FMO DATABASE

FMODB ID: R8298

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1554024.999009
FMO2-HF: Nuclear repulsion	1492892.204498
FMO2-HF: Total energy	-61132.794511
FMO2-MP2: Total energy	-61311.827183

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.
-15.366	-11.356	0.366	-2.386	-1.99	-0.015

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 : -0.013 / q_NPA : -0.010

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	-0.826	-0.889	2.569	-11.779	-7.890	0.367	-2.381	-1.875	-0.015
4	A	1230	ASP	-1	-0.907	-0.952	5.134	-2.589	-2.468	-0.001	-0.005	-0.115	0.000
5	A	1231	TYR	0	-0.055	-0.053	7.076	0.573	0.573	0.000	0.000	0.000	0.000
6	A	1232	SER	0	-0.002	0.015	10.832	0.057	0.057	0.000	0.000	0.000	0.000
7	A	1233	VAL	0	-0.011	-0.014	14.036	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	1234	VAL	0	0.018	0.031	16.579	0.071	0.071	0.000	0.000	0.000	0.000
9	A	1235	ASN	0	-0.003	-0.015	18.952	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	1236	ARG	1	0.815	0.913	21.957	0.351	0.351	0.000	0.000	0.000	0.000
11	A	1237	PHE	0	-0.039	-0.010	25.411	0.024	0.024	0.000	0.000	0.000	0.000
12	A	1238	GLU	-1	-0.869	-0.911	26.313	-0.224	-0.224	0.000	0.000	0.000	0.000
13	A	1239	SER	0	-0.053	-0.022	28.795	0.014	0.014	0.000	0.000	0.000	0.000
14	A	1240	HIS	0	-0.017	-0.010	28.478	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	1241	GLY	0	0.055	0.036	30.068	0.015	0.015	0.000	0.000	0.000	0.000
16	A	1242	GLY	0	-0.026	-0.013	31.984	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	1243	GLY	0	-0.002	-0.027	31.237	0.001	0.001	0.000	0.000	0.000	0.000
18	A	1244	TRP	0	0.006	0.019	30.059	0.009	0.009	0.000	0.000	0.000	0.000
19	A	1245	GLY	0	0.005	-0.004	31.943	0.007	0.007	0.000	0.000	0.000	0.000
20	A	1246	TYR	0	-0.017	0.006	28.094	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	1247	SER	0	0.006	-0.015	33.534	0.017	0.017	0.000	0.000	0.000	0.000
22	A	1248	ALA	0	0.016	-0.001	34.567	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	1249	HIS	0	0.004	0.003	35.027	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	1250	SER	0	0.015	0.019	33.018	0.004	0.004	0.000	0.000	0.000	0.000
25	A	1251	VAL	0	-0.030	-0.011	31.053	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	1252	GLU	-1	-0.730	-0.827	28.178	-0.243	-0.243	0.000	0.000	0.000	0.000
27	A	1253	ALA	0	-0.019	-0.027	29.009	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	1254	ILE	0	-0.027	-0.008	26.669	0.020	0.020	0.000	0.000	0.000	0.000
29	A	1255	ARG	1	0.822	0.920	28.602	0.207	0.207	0.000	0.000	0.000	0.000
30	A	1256	PHE	0	-0.023	-0.022	23.664	0.004	0.004	0.000	0.000	0.000	0.000
31	A	1257	SER	0	0.032	-0.010	27.450	0.008	0.008	0.000	0.000	0.000	0.000
32	A	1258	ALA	0	0.049	0.023	24.286	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	1259	ASP	-1	-0.840	-0.893	26.285	-0.307	-0.307	0.000	0.000	0.000	0.000
34	A	1260	THR	0	-0.047	-0.040	22.800	0.024	0.024	0.000	0.000	0.000	0.000
35	A	1261	ASP	-1	-0.866	-0.928	22.897	-0.393	-0.393	0.000	0.000	0.000	0.000
36	A	1262	ILE	0	-0.047	-0.029	19.181	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	1263	LEU	0	0.013	0.008	15.207	0.032	0.032	0.000	0.000	0.000	0.000
38	A	1264	LEU	0	-0.003	0.001	16.026	-0.111	-0.111	0.000	0.000	0.000	0.000
