FMO DATABASE

FMODB ID: 53L1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1133172.439302
FMO2-HF: Nuclear repulsion	1072421.869103
FMO2-HF: Total energy	-60750.570199
FMO2-MP2: Total energy	-60927.10113

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.
-8.356	-4.542	8.264	-2.826	-9.254	0.001

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 : -0.008 / q_NPA : -0.007

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	0.023	0.005	3.878	-1.333	1.746	-0.021	-1.687	-1.372	0.000
4	B	445	VAL	0	-0.020	0.001	5.010	0.274	0.389	-0.001	-0.014	-0.099	0.000
5	B	446	GLY	0	0.065	0.038	2.128	-0.799	-0.759	4.117	-2.307	-1.851	0.005
6	B	447	LYS	1	0.869	0.898	2.074	-3.742	-5.333	3.221	1.956	-3.586	0.004
7	B	448	LYS	1	0.890	0.934	3.825	-1.926	-1.681	0.017	-0.045	-0.217	0.000
8	B	449	LEU	0	0.007	0.005	5.983	-0.331	-0.331	0.000	0.000	0.000	0.000
9	B	450	HIS	0	-0.004	-0.001	7.162	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	451	GLU	-1	-0.844	-0.906	8.755	0.654	0.654	0.000	0.000	0.000	0.000
11	B	452	TYR	0	-0.018	-0.032	10.756	-0.126	-0.126	0.000	0.000	0.000	0.000
12	B	453	ASN	0	0.040	0.022	11.321	-0.169	-0.169	0.000	0.000	0.000	0.000
13	B	454	THR	0	-0.014	-0.016	13.011	-0.062	-0.062	0.000	0.000	0.000	0.000
14	B	455	GLN	0	0.016	-0.004	15.052	-0.097	-0.097	0.000	0.000	0.000	0.000
15	B	456	PHE	0	-0.004	0.004	15.897	-0.056	-0.056	0.000	0.000	0.000	0.000
16	B	457	GLN	0	-0.016	-0.022	16.566	-0.088	-0.088	0.000	0.000	0.000	0.000
17	B	458	GLU	-1	-0.906	-0.919	19.498	0.292	0.292	0.000	0.000	0.000	0.000
18	B	459	LYS	1	0.921	0.945	19.388	-0.351	-0.351	0.000	0.000	0.000	0.000
19	B	460	SER	0	-0.022	-0.013	21.369	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	461	ARG	1	0.972	0.992	23.315	-0.253	-0.253	0.000	0.000	0.000	0.000
21	B	462	GLU	-1	-0.984	-0.985	25.266	0.175	0.175	0.000	0.000	0.000	0.000
22	B	463	TYR	0	-0.002	-0.011	26.412	-0.023	-0.023	0.000	0.000	0.000	0.000
23	B	464	ASP	-1	-0.880	-0.947	26.417	0.215	0.215	0.000	0.000	0.000	0.000
24	B	465	ARG	1	0.920	0.954	29.334	-0.172	-0.172	0.000	0.000	0.000	0.000
25	B	466	LEU	0	-0.019	0.000	30.955	-0.012	-0.012	0.000	0.000	0.000	0.000
26	B	467	TYR	0	0.021	0.002	32.041	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	468	GLU	-1	-0.916	-0.948	33.646	0.123	0.123	0.000	0.000	0.000	0.000
28	B	469	GLU	-1	-0.864	-0.894	35.455	0.097	0.097	0.000	0.000	0.000	0.000
29	B	470	TYR	0	-0.022	-0.038	36.512	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	471	THR	0	0.001	-0.010	36.938	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	472	ARG	1	0.813	0.888	39.550	-0.106	-0.106	0.000	0.000	0.000	0.000
