FMO DATABASE

FMODB ID: ZV86N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1552037.079082
FMO2-HF: Nuclear repulsion	1490904.338342
FMO2-HF: Total energy	-61132.74074
FMO2-MP2: Total energy	-61311.684409

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.
-11.398	-8.649	0.007	-1.536	-1.22	-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 : -0.006 / q_NPA : -0.012

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	-0.837	-0.904	3.211	-7.617	-4.868	0.007	-1.536	-1.220	-0.001
4	A	1230	ASP	-1	-0.909	-0.945	5.474	-2.952	-2.952	0.000	0.000	0.000	0.000
5	A	1231	TYR	0	-0.047	-0.049	7.221	0.594	0.594	0.000	0.000	0.000	0.000
6	A	1232	SER	0	-0.011	0.009	10.999	0.015	0.015	0.000	0.000	0.000	0.000
7	A	1233	VAL	0	-0.010	-0.010	14.155	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	1234	VAL	0	0.013	0.026	16.769	0.063	0.063	0.000	0.000	0.000	0.000
9	A	1235	ASN	0	0.001	-0.011	19.403	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	1236	ARG	1	0.848	0.928	22.569	0.364	0.364	0.000	0.000	0.000	0.000
11	A	1237	PHE	0	-0.055	-0.009	25.770	0.026	0.026	0.000	0.000	0.000	0.000
12	A	1238	GLU	-1	-0.857	-0.910	26.574	-0.256	-0.256	0.000	0.000	0.000	0.000
13	A	1239	SER	0	-0.055	-0.025	28.968	0.011	0.011	0.000	0.000	0.000	0.000
14	A	1240	HIS	0	-0.017	-0.004	28.803	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	1241	GLY	0	0.048	0.027	30.367	0.016	0.016	0.000	0.000	0.000	0.000
16	A	1242	GLY	0	-0.005	0.000	32.575	0.003	0.003	0.000	0.000	0.000	0.000
17	A	1243	GLY	0	-0.023	-0.024	31.935	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	1244	TRP	0	0.011	0.030	30.775	0.009	0.009	0.000	0.000	0.000	0.000
19	A	1245	GLY	0	0.013	0.001	31.931	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	1246	TYR	0	0.001	0.004	28.478	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	1247	SER	0	-0.009	-0.015	33.697	0.017	0.017	0.000	0.000	0.000	0.000
22	A	1248	ALA	0	0.018	-0.006	34.825	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	1249	HIS	0	-0.016	-0.009	35.207	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	1250	SER	0	0.002	0.019	33.367	0.004	0.004	0.000	0.000	0.000	0.000
25	A	1251	VAL	0	-0.029	-0.010	31.436	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	1252	GLU	-1	-0.767	-0.846	28.536	-0.245	-0.245	0.000	0.000	0.000	0.000
27	A	1253	ALA	0	0.000	-0.018	29.281	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	1254	ILE	0	-0.036	-0.010	27.186	0.019	0.019	0.000	0.000	0.000	0.000
29	A	1255	ARG	1	0.836	0.920	29.039	0.210	0.210	0.000	0.000	0.000	0.000
30	A	1256	PHE	0	-0.014	-0.023	24.014	0.000	0.000	0.000	0.000	0.000	0.000
31	A	1257	SER	0	0.023	-0.005	28.068	0.006	0.006	0.000	0.000	0.000	0.000
32	A	1258	ALA	0	0.036	0.031	24.468	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	1259	ASP	-1	-0.834	-0.907	26.482	-0.321	-0.321	0.000	0.000	0.000	0.000
34	A	1260	THR	0	-0.017	-0.026	23.261	0.024	0.024	0.000	0.000	0.000	0.000
35	A	1261	ASP	-1	-0.877	-0.926	23.338	-0.394	-0.394	0.000	0.000	0.000	0.000
36	A	1262	ILE	0	-0.054	-0.032	19.522	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	1263	LEU	0	0.002	0.008	15.304	0.041	0.041	0.000	0.000	0.000	0.000
38	A	1264	LEU	0	-0.007	-0.007	16.798	-0.101	-0.101	0.000	0.000	0.000	0.000
