	0.075	0.075	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.832	0.924	23.079	0.118	0.118	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.911	-0.923	26.797	-0.056	-0.056	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.778	0.860	25.453	0.060	0.060	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.958	-0.989	25.516	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.945	-0.958	20.962	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.768	-0.860	20.557	-0.093	-0.093	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.059	-0.027	17.541	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.827	-0.924	21.718	-0.115	-0.115	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.065	-0.031	20.011	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	25	HIS	0	-0.014	-0.017	23.308	0.034	0.034	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.034	-0.015	23.849	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.056	-0.034	23.489	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.780	-0.874	19.843	-0.278	-0.278	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.028	-0.020	14.779	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.002	0.017	14.720	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.058	-0.059	8.214	-0.090	-0.090	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.027	0.023	10.054	0.066	0.066	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.021	-0.010	5.675	-0.250	-0.250	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.919	0.943	5.789	0.679	0.679	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.021	-0.007	6.360	0.089	0.089	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.012	-0.001	8.182	0.007	0.007	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.066	0.032	10.501	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.016	-0.015	9.638	0.026	0.026	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.043	-0.019	12.291	0.007	0.007	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.026	-0.008	14.194	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.013	0.002	16.032	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	42	PHE	0	-0.011	-0.004	14.946	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.047	-0.015	14.442	0.011	0.011	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.920	-0.966	16.065	-0.039	-0.039	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.009	-0.006	15.438	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.005	-0.014	16.606	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.752	-0.845	12.668	-0.356	-0.356	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.043	-0.025	15.565	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.790	0.895	17.915	0.140	0.140	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.019	0.021	18.041	0.016	0.016	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.857	-0.949	19.596	-0.148	-0.148	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.904	-0.936	22.206	-0.080	-0.080	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.051	-0.017	16.266	0.013	0.013	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.003	0.015	20.487	0.019	0.019	0.000	0.000	0.000	0.000
53	A	55	TRP	0	-0.024	-0.017	20.411	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	56	LEU	0	-0.003	0.015	14.594	0.007	0.007	0.000	0.000	0.000	0.000
55	A	57	ASN	0	0.043	0.014	13.778	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.057	-0.047	11.987	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	59	TYR	0	-0.084	-0.031	11.363	0.060	0.060	0.000	0.000	0.000	0.000
58	A	60	ASN	0	0.049	0.001	13.243	-0.096	-0.096	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.799	-0.870	10.892	-0.988	-0.988	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.016	0.004	15.281	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.003	-0.014	18.856	0.026	0.026	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.039	-0.011	16.590	0.021	0.021	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.862	-0.919	17.599	-0.119	-0.119	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.843	0.896	9.991	0.192	0.192	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.033	0.020	15.948	0.028	0.028	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.853	-0.920	16.788	-0.109	-0.109	0.000	0.000	0.000	0.000
67	A	69	PHE	0	-0.023	-0.021	15.095	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.009	0.013	19.931	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.044	0.011	20.357	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.007	-0.024	21.223	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.058	-0.017	23.487	0.006	0.006	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.012	0.002	18.543	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.788	-0.858	20.737	-0.257	-0.257	0.000	0.000	0.000	0.000
74	A	76	TYR	0	-0.042	-0.025	13.083	-0.083	-0.083	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.025	-0.019	15.542	0.021	0.021	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.007	0.020	14.145	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.806	0.895	8.920	0.528	0.528	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.857	0.926	7.974	1.317	1.317	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.847	0.909	4.408	1.521	1.635	-0.001	-0.032	-0.081	0.000
80	A	82	ILE	0	-0.008	-0.009	2.416	0.008	1.458	0.527	-0.728	-1.249	0.000
81	A	83	SER	0	0.003	-0.003	3.001	-3.879	-2.598	0.083	-0.827	-0.536	-0.008
82	A	84	PRO	0	-0.033	-0.014	5.330	0.303	0.303	0.000	0.000	0.000	0.000
83	A	85	PRO	0	0.039	0.026	7.892	-0.053	-0.053	0.000	0.000	0.000	0.000

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