FMO DATABASE

FMODB ID: 824QY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1422558.584897
FMO2-HF: Nuclear repulsion	1363647.918522
FMO2-HF: Total energy	-58910.666375
FMO2-MP2: Total energy	-59083.685957

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.
-29.758	-19.974	3.969	-6.364	-7.386	0.018

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 : 0.073 / q_NPA : 0.021

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	0.005	0.012	2.181	-10.761	-6.796	3.056	-3.397	-3.624	0.029
4	A	1248	LEU	0	0.001	0.016	4.007	-2.531	-2.280	0.002	-0.080	-0.172	0.000
5	A	1249	THR	0	0.043	0.005	5.365	0.277	0.277	0.000	0.000	0.000	0.000
6	A	1250	PRO	0	0.051	0.003	8.025	0.144	0.144	0.000	0.000	0.000	0.000
7	A	1251	MET	0	0.000	-0.002	8.311	0.306	0.306	0.000	0.000	0.000	0.000
8	A	1252	HIS	0	0.018	0.017	4.443	0.869	0.928	-0.001	-0.003	-0.054	0.000
9	A	1253	LEU	0	0.003	0.012	10.117	0.186	0.186	0.000	0.000	0.000	0.000
10	A	1254	ARG	1	0.943	0.963	13.232	0.979	0.979	0.000	0.000	0.000	0.000
11	A	1255	LYS	1	0.930	0.980	10.433	1.411	1.411	0.000	0.000	0.000	0.000
12	A	1256	ALA	0	0.019	0.000	13.797	0.092	0.092	0.000	0.000	0.000	0.000
13	A	1257	LYS	1	0.899	0.954	15.404	0.543	0.543	0.000	0.000	0.000	0.000
14	A	1258	LEU	0	0.024	0.026	17.597	0.048	0.048	0.000	0.000	0.000	0.000
15	A	1259	MET	0	0.007	0.008	14.734	0.000	0.000	0.000	0.000	0.000	0.000
16	A	1260	PHE	0	0.017	0.029	19.082	0.054	0.054	0.000	0.000	0.000	0.000
17	A	1261	PHE	0	-0.018	-0.012	21.682	0.039	0.039	0.000	0.000	0.000	0.000
18	A	1262	TRP	0	0.003	-0.006	21.746	0.008	0.008	0.000	0.000	0.000	0.000
19	A	1263	VAL	0	-0.037	-0.009	19.083	0.025	0.025	0.000	0.000	0.000	0.000
20	A	1264	ARG	1	0.853	0.924	21.692	0.206	0.206	0.000	0.000	0.000	0.000
21	A	1265	TYR	0	-0.089	-0.066	22.730	0.011	0.011	0.000	0.000	0.000	0.000
22	A	1266	PRO	0	0.040	0.051	17.785	0.018	0.018	0.000	0.000	0.000	0.000
23	A	1267	SER	0	0.057	0.027	19.259	0.006	0.006	0.000	0.000	0.000	0.000
24	A	1268	SER	0	0.052	-0.014	15.133	-0.051	-0.051	0.000	0.000	0.000	0.000
25	A	1269	ALA	0	-0.012	0.002	14.373	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	1270	VAL	0	0.037	0.027	15.215	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	1271	LEU	0	0.001	-0.007	12.652	-0.069	-0.069	0.000	0.000	0.000	0.000
28	A	1272	LYS	1	0.947	0.964	10.377	-0.154	-0.154	0.000	0.000	0.000	0.000
29	A	1273	MET	0	-0.005	0.013	10.596	-0.113	-0.113	0.000	0.000	0.000	0.000
30	A	1274	TYR	0	0.011	-0.011	12.809	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	1275	PHE	0	-0.062	-0.028	7.959	-0.046	-0.046	0.000	0.000	0.000	0.000
32	A	1276	PRO	0	0.042	0.011	7.265	-0.329	-0.329	0.000	0.000	0.000	0.000
33	A	1277	ASP	-1	-0.837	-0.907	4.984	-3.564	-3.564	0.000	0.000	0.000	0.000
34	A	1278	ILE	0	-0.034	-0.009	2.638	-7.895	-5.152	0.564	-1.598	-1.708	-0.019
35	A	1279	LYS	1	0.939	0.966	2.872	-8.479	-5.717	0.349	-1.279	-1.832	0.008
36	A	1280	PHE	0	-0.018	-0.026	4.721	0.485	0.489	-0.001	-0.007	0.004	0.000
37	A	1281	ASN	0	0.014	0.013	7.367	0.098	0.098	0.000	0.000	0.000	0.000
38	A	1282	LYS	1	1.022	0.999	10.546	-0.443	-0.443	0.000	0.000	0.000	0.000
39	A	1283	ASN	0	0.034	0.015	10.944	-0.149	-0.149	0.000	0.000	0.000	0.000