39	A	1265	GLY	0	0.060	0.019	13.937	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	1266	GLY	0	0.004	-0.008	14.988	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	1267	LEU	0	-0.041	-0.010	16.661	0.072	0.072	0.000	0.000	0.000	0.000
42	A	1268	GLY	0	0.017	0.017	17.940	-0.064	-0.064	0.000	0.000	0.000	0.000
43	A	1269	LEU	0	-0.029	-0.024	19.064	0.074	0.074	0.000	0.000	0.000	0.000
44	A	1270	PHE	0	0.020	0.006	20.792	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	1271	GLY	0	0.061	0.013	22.864	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	1272	GLY	0	-0.025	-0.008	22.648	0.026	0.026	0.000	0.000	0.000	0.000
47	A	1273	ARG	1	0.755	0.842	23.935	0.216	0.216	0.000	0.000	0.000	0.000
48	A	1274	GLY	0	-0.002	0.002	25.440	0.021	0.021	0.000	0.000	0.000	0.000
49	A	1275	GLH	0	-0.085	-0.065	21.471	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	1276	TYR	0	-0.067	-0.052	23.391	0.020	0.020	0.000	0.000	0.000	0.000
51	A	1277	THR	0	-0.031	-0.015	23.642	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	1278	ALA	0	0.021	-0.001	22.819	0.013	0.013	0.000	0.000	0.000	0.000
53	A	1279	LYS	1	0.788	0.909	23.246	0.345	0.345	0.000	0.000	0.000	0.000
54	A	1280	ILE	0	-0.003	0.001	19.428	0.045	0.045	0.000	0.000	0.000	0.000
55	A	1281	LYS	1	0.801	0.897	23.986	0.330	0.330	0.000	0.000	0.000	0.000
56	A	1282	LEU	0	0.044	0.030	22.243	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	1283	PHE	0	-0.034	-0.025	25.479	0.016	0.016	0.000	0.000	0.000	0.000
58	A	1284	GLU	-1	-0.797	-0.892	28.423	-0.342	-0.342	0.000	0.000	0.000	0.000
59	A	1285	LEU	0	-0.070	-0.042	29.848	0.021	0.021	0.000	0.000	0.000	0.000
60	A	1286	GLY	0	0.050	0.045	32.136	0.017	0.017	0.000	0.000	0.000	0.000
61	A	1287	PRO	0	0.005	0.002	33.126	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	1288	ASP	-1	-0.859	-0.936	34.513	-0.187	-0.187	0.000	0.000	0.000	0.000
63	A	1289	GLY	0	0.007	0.007	34.463	0.007	0.007	0.000	0.000	0.000	0.000
64	A	1290	GLY	0	0.043	0.024	34.646	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	1291	ASP	-1	-0.964	-0.992	35.444	-0.180	-0.180	0.000	0.000	0.000	0.000
66	A	1292	HIS	0	-0.063	-0.035	38.792	0.008	0.008	0.000	0.000	0.000	0.000
67	A	1293	GLU	-1	-0.727	-0.836	34.872	-0.237	-0.237	0.000	0.000	0.000	0.000
68	A	1294	THR	0	0.033	0.014	36.801	0.006	0.006	0.000	0.000	0.000	0.000
69	A	1295	ASP	-1	-0.848	-0.932	36.249	-0.207	-0.207	0.000	0.000	0.000	0.000
70	A	1296	GLY	0	0.045	0.031	33.285	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	1297	ASP	-1	-0.900	-0.939	32.091	-0.232	-0.232	0.000	0.000	0.000	0.000
72	A	1298	LEU	0	-0.081	-0.053	27.738	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	1299	LEU	0	0.025	0.020	25.050	0.002	0.002	0.000	0.000	0.000	0.000
74	A	1300	ALA	0	0.026	0.014	21.991	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	1301	GLU	-1	-0.866	-0.945	23.481	-0.301	-0.301	0.000	0.000	0.000	0.000
76	A	1302	THR	0	0.066	0.069	18.942	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	1303	ASP	-1	-0.826	-0.925	21.054	-0.276	-0.276	0.000	0.000	0.000	0.000
78	A	1304	VAL	0	-0.098	-0.046	22.280	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	1305	LEU	0	0.014	0.016	16.438	0.016	0.016	0.000	0.000	0.000	0.000
