FMO DATABASE

FMODB ID: 6Y2NZ

Calculation Name: 3GBW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GBW

Chain ID: A

ChEMBL ID:

UniProt ID: Q7TPH6

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1552359.088251
FMO2-HF: Nuclear repulsion	1491226.788363
FMO2-HF: Total energy	-61132.299888
FMO2-MP2: Total energy	-61311.147254

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:1227:SER)

Summations of interaction energy for fragment #1(A:1227:SER)

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.
-11.581	-9.125	0.002	-1.346	-1.112	-0.001

Interaction energy analysis for fragmet #1(A:1227:SER)

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 : -0.020

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	1229	GLU	-1	-0.930	-0.954	3.287	-7.615	-5.159	0.002	-1.346	-1.112	-0.001
4	A	1230	ASP	-1	-0.915	-0.947	5.501	-3.306	-3.306	0.000	0.000	0.000	0.000
5	A	1231	TYR	0	-0.014	-0.016	7.287	0.583	0.583	0.000	0.000	0.000	0.000
6	A	1232	SER	0	-0.033	-0.002	11.067	0.086	0.086	0.000	0.000	0.000	0.000
7	A	1233	VAL	0	0.002	-0.007	14.228	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	1234	VAL	0	0.017	0.026	16.859	0.061	0.061	0.000	0.000	0.000	0.000
9	A	1235	ASN	0	0.004	-0.011	19.756	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	1236	ARG	1	0.859	0.935	22.672	0.372	0.372	0.000	0.000	0.000	0.000
11	A	1237	PHE	0	-0.061	-0.014	25.876	0.027	0.027	0.000	0.000	0.000	0.000
12	A	1238	GLU	-1	-0.906	-0.946	26.686	-0.281	-0.281	0.000	0.000	0.000	0.000
13	A	1239	SER	0	-0.050	-0.020	29.080	0.009	0.009	0.000	0.000	0.000	0.000
14	A	1240	HIS	0	-0.001	0.007	28.784	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	1241	GLY	0	0.041	0.021	30.319	0.016	0.016	0.000	0.000	0.000	0.000
16	A	1242	GLY	0	-0.025	-0.015	32.538	0.002	0.002	0.000	0.000	0.000	0.000
17	A	1243	GLY	0	-0.025	-0.024	31.908	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	1244	TRP	0	0.003	0.015	30.686	0.009	0.009	0.000	0.000	0.000	0.000
19	A	1245	GLY	0	0.021	0.005	31.907	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	1246	TYR	0	0.004	0.009	28.492	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	1247	SER	0	-0.004	-0.017	33.675	0.017	0.017	0.000	0.000	0.000	0.000
22	A	1248	ALA	0	0.002	-0.014	34.805	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	1249	HIS	0	-0.020	-0.016	35.193	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	1250	SER	0	0.016	0.037	33.341	0.004	0.004	0.000	0.000	0.000	0.000
25	A	1251	VAL	0	-0.024	-0.014	31.299	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	1252	GLU	-1	-0.771	-0.865	28.493	-0.242	-0.242	0.000	0.000	0.000	0.000
27	A	1253	ALA	0	-0.003	-0.018	29.359	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	1254	ILE	0	-0.039	-0.010	27.279	0.018	0.018	0.000	0.000	0.000	0.000
29	A	1255	ARG	1	0.839	0.918	29.115	0.208	0.208	0.000	0.000	0.000	0.000
30	A	1256	PHE	0	-0.007	-0.019	24.089	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	1257	SER	0	0.021	0.003	28.120	0.009	0.009	0.000	0.000	0.000	0.000
32	A	1258	ALA	0	0.035	0.030	24.493	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	1259	ASP	-1	-0.845	-0.916	26.530	-0.325	-0.325	0.000	0.000	0.000	0.000
34	A	1260	THR	0	-0.009	-0.016	23.059	0.023	0.023	0.000	0.000	0.000	0.000
35	A	1261	ASP	-1	-0.881	-0.932	23.347	-0.382	-0.382	0.000	0.000	0.000	0.000
