FMO DATABASE

FMODB ID: YVG52

Calculation Name: 2WWE-A-Xray372

Preferred Name: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit gamma

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2WWE

Chain ID: A

ChEMBL ID: CHEMBL1163120

UniProt ID: O75747

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	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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-952152.757687
FMO2-HF: Nuclear repulsion	906188.168138
FMO2-HF: Total energy	-45964.589549
FMO2-MP2: Total energy	-46099.651888

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:-6:ASN)

Summations of interaction energy for fragment #1(A:-6:ASN)

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.
-22.88	-16.115	3.035	-3.955	-5.845	-0.026

Interaction energy analysis for fragmet #1(A:-6:ASN)

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 : -0.024

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	A	-4	TYR	0	0.029	0.014	2.744	-2.240	0.340	0.968	-1.175	-2.373	0.009
4	A	-3	PHE	0	-0.026	-0.017	6.080	0.663	0.663	0.000	0.000	0.000	0.000
5	A	-2	GLN	0	0.013	0.008	6.874	0.583	0.583	0.000	0.000	0.000	0.000
6	A	-1	SER	0	0.012	-0.001	10.003	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	0	MET	0	0.031	0.003	12.112	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	1203	SER	0	0.015	0.025	9.007	0.024	0.024	0.000	0.000	0.000	0.000
9	A	1204	ILE	0	0.012	0.010	10.993	0.120	0.120	0.000	0.000	0.000	0.000
10	A	1205	GLU	-1	-0.967	-0.976	12.425	-1.057	-1.057	0.000	0.000	0.000	0.000
11	A	1206	ARG	1	0.950	0.973	14.981	0.436	0.436	0.000	0.000	0.000	0.000
12	A	1207	ALA	0	0.023	0.010	18.061	0.046	0.046	0.000	0.000	0.000	0.000
13	A	1208	THR	0	-0.021	-0.006	20.258	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	1209	ILE	0	-0.049	-0.031	23.962	0.029	0.029	0.000	0.000	0.000	0.000
15	A	1210	LEU	0	-0.025	-0.014	26.983	0.010	0.010	0.000	0.000	0.000	0.000
16	A	1211	GLY	0	0.003	0.004	29.603	0.015	0.015	0.000	0.000	0.000	0.000
17	A	1212	PHE	0	-0.048	-0.016	30.784	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	1213	SER	0	-0.014	-0.017	30.733	0.013	0.013	0.000	0.000	0.000	0.000
19	A	1214	LYS	1	0.878	0.925	30.592	0.125	0.125	0.000	0.000	0.000	0.000
20	A	1215	LYS	1	0.830	0.890	30.077	0.111	0.111	0.000	0.000	0.000	0.000
21	A	1216	SER	0	0.041	0.016	34.084	0.004	0.004	0.000	0.000	0.000	0.000
22	A	1217	SER	0	0.036	0.027	33.937	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	1218	ASN	0	-0.043	-0.018	33.560	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	1219	LEU	0	-0.058	-0.026	28.776	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	1220	TYR	0	0.018	0.002	27.291	0.013	0.013	0.000	0.000	0.000	0.000
26	A	1221	LEU	0	-0.019	-0.010	27.378	0.000	0.000	0.000	0.000	0.000	0.000
27	A	1222	ILE	0	-0.015	-0.008	21.849	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	1223	GLN	0	0.016	0.003	23.506	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	1224	VAL	0	-0.001	0.001	17.259	-0.050	-0.050	0.000	0.000	0.000	0.000
30	A	1225	THR	0	-0.026	-0.014	19.033	0.069	0.069	0.000	0.000	0.000	0.000