80	A	1306	ALA	0	-0.002	-0.017	21.050	0.011	0.011	0.000	0.000	0.000	0.000
81	A	1307	TYR	0	-0.068	-0.045	18.667	-0.043	-0.043	0.000	0.000	0.000	0.000
82	A	1308	ASP	-1	-0.837	-0.888	18.886	-0.256	-0.256	0.000	0.000	0.000	0.000
83	A	1309	CYS	0	0.028	0.023	18.243	-0.062	-0.062	0.000	0.000	0.000	0.000
84	A	1310	ALA	0	0.040	0.028	18.772	0.048	0.048	0.000	0.000	0.000	0.000
85	A	1311	ALA	0	0.017	0.008	20.713	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	1312	ARG	1	0.885	0.936	23.275	0.199	0.199	0.000	0.000	0.000	0.000
87	A	1313	GLU	-1	-0.879	-0.926	18.136	-0.429	-0.429	0.000	0.000	0.000	0.000
88	A	1314	LYS	1	0.826	0.896	18.062	0.446	0.446	0.000	0.000	0.000	0.000
89	A	1315	TYR	0	0.009	0.004	15.372	-0.086	-0.086	0.000	0.000	0.000	0.000
90	A	1316	ALA	0	0.040	0.012	12.922	0.041	0.041	0.000	0.000	0.000	0.000
91	A	1317	MET	0	-0.039	-0.007	14.269	-0.087	-0.087	0.000	0.000	0.000	0.000
92	A	1318	MET	0	0.015	0.006	10.986	0.081	0.081	0.000	0.000	0.000	0.000
93	A	1319	PHE	0	-0.029	-0.030	15.248	0.140	0.140	0.000	0.000	0.000	0.000
94	A	1320	ASP	-1	-0.913	-0.966	15.458	-0.772	-0.772	0.000	0.000	0.000	0.000
95	A	1321	GLU	-1	-0.927	-0.964	14.960	-0.995	-0.995	0.000	0.000	0.000	0.000
96	A	1322	PRO	0	-0.061	-0.014	13.706	0.060	0.060	0.000	0.000	0.000	0.000
97	A	1323	VAL	0	-0.023	-0.020	16.305	0.090	0.090	0.000	0.000	0.000	0.000
98	A	1324	LEU	0	-0.046	-0.022	19.771	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	1325	LEU	0	-0.056	-0.016	21.153	0.041	0.041	0.000	0.000	0.000	0.000
100	A	1326	GLN	0	0.013	-0.002	23.707	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	1327	ALA	0	0.037	0.013	26.519	0.004	0.004	0.000	0.000	0.000	0.000
102	A	1328	GLY	0	-0.059	-0.030	27.821	0.022	0.022	0.000	0.000	0.000	0.000
103	A	1329	TRP	0	-0.062	-0.027	28.939	0.023	0.023	0.000	0.000	0.000	0.000
104	A	1330	TRP	0	-0.021	0.020	28.989	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	1331	TYR	0	0.021	-0.007	26.712	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	1332	VAL	0	-0.062	-0.036	28.467	0.017	0.017	0.000	0.000	0.000	0.000
107	A	1333	ALA	0	0.054	0.049	24.364	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	1334	TRP	0	-0.020	-0.025	25.616	0.036	0.036	0.000	0.000	0.000	0.000
109	A	1335	ALA	0	0.069	0.016	25.010	-0.036	-0.036	0.000	0.000	0.000	0.000
110	A	1336	ARG	1	0.869	0.951	26.644	0.256	0.256	0.000	0.000	0.000	0.000
111	A	1337	VAL	0	0.034	0.021	25.384	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	1338	SER	0	-0.049	-0.035	27.374	0.033	0.033	0.000	0.000	0.000	0.000
113	A	1339	GLY	0	0.021	0.012	27.769	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	1340	PRO	0	-0.010	0.014	28.283	0.013	0.013	0.000	0.000	0.000	0.000
115	A	1341	SER	0	0.029	0.007	30.198	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	1342	SER	0	-0.024	0.009	26.474	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	1343	ASP	-1	-0.800	-0.885	25.359	-0.220	-0.220	0.000	0.000	0.000	0.000
118	A	1344	CYS	0	-0.078	0.011	27.645	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	1345	GLY	0	0.069	0.037	28.443	0.007	0.007	0.000	0.000	0.000	0.000
120	A	1346	SER	0	-0.045	-0.052	29.022	0.015	0.015	0.000	0.000	0.000	0.000