36	A	1262	ILE	0	-0.054	-0.034	19.505	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	1263	LEU	0	0.001	0.005	15.131	0.045	0.045	0.000	0.000	0.000	0.000
38	A	1264	LEU	0	-0.009	-0.009	16.831	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	1265	GLY	0	0.066	0.020	14.551	0.014	0.014	0.000	0.000	0.000	0.000
40	A	1266	GLY	0	0.017	-0.004	15.564	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	1267	LEU	0	-0.058	-0.020	17.186	0.047	0.047	0.000	0.000	0.000	0.000
42	A	1268	GLY	0	0.015	0.016	18.356	-0.046	-0.046	0.000	0.000	0.000	0.000
43	A	1269	LEU	0	-0.029	-0.027	19.195	0.079	0.079	0.000	0.000	0.000	0.000
44	A	1270	PHE	0	0.034	0.014	20.879	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	1271	GLY	0	0.074	0.021	23.084	0.006	0.006	0.000	0.000	0.000	0.000
46	A	1272	GLY	0	-0.001	0.013	23.029	0.021	0.021	0.000	0.000	0.000	0.000
47	A	1273	ARG	1	0.788	0.887	24.209	0.242	0.242	0.000	0.000	0.000	0.000
48	A	1274	GLY	0	-0.007	-0.001	25.516	0.022	0.022	0.000	0.000	0.000	0.000
49	A	1275	GLH	0	-0.097	-0.067	22.224	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	1276	TYR	0	-0.047	-0.033	23.590	0.017	0.017	0.000	0.000	0.000	0.000
51	A	1277	THR	0	-0.020	-0.009	23.608	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	1278	ALA	0	0.042	0.006	22.602	0.007	0.007	0.000	0.000	0.000	0.000
53	A	1279	LYS	1	0.830	0.929	22.791	0.275	0.275	0.000	0.000	0.000	0.000
54	A	1280	ILE	0	0.019	0.004	19.196	0.029	0.029	0.000	0.000	0.000	0.000
55	A	1281	LYS	1	0.833	0.916	23.686	0.296	0.296	0.000	0.000	0.000	0.000
56	A	1282	LEU	0	0.034	0.030	22.494	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	1283	PHE	0	-0.028	-0.020	25.534	0.021	0.021	0.000	0.000	0.000	0.000
58	A	1284	GLU	-1	-0.866	-0.939	28.838	-0.293	-0.293	0.000	0.000	0.000	0.000
59	A	1285	LEU	0	-0.078	-0.045	30.048	0.021	0.021	0.000	0.000	0.000	0.000
60	A	1286	GLY	0	0.064	0.041	32.187	0.017	0.017	0.000	0.000	0.000	0.000
61	A	1287	PRO	0	-0.004	-0.007	33.590	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	1288	ASP	-1	-0.850	-0.919	35.102	-0.176	-0.176	0.000	0.000	0.000	0.000
63	A	1289	GLY	0	-0.015	-0.007	35.052	0.006	0.006	0.000	0.000	0.000	0.000
64	A	1290	GLY	0	-0.015	-0.012	35.644	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	1291	ASP	-1	-0.971	-0.983	36.248	-0.176	-0.176	0.000	0.000	0.000	0.000
66	A	1292	HIS	0	-0.053	-0.038	39.367	0.007	0.007	0.000	0.000	0.000	0.000
67	A	1293	GLU	-1	-0.791	-0.870	35.050	-0.232	-0.232	0.000	0.000	0.000	0.000
68	A	1294	THR	0	0.016	-0.002	37.350	0.008	0.008	0.000	0.000	0.000	0.000
69	A	1295	ASP	-1	-0.922	-0.983	37.000	-0.177	-0.177	0.000	0.000	0.000	0.000
70	A	1296	GLY	0	-0.018	-0.009	33.514	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	1297	ASP	-1	-0.883	-0.922	31.731	-0.195	-0.195	0.000	0.000	0.000	0.000
72	A	1298	LEU	0	-0.101	-0.058	27.227	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	1299	LEU	0	0.003	-0.003	24.793	0.005	0.005	0.000	0.000	0.000	0.000
74	A	1300	ALA	0	0.030	0.019	21.431	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	1301	GLU	-1	-0.949	-0.995	22.946	-0.247	-0.247	0.000	0.000	0.000	0.000
76	A	1302	THR	0	0.105	0.089	19.178	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	1303	ASP	-1	-0.888	-0.933	21.399	-0.222	-0.222	0.000	0.000	0.000	0.000