39	A	1265	GLY	0	0.060	0.017	14.501	0.004	0.004	0.000	0.000	0.000	0.000
40	A	1266	GLY	0	0.018	-0.003	15.526	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	1267	LEU	0	-0.058	-0.018	17.115	0.054	0.054	0.000	0.000	0.000	0.000
42	A	1268	GLY	0	0.014	0.016	18.399	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	1269	LEU	0	-0.028	-0.025	19.157	0.078	0.078	0.000	0.000	0.000	0.000
44	A	1270	PHE	0	0.033	0.011	20.916	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	1271	GLY	0	0.072	0.022	23.100	0.002	0.002	0.000	0.000	0.000	0.000
46	A	1272	GLY	0	-0.004	0.009	23.060	0.022	0.022	0.000	0.000	0.000	0.000
47	A	1273	ARG	1	0.751	0.847	24.219	0.236	0.236	0.000	0.000	0.000	0.000
48	A	1274	GLY	0	-0.008	-0.001	25.512	0.021	0.021	0.000	0.000	0.000	0.000
49	A	1275	GLH	0	-0.091	-0.075	21.905	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	1276	TYR	0	-0.048	-0.026	23.538	0.018	0.018	0.000	0.000	0.000	0.000
51	A	1277	THR	0	-0.032	-0.016	23.623	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	1278	ALA	0	0.032	0.001	22.694	0.012	0.012	0.000	0.000	0.000	0.000
53	A	1279	LYS	1	0.816	0.925	22.804	0.308	0.308	0.000	0.000	0.000	0.000
54	A	1280	ILE	0	0.020	0.008	19.219	0.033	0.033	0.000	0.000	0.000	0.000
55	A	1281	LYS	1	0.804	0.899	23.696	0.314	0.314	0.000	0.000	0.000	0.000
56	A	1282	LEU	0	0.035	0.029	22.580	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	1283	PHE	0	-0.033	-0.026	25.585	0.019	0.019	0.000	0.000	0.000	0.000
58	A	1284	GLU	-1	-0.786	-0.894	28.849	-0.329	-0.329	0.000	0.000	0.000	0.000
59	A	1285	LEU	0	-0.085	-0.050	30.125	0.022	0.022	0.000	0.000	0.000	0.000
60	A	1286	GLY	0	0.065	0.041	32.279	0.017	0.017	0.000	0.000	0.000	0.000
61	A	1287	PRO	0	0.010	0.002	33.702	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	1288	ASP	-1	-0.880	-0.938	35.070	-0.183	-0.183	0.000	0.000	0.000	0.000
63	A	1289	GLY	0	0.000	0.002	35.002	0.007	0.007	0.000	0.000	0.000	0.000
64	A	1290	GLY	0	0.014	0.007	35.580	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	1291	ASP	-1	-0.949	-0.971	36.190	-0.180	-0.180	0.000	0.000	0.000	0.000
66	A	1292	HIS	0	-0.049	-0.029	39.284	0.008	0.008	0.000	0.000	0.000	0.000
67	A	1293	GLU	-1	-0.769	-0.848	35.159	-0.237	-0.237	0.000	0.000	0.000	0.000
68	A	1294	THR	0	0.047	0.020	37.428	0.008	0.008	0.000	0.000	0.000	0.000
69	A	1295	ASP	-1	-0.858	-0.948	36.939	-0.198	-0.198	0.000	0.000	0.000	0.000
70	A	1296	GLY	0	0.032	0.029	33.571	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	1297	ASP	-1	-0.903	-0.935	31.843	-0.213	-0.213	0.000	0.000	0.000	0.000
72	A	1298	LEU	0	-0.101	-0.058	27.310	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	1299	LEU	0	0.014	0.003	24.791	0.006	0.006	0.000	0.000	0.000	0.000
74	A	1300	ALA	0	0.028	0.019	21.427	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	1301	GLU	-1	-0.858	-0.948	22.906	-0.276	-0.276	0.000	0.000	0.000	0.000
76	A	1302	THR	0	0.089	0.079	19.271	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	1303	ASP	-1	-0.896	-0.939	21.398	-0.258	-0.258	0.000	0.000	0.000	0.000
78	A	1304	VAL	0	-0.089	-0.056	22.213	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	1305	LEU	0	0.024	0.023	16.410	0.024	0.024	0.000	0.000	0.000	0.000
