FMO DATABASE

FMODB ID: 43M1N

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:

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129873.604982
FMO2-HF: Nuclear repulsion	1069124.125257
FMO2-HF: Total energy	-60749.479725
FMO2-MP2: Total energy	-60926.11979

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.
-7.389	-1.981	5.239	-2.589	-8.06	0.002

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 : -0.007 / q_NPA : -0.008

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	0.004	0.005	3.809	-0.778	1.539	-0.026	-1.204	-1.088	0.002
4	B	445	VAL	0	0.003	0.003	5.158	0.043	0.121	-0.001	-0.011	-0.067	0.000
5	B	446	GLY	0	0.042	0.025	2.216	-1.028	-0.286	2.042	-1.375	-1.409	0.003
6	B	447	LYS	1	0.900	0.939	2.226	-4.044	-3.775	2.536	0.572	-3.377	0.002
7	B	448	LYS	1	0.897	0.929	3.661	-1.269	-1.127	0.021	0.038	-0.201	0.000
8	B	449	LEU	0	-0.005	0.001	5.873	-0.239	-0.239	0.000	0.000	0.000	0.000
9	B	450	HIS	0	0.003	0.012	6.972	0.035	0.035	0.000	0.000	0.000	0.000
10	B	451	GLU	-1	-0.844	-0.920	8.560	0.526	0.526	0.000	0.000	0.000	0.000
11	B	452	TYR	0	-0.031	-0.047	10.468	-0.112	-0.112	0.000	0.000	0.000	0.000
12	B	453	ASN	0	-0.006	0.001	11.504	-0.129	-0.129	0.000	0.000	0.000	0.000
13	B	454	THR	0	0.013	-0.008	13.217	-0.041	-0.041	0.000	0.000	0.000	0.000
14	B	455	GLN	0	0.031	0.016	15.015	-0.065	-0.065	0.000	0.000	0.000	0.000
15	B	456	PHE	0	0.008	0.009	15.871	-0.045	-0.045	0.000	0.000	0.000	0.000
16	B	457	GLN	0	0.021	-0.008	17.020	-0.064	-0.064	0.000	0.000	0.000	0.000
17	B	458	GLU	-1	-0.936	-0.941	19.701	0.235	0.235	0.000	0.000	0.000	0.000
18	B	459	LYS	1	0.925	0.952	19.231	-0.280	-0.280	0.000	0.000	0.000	0.000
19	B	460	SER	0	-0.018	-0.011	21.023	-0.015	-0.015	0.000	0.000	0.000	0.000
20	B	461	ARG	1	0.954	0.985	23.000	-0.209	-0.209	0.000	0.000	0.000	0.000
21	B	462	GLU	-1	-0.989	-0.996	25.096	0.144	0.144	0.000	0.000	0.000	0.000
22	B	463	TYR	0	0.012	0.015	26.294	-0.020	-0.020	0.000	0.000	0.000	0.000
23	B	464	ASP	-1	-0.847	-0.931	26.881	0.179	0.179	0.000	0.000	0.000	0.000
24	B	465	ARG	1	0.887	0.929	29.313	-0.146	-0.146	0.000	0.000	0.000	0.000
25	B	466	LEU	0	-0.012	0.006	30.657	-0.009	-0.009	0.000	0.000	0.000	0.000
26	B	467	TYR	0	0.004	-0.002	31.908	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	468	GLU	-1	-0.909	-0.946	33.640	0.103	0.103	0.000	0.000	0.000	0.000
28	B	469	GLU	-1	-0.873	-0.916	35.471	0.082	0.082	0.000	0.000	0.000	0.000
29	B	470	TYR	0	-0.021	-0.034	36.189	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	471	THR	0	-0.029	-0.028	36.914	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	472	ARG	1	0.795	0.862	39.458	-0.088	-0.088	0.000	0.000	0.000	0.000
