FMO DATABASE

FMODB ID: J37V9

Calculation Name: 1MIJ-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1MIJ

Chain ID: A

ChEMBL ID:
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UniProt ID: P29617

Base Structure: X-ray

Registration Date: 2023-06-19

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1426442.553682
FMO2-HF: Nuclear repulsion	1367531.022242
FMO2-HF: Total energy	-58911.531441
FMO2-MP2: Total energy	-59084.512851

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:1245:SER)

Summations of interaction energy for fragment #1(A:1245: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.
-28.917	-20.608	5.8	-6.186	-7.922	0.037

Interaction energy analysis for fragmet #1(A:1245:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / 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	1247	THR	0	-0.043	-0.015	2.200	-7.805	-4.185	2.874	-3.062	-3.432	0.029
4	A	1248	LEU	0	-0.002	0.017	3.157	-4.810	-3.854	0.058	-0.463	-0.551	-0.003
5	A	1249	THR	0	0.054	0.004	4.706	0.327	0.392	-0.001	-0.003	-0.061	0.000
6	A	1250	PRO	0	0.065	0.007	7.310	0.209	0.209	0.000	0.000	0.000	0.000
7	A	1251	MET	0	-0.001	0.005	8.859	0.325	0.325	0.000	0.000	0.000	0.000
8	A	1252	HIS	0	0.035	0.029	4.127	0.834	0.897	-0.001	-0.006	-0.056	0.000
9	A	1253	LEU	0	0.007	0.012	9.739	0.229	0.229	0.000	0.000	0.000	0.000
10	A	1254	ARG	1	0.917	0.956	12.897	1.068	1.068	0.000	0.000	0.000	0.000
11	A	1255	LYS	1	0.866	0.949	9.721	1.704	1.704	0.000	0.000	0.000	0.000
12	A	1256	ALA	0	0.004	-0.001	13.100	0.112	0.112	0.000	0.000	0.000	0.000
13	A	1257	LYS	1	0.777	0.882	14.747	0.558	0.558	0.000	0.000	0.000	0.000
14	A	1258	LEU	0	0.011	0.009	16.745	0.064	0.064	0.000	0.000	0.000	0.000
15	A	1259	MET	0	0.010	0.011	14.742	0.007	0.007	0.000	0.000	0.000	0.000
16	A	1260	PHE	0	-0.002	0.017	18.572	0.061	0.061	0.000	0.000	0.000	0.000
17	A	1261	PHE	0	-0.017	-0.011	21.035	0.045	0.045	0.000	0.000	0.000	0.000
18	A	1262	TRP	0	0.028	0.015	21.390	0.008	0.008	0.000	0.000	0.000	0.000
19	A	1263	VAL	0	-0.013	-0.011	18.972	0.028	0.028	0.000	0.000	0.000	0.000
20	A	1264	ARG	1	0.820	0.886	21.304	0.240	0.240	0.000	0.000	0.000	0.000
21	A	1265	TYR	0	-0.075	-0.038	22.544	0.008	0.008	0.000	0.000	0.000	0.000
22	A	1266	PRO	0	0.027	0.042	17.813	0.025	0.025	0.000	0.000	0.000	0.000
23	A	1267	SER	0	0.055	0.019	19.029	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	1268	SER	0	0.045	-0.007	15.320	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	1269	ALA	0	-0.013	0.005	14.572	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	1270	VAL	0	0.039	0.028	15.613	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	1271	LEU	0	-0.016	-0.015	12.839	-0.073	-0.073	0.000	0.000	0.000	0.000
28	A	1272	LYS	1	0.938	0.958	10.766	-0.183	-0.183	0.000	0.000	0.000	0.000
29	A	1273	MET	0	-0.013	0.016	11.225	-0.076	-0.076	0.000	0.000	0.000	0.000
