FMO DATABASE

FMODB ID: 1NL1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-953845.763659
FMO2-HF: Nuclear repulsion	907880.500272
FMO2-HF: Total energy	-45965.263387
FMO2-MP2: Total energy	-46100.355928

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.
-24.909	-19.878	8.552	-5.775	-7.806	-0.051

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 : -0.049 / q_NPA : -0.035

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	-0.017	-0.019	2.238	-0.128	1.957	2.344	-1.537	-2.892	0.007
4	A	-3	PHE	0	-0.017	-0.017	5.750	0.866	0.866	0.000	0.000	0.000	0.000
5	A	-2	GLN	0	-0.005	0.007	6.862	0.687	0.687	0.000	0.000	0.000	0.000
6	A	-1	SER	0	0.028	0.003	9.820	-0.102	-0.102	0.000	0.000	0.000	0.000
7	A	0	MET	0	-0.006	-0.014	11.643	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	1203	SER	0	0.039	0.043	8.559	0.067	0.067	0.000	0.000	0.000	0.000
9	A	1204	ILE	0	-0.033	-0.015	10.441	0.128	0.128	0.000	0.000	0.000	0.000
10	A	1205	GLU	-1	-0.880	-0.915	11.960	-1.224	-1.224	0.000	0.000	0.000	0.000
11	A	1206	ARG	1	0.873	0.918	14.523	0.523	0.523	0.000	0.000	0.000	0.000
12	A	1207	ALA	0	0.031	0.014	17.575	0.046	0.046	0.000	0.000	0.000	0.000
13	A	1208	THR	0	-0.006	0.000	19.865	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	1209	ILE	0	-0.053	-0.022	23.610	0.031	0.031	0.000	0.000	0.000	0.000
15	A	1210	LEU	0	-0.023	-0.007	26.597	0.002	0.002	0.000	0.000	0.000	0.000
16	A	1211	GLY	0	0.001	0.002	29.363	0.017	0.017	0.000	0.000	0.000	0.000
17	A	1212	PHE	0	-0.027	-0.006	30.611	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	1213	SER	0	-0.035	-0.033	30.266	0.010	0.010	0.000	0.000	0.000	0.000
19	A	1214	LYS	1	0.867	0.910	29.983	0.129	0.129	0.000	0.000	0.000	0.000
20	A	1215	LYS	1	0.818	0.908	28.619	0.113	0.113	0.000	0.000	0.000	0.000
21	A	1216	SER	0	0.018	-0.004	33.751	0.004	0.004	0.000	0.000	0.000	0.000
22	A	1217	SER	0	0.036	0.019	33.418	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	1218	ASN	0	-0.036	-0.012	33.317	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	1219	LEU	0	-0.056	-0.023	27.984	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	1220	TYR	0	0.016	0.007	27.196	0.012	0.012	0.000	0.000	0.000	0.000
26	A	1221	LEU	0	-0.012	-0.005	27.110	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	1222	ILE	0	-0.014	-0.014	21.797	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	1223	GLN	0	0.018	0.011	23.155	0.020	0.020	0.000	0.000	0.000	0.000
29	A	1224	VAL	0	-0.012	-0.007	16.908	-0.056	-0.056	0.000	0.000	0.000	0.000
30	A	1225	THR	0	-0.040	-0.025	18.421	0.066	0.066	0.000	0.000	0.000	0.000
31	A	1226	HIS	0	0.028	0.017	14.067	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	1227	SER	0	0.024	-0.001	12.343	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	1228	ASN	0	-0.028	-0.019	14.608	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	1229	ASN	0	-0.046	-0.028	17.329	0.025	0.025	0.000	0.000	0.000	0.000
35	A	1230	GLU	-1	-0.868	-0.914	19.059	-0.093	-0.093	0.000	0.000	0.000	0.000