40	A	1284	ASN	0	0.044	0.011	6.541	-0.289	-0.289	0.000	0.000	0.000	0.000
41	A	1285	THR	0	0.025	0.015	10.179	-0.261	-0.261	0.000	0.000	0.000	0.000
42	A	1286	ALA	0	-0.004	-0.003	12.318	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	1287	GLN	0	-0.005	0.003	10.057	0.023	0.023	0.000	0.000	0.000	0.000
44	A	1288	LEU	0	0.015	0.002	10.211	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	1289	VAL	0	-0.004	-0.005	13.420	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	1290	LYS	1	0.915	0.963	16.724	0.094	0.094	0.000	0.000	0.000	0.000
47	A	1291	TRP	0	0.023	0.012	10.584	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	1292	PHE	0	0.077	0.027	15.531	0.013	0.013	0.000	0.000	0.000	0.000
49	A	1293	SER	0	-0.069	-0.023	19.715	0.023	0.023	0.000	0.000	0.000	0.000
50	A	1294	ASN	0	0.059	0.021	19.369	0.036	0.036	0.000	0.000	0.000	0.000
51	A	1295	PHE	0	-0.049	-0.024	17.017	0.005	0.005	0.000	0.000	0.000	0.000
52	A	1296	ARG	1	0.941	0.962	22.010	0.182	0.182	0.000	0.000	0.000	0.000
53	A	1297	GLU	-1	-0.967	-0.958	25.315	-0.115	-0.115	0.000	0.000	0.000	0.000
54	A	1298	PHE	0	0.011	-0.003	25.753	0.009	0.009	0.000	0.000	0.000	0.000
55	A	1299	TYR	0	-0.002	-0.019	26.942	0.004	0.004	0.000	0.000	0.000	0.000
56	A	1300	TYR	0	0.043	0.007	28.630	0.008	0.008	0.000	0.000	0.000	0.000
57	A	1301	ILE	0	-0.004	0.025	29.888	0.009	0.009	0.000	0.000	0.000	0.000
58	A	1302	GLN	0	-0.038	-0.023	30.571	0.011	0.011	0.000	0.000	0.000	0.000
59	A	1303	MET	0	-0.057	-0.018	31.716	0.008	0.008	0.000	0.000	0.000	0.000
60	A	1304	GLU	-1	-0.846	-0.925	34.802	-0.076	-0.076	0.000	0.000	0.000	0.000
61	A	1305	LYS	1	0.961	0.983	35.491	0.124	0.124	0.000	0.000	0.000	0.000
62	A	1306	TYR	0	0.026	0.001	37.201	0.004	0.004	0.000	0.000	0.000	0.000
63	A	1307	ALA	0	0.018	0.012	38.963	0.004	0.004	0.000	0.000	0.000	0.000
64	A	1308	ARG	1	0.823	0.881	40.631	0.075	0.075	0.000	0.000	0.000	0.000
65	A	1309	GLN	0	-0.043	-0.008	40.355	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	1310	ALA	0	0.009	0.003	43.208	0.003	0.003	0.000	0.000	0.000	0.000
67	A	1311	VAL	0	-0.050	-0.021	45.068	0.003	0.003	0.000	0.000	0.000	0.000
68	A	1312	THR	0	-0.081	-0.038	46.362	0.004	0.004	0.000	0.000	0.000	0.000
69	A	1313	GLU	-1	-1.000	-0.978	46.973	-0.072	-0.072	0.000	0.000	0.000	0.000
70	A	1327	SER	0	0.041	0.010	37.785	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	1328	GLU	-1	-0.760	-0.858	35.873	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	1329	LEU	0	0.041	0.023	33.508	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	1330	TYR	0	-0.014	-0.056	31.917	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	1331	ARG	1	0.872	0.935	31.215	0.156	0.156	0.000	0.000	0.000	0.000
75	A	1332	VAL	0	-0.018	-0.005	30.518	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	1333	LEU	0	-0.030	-0.024	28.359	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	1334	ASN	0	0.027	0.004	26.727	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	1335	LEU	0	0.014	0.014	26.033	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	1336	HIS	0	-0.081	-0.042	22.978	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	1337	TYR	0	-0.091	-0.071	21.705	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	1338	ASN	0	-0.017	-0.024	21.489	-0.078	-0.078	0.000	0.000	0.000	0.000