32	B	473	THR	0	-0.028	-0.047	40.953	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	474	SER	0	-0.006	-0.003	42.258	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	475	GLN	0	-0.011	-0.011	43.955	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	476	GLU	-1	-0.774	-0.872	45.517	0.079	0.079	0.000	0.000	0.000	0.000
36	B	477	ILE	0	-0.035	-0.015	45.304	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	478	GLN	0	0.040	0.026	48.406	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	479	MET	0	-0.005	0.006	49.936	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	480	LYS	1	0.852	0.920	48.798	-0.074	-0.074	0.000	0.000	0.000	0.000
40	B	481	ARG	1	0.904	0.941	49.522	-0.064	-0.064	0.000	0.000	0.000	0.000
41	B	482	THR	0	0.024	0.005	54.338	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	483	ALA	0	-0.004	0.002	56.229	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	484	ILE	0	-0.015	-0.009	56.102	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	485	GLU	-1	-0.930	-0.962	58.274	0.047	0.047	0.000	0.000	0.000	0.000
45	B	486	ALA	0	0.028	0.017	60.955	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	487	PHE	0	-0.007	0.001	60.225	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	488	ASN	0	-0.019	-0.018	62.489	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	489	GLU	-1	-0.796	-0.882	65.530	0.035	0.035	0.000	0.000	0.000	0.000
49	B	490	THR	0	-0.052	-0.043	66.023	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	491	ILE	0	-0.049	-0.030	66.193	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	492	LYS	1	0.837	0.911	68.699	-0.036	-0.036	0.000	0.000	0.000	0.000
52	B	493	ILE	0	0.065	0.041	70.753	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	494	PHE	0	-0.052	-0.033	70.740	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	495	GLU	-1	-0.876	-0.943	73.048	0.030	0.030	0.000	0.000	0.000	0.000
55	B	496	GLU	-1	-0.905	-0.963	75.394	0.030	0.030	0.000	0.000	0.000	0.000
56	B	497	GLN	0	-0.020	0.009	77.629	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	498	CYS	0	-0.094	-0.049	78.132	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	499	GLN	0	0.035	0.001	78.668	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	500	THR	0	-0.061	-0.030	81.734	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	501	GLN	0	-0.067	-0.038	83.152	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	502	GLU	-1	-0.825	-0.880	84.757	0.023	0.023	0.000	0.000	0.000	0.000
62	B	503	ARG	1	0.905	0.965	85.529	-0.024	-0.024	0.000	0.000	0.000	0.000
63	B	504	TYR	0	0.045	0.012	87.470	0.000	0.000	0.000	0.000	0.000	0.000
64	B	505	SER	0	-0.042	-0.029	88.878	0.000	0.000	0.000	0.000	0.000	0.000
65	B	506	LYS	1	0.981	0.972	91.221	-0.020	-0.020	0.000	0.000	0.000	0.000
66	B	507	GLU	-1	-0.934	-0.973	93.029	0.020	0.020	0.000	0.000	0.000	0.000
