FMO DATABASE

FMODB ID: K3143

Calculation Name: 2RD0-B-Xray372

Preferred Name: PI3-kinase p85-alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2RD0

Chain ID: B

ChEMBL ID: CHEMBL2506

UniProt ID: P27986

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1128709.84308
FMO2-HF: Nuclear repulsion	1067961.987166
FMO2-HF: Total energy	-60747.855914
FMO2-MP2: Total energy	-60924.585262

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(B:442:ILE)

Summations of interaction energy for fragment #1(B:442:ILE)

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.
-4.283	-2.804	9.506	-1.717	-9.265	-0.014

Interaction energy analysis for fragmet #1(B:442:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.032

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

Sort

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	B	444	ALA	0	0.009	0.011	3.809	-0.813	1.000	-0.024	-0.882	-0.907	-0.003
4	B	445	VAL	0	-0.008	-0.005	5.328	-0.180	-0.102	-0.001	-0.015	-0.062	0.000
5	B	446	GLY	0	0.052	0.024	2.189	-0.138	-0.877	4.194	-1.703	-1.750	-0.003
6	B	447	LYS	1	0.972	0.964	2.151	-0.307	-2.159	3.978	1.705	-3.831	-0.001
7	B	448	LYS	1	0.978	0.985	3.780	-0.729	-0.531	0.014	-0.005	-0.207	0.000
8	B	449	LEU	0	0.020	0.004	5.632	-0.138	-0.138	0.000	0.000	0.000	0.000
9	B	450	HIS	0	-0.003	0.011	7.108	-0.017	-0.017	0.000	0.000	0.000	0.000
10	B	451	GLU	-1	-0.918	-0.967	8.616	0.140	0.140	0.000	0.000	0.000	0.000
11	B	452	TYR	0	-0.046	-0.056	10.329	-0.052	-0.052	0.000	0.000	0.000	0.000
12	B	453	ASN	0	-0.011	-0.003	11.585	-0.038	-0.038	0.000	0.000	0.000	0.000
13	B	454	THR	0	0.009	-0.015	13.244	-0.018	-0.018	0.000	0.000	0.000	0.000
14	B	455	GLN	0	0.060	0.028	15.105	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	456	PHE	0	-0.064	-0.027	15.668	-0.020	-0.020	0.000	0.000	0.000	0.000
16	B	457	GLN	0	0.051	0.002	16.994	-0.024	-0.024	0.000	0.000	0.000	0.000
17	B	458	GLU	-1	-0.989	-0.968	19.699	0.071	0.071	0.000	0.000	0.000	0.000
18	B	459	LYS	1	0.969	0.992	17.981	-0.107	-0.107	0.000	0.000	0.000	0.000
19	B	460	SER	0	-0.027	-0.019	21.035	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	461	ARG	1	0.966	0.991	23.008	-0.073	-0.073	0.000	0.000	0.000	0.000
21	B	462	GLU	-1	-0.982	-0.996	25.099	0.048	0.048	0.000	0.000	0.000	0.000
22	B	463	TYR	0	0.009	0.011	26.281	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	464	ASP	-1	-0.846	-0.929	27.479	0.077	0.077	0.000	0.000	0.000	0.000
24	B	465	ARG	1	0.895	0.927	29.351	-0.052	-0.052	0.000	0.000	0.000	0.000
25	B	466	LEU	0	0.006	0.018	30.450	-0.004	-0.004	0.000	0.000	0.000	0.000
26	B	467	TYR	0	0.003	-0.011	31.844	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	468	GLU	-1	-0.926	-0.954	33.640	0.044	0.044	0.000	0.000	0.000	0.000
28	B	469	GLU	-1	-0.934	-0.958	35.489	0.030	0.030	0.000	0.000	0.000	0.000