36	A	1231	THR	0	-0.096	-0.050	19.585	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	1232	SER	0	0.013	0.003	18.469	0.033	0.033	0.000	0.000	0.000	0.000
38	A	1233	LEU	0	-0.017	-0.017	21.555	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	1234	THR	0	0.006	0.003	20.613	0.011	0.011	0.000	0.000	0.000	0.000
40	A	1235	GLU	-1	-0.755	-0.848	23.299	-0.145	-0.145	0.000	0.000	0.000	0.000
41	A	1236	LYS	1	0.850	0.945	20.853	0.257	0.257	0.000	0.000	0.000	0.000
42	A	1237	SER	0	0.026	-0.016	25.534	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	1238	PHE	0	0.030	0.007	25.996	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	1239	GLU	-1	-0.809	-0.876	26.305	-0.260	-0.260	0.000	0.000	0.000	0.000
45	A	1240	GLN	0	0.012	0.009	23.285	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	1241	PHE	0	0.062	0.028	21.040	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	1242	SER	0	-0.026	-0.023	21.639	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	1243	LYS	1	0.831	0.918	20.985	0.230	0.230	0.000	0.000	0.000	0.000
49	A	1244	LEU	0	0.031	0.022	15.214	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	1245	HIS	0	0.099	0.069	17.646	-0.094	-0.094	0.000	0.000	0.000	0.000
51	A	1246	SER	0	-0.048	-0.022	19.085	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	1247	GLN	0	0.005	0.007	16.184	0.082	0.082	0.000	0.000	0.000	0.000
53	A	1248	LEU	0	0.081	0.040	12.606	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	1249	GLN	0	-0.015	-0.025	14.920	-0.084	-0.084	0.000	0.000	0.000	0.000
55	A	1250	LYS	1	0.830	0.924	17.057	0.448	0.448	0.000	0.000	0.000	0.000
56	A	1251	GLN	0	-0.004	-0.006	8.828	0.146	0.146	0.000	0.000	0.000	0.000
57	A	1252	PHE	0	0.029	0.008	7.610	-0.096	-0.096	0.000	0.000	0.000	0.000
58	A	1253	ALA	0	0.029	0.027	12.629	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	1254	SER	0	-0.085	-0.051	12.894	0.124	0.124	0.000	0.000	0.000	0.000
60	A	1255	LEU	0	0.004	0.013	8.782	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	1256	THR	0	-0.025	-0.014	13.376	0.197	0.197	0.000	0.000	0.000	0.000
62	A	1257	LEU	0	-0.004	0.006	13.670	-0.057	-0.057	0.000	0.000	0.000	0.000
63	A	1258	PRO	0	0.014	0.015	16.483	0.086	0.086	0.000	0.000	0.000	0.000
64	A	1259	GLU	-1	-0.844	-0.937	19.395	-0.460	-0.460	0.000	0.000	0.000	0.000
65	A	1260	PHE	0	-0.011	0.011	22.244	0.003	0.003	0.000	0.000	0.000	0.000
66	A	1261	PRO	0	0.014	-0.003	24.042	0.039	0.039	0.000	0.000	0.000	0.000
67	A	1262	HIS	1	0.801	0.914	26.978	0.441	0.441	0.000	0.000	0.000	0.000
68	A	1263	TRP	0	0.048	-0.001	29.481	0.029	0.029	0.000	0.000	0.000	0.000
69	A	1264	TRP	0	0.044	0.026	29.656	0.016	0.016	0.000	0.000	0.000	0.000
70	A	1265	HIS	0	-0.053	-0.018	33.023	0.002	0.002	0.000	0.000	0.000	0.000
71	A	1266	LEU	0	0.079	0.031	36.499	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	1267	PRO	0	-0.002	-0.014	37.015	0.003	0.003	0.000	0.000	0.000	0.000
73	A	1268	PHE	0	-0.004	0.004	29.688	0.000	0.000	0.000	0.000	0.000	0.000
