FMO DATABASE

FMODB ID: VQ6Q1

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-560839.368514
FMO2-HF: Nuclear repulsion	528415.413157
FMO2-HF: Total energy	-32423.955357
FMO2-MP2: Total energy	-32520.957245

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.
-3.256	2.416	0.729	-3.209	-3.192	-0.009

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 : 0.028

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	-0.009	0.000	3.868	-1.347	1.556	-0.019	-1.707	-1.177	0.003
4	A	6	TYR	0	-0.040	-0.023	6.456	-0.130	-0.130	0.000	0.000	0.000	0.000
5	A	7	GLN	0	0.020	0.001	10.222	-0.002	-0.002	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.012	-0.030	12.996	0.037	0.037	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.807	0.881	16.549	0.277	0.277	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.026	0.024	19.804	0.021	0.021	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.036	-0.027	22.603	0.001	0.001	0.000	0.000	0.000	0.000
10	A	12	TYR	0	-0.047	-0.026	25.832	0.018	0.018	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.867	-0.930	26.186	-0.157	-0.157	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.082	-0.062	24.603	0.010	0.010	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.928	0.970	26.895	0.073	0.073	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.798	0.897	23.394	0.107	0.107	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.892	-0.916	27.015	-0.056	-0.056	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.761	0.849	25.975	0.065	0.065	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.961	-0.982	25.906	-0.047	-0.047	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.922	-0.960	21.561	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.782	-0.880	20.850	-0.090	-0.090	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.076	-0.016	17.839	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.825	-0.925	21.834	-0.111	-0.111	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.060	-0.032	20.438	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	25	HIS	0	-0.018	-0.020	23.859	0.032	0.032	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.036	-0.010	24.545	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.035	-0.019	23.915	0.002	0.002	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.778	-0.873	20.404	-0.260	-0.260	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.020	-0.013	14.991	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.005	0.013	15.351	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.061	-0.061	8.668	-0.071	-0.071	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.044	0.031	10.437	0.065	0.065	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.010	-0.008	6.054	-0.233	-0.233	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.895	0.933	6.057	0.736	0.736	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.011	-0.006	6.508	0.102	0.102	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.004	0.001	8.221	0.025	0.025	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.047	0.022	10.868	0.006	0.006	0.000	0.000	0.000	0.000
36	A	38	VAL	0	0.009	-0.004	10.059	0.026	0.026	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.049	-0.021	12.234	0.018	0.018	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.022	-0.005	14.113	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.007	0.006	15.799	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	42	PHE	0	-0.014	0.004	14.917	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.027	-0.022	14.405	0.016	0.016	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.922	-0.963	16.353	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.004	-0.013	15.908	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.011	-0.004	16.985	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.738	-0.823	12.868	-0.414	-0.414	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.026	-0.010	15.425	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.797	0.904	18.020	0.147	0.147	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.016	0.024	18.386	0.014	0.014	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.864	-0.953	19.749	-0.151	-0.151	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.899	-0.935	21.881	-0.089	-0.089	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.045	-0.021	16.074	0.012	0.012	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.002	0.020	20.294	0.017	0.017	0.000	0.000	0.000	0.000
53	A	55	TRP	0	-0.036	-0.027	20.446	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.003	0.012	14.825	0.003	0.003	0.000	0.000	0.000	0.000
55	A	57	ASN	0	0.057	0.026	14.049	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.042	-0.042	12.336	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	59	TYR	0	-0.077	-0.028	11.586	0.055	0.055	0.000	0.000	0.000	0.000
58	A	60	ASN	0	0.045	0.011	13.779	-0.089	-0.089	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.794	-0.869	11.157	-0.902	-0.902	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.022	0.003	15.581	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.016	-0.023	18.908	0.027	0.027	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.030	-0.006	17.046	0.023	0.023	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.816	-0.901	17.446	-0.124	-0.124	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.786	0.873	11.274	0.164	0.164	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.044	0.030	16.484	0.030	0.030	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.858	-0.917	17.004	-0.109	-0.109	0.000	0.000	0.000	0.000
67	A	69	PHE	0	-0.012	-0.017	15.413	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.022	0.031	20.218	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.029	-0.005	20.388	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	72	THR	0	0.001	-0.024	21.163	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.055	-0.012	23.647	0.008	0.008	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.025	-0.012	18.729	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.766	-0.844	20.895	-0.255	-0.255	0.000	0.000	0.000	0.000
74	A	76	TYR	0	-0.055	-0.055	13.243	-0.063	-0.063	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.034	-0.020	15.737	0.020	0.020	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.004	0.014	14.394	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.800	0.887	9.155	0.532	0.532	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.839	0.916	7.984	1.192	1.192	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.877	0.916	4.525	1.613	1.734	-0.001	-0.037	-0.083	0.000
80	A	82	ILE	0	-0.010	-0.004	2.400	0.328	1.445	0.561	-0.503	-1.175	-0.001
81	A	83	SER	0	-0.004	-0.006	2.831	-4.225	-2.694	0.188	-0.962	-0.757	-0.011
82	A	84	PRO	0	-0.011	-0.008	5.062	0.289	0.289	0.000	0.000	0.000	0.000
83	A	85	PRO	0	0.025	0.026	7.786	-0.071	-0.071	0.000	0.000	0.000	0.000

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