29	B	470	TYR	0	0.008	0.037	36.209	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	471	THR	0	-0.022	-0.024	36.952	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	472	ARG	1	0.963	0.979	39.477	-0.032	-0.032	0.000	0.000	0.000	0.000
32	B	473	THR	0	-0.065	-0.081	40.416	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	474	SER	0	0.013	0.019	42.536	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	475	GLN	0	0.012	-0.004	43.903	0.000	0.000	0.000	0.000	0.000	0.000
35	B	476	GLU	-1	-0.940	-0.957	45.646	0.024	0.024	0.000	0.000	0.000	0.000
36	B	477	ILE	0	-0.050	-0.027	45.602	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	478	GLN	0	-0.004	-0.014	48.759	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	479	MET	0	0.002	0.008	50.404	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	480	LYS	1	0.908	0.964	48.692	-0.022	-0.022	0.000	0.000	0.000	0.000
40	B	481	ARG	1	0.907	0.949	49.873	-0.022	-0.022	0.000	0.000	0.000	0.000
41	B	482	THR	0	0.069	0.031	54.557	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	483	ALA	0	-0.035	-0.006	56.348	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	484	ILE	0	-0.004	-0.005	56.418	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	485	GLU	-1	-0.896	-0.942	58.489	0.017	0.017	0.000	0.000	0.000	0.000
45	B	486	ALA	0	0.025	0.018	61.022	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	487	PHE	0	-0.004	-0.014	59.936	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	488	ASN	0	-0.037	-0.018	62.263	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	489	GLU	-1	-0.860	-0.939	65.577	0.013	0.013	0.000	0.000	0.000	0.000
49	B	490	THR	0	-0.036	-0.010	66.310	0.000	0.000	0.000	0.000	0.000	0.000
50	B	491	ILE	0	-0.038	-0.040	65.889	0.000	0.000	0.000	0.000	0.000	0.000
51	B	492	LYS	1	0.908	0.948	68.951	-0.013	-0.013	0.000	0.000	0.000	0.000
52	B	493	ILE	0	0.037	0.030	70.804	0.000	0.000	0.000	0.000	0.000	0.000
53	B	494	PHE	0	-0.081	-0.043	70.840	0.000	0.000	0.000	0.000	0.000	0.000
54	B	495	GLU	-1	-0.889	-0.957	73.504	0.009	0.009	0.000	0.000	0.000	0.000
55	B	496	GLU	-1	-0.931	-0.976	75.717	0.010	0.010	0.000	0.000	0.000	0.000
56	B	497	GLN	0	0.040	0.056	78.098	0.000	0.000	0.000	0.000	0.000	0.000
57	B	498	CYS	0	-0.094	-0.056	78.238	0.000	0.000	0.000	0.000	0.000	0.000
58	B	499	GLN	0	0.029	0.006	79.187	0.000	0.000	0.000	0.000	0.000	0.000
59	B	500	THR	0	-0.042	-0.030	81.868	0.000	0.000	0.000	0.000	0.000	0.000
60	B	501	GLN	0	-0.066	-0.034	83.822	0.000	0.000	0.000	0.000	0.000	0.000
61	B	502	GLU	-1	-0.824	-0.880	84.933	0.007	0.007	0.000	0.000	0.000	0.000
62	B	503	ARG	1	0.893	0.939	85.524	-0.008	-0.008	0.000	0.000	0.000	0.000
63	B	504	TYR	0	0.046	0.037	88.672	0.000	0.000	0.000	0.000	0.000	0.000
64	B	505	SER	0	-0.045	-0.048	88.481	0.000	0.000	0.000	0.000	0.000	0.000