31	A	1226	HIS	0	0.015	-0.001	14.750	-0.084	-0.084	0.000	0.000	0.000	0.000
32	A	1227	SER	0	0.022	0.020	12.563	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	1228	ASN	0	-0.008	-0.010	14.904	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	1229	ASN	0	-0.035	-0.034	17.522	0.027	0.027	0.000	0.000	0.000	0.000
35	A	1230	GLU	-1	-0.930	-0.930	19.295	-0.075	-0.075	0.000	0.000	0.000	0.000
36	A	1231	THR	0	-0.053	-0.037	19.856	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	1232	SER	0	-0.001	-0.013	19.018	0.034	0.034	0.000	0.000	0.000	0.000
38	A	1233	LEU	0	-0.033	-0.026	21.990	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	1234	THR	0	0.047	0.023	21.010	0.012	0.012	0.000	0.000	0.000	0.000
40	A	1235	GLU	-1	-0.754	-0.840	23.598	-0.138	-0.138	0.000	0.000	0.000	0.000
41	A	1236	LYS	1	0.808	0.913	21.041	0.265	0.265	0.000	0.000	0.000	0.000
42	A	1237	SER	0	0.087	0.047	25.904	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	1238	PHE	0	0.041	0.008	26.670	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	1239	GLU	-1	-0.871	-0.947	27.027	-0.247	-0.247	0.000	0.000	0.000	0.000
45	A	1240	GLN	0	0.004	0.003	23.670	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	1241	PHE	0	0.042	0.017	21.963	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	1242	SER	0	-0.009	-0.001	22.442	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	1243	LYS	1	0.896	0.953	21.275	0.284	0.284	0.000	0.000	0.000	0.000
49	A	1244	LEU	0	0.050	0.029	16.057	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	1245	HIS	0	0.091	0.088	18.221	-0.088	-0.088	0.000	0.000	0.000	0.000
51	A	1246	SER	0	-0.064	-0.034	19.386	-0.038	-0.038	0.000	0.000	0.000	0.000
52	A	1247	GLN	0	-0.065	-0.051	16.683	0.002	0.002	0.000	0.000	0.000	0.000
53	A	1248	LEU	0	0.079	0.038	13.182	-0.044	-0.044	0.000	0.000	0.000	0.000
54	A	1249	GLN	0	-0.007	-0.010	15.316	-0.083	-0.083	0.000	0.000	0.000	0.000
55	A	1250	LYS	1	0.863	0.942	17.524	0.395	0.395	0.000	0.000	0.000	0.000
56	A	1251	GLN	0	-0.026	-0.001	9.531	0.150	0.150	0.000	0.000	0.000	0.000
57	A	1252	PHE	0	-0.008	-0.015	8.126	-0.136	-0.136	0.000	0.000	0.000	0.000
58	A	1253	ALA	0	0.035	0.019	13.051	0.015	0.015	0.000	0.000	0.000	0.000
59	A	1254	SER	0	-0.019	-0.009	13.086	0.091	0.091	0.000	0.000	0.000	0.000
60	A	1255	LEU	0	-0.041	-0.005	9.397	-0.040	-0.040	0.000	0.000	0.000	0.000
61	A	1256	THR	0	-0.002	0.000	13.850	0.182	0.182	0.000	0.000	0.000	0.000
62	A	1257	LEU	0	-0.024	-0.005	14.040	-0.076	-0.076	0.000	0.000	0.000	0.000
63	A	1258	PRO	0	0.022	0.021	16.996	0.079	0.079	0.000	0.000	0.000	0.000
64	A	1259	GLU	-1	-0.932	-0.976	19.930	-0.517	-0.517	0.000	0.000	0.000	0.000
65	A	1260	PHE	0	-0.010	0.008	22.830	0.004	0.004	0.000	0.000	0.000	0.000
66	A	1261	PRO	0	0.006	-0.008	24.397	0.032	0.032	0.000	0.000	0.000	0.000
67	A	1262	HIS	1	0.881	0.949	27.642	0.379	0.379	0.000	0.000	0.000	0.000
68	A	1263	TRP	0	0.058	0.015	29.757	0.026	0.026	0.000	0.000	0.000	0.000
69	A	1264	TRP	0	0.051	0.025	30.665	0.015	0.015	0.000	0.000	0.000	0.000
70	A	1265	HIS	0	-0.058	-0.028	33.965	0.002	0.002	0.000	0.000	0.000	0.000