32	B	473	THR	0	-0.030	-0.030	40.887	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	474	SER	0	0.009	0.015	42.480	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	475	GLN	0	0.005	-0.005	44.159	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	476	GLU	-1	-0.796	-0.859	45.564	0.068	0.068	0.000	0.000	0.000	0.000
36	B	477	ILE	0	-0.028	-0.012	45.631	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	478	GLN	0	0.037	0.016	48.399	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	479	MET	0	-0.013	-0.004	50.233	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	480	LYS	1	0.897	0.943	49.009	-0.061	-0.061	0.000	0.000	0.000	0.000
40	B	481	ARG	1	0.887	0.939	49.814	-0.052	-0.052	0.000	0.000	0.000	0.000
41	B	482	THR	0	0.030	0.012	54.614	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	483	ALA	0	-0.012	0.003	56.353	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	484	ILE	0	-0.005	0.001	56.506	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	485	GLU	-1	-0.911	-0.949	58.547	0.039	0.039	0.000	0.000	0.000	0.000
45	B	486	ALA	0	0.022	0.017	61.028	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	487	PHE	0	-0.004	-0.011	59.999	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	488	ASN	0	-0.038	-0.020	62.518	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	489	GLU	-1	-0.777	-0.867	65.617	0.030	0.030	0.000	0.000	0.000	0.000
49	B	490	THR	0	-0.035	-0.023	66.247	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	491	ILE	0	-0.046	-0.039	65.938	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	492	LYS	1	0.832	0.885	68.561	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	493	ILE	0	0.030	0.026	70.810	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	494	PHE	0	-0.084	-0.043	70.814	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	495	GLU	-1	-0.874	-0.946	73.268	0.025	0.025	0.000	0.000	0.000	0.000
55	B	496	GLU	-1	-0.929	-0.974	75.734	0.025	0.025	0.000	0.000	0.000	0.000
56	B	497	GLN	0	0.020	0.038	78.135	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	498	CYS	0	-0.077	-0.048	78.232	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	499	GLN	0	0.028	0.011	79.700	0.000	0.000	0.000	0.000	0.000	0.000
59	B	500	THR	0	-0.042	-0.024	82.007	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	501	GLN	0	-0.084	-0.043	83.805	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	502	GLU	-1	-0.847	-0.906	85.078	0.019	0.019	0.000	0.000	0.000	0.000
62	B	503	ARG	1	0.899	0.954	85.422	-0.020	-0.020	0.000	0.000	0.000	0.000
63	B	504	TYR	0	0.048	0.022	87.963	0.000	0.000	0.000	0.000	0.000	0.000
64	B	505	SER	0	-0.042	-0.040	88.561	0.000	0.000	0.000	0.000	0.000	0.000
65	B	506	LYS	1	0.981	0.965	91.068	-0.017	-0.017	0.000	0.000	0.000	0.000
66	B	507	GLU	-1	-0.976	-0.966	92.852	0.016	0.016	0.000	0.000	0.000	0.000