65	B	506	LYS	1	0.968	0.957	91.044	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	507	GLU	-1	-0.952	-0.960	92.807	0.006	0.006	0.000	0.000	0.000	0.000
67	B	508	TYR	0	-0.105	-0.047	93.718	0.000	0.000	0.000	0.000	0.000	0.000
68	B	509	ILE	0	-0.047	-0.005	93.024	0.000	0.000	0.000	0.000	0.000	0.000
69	B	521	ILE	0	0.016	-0.012	96.027	0.000	0.000	0.000	0.000	0.000	0.000
70	B	522	GLN	0	0.086	0.035	95.496	0.000	0.000	0.000	0.000	0.000	0.000
71	B	523	ARG	1	0.930	0.984	91.843	-0.005	-0.005	0.000	0.000	0.000	0.000
72	B	524	ILE	0	-0.009	-0.010	89.316	0.000	0.000	0.000	0.000	0.000	0.000
73	B	525	MET	0	0.031	0.012	87.798	0.000	0.000	0.000	0.000	0.000	0.000
74	B	526	HIS	0	0.050	0.019	81.119	0.000	0.000	0.000	0.000	0.000	0.000
75	B	527	ASN	0	-0.031	-0.026	82.062	0.000	0.000	0.000	0.000	0.000	0.000
76	B	528	TYR	0	0.141	0.059	81.407	0.000	0.000	0.000	0.000	0.000	0.000
77	B	529	ASP	-1	-0.923	-0.968	81.282	0.007	0.007	0.000	0.000	0.000	0.000
78	B	530	LYS	1	0.871	0.941	77.119	-0.008	-0.008	0.000	0.000	0.000	0.000
79	B	531	LEU	0	-0.021	0.002	76.823	0.000	0.000	0.000	0.000	0.000	0.000
80	B	532	LYS	1	0.958	0.997	76.319	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	533	SER	0	-0.005	-0.008	74.873	0.000	0.000	0.000	0.000	0.000	0.000
82	B	534	ARG	1	0.974	0.994	67.757	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	535	ILE	0	0.044	0.022	70.908	0.000	0.000	0.000	0.000	0.000	0.000
84	B	536	SER	0	-0.017	-0.004	70.066	0.000	0.000	0.000	0.000	0.000	0.000
85	B	537	GLU	-1	-0.896	-0.946	67.972	0.010	0.010	0.000	0.000	0.000	0.000
86	B	538	ILE	0	-0.068	-0.006	66.210	0.001	0.001	0.000	0.000	0.000	0.000
87	B	539	ILE	0	0.011	0.006	65.201	0.001	0.001	0.000	0.000	0.000	0.000
88	B	540	ASP	-1	-0.873	-0.950	64.459	0.010	0.010	0.000	0.000	0.000	0.000
89	B	541	SER	0	-0.115	-0.086	62.188	0.000	0.000	0.000	0.000	0.000	0.000
90	B	542	ARG	1	0.878	0.938	60.589	-0.012	-0.012	0.000	0.000	0.000	0.000
91	B	543	ARG	1	0.945	0.994	59.922	-0.009	-0.009	0.000	0.000	0.000	0.000
92	B	544	ARG	1	0.969	0.986	58.363	-0.011	-0.011	0.000	0.000	0.000	0.000
93	B	545	LEU	0	0.001	0.018	55.305	0.001	0.001	0.000	0.000	0.000	0.000
94	B	546	GLU	-1	-0.869	-0.945	55.142	0.014	0.014	0.000	0.000	0.000	0.000
95	B	547	GLU	-1	-0.981	-0.992	54.678	0.012	0.012	0.000	0.000	0.000	0.000
96	B	548	ASP	-1	-0.907	-0.950	52.090	0.016	0.016	0.000	0.000	0.000	0.000
97	B	549	LEU	0	-0.069	-0.029	50.534	0.001	0.001	0.000	0.000	0.000	0.000
98	B	550	LYS	1	0.945	0.957	49.706	-0.017	-0.017	0.000	0.000	0.000	0.000
99	B	551	LYS	1	0.992	1.015	47.284	-0.014	-0.014	0.000	0.000	0.000	0.000
100	B	552	GLN	0	0.143	0.053	45.202	0.001	0.001	0.000	0.000	0.000	0.000
101	B	553	ALA	0	-0.052	-0.004	45.085	0.001	0.001	0.000	0.000	0.000	0.000
102	B	554	ALA	0	-0.074	-0.051	44.532	0.001	0.001	0.000	0.000	0.000	0.000