67	B	508	TYR	0	-0.057	-0.012	94.040	0.000	0.000	0.000	0.000	0.000	0.000
68	B	509	ILE	0	-0.095	-0.033	93.404	0.000	0.000	0.000	0.000	0.000	0.000
69	B	521	ILE	0	0.022	0.010	95.903	0.000	0.000	0.000	0.000	0.000	0.000
70	B	522	GLN	0	0.094	0.046	95.350	0.001	0.001	0.000	0.000	0.000	0.000
71	B	523	ARG	1	0.905	0.944	91.986	-0.021	-0.021	0.000	0.000	0.000	0.000
72	B	524	ILE	0	0.003	0.003	89.060	0.001	0.001	0.000	0.000	0.000	0.000
73	B	525	MET	0	0.032	0.017	87.581	0.000	0.000	0.000	0.000	0.000	0.000
74	B	526	HIS	0	0.067	0.014	80.917	0.001	0.001	0.000	0.000	0.000	0.000
75	B	527	ASN	0	-0.042	-0.018	82.518	0.001	0.001	0.000	0.000	0.000	0.000
76	B	528	TYR	0	0.124	0.043	81.395	0.001	0.001	0.000	0.000	0.000	0.000
77	B	529	ASP	-1	-0.875	-0.941	81.008	0.026	0.026	0.000	0.000	0.000	0.000
78	B	530	LYS	1	0.854	0.931	77.152	-0.028	-0.028	0.000	0.000	0.000	0.000
79	B	531	LEU	0	-0.010	0.012	76.691	0.001	0.001	0.000	0.000	0.000	0.000
80	B	532	LYS	1	0.874	0.939	76.213	-0.025	-0.025	0.000	0.000	0.000	0.000
81	B	533	SER	0	-0.008	-0.005	74.235	0.000	0.000	0.000	0.000	0.000	0.000
82	B	534	ARG	1	0.851	0.921	67.634	-0.038	-0.038	0.000	0.000	0.000	0.000
83	B	535	ILE	0	0.042	0.019	71.039	0.001	0.001	0.000	0.000	0.000	0.000
84	B	536	SER	0	0.023	0.009	70.155	0.001	0.001	0.000	0.000	0.000	0.000
85	B	537	GLU	-1	-0.840	-0.900	67.953	0.039	0.039	0.000	0.000	0.000	0.000
86	B	538	ILE	0	-0.038	0.008	66.231	0.002	0.002	0.000	0.000	0.000	0.000
87	B	539	ILE	0	0.039	0.021	65.304	0.002	0.002	0.000	0.000	0.000	0.000
88	B	540	ASP	-1	-0.834	-0.927	64.518	0.040	0.040	0.000	0.000	0.000	0.000
89	B	541	SER	0	-0.107	-0.074	62.018	0.002	0.002	0.000	0.000	0.000	0.000
90	B	542	ARG	1	0.855	0.931	60.621	-0.039	-0.039	0.000	0.000	0.000	0.000
91	B	543	ARG	1	0.883	0.943	59.862	-0.039	-0.039	0.000	0.000	0.000	0.000
92	B	544	ARG	1	0.932	0.966	58.276	-0.045	-0.045	0.000	0.000	0.000	0.000
93	B	545	LEU	0	0.017	0.024	54.881	0.002	0.002	0.000	0.000	0.000	0.000
94	B	546	GLU	-1	-0.850	-0.924	55.118	0.046	0.046	0.000	0.000	0.000	0.000
95	B	547	GLU	-1	-0.940	-0.974	54.798	0.048	0.048	0.000	0.000	0.000	0.000
96	B	548	ASP	-1	-0.896	-0.946	52.128	0.062	0.062	0.000	0.000	0.000	0.000
97	B	549	LEU	0	-0.072	-0.027	50.396	0.003	0.003	0.000	0.000	0.000	0.000
98	B	550	LYS	1	0.938	0.956	50.030	-0.051	-0.051	0.000	0.000	0.000	0.000
99	B	551	LYS	1	0.873	0.940	45.321	-0.072	-0.072	0.000	0.000	0.000	0.000
100	B	552	GLN	0	0.049	0.009	46.025	0.001	0.001	0.000	0.000	0.000	0.000
101	B	553	ALA	0	-0.011	0.002	45.221	0.003	0.003	0.000	0.000	0.000	0.000
102	B	554	ALA	0	-0.080	-0.025	45.269	0.001	0.001	0.000	0.000	0.000	0.000
103	B	555	GLU	-1	-0.764	-0.878	41.568	0.082	0.082	0.000	0.000	0.000	0.000