71	A	1266	LEU	0	0.082	0.029	36.894	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	1267	PRO	0	-0.001	-0.018	37.170	0.003	0.003	0.000	0.000	0.000	0.000
73	A	1268	PHE	0	-0.003	0.012	30.218	0.003	0.003	0.000	0.000	0.000	0.000
74	A	1269	THR	0	0.008	-0.001	35.604	0.002	0.002	0.000	0.000	0.000	0.000
75	A	1270	ASN	0	-0.015	-0.005	38.021	0.009	0.009	0.000	0.000	0.000	0.000
76	A	1271	SER	0	-0.028	0.004	37.793	0.003	0.003	0.000	0.000	0.000	0.000
77	A	1272	ASP	-1	-0.780	-0.905	35.607	-0.191	-0.191	0.000	0.000	0.000	0.000
78	A	1273	HIS	0	0.012	-0.001	33.978	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	1274	ARG	1	0.823	0.933	32.548	0.263	0.263	0.000	0.000	0.000	0.000
80	A	1275	ARG	1	0.900	0.952	31.448	0.193	0.193	0.000	0.000	0.000	0.000
81	A	1276	PHE	0	0.021	0.005	29.551	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	1277	ARG	1	0.952	0.984	28.372	0.305	0.305	0.000	0.000	0.000	0.000
83	A	1278	ASP	-1	-0.821	-0.919	27.816	-0.366	-0.366	0.000	0.000	0.000	0.000
84	A	1279	LEU	0	-0.024	-0.013	25.199	-0.038	-0.038	0.000	0.000	0.000	0.000
85	A	1280	ASN	0	0.079	0.041	23.779	-0.051	-0.051	0.000	0.000	0.000	0.000
86	A	1281	HIS	0	-0.076	-0.044	23.125	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	1282	TYR	0	-0.040	-0.055	19.400	-0.059	-0.059	0.000	0.000	0.000	0.000
88	A	1283	MET	0	-0.027	-0.015	19.387	-0.069	-0.069	0.000	0.000	0.000	0.000
89	A	1284	GLU	-1	-0.813	-0.888	18.134	-0.639	-0.639	0.000	0.000	0.000	0.000
90	A	1285	GLN	0	-0.026	-0.025	17.733	-0.116	-0.116	0.000	0.000	0.000	0.000
91	A	1286	ILE	0	-0.060	-0.025	15.228	-0.136	-0.136	0.000	0.000	0.000	0.000
92	A	1287	LEU	0	-0.044	-0.013	13.399	-0.162	-0.162	0.000	0.000	0.000	0.000
93	A	1288	ASN	0	-0.049	-0.032	13.126	-0.176	-0.176	0.000	0.000	0.000	0.000
94	A	1289	VAL	0	-0.013	0.018	11.440	0.025	0.025	0.000	0.000	0.000	0.000
95	A	1290	SER	0	0.022	-0.011	7.267	0.074	0.074	0.000	0.000	0.000	0.000
96	A	1291	HIS	0	0.004	0.011	2.241	-3.550	-2.409	0.990	-0.730	-1.401	-0.005
97	A	1292	GLU	-1	-0.848	-0.948	2.371	-21.026	-17.982	1.077	-2.050	-2.071	-0.030
98	A	1293	VAL	0	0.000	0.012	5.523	1.170	1.170	0.000	0.000	0.000	0.000
99	A	1294	THR	0	0.016	0.005	8.648	0.417	0.417	0.000	0.000	0.000	0.000
100	A	1295	ASN	0	-0.079	-0.043	5.229	1.279	1.279	0.000	0.000	0.000	0.000
101	A	1296	SER	0	-0.024	-0.008	6.892	0.518	0.518	0.000	0.000	0.000	0.000
102	A	1297	ASP	-1	-0.866	-0.942	8.700	0.080	0.080	0.000	0.000	0.000	0.000
103	A	1298	CYS	0	-0.055	-0.019	10.921	0.054	0.054	0.000	0.000	0.000	0.000
104	A	1299	VAL	0	0.040	0.016	11.681	0.133	0.133	0.000	0.000	0.000	0.000
105	A	1300	LEU	0	0.019	0.010	8.456	0.125	0.125	0.000	0.000	0.000	0.000
106	A	1301	SER	0	0.010	0.007	12.788	0.131	0.131	0.000	0.000	0.000	0.000
107	A	1302	PHE	0	-0.080	-0.033	15.526	0.071	0.071	0.000	0.000	0.000	0.000
108	A	1303	PHE	0	-0.005	-0.038	15.419	0.056	0.056	0.000	0.000	0.000	0.000
109	A	1304	LEU	0	0.025	0.022	13.546	0.035	0.035	0.000	0.000	0.000	0.000
110	A	1305	SER	0	-0.047	-0.001	17.427	0.062	0.062	0.000	0.000	0.000	0.000
111	A	1306	GLU	-1	-0.917	-0.946	19.997	-0.118	-0.118	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-6:ASN)