80	A	1306	ALA	0	-0.002	-0.017	21.048	0.002	0.002	0.000	0.000	0.000	0.000
81	A	1307	TYR	0	-0.056	-0.042	18.587	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	1308	ASP	-1	-0.848	-0.888	18.771	-0.266	-0.266	0.000	0.000	0.000	0.000
83	A	1309	CYS	0	0.026	0.005	18.178	-0.060	-0.060	0.000	0.000	0.000	0.000
84	A	1310	ALA	0	0.012	0.019	18.750	0.052	0.052	0.000	0.000	0.000	0.000
85	A	1311	ALA	0	0.041	0.002	20.634	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	1312	ARG	1	0.896	0.943	22.802	0.211	0.211	0.000	0.000	0.000	0.000
87	A	1313	GLU	-1	-0.934	-0.954	18.145	-0.474	-0.474	0.000	0.000	0.000	0.000
88	A	1314	LYS	1	0.858	0.933	18.419	0.485	0.485	0.000	0.000	0.000	0.000
89	A	1315	TYR	0	0.006	0.001	15.370	-0.074	-0.074	0.000	0.000	0.000	0.000
90	A	1316	ALA	0	0.032	0.014	13.140	0.040	0.040	0.000	0.000	0.000	0.000
91	A	1317	MET	0	-0.038	-0.008	14.552	-0.047	-0.047	0.000	0.000	0.000	0.000
92	A	1318	MET	0	0.014	0.004	11.447	0.049	0.049	0.000	0.000	0.000	0.000
93	A	1319	PHE	0	-0.023	-0.026	15.395	0.141	0.141	0.000	0.000	0.000	0.000
94	A	1320	ASP	-1	-0.916	-0.960	15.279	-0.678	-0.678	0.000	0.000	0.000	0.000
95	A	1321	GLU	-1	-0.937	-0.974	14.500	-0.903	-0.903	0.000	0.000	0.000	0.000
96	A	1322	PRO	0	-0.054	-0.013	13.485	0.056	0.056	0.000	0.000	0.000	0.000
97	A	1323	VAL	0	-0.014	-0.007	16.283	0.092	0.092	0.000	0.000	0.000	0.000
98	A	1324	LEU	0	-0.038	-0.017	19.864	-0.034	-0.034	0.000	0.000	0.000	0.000
99	A	1325	LEU	0	-0.050	-0.020	21.316	0.047	0.047	0.000	0.000	0.000	0.000
100	A	1326	GLN	0	0.010	0.003	24.201	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	1327	ALA	0	0.041	0.013	27.178	0.005	0.005	0.000	0.000	0.000	0.000
102	A	1328	GLY	0	-0.058	-0.026	28.239	0.023	0.023	0.000	0.000	0.000	0.000
103	A	1329	TRP	0	-0.066	-0.027	29.447	0.024	0.024	0.000	0.000	0.000	0.000
104	A	1330	TRP	0	-0.009	0.020	29.478	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	1331	TYR	0	0.035	0.000	27.060	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	1332	VAL	0	-0.067	-0.036	28.931	0.013	0.013	0.000	0.000	0.000	0.000
107	A	1333	ALA	0	0.040	0.036	24.705	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	1334	TRP	0	-0.012	-0.023	25.852	0.035	0.035	0.000	0.000	0.000	0.000
109	A	1335	ALA	0	0.069	0.019	25.016	-0.034	-0.034	0.000	0.000	0.000	0.000
110	A	1336	ARG	1	0.879	0.954	26.650	0.246	0.246	0.000	0.000	0.000	0.000
111	A	1337	VAL	0	0.031	0.017	25.527	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	1338	SER	0	-0.052	-0.027	27.487	0.031	0.031	0.000	0.000	0.000	0.000
113	A	1339	GLY	0	0.048	0.015	27.762	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	1340	PRO	0	-0.032	0.001	28.538	0.011	0.011	0.000	0.000	0.000	0.000
115	A	1341	SER	0	0.005	-0.006	30.385	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	1342	SER	0	-0.006	0.009	26.781	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1343	ASP	-1	-0.797	-0.886	25.526	-0.246	-0.246	0.000	0.000	0.000	0.000
118	A	1344	CYS	0	-0.064	0.001	27.917	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	1345	GLY	0	0.057	0.030	28.762	0.002	0.002	0.000	0.000	0.000	0.000
120	A	1346	SER	0	-0.050	-0.050	29.317	0.018	0.018	0.000	0.000	0.000	0.000