121	A	1347	HIS	0	-0.016	-0.023	30.771	0.001	0.001	0.000	0.000	0.000	0.000
122	A	1348	GLY	0	0.002	0.015	29.861	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	1349	GLN	0	-0.026	-0.029	29.401	0.019	0.019	0.000	0.000	0.000	0.000
124	A	1350	ALA	0	0.017	-0.001	30.110	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	1351	SER	0	-0.060	-0.043	29.659	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1352	ILE	0	-0.014	0.001	24.331	0.011	0.011	0.000	0.000	0.000	0.000
127	A	1353	THR	0	-0.006	0.002	25.796	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	1354	THR	0	-0.006	-0.023	20.290	0.012	0.012	0.000	0.000	0.000	0.000
129	A	1355	ASP	-1	-0.923	-0.968	19.467	-0.358	-0.358	0.000	0.000	0.000	0.000
130	A	1356	ASP	-1	-0.863	-0.891	18.496	-0.507	-0.507	0.000	0.000	0.000	0.000
131	A	1357	GLY	0	-0.037	-0.020	20.598	0.020	0.020	0.000	0.000	0.000	0.000
132	A	1358	VAL	0	-0.021	0.002	21.199	0.022	0.022	0.000	0.000	0.000	0.000
133	A	1359	ILE	0	-0.036	-0.009	23.965	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	1360	PHE	0	0.040	0.010	20.217	0.001	0.001	0.000	0.000	0.000	0.000
135	A	1361	GLN	0	-0.040	-0.024	26.183	0.035	0.035	0.000	0.000	0.000	0.000
136	A	1362	PHE	0	0.006	-0.008	24.100	-0.021	-0.021	0.000	0.000	0.000	0.000
137	A	1363	LYS	1	0.861	0.926	30.103	0.230	0.230	0.000	0.000	0.000	0.000
138	A	1364	SER	0	0.044	0.015	32.349	-0.016	-0.016	0.000	0.000	0.000	0.000
139	A	1365	SER	0	-0.044	-0.029	32.272	0.004	0.004	0.000	0.000	0.000	0.000
140	A	1366	LYS	1	0.803	0.873	34.225	0.195	0.195	0.000	0.000	0.000	0.000
141	A	1367	LYS	1	0.763	0.881	32.239	0.253	0.253	0.000	0.000	0.000	0.000
142	A	1368	SER	0	-0.073	-0.032	33.005	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	1369	ASN	0	-0.013	-0.024	34.166	0.009	0.009	0.000	0.000	0.000	0.000
144	A	1370	ASN	0	-0.065	-0.038	32.152	0.027	0.027	0.000	0.000	0.000	0.000
145	A	1371	GLY	0	0.005	0.001	34.640	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	1372	THR	0	-0.057	-0.029	29.445	0.002	0.002	0.000	0.000	0.000	0.000
147	A	1373	ASP	-1	-0.789	-0.868	32.845	-0.207	-0.207	0.000	0.000	0.000	0.000
148	A	1374	VAL	0	0.014	0.006	31.672	-0.018	-0.018	0.000	0.000	0.000	0.000
149	A	1375	ASN	0	-0.060	-0.027	31.734	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	1376	ALA	0	-0.012	-0.028	32.030	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1377	GLY	0	0.028	0.015	30.861	-0.007	-0.007	0.000	0.000	0.000	0.000
152	A	1378	GLN	0	0.028	-0.018	24.741	-0.037	-0.037	0.000	0.000	0.000	0.000
153	A	1379	ILE	0	-0.013	-0.001	23.271	0.009	0.009	0.000	0.000	0.000	0.000
154	A	1380	PRO	0	-0.015	-0.004	21.746	0.006	0.006	0.000	0.000	0.000	0.000
155	A	1381	GLN	0	-0.023	-0.014	17.466	-0.039	-0.039	0.000	0.000	0.000	0.000
156	A	1382	LEU	0	0.018	0.031	19.661	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	1383	LEU	0	-0.024	0.000	14.021	-0.003	-0.003	0.000	0.000	0.000	0.000
158	A	1384	TYR	0	-0.044	-0.061	15.149	-0.035	-0.035	0.000	0.000	0.000	0.000
159	A	1385	ARG	1	0.872	0.934	8.846	1.951	1.951	0.000	0.000	0.000	0.000
160	A	1386	LEU	0	0.034	0.019	14.393	0.095	0.095	0.000	0.000	0.000	0.000
161	A	1387	PRO	0	-0.025	-0.001	15.844	-0.063	-0.063	0.000	0.000	0.000	0.000

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