78	A	1304	VAL	0	-0.100	-0.068	22.206	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	1305	LEU	0	0.035	0.026	16.371	0.027	0.027	0.000	0.000	0.000	0.000
80	A	1306	ALA	0	-0.013	-0.019	21.008	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	1307	TYR	0	-0.044	-0.037	18.532	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	1308	ASP	-1	-0.843	-0.897	18.774	-0.275	-0.275	0.000	0.000	0.000	0.000
83	A	1309	CYS	0	0.026	0.006	18.177	-0.061	-0.061	0.000	0.000	0.000	0.000
84	A	1310	ALA	0	0.008	0.018	18.750	0.054	0.054	0.000	0.000	0.000	0.000
85	A	1311	ALA	0	0.028	-0.006	20.631	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	1312	ARG	1	0.878	0.933	22.785	0.236	0.236	0.000	0.000	0.000	0.000
87	A	1313	GLU	-1	-0.948	-0.955	18.138	-0.515	-0.515	0.000	0.000	0.000	0.000
88	A	1314	LYS	1	0.895	0.952	18.315	0.539	0.539	0.000	0.000	0.000	0.000
89	A	1315	TYR	0	0.000	-0.003	14.887	-0.067	-0.067	0.000	0.000	0.000	0.000
90	A	1316	ALA	0	0.031	0.015	13.079	0.042	0.042	0.000	0.000	0.000	0.000
91	A	1317	MET	0	-0.038	-0.008	14.515	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	1318	MET	0	0.014	0.004	11.556	0.030	0.030	0.000	0.000	0.000	0.000
93	A	1319	PHE	0	-0.020	-0.026	15.399	0.141	0.141	0.000	0.000	0.000	0.000
94	A	1320	ASP	-1	-0.917	-0.958	15.292	-0.579	-0.579	0.000	0.000	0.000	0.000
95	A	1321	GLU	-1	-0.938	-0.973	14.387	-0.741	-0.741	0.000	0.000	0.000	0.000
96	A	1322	PRO	0	-0.059	-0.015	13.383	0.042	0.042	0.000	0.000	0.000	0.000
97	A	1323	VAL	0	-0.004	-0.001	16.221	0.092	0.092	0.000	0.000	0.000	0.000
98	A	1324	LEU	0	-0.044	-0.020	19.788	-0.039	-0.039	0.000	0.000	0.000	0.000
99	A	1325	LEU	0	-0.053	-0.027	21.201	0.049	0.049	0.000	0.000	0.000	0.000
100	A	1326	GLN	0	0.013	-0.006	24.068	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	1327	ALA	0	0.046	0.019	27.097	0.003	0.003	0.000	0.000	0.000	0.000
102	A	1328	GLY	0	-0.058	-0.026	28.262	0.024	0.024	0.000	0.000	0.000	0.000
103	A	1329	TRP	0	-0.043	-0.016	29.407	0.023	0.023	0.000	0.000	0.000	0.000
104	A	1330	TRP	0	-0.014	0.006	29.520	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	1331	TYR	0	0.082	0.041	27.092	0.003	0.003	0.000	0.000	0.000	0.000
106	A	1332	VAL	0	-0.065	-0.034	28.975	0.010	0.010	0.000	0.000	0.000	0.000
107	A	1333	ALA	0	0.046	0.037	24.796	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	1334	TRP	0	-0.009	-0.023	25.943	0.034	0.034	0.000	0.000	0.000	0.000
109	A	1335	ALA	0	0.072	0.017	24.952	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	1336	ARG	1	0.882	0.964	26.606	0.228	0.228	0.000	0.000	0.000	0.000
111	A	1337	VAL	0	0.045	0.024	25.438	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	1338	SER	0	-0.066	-0.035	27.475	0.029	0.029	0.000	0.000	0.000	0.000
113	A	1339	GLY	0	0.055	0.019	27.754	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	1340	PRO	0	-0.028	0.002	28.526	0.011	0.011	0.000	0.000	0.000	0.000
115	A	1341	SER	0	0.004	-0.005	30.373	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	1342	SER	0	-0.009	0.013	26.781	0.001	0.001	0.000	0.000	0.000	0.000
117	A	1343	ASP	-1	-0.799	-0.898	25.245	-0.270	-0.270	0.000	0.000	0.000	0.000
118	A	1344	CYS	0	-0.069	-0.002	27.888	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	1345	GLY	0	0.049	0.028	28.851	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	1346	SER	0	-0.046	-0.052	29.348	0.019	0.019	0.000	0.000	0.000	0.000