30	A	1274	TYR	0	0.026	-0.015	13.273	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	1275	PHE	0	-0.061	-0.029	8.343	-0.096	-0.096	0.000	0.000	0.000	0.000
32	A	1276	PRO	0	0.063	0.032	7.704	-0.239	-0.239	0.000	0.000	0.000	0.000
33	A	1277	ASP	-1	-0.831	-0.912	5.283	-2.980	-2.980	0.000	0.000	0.000	0.000
34	A	1278	ILE	0	-0.054	-0.019	3.197	-5.505	-3.843	0.044	-0.822	-0.884	-0.007
35	A	1279	LYS	1	0.972	0.981	2.532	-11.926	-10.010	2.827	-1.822	-2.921	0.018
36	A	1280	PHE	0	-0.018	-0.023	4.847	0.263	0.290	-0.001	-0.008	-0.017	0.000
37	A	1281	ASN	0	0.009	0.008	7.481	0.107	0.107	0.000	0.000	0.000	0.000
38	A	1282	LYS	1	1.014	1.013	10.659	-0.440	-0.440	0.000	0.000	0.000	0.000
39	A	1283	ASN	0	0.030	0.014	11.451	-0.151	-0.151	0.000	0.000	0.000	0.000
40	A	1284	ASN	0	0.048	0.012	6.470	-0.150	-0.150	0.000	0.000	0.000	0.000
41	A	1285	THR	0	0.005	-0.014	10.143	-0.250	-0.250	0.000	0.000	0.000	0.000
42	A	1286	ALA	0	-0.006	-0.002	12.647	-0.072	-0.072	0.000	0.000	0.000	0.000
43	A	1287	GLN	0	-0.005	0.003	9.870	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	1288	LEU	0	0.027	0.018	9.844	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	1289	VAL	0	0.012	0.002	13.179	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1290	LYS	1	0.855	0.936	16.653	0.175	0.175	0.000	0.000	0.000	0.000
47	A	1291	TRP	0	0.000	-0.002	9.719	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	1292	PHE	0	0.087	0.024	14.859	0.016	0.016	0.000	0.000	0.000	0.000
49	A	1293	SER	0	-0.016	-0.010	18.840	0.036	0.036	0.000	0.000	0.000	0.000
50	A	1294	ASN	0	0.022	0.009	19.299	0.043	0.043	0.000	0.000	0.000	0.000
51	A	1295	PHE	0	-0.034	-0.005	16.198	0.013	0.013	0.000	0.000	0.000	0.000
52	A	1296	ARG	1	0.922	0.959	21.374	0.229	0.229	0.000	0.000	0.000	0.000
53	A	1297	GLU	-1	-0.920	-0.958	24.096	-0.148	-0.148	0.000	0.000	0.000	0.000
54	A	1298	PHE	0	0.018	0.000	25.031	0.012	0.012	0.000	0.000	0.000	0.000
55	A	1299	TYR	0	-0.005	-0.018	26.322	0.006	0.006	0.000	0.000	0.000	0.000
56	A	1300	TYR	0	0.019	-0.023	28.032	0.011	0.011	0.000	0.000	0.000	0.000
57	A	1301	ILE	0	-0.004	0.021	28.983	0.012	0.012	0.000	0.000	0.000	0.000
58	A	1302	GLN	0	0.013	0.004	29.895	0.016	0.016	0.000	0.000	0.000	0.000
59	A	1303	MET	0	-0.045	-0.008	30.877	0.008	0.008	0.000	0.000	0.000	0.000
60	A	1304	GLU	-1	-0.754	-0.865	34.212	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	1305	LYS	1	0.916	0.964	33.870	0.158	0.158	0.000	0.000	0.000	0.000
62	A	1306	TYR	0	0.029	0.005	36.538	0.004	0.004	0.000	0.000	0.000	0.000
63	A	1307	ALA	0	0.017	0.009	38.261	0.005	0.005	0.000	0.000	0.000	0.000
64	A	1308	ARG	1	0.811	0.871	39.711	0.088	0.088	0.000	0.000	0.000	0.000
65	A	1309	GLN	0	-0.029	0.000	39.415	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	1310	ALA	0	0.011	0.006	42.401	0.004	0.004	0.000	0.000	0.000	0.000