103	B	555	GLU	-1	-0.886	-0.939	40.290	0.024	0.024	0.000	0.000	0.000	0.000
104	B	556	TYR	0	-0.020	-0.007	40.845	0.000	0.000	0.000	0.000	0.000	0.000
105	B	557	ARG	1	0.925	0.943	40.233	-0.017	-0.017	0.000	0.000	0.000	0.000
106	B	558	GLU	-1	-0.900	-0.932	37.687	0.022	0.022	0.000	0.000	0.000	0.000
107	B	559	ILE	0	-0.011	-0.014	35.976	0.002	0.002	0.000	0.000	0.000	0.000
108	B	560	ASP	-1	-0.893	-0.959	35.378	0.036	0.036	0.000	0.000	0.000	0.000
109	B	561	LYS	1	0.883	0.955	34.923	-0.019	-0.019	0.000	0.000	0.000	0.000
110	B	562	ARG	1	0.929	0.952	31.937	-0.026	-0.026	0.000	0.000	0.000	0.000
111	B	563	MET	0	0.079	0.048	30.742	0.004	0.004	0.000	0.000	0.000	0.000
112	B	564	ASN	0	-0.098	-0.037	30.615	0.007	0.007	0.000	0.000	0.000	0.000
113	B	565	SER	0	-0.034	-0.027	29.544	-0.004	-0.004	0.000	0.000	0.000	0.000
114	B	566	ILE	0	0.023	0.023	25.053	0.001	0.001	0.000	0.000	0.000	0.000
115	B	567	LYS	1	0.935	0.989	25.400	-0.053	-0.053	0.000	0.000	0.000	0.000
116	B	568	PRO	0	0.020	0.007	25.229	0.007	0.007	0.000	0.000	0.000	0.000
117	B	569	ASP	-1	-0.835	-0.911	21.497	0.065	0.065	0.000	0.000	0.000	0.000
118	B	570	LEU	0	-0.009	-0.021	21.051	0.010	0.010	0.000	0.000	0.000	0.000
119	B	571	ILE	0	-0.043	-0.045	20.610	0.015	0.015	0.000	0.000	0.000	0.000
120	B	572	GLN	0	-0.001	-0.012	19.899	0.010	0.010	0.000	0.000	0.000	0.000
121	B	573	LEU	0	0.011	0.028	16.373	0.010	0.010	0.000	0.000	0.000	0.000
122	B	574	ARG	1	0.891	0.993	15.960	-0.109	-0.109	0.000	0.000	0.000	0.000
123	B	575	LYS	1	0.979	0.978	16.095	-0.105	-0.105	0.000	0.000	0.000	0.000
124	B	576	THR	0	0.016	0.024	11.389	0.009	0.009	0.000	0.000	0.000	0.000
125	B	577	ARG	1	0.939	0.964	11.267	-0.198	-0.198	0.000	0.000	0.000	0.000
126	B	578	ASP	-1	-0.997	-1.007	11.452	0.251	0.251	0.000	0.000	0.000	0.000
127	B	579	GLN	0	0.002	0.014	12.940	0.001	0.001	0.000	0.000	0.000	0.000
128	B	580	TYR	0	-0.032	0.000	7.421	0.005	0.005	0.000	0.000	0.000	0.000
129	B	581	LEU	0	0.009	0.013	8.552	0.058	0.058	0.000	0.000	0.000	0.000
130	B	582	MET	0	-0.037	-0.028	8.317	0.012	0.012	0.000	0.000	0.000	0.000
131	B	583	TRP	0	0.006	0.005	2.415	-1.736	-0.040	1.344	-0.783	-2.256	-0.007
132	B	593	LYS	1	0.988	0.995	13.743	-0.191	-0.191	0.000	0.000	0.000	0.000
133	B	594	LEU	0	0.016	-0.004	10.514	0.024	0.024	0.000	0.000	0.000	0.000
134	B	595	ASN	0	-0.012	-0.014	11.451	-0.016	-0.016	0.000	0.000	0.000	0.000
135	B	596	GLU	-1	-0.947	-0.973	9.146	0.236	0.236	0.000	0.000	0.000	0.000
136	B	597	TRP	0	-0.014	-0.015	4.438	-0.194	0.091	0.001	-0.034	-0.252	0.000
137	B	598	LEU	0	0.002	0.011	9.323	-0.008	-0.008	0.000	0.000	0.000	0.000
138	B	599	GLY	0	-0.007	0.011	12.703	-0.020	-0.020	0.000	0.000	0.000	0.000
139	B	600	ASN	0	0.023	0.018	10.890	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:442:ILE)