121	A	1347	HIS	0	-0.009	-0.017	31.002	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	1348	GLY	0	-0.014	0.005	30.184	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	1349	GLN	0	-0.031	-0.025	29.498	0.022	0.022	0.000	0.000	0.000	0.000
124	A	1350	ALA	0	0.005	-0.003	30.612	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	1351	SER	0	-0.048	-0.038	30.333	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	1352	ILE	0	0.009	0.013	24.706	0.009	0.009	0.000	0.000	0.000	0.000
127	A	1353	THR	0	-0.012	-0.001	26.360	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	1354	THR	0	-0.010	-0.027	20.701	0.012	0.012	0.000	0.000	0.000	0.000
129	A	1355	ASP	-1	-0.909	-0.960	20.016	-0.410	-0.410	0.000	0.000	0.000	0.000
130	A	1356	ASP	-1	-0.879	-0.903	19.087	-0.545	-0.545	0.000	0.000	0.000	0.000
131	A	1357	GLY	0	-0.034	-0.020	21.326	0.018	0.018	0.000	0.000	0.000	0.000
132	A	1358	VAL	0	-0.034	0.001	21.757	0.023	0.023	0.000	0.000	0.000	0.000
133	A	1359	ILE	0	-0.040	-0.013	24.494	0.004	0.004	0.000	0.000	0.000	0.000
134	A	1360	PHE	0	0.018	-0.004	20.766	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	1361	GLN	0	-0.026	-0.016	26.856	0.031	0.031	0.000	0.000	0.000	0.000
136	A	1362	PHE	0	0.013	-0.007	24.562	-0.020	-0.020	0.000	0.000	0.000	0.000
137	A	1363	LYS	1	0.845	0.915	30.568	0.233	0.233	0.000	0.000	0.000	0.000
138	A	1364	SER	0	0.049	0.016	32.807	-0.016	-0.016	0.000	0.000	0.000	0.000
139	A	1365	SER	0	-0.037	-0.025	32.814	0.003	0.003	0.000	0.000	0.000	0.000
140	A	1366	LYS	1	0.809	0.883	34.834	0.190	0.190	0.000	0.000	0.000	0.000
141	A	1367	LYS	1	0.791	0.894	32.823	0.241	0.241	0.000	0.000	0.000	0.000
142	A	1368	SER	0	-0.077	-0.032	33.461	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	1369	ASN	0	-0.018	-0.022	34.689	0.007	0.007	0.000	0.000	0.000	0.000
144	A	1370	ASN	0	-0.060	-0.052	32.854	0.027	0.027	0.000	0.000	0.000	0.000
145	A	1371	GLY	0	0.017	0.010	35.157	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	1372	THR	0	-0.047	-0.028	29.751	-0.002	-0.002	0.000	0.000	0.000	0.000
147	A	1373	ASP	-1	-0.811	-0.882	33.077	-0.211	-0.211	0.000	0.000	0.000	0.000
148	A	1374	VAL	0	0.014	0.007	32.188	-0.017	-0.017	0.000	0.000	0.000	0.000
149	A	1375	ASN	0	-0.059	-0.027	32.252	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	1376	ALA	0	0.004	-0.015	32.346	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	1377	GLY	0	0.028	0.016	31.069	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	1378	GLN	0	0.036	-0.015	25.002	-0.042	-0.042	0.000	0.000	0.000	0.000
153	A	1379	ILE	0	-0.023	-0.011	23.548	0.008	0.008	0.000	0.000	0.000	0.000
154	A	1380	PRO	0	-0.022	-0.005	21.974	0.006	0.006	0.000	0.000	0.000	0.000
155	A	1381	GLN	0	-0.015	-0.019	17.959	-0.044	-0.044	0.000	0.000	0.000	0.000
156	A	1382	LEU	0	-0.002	0.025	19.898	0.000	0.000	0.000	0.000	0.000	0.000
157	A	1383	LEU	0	-0.006	0.007	14.183	-0.014	-0.014	0.000	0.000	0.000	0.000
158	A	1384	TYR	0	-0.040	-0.057	15.481	-0.017	-0.017	0.000	0.000	0.000	0.000
159	A	1385	ARG	1	0.876	0.945	9.495	2.024	2.024	0.000	0.000	0.000	0.000
160	A	1386	LEU	0	0.026	0.020	14.921	0.096	0.096	0.000	0.000	0.000	0.000
161	A	1387	PRO	0	-0.019	0.003	16.276	-0.056	-0.056	0.000	0.000	0.000	0.000

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