67	A	1311	VAL	0	-0.039	-0.018	44.211	0.003	0.003	0.000	0.000	0.000	0.000
68	A	1312	THR	0	-0.044	-0.018	45.543	0.005	0.005	0.000	0.000	0.000	0.000
69	A	1313	GLU	-1	-1.037	-1.013	46.139	-0.083	-0.083	0.000	0.000	0.000	0.000
70	A	1327	SER	0	0.084	0.030	37.218	0.001	0.001	0.000	0.000	0.000	0.000
71	A	1328	GLU	-1	-0.770	-0.847	35.316	-0.186	-0.186	0.000	0.000	0.000	0.000
72	A	1329	LEU	0	0.016	0.011	32.843	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	1330	TYR	0	-0.024	-0.055	31.573	-0.020	-0.020	0.000	0.000	0.000	0.000
74	A	1331	ARG	1	0.850	0.899	30.691	0.171	0.171	0.000	0.000	0.000	0.000
75	A	1332	VAL	0	-0.006	-0.004	29.831	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	1333	LEU	0	-0.023	-0.012	27.629	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	1334	ASN	0	0.027	0.010	26.071	-0.044	-0.044	0.000	0.000	0.000	0.000
78	A	1335	LEU	0	0.018	0.016	25.403	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	1336	HIS	0	0.019	0.028	22.676	-0.040	-0.040	0.000	0.000	0.000	0.000
80	A	1337	TYR	0	-0.064	-0.051	21.077	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	1338	ASN	0	0.010	-0.019	20.776	-0.088	-0.088	0.000	0.000	0.000	0.000
82	A	1339	ARG	1	0.865	0.939	21.332	0.368	0.368	0.000	0.000	0.000	0.000
83	A	1340	ASN	0	-0.020	-0.023	20.732	0.005	0.005	0.000	0.000	0.000	0.000
84	A	1341	ASN	0	0.021	0.009	23.340	0.012	0.012	0.000	0.000	0.000	0.000
85	A	1342	HIS	0	-0.001	0.009	18.527	-0.054	-0.054	0.000	0.000	0.000	0.000
86	A	1343	ILE	0	-0.005	0.016	21.412	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	1344	GLU	-1	-0.875	-0.927	24.329	-0.237	-0.237	0.000	0.000	0.000	0.000
88	A	1345	VAL	0	-0.032	-0.019	26.465	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	1346	PRO	0	0.033	0.028	25.717	0.024	0.024	0.000	0.000	0.000	0.000
90	A	1347	GLN	0	0.077	0.017	28.820	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1348	ASN	0	0.005	-0.011	28.829	0.021	0.021	0.000	0.000	0.000	0.000
92	A	1349	PHE	0	0.009	0.006	26.311	0.006	0.006	0.000	0.000	0.000	0.000
93	A	1350	ARG	1	0.937	0.971	29.039	0.226	0.226	0.000	0.000	0.000	0.000
94	A	1351	PHE	0	0.035	0.021	32.505	0.011	0.011	0.000	0.000	0.000	0.000
95	A	1352	VAL	0	0.020	0.020	28.880	0.013	0.013	0.000	0.000	0.000	0.000
96	A	1353	VAL	0	0.016	0.023	30.405	0.010	0.010	0.000	0.000	0.000	0.000
97	A	1354	GLU	-1	-0.857	-0.905	32.805	-0.134	-0.134	0.000	0.000	0.000	0.000
98	A	1355	SER	0	-0.024	-0.022	35.240	0.014	0.014	0.000	0.000	0.000	0.000
99	A	1356	THR	0	-0.039	-0.032	32.403	0.007	0.007	0.000	0.000	0.000	0.000
100	A	1357	LEU	0	0.004	-0.001	35.060	0.008	0.008	0.000	0.000	0.000	0.000
101	A	1358	ARG	1	0.938	0.972	37.570	0.129	0.129	0.000	0.000	0.000	0.000
102	A	1359	GLU	-1	-0.836	-0.871	37.512	-0.086	-0.086	0.000	0.000	0.000	0.000
103	A	1360	PHE	0	-0.038	-0.034	33.905	0.005	0.005	0.000	0.000	0.000	0.000