67	B	508	TYR	0	-0.101	-0.048	94.108	0.000	0.000	0.000	0.000	0.000	0.000
68	B	509	ILE	0	-0.034	-0.002	93.033	0.000	0.000	0.000	0.000	0.000	0.000
69	B	521	ILE	0	0.004	-0.015	96.073	0.000	0.000	0.000	0.000	0.000	0.000
70	B	522	GLN	0	0.113	0.052	95.357	0.000	0.000	0.000	0.000	0.000	0.000
71	B	523	ARG	1	0.912	0.972	91.791	-0.018	-0.018	0.000	0.000	0.000	0.000
72	B	524	ILE	0	-0.003	-0.011	89.207	0.001	0.001	0.000	0.000	0.000	0.000
73	B	525	MET	0	0.038	0.016	87.820	0.000	0.000	0.000	0.000	0.000	0.000
74	B	526	HIS	0	0.062	0.024	81.107	0.001	0.001	0.000	0.000	0.000	0.000
75	B	527	ASN	0	-0.015	-0.020	82.246	0.001	0.001	0.000	0.000	0.000	0.000
76	B	528	TYR	0	0.137	0.065	81.421	0.001	0.001	0.000	0.000	0.000	0.000
77	B	529	ASP	-1	-0.869	-0.947	81.324	0.021	0.021	0.000	0.000	0.000	0.000
78	B	530	LYS	1	0.842	0.929	77.273	-0.024	-0.024	0.000	0.000	0.000	0.000
79	B	531	LEU	0	-0.017	0.007	76.814	0.001	0.001	0.000	0.000	0.000	0.000
80	B	532	LYS	1	0.903	0.968	76.353	-0.021	-0.021	0.000	0.000	0.000	0.000
81	B	533	SER	0	0.000	-0.003	74.437	0.000	0.000	0.000	0.000	0.000	0.000
82	B	534	ARG	1	0.868	0.924	67.523	-0.032	-0.032	0.000	0.000	0.000	0.000
83	B	535	ILE	0	0.054	0.023	70.942	0.001	0.001	0.000	0.000	0.000	0.000
84	B	536	SER	0	0.008	0.003	70.122	0.001	0.001	0.000	0.000	0.000	0.000
85	B	537	GLU	-1	-0.843	-0.901	68.014	0.032	0.032	0.000	0.000	0.000	0.000
86	B	538	ILE	0	-0.051	0.002	66.339	0.002	0.002	0.000	0.000	0.000	0.000
87	B	539	ILE	0	0.027	0.016	65.250	0.001	0.001	0.000	0.000	0.000	0.000
88	B	540	ASP	-1	-0.820	-0.922	64.540	0.032	0.032	0.000	0.000	0.000	0.000
89	B	541	SER	0	-0.107	-0.073	62.220	0.002	0.002	0.000	0.000	0.000	0.000
90	B	542	ARG	1	0.871	0.924	60.640	-0.032	-0.032	0.000	0.000	0.000	0.000
91	B	543	ARG	1	0.885	0.958	59.997	-0.031	-0.031	0.000	0.000	0.000	0.000
92	B	544	ARG	1	0.937	0.973	58.463	-0.037	-0.037	0.000	0.000	0.000	0.000
93	B	545	LEU	0	-0.008	0.008	54.981	0.002	0.002	0.000	0.000	0.000	0.000
94	B	546	GLU	-1	-0.854	-0.928	55.215	0.037	0.037	0.000	0.000	0.000	0.000
95	B	547	GLU	-1	-0.962	-0.985	54.783	0.039	0.039	0.000	0.000	0.000	0.000
96	B	548	ASP	-1	-0.902	-0.949	52.164	0.050	0.050	0.000	0.000	0.000	0.000
97	B	549	LEU	0	-0.072	-0.029	50.526	0.003	0.003	0.000	0.000	0.000	0.000
98	B	550	LYS	1	0.963	0.966	49.801	-0.041	-0.041	0.000	0.000	0.000	0.000
99	B	551	LYS	1	0.987	1.013	46.932	-0.051	-0.051	0.000	0.000	0.000	0.000
100	B	552	GLN	0	0.100	0.037	45.635	0.001	0.001	0.000	0.000	0.000	0.000
101	B	553	ALA	0	-0.029	0.007	45.176	0.003	0.003	0.000	0.000	0.000	0.000
102	B	554	ALA	0	-0.103	-0.064	44.663	0.002	0.002	0.000	0.000	0.000	0.000
103	B	555	GLU	-1	-0.888	-0.937	40.843	0.073	0.073	0.000	0.000	0.000	0.000