104	B	556	TYR	0	-0.017	0.004	40.505	0.002	0.002	0.000	0.000	0.000	0.000
105	B	557	ARG	1	0.908	0.938	40.235	-0.063	-0.063	0.000	0.000	0.000	0.000
106	B	558	GLU	-1	-0.799	-0.878	36.900	0.097	0.097	0.000	0.000	0.000	0.000
107	B	559	ILE	0	-0.014	-0.014	35.729	0.006	0.006	0.000	0.000	0.000	0.000
108	B	560	ASP	-1	-0.830	-0.896	35.323	0.104	0.104	0.000	0.000	0.000	0.000
109	B	561	LYS	1	0.841	0.913	34.941	-0.089	-0.089	0.000	0.000	0.000	0.000
110	B	562	ARG	1	0.914	0.953	30.436	-0.128	-0.128	0.000	0.000	0.000	0.000
111	B	563	MET	0	0.016	0.018	31.140	0.011	0.011	0.000	0.000	0.000	0.000
112	B	564	ASN	0	-0.033	-0.042	30.462	0.016	0.016	0.000	0.000	0.000	0.000
113	B	565	SER	0	-0.013	0.004	29.552	-0.005	-0.005	0.000	0.000	0.000	0.000
114	B	566	ILE	0	-0.012	0.001	25.550	0.005	0.005	0.000	0.000	0.000	0.000
115	B	567	LYS	1	0.877	0.941	25.793	-0.124	-0.124	0.000	0.000	0.000	0.000
116	B	568	PRO	0	0.008	0.012	25.498	0.011	0.011	0.000	0.000	0.000	0.000
117	B	569	ASP	-1	-0.870	-0.935	21.922	0.243	0.243	0.000	0.000	0.000	0.000
118	B	570	LEU	0	0.028	0.010	21.189	0.025	0.025	0.000	0.000	0.000	0.000
119	B	571	ILE	0	-0.010	-0.017	21.003	0.026	0.026	0.000	0.000	0.000	0.000
120	B	572	GLN	0	-0.025	-0.019	20.051	0.004	0.004	0.000	0.000	0.000	0.000
121	B	573	LEU	0	0.016	0.014	16.430	0.029	0.029	0.000	0.000	0.000	0.000
122	B	574	ARG	1	0.868	0.977	16.164	-0.273	-0.273	0.000	0.000	0.000	0.000
123	B	575	LYS	1	0.903	0.941	15.820	-0.220	-0.220	0.000	0.000	0.000	0.000
124	B	576	THR	0	0.020	0.020	11.952	-0.005	-0.005	0.000	0.000	0.000	0.000
125	B	577	ARG	1	0.887	0.932	11.052	-0.508	-0.508	0.000	0.000	0.000	0.000
126	B	578	ASP	-1	-0.830	-0.903	11.081	0.458	0.458	0.000	0.000	0.000	0.000
127	B	579	GLN	0	-0.020	-0.018	12.653	0.008	0.008	0.000	0.000	0.000	0.000
128	B	580	TYR	0	-0.011	0.008	7.105	-0.048	-0.048	0.000	0.000	0.000	0.000
129	B	581	LEU	0	-0.004	0.003	7.420	0.258	0.258	0.000	0.000	0.000	0.000
130	B	582	MET	0	-0.055	-0.027	8.500	0.131	0.131	0.000	0.000	0.000	0.000
131	B	583	TRP	0	-0.028	-0.004	2.646	-2.173	-0.247	0.931	-0.729	-2.129	-0.008
132	B	593	LYS	1	0.969	0.983	14.428	-0.460	-0.460	0.000	0.000	0.000	0.000
133	B	594	LEU	0	0.024	0.006	10.730	0.110	0.110	0.000	0.000	0.000	0.000
134	B	595	ASN	0	-0.011	-0.015	10.940	0.013	0.013	0.000	0.000	0.000	0.000
135	B	596	GLU	-1	-0.803	-0.899	7.747	1.977	1.977	0.000	0.000	0.000	0.000
136	B	597	TRP	0	0.007	-0.003	5.180	0.258	0.258	0.000	0.000	0.000	0.000
137	B	598	LEU	0	0.000	-0.007	9.007	-0.066	-0.066	0.000	0.000	0.000	0.000
138	B	599	GLY	0	-0.023	0.016	12.178	-0.090	-0.090	0.000	0.000	0.000	0.000
139	B	600	ASN	0	-0.011	-0.003	11.135	-0.034	-0.034	0.000	0.000	0.000	0.000

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