104	A	1361	PHE	0	0.005	0.013	39.213	0.005	0.005	0.000	0.000	0.000	0.000
105	A	1362	ARG	1	0.857	0.884	41.556	0.092	0.092	0.000	0.000	0.000	0.000
106	A	1363	ALA	0	-0.044	-0.014	41.376	0.005	0.005	0.000	0.000	0.000	0.000
107	A	1364	ILE	0	0.007	-0.013	40.228	0.004	0.004	0.000	0.000	0.000	0.000
108	A	1365	GLN	0	-0.006	0.005	44.376	0.003	0.003	0.000	0.000	0.000	0.000
109	A	1366	GLY	0	-0.022	-0.001	46.896	0.003	0.003	0.000	0.000	0.000	0.000
110	A	1367	GLY	0	0.038	0.025	47.631	0.004	0.004	0.000	0.000	0.000	0.000
111	A	1368	LYS	1	0.829	0.889	44.512	0.054	0.054	0.000	0.000	0.000	0.000
112	A	1369	ASP	-1	-0.841	-0.918	41.950	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	1370	THR	0	-0.009	-0.010	42.737	0.001	0.001	0.000	0.000	0.000	0.000
114	A	1371	GLU	-1	-0.816	-0.879	44.043	-0.046	-0.046	0.000	0.000	0.000	0.000
115	A	1372	GLN	0	0.018	-0.004	42.060	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	1373	SER	0	-0.078	-0.048	38.059	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1374	TRP	0	0.104	0.081	38.303	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	1375	LYS	1	0.868	0.939	34.234	0.095	0.095	0.000	0.000	0.000	0.000
119	A	1376	LYS	1	0.922	0.956	31.814	0.058	0.058	0.000	0.000	0.000	0.000
120	A	1377	SER	0	-0.037	-0.021	35.235	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	1378	ILE	0	0.076	0.039	34.276	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	1379	TYR	0	-0.028	-0.014	30.818	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	1380	LYS	1	0.984	0.999	31.173	0.048	0.048	0.000	0.000	0.000	0.000
124	A	1381	ILE	0	0.011	0.025	33.477	0.003	0.003	0.000	0.000	0.000	0.000
125	A	1382	ILE	0	0.055	0.012	29.081	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	1383	SER	0	-0.067	-0.050	28.052	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	1384	ARG	1	0.870	0.935	28.480	0.088	0.088	0.000	0.000	0.000	0.000
128	A	1385	MET	0	-0.040	-0.005	30.027	0.003	0.003	0.000	0.000	0.000	0.000
129	A	1386	ASP	-1	-0.765	-0.862	23.905	-0.266	-0.266	0.000	0.000	0.000	0.000
130	A	1387	ASP	-1	-0.858	-0.919	25.044	-0.232	-0.232	0.000	0.000	0.000	0.000
131	A	1388	PRO	0	-0.006	-0.013	23.242	-0.029	-0.029	0.000	0.000	0.000	0.000
132	A	1389	VAL	0	-0.010	0.003	17.470	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	1390	PRO	0	0.015	0.017	20.512	0.000	0.000	0.000	0.000	0.000	0.000
134	A	1391	GLU	-1	-0.726	-0.855	18.575	-0.459	-0.459	0.000	0.000	0.000	0.000
135	A	1392	TYR	0	0.036	0.025	17.364	-0.037	-0.037	0.000	0.000	0.000	0.000
136	A	1393	PHE	0	-0.006	-0.008	15.269	-0.093	-0.093	0.000	0.000	0.000	0.000
137	A	1394	LYS	1	0.743	0.862	12.837	0.277	0.277	0.000	0.000	0.000	0.000
138	A	1395	SER	0	-0.035	-0.010	12.218	-0.055	-0.055	0.000	0.000	0.000	0.000
139	A	1396	PRO	0	-0.040	-0.009	9.916	-0.119	-0.119	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1245:SER)