104	B	556	TYR	0	-0.012	0.000	40.653	0.001	0.001	0.000	0.000	0.000	0.000
105	B	557	ARG	1	0.924	0.941	40.348	-0.049	-0.049	0.000	0.000	0.000	0.000
106	B	558	GLU	-1	-0.810	-0.875	37.289	0.072	0.072	0.000	0.000	0.000	0.000
107	B	559	ILE	0	-0.009	-0.016	35.845	0.004	0.004	0.000	0.000	0.000	0.000
108	B	560	ASP	-1	-0.850	-0.911	35.490	0.082	0.082	0.000	0.000	0.000	0.000
109	B	561	LYS	1	0.813	0.890	35.041	-0.065	-0.065	0.000	0.000	0.000	0.000
110	B	562	ARG	1	0.929	0.961	30.870	-0.095	-0.095	0.000	0.000	0.000	0.000
111	B	563	MET	0	0.051	0.041	30.904	0.011	0.011	0.000	0.000	0.000	0.000
112	B	564	ASN	0	-0.120	-0.057	30.754	0.011	0.011	0.000	0.000	0.000	0.000
113	B	565	SER	0	-0.019	-0.018	29.577	-0.009	-0.009	0.000	0.000	0.000	0.000
114	B	566	ILE	0	0.018	0.021	25.212	0.002	0.002	0.000	0.000	0.000	0.000
115	B	567	LYS	1	0.953	0.983	25.575	-0.106	-0.106	0.000	0.000	0.000	0.000
116	B	568	PRO	0	0.010	0.010	25.376	0.010	0.010	0.000	0.000	0.000	0.000
117	B	569	ASP	-1	-0.859	-0.923	22.213	0.173	0.173	0.000	0.000	0.000	0.000
118	B	570	LEU	0	-0.005	-0.019	21.042	0.018	0.018	0.000	0.000	0.000	0.000
119	B	571	ILE	0	-0.034	-0.036	20.721	0.025	0.025	0.000	0.000	0.000	0.000
120	B	572	GLN	0	-0.019	-0.015	20.245	0.006	0.006	0.000	0.000	0.000	0.000
121	B	573	LEU	0	0.015	0.025	16.227	0.014	0.014	0.000	0.000	0.000	0.000
122	B	574	ARG	1	0.871	0.977	16.074	-0.220	-0.220	0.000	0.000	0.000	0.000
123	B	575	LYS	1	0.914	0.936	15.916	-0.181	-0.181	0.000	0.000	0.000	0.000
124	B	576	THR	0	0.013	0.019	11.660	-0.007	-0.007	0.000	0.000	0.000	0.000
125	B	577	ARG	1	0.901	0.933	11.076	-0.411	-0.411	0.000	0.000	0.000	0.000
126	B	578	ASP	-1	-0.836	-0.887	11.282	0.380	0.380	0.000	0.000	0.000	0.000
127	B	579	GLN	0	-0.029	-0.020	12.954	-0.003	-0.003	0.000	0.000	0.000	0.000
128	B	580	TYR	0	-0.011	0.010	7.483	-0.009	-0.009	0.000	0.000	0.000	0.000
129	B	581	LEU	0	0.000	0.008	8.361	0.170	0.170	0.000	0.000	0.000	0.000
130	B	582	MET	0	-0.045	-0.032	8.547	0.163	0.163	0.000	0.000	0.000	0.000
131	B	583	TRP	0	-0.002	0.008	2.651	-1.681	0.179	0.667	-0.609	-1.918	-0.005
132	B	593	LYS	1	0.984	0.991	14.146	-0.493	-0.493	0.000	0.000	0.000	0.000
133	B	594	LEU	0	0.017	-0.001	10.723	0.125	0.125	0.000	0.000	0.000	0.000
134	B	595	ASN	0	-0.027	-0.022	10.914	-0.007	-0.007	0.000	0.000	0.000	0.000
135	B	596	GLU	-1	-0.869	-0.932	8.113	1.809	1.809	0.000	0.000	0.000	0.000
136	B	597	TRP	0	0.021	-0.008	4.858	0.284	0.284	0.000	0.000	0.000	0.000
137	B	598	LEU	0	0.004	0.006	9.016	-0.075	-0.075	0.000	0.000	0.000	0.000
138	B	599	GLY	0	-0.011	0.008	12.411	-0.056	-0.056	0.000	0.000	0.000	0.000
139	B	600	ASN	0	0.017	0.015	10.895	-0.046	-0.046	0.000	0.000	0.000	0.000

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