121	A	1347	HIS	0	0.014	-0.003	31.117	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	1348	GLY	0	-0.020	0.006	30.289	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	1349	GLN	0	-0.012	-0.004	29.559	0.026	0.026	0.000	0.000	0.000	0.000
124	A	1350	ALA	0	0.007	-0.008	30.703	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	1351	SER	0	-0.043	-0.034	30.435	0.001	0.001	0.000	0.000	0.000	0.000
126	A	1352	ILE	0	0.012	0.019	24.825	0.008	0.008	0.000	0.000	0.000	0.000
127	A	1353	THR	0	-0.021	-0.006	26.373	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1354	THR	0	-0.021	-0.030	20.861	0.012	0.012	0.000	0.000	0.000	0.000
129	A	1355	ASP	-1	-0.890	-0.949	20.092	-0.443	-0.443	0.000	0.000	0.000	0.000
130	A	1356	ASP	-1	-0.892	-0.915	19.122	-0.577	-0.577	0.000	0.000	0.000	0.000
131	A	1357	GLY	0	-0.034	-0.022	21.371	0.022	0.022	0.000	0.000	0.000	0.000
132	A	1358	VAL	0	-0.030	0.004	21.767	0.026	0.026	0.000	0.000	0.000	0.000
133	A	1359	ILE	0	-0.022	-0.004	24.541	0.001	0.001	0.000	0.000	0.000	0.000
134	A	1360	PHE	0	0.009	-0.010	20.993	0.000	0.000	0.000	0.000	0.000	0.000
135	A	1361	GLN	0	-0.036	-0.022	26.922	0.035	0.035	0.000	0.000	0.000	0.000
136	A	1362	PHE	0	0.017	0.000	24.720	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	1363	LYS	1	0.906	0.956	30.648	0.241	0.241	0.000	0.000	0.000	0.000
138	A	1364	SER	0	0.058	0.018	32.889	-0.015	-0.015	0.000	0.000	0.000	0.000
139	A	1365	SER	0	-0.028	-0.002	32.882	0.005	0.005	0.000	0.000	0.000	0.000
140	A	1366	LYS	1	0.890	0.935	34.914	0.178	0.178	0.000	0.000	0.000	0.000
141	A	1367	LYS	1	0.841	0.928	32.569	0.235	0.235	0.000	0.000	0.000	0.000
142	A	1368	SER	0	-0.079	-0.034	33.555	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	1369	ASN	0	-0.011	-0.012	34.762	0.006	0.006	0.000	0.000	0.000	0.000
144	A	1370	ASN	0	-0.086	-0.078	32.813	0.025	0.025	0.000	0.000	0.000	0.000
145	A	1371	GLY	0	0.028	0.015	35.114	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	1372	THR	0	-0.030	-0.009	29.869	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	1373	ASP	-1	-0.865	-0.908	33.127	-0.211	-0.211	0.000	0.000	0.000	0.000
148	A	1374	VAL	0	-0.003	-0.016	32.289	-0.017	-0.017	0.000	0.000	0.000	0.000
149	A	1375	ASN	0	-0.017	0.000	32.352	-0.014	-0.014	0.000	0.000	0.000	0.000
150	A	1376	ALA	0	0.006	-0.010	32.450	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	1377	GLY	0	0.028	0.021	31.024	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	1378	GLN	0	0.042	-0.013	25.086	-0.046	-0.046	0.000	0.000	0.000	0.000
153	A	1379	ILE	0	-0.025	-0.008	23.695	0.007	0.007	0.000	0.000	0.000	0.000
154	A	1380	PRO	0	-0.031	-0.007	22.046	0.004	0.004	0.000	0.000	0.000	0.000
155	A	1381	GLN	0	-0.016	-0.015	17.924	-0.043	-0.043	0.000	0.000	0.000	0.000
156	A	1382	LEU	0	-0.002	0.023	19.985	0.007	0.007	0.000	0.000	0.000	0.000
157	A	1383	LEU	0	-0.008	0.005	14.284	-0.023	-0.023	0.000	0.000	0.000	0.000
158	A	1384	TYR	0	-0.023	-0.042	15.575	-0.004	-0.004	0.000	0.000	0.000	0.000
159	A	1385	ARG	1	0.945	0.974	9.294	1.828	1.828	0.000	0.000	0.000	0.000
160	A	1386	LEU	0	0.038	0.025	14.950	0.102	0.102	0.000	0.000	0.000	0.000
161	A	1387	PRO	0	-0.028	-0.001	16.272	-0.059	-0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1227:SER)