74	A	1269	THR	0	0.003	-0.004	35.189	0.003	0.003	0.000	0.000	0.000	0.000
75	A	1270	ASN	0	-0.019	-0.013	37.380	0.007	0.007	0.000	0.000	0.000	0.000
76	A	1271	SER	0	-0.010	0.004	37.304	0.004	0.004	0.000	0.000	0.000	0.000
77	A	1272	ASP	-1	-0.765	-0.887	34.944	-0.206	-0.206	0.000	0.000	0.000	0.000
78	A	1273	HIS	0	0.018	0.009	33.339	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	1274	ARG	1	0.820	0.916	31.249	0.297	0.297	0.000	0.000	0.000	0.000
80	A	1275	ARG	1	0.848	0.914	30.819	0.201	0.201	0.000	0.000	0.000	0.000
81	A	1276	PHE	0	0.018	0.001	29.017	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	1277	ARG	1	0.906	0.947	27.812	0.341	0.341	0.000	0.000	0.000	0.000
83	A	1278	ASP	-1	-0.767	-0.869	27.285	-0.402	-0.402	0.000	0.000	0.000	0.000
84	A	1279	LEU	0	-0.013	0.001	24.586	-0.041	-0.041	0.000	0.000	0.000	0.000
85	A	1280	ASN	0	0.040	0.015	23.215	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	1281	HIS	0	-0.059	-0.036	22.521	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	1282	TYR	0	-0.012	-0.021	18.870	-0.060	-0.060	0.000	0.000	0.000	0.000
88	A	1283	MET	0	-0.036	-0.020	18.876	-0.082	-0.082	0.000	0.000	0.000	0.000
89	A	1284	GLU	-1	-0.831	-0.908	17.665	-0.708	-0.708	0.000	0.000	0.000	0.000
90	A	1285	GLN	0	-0.032	-0.017	17.371	-0.135	-0.135	0.000	0.000	0.000	0.000
91	A	1286	ILE	0	-0.036	-0.020	14.829	-0.167	-0.167	0.000	0.000	0.000	0.000
92	A	1287	LEU	0	-0.046	-0.014	12.846	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	1288	ASN	0	-0.034	-0.018	12.294	-0.253	-0.253	0.000	0.000	0.000	0.000
94	A	1289	VAL	0	-0.034	0.005	11.221	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	1290	SER	0	-0.013	-0.043	5.751	0.333	0.333	0.000	0.000	0.000	0.000
96	A	1291	HIS	0	0.008	0.012	2.642	-4.021	-2.418	0.985	-0.971	-1.616	-0.011
97	A	1292	GLU	-1	-0.728	-0.851	2.011	-25.497	-24.214	5.224	-3.263	-3.244	-0.047
98	A	1293	VAL	0	-0.006	0.006	5.157	1.504	1.564	-0.001	-0.004	-0.054	0.000
99	A	1294	THR	0	0.007	0.000	8.417	0.501	0.501	0.000	0.000	0.000	0.000
100	A	1295	ASN	0	-0.078	-0.046	5.136	1.304	1.304	0.000	0.000	0.000	0.000
101	A	1296	SER	0	-0.021	-0.014	6.511	0.606	0.606	0.000	0.000	0.000	0.000
102	A	1297	ASP	-1	-0.855	-0.925	8.391	0.075	0.075	0.000	0.000	0.000	0.000
103	A	1298	CYS	0	-0.062	-0.019	10.863	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	1299	VAL	0	0.042	0.021	11.448	0.113	0.113	0.000	0.000	0.000	0.000
105	A	1300	LEU	0	0.013	0.011	7.947	0.118	0.118	0.000	0.000	0.000	0.000
106	A	1301	SER	0	0.004	-0.024	12.507	0.097	0.097	0.000	0.000	0.000	0.000
107	A	1302	PHE	0	-0.080	-0.018	15.285	0.062	0.062	0.000	0.000	0.000	0.000
108	A	1303	PHE	0	0.008	-0.025	15.140	0.055	0.055	0.000	0.000	0.000	0.000
109	A	1304	LEU	0	0.001	0.010	13.166	0.033	0.033	0.000	0.000	0.000	0.000
110	A	1305	SER	0	-0.006	0.000	17.194	0.074	0.074	0.000	0.000	0.000	0.000
111	A	1306	GLU	-1	-0.893	-0.931	19.975	-0.148	-0.148	0.000	0.000	0.000	0.000

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