82	A	1339	ARG	1	0.931	0.993	22.207	0.330	0.330	0.000	0.000	0.000	0.000
83	A	1340	ASN	0	-0.028	-0.027	21.196	0.047	0.047	0.000	0.000	0.000	0.000
84	A	1341	ASN	0	0.004	0.009	23.854	0.009	0.009	0.000	0.000	0.000	0.000
85	A	1342	HIS	0	-0.033	-0.010	20.016	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	1343	ILE	0	-0.009	0.004	21.895	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	1344	GLU	-1	-0.880	-0.925	24.708	-0.217	-0.217	0.000	0.000	0.000	0.000
88	A	1345	VAL	0	-0.061	-0.039	27.238	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	1346	PRO	0	0.039	0.031	26.004	0.019	0.019	0.000	0.000	0.000	0.000
90	A	1347	GLN	0	0.092	0.027	29.056	0.003	0.003	0.000	0.000	0.000	0.000
91	A	1348	ASN	0	0.009	-0.033	29.033	0.019	0.019	0.000	0.000	0.000	0.000
92	A	1349	PHE	0	-0.016	0.002	27.109	0.005	0.005	0.000	0.000	0.000	0.000
93	A	1350	ARG	1	0.956	0.979	29.657	0.194	0.194	0.000	0.000	0.000	0.000
94	A	1351	PHE	0	0.033	0.032	33.207	0.010	0.010	0.000	0.000	0.000	0.000
95	A	1352	VAL	0	0.022	0.021	29.635	0.012	0.012	0.000	0.000	0.000	0.000
96	A	1353	VAL	0	0.014	0.025	31.175	0.009	0.009	0.000	0.000	0.000	0.000
97	A	1354	GLU	-1	-0.840	-0.917	33.565	-0.121	-0.121	0.000	0.000	0.000	0.000
98	A	1355	SER	0	-0.060	-0.045	35.244	0.012	0.012	0.000	0.000	0.000	0.000
99	A	1356	THR	0	-0.028	-0.026	33.133	0.007	0.007	0.000	0.000	0.000	0.000
100	A	1357	LEU	0	0.015	0.008	35.721	0.008	0.008	0.000	0.000	0.000	0.000
101	A	1358	ARG	1	0.954	0.980	38.183	0.109	0.109	0.000	0.000	0.000	0.000
102	A	1359	GLU	-1	-0.946	-0.970	37.614	-0.071	-0.071	0.000	0.000	0.000	0.000
103	A	1360	PHE	0	-0.017	-0.026	34.655	0.004	0.004	0.000	0.000	0.000	0.000
104	A	1361	PHE	0	0.013	0.011	40.033	0.004	0.004	0.000	0.000	0.000	0.000
105	A	1362	ARG	1	0.952	0.977	42.014	0.078	0.078	0.000	0.000	0.000	0.000
106	A	1363	ALA	0	-0.025	-0.007	42.148	0.004	0.004	0.000	0.000	0.000	0.000
107	A	1364	ILE	0	0.009	-0.001	41.105	0.003	0.003	0.000	0.000	0.000	0.000
108	A	1365	GLN	0	0.008	0.016	44.977	0.003	0.003	0.000	0.000	0.000	0.000
109	A	1366	GLY	0	-0.055	-0.021	47.457	0.003	0.003	0.000	0.000	0.000	0.000
110	A	1367	GLY	0	0.027	0.011	48.230	0.003	0.003	0.000	0.000	0.000	0.000
111	A	1368	LYS	1	0.968	0.965	45.226	0.050	0.050	0.000	0.000	0.000	0.000
112	A	1369	ASP	-1	-0.847	-0.921	42.608	-0.056	-0.056	0.000	0.000	0.000	0.000
113	A	1370	THR	0	-0.040	-0.010	43.489	0.001	0.001	0.000	0.000	0.000	0.000
114	A	1371	GLU	-1	-0.927	-0.949	44.758	-0.034	-0.034	0.000	0.000	0.000	0.000
115	A	1372	GLN	0	0.006	-0.011	42.267	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	1373	SER	0	-0.065	-0.055	38.569	0.001	0.001	0.000	0.000	0.000	0.000
117	A	1374	TRP	0	0.084	0.069	39.371	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	1375	LYS	1	0.961	0.984	34.116	0.075	0.075	0.000	0.000	0.000	0.000
119	A	1376	LYS	1	0.915	0.962	32.237	0.043	0.043	0.000	0.000	0.000	0.000
120	A	1377	SER	0	0.000	-0.002	35.217	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	1378	ILE	0	0.098	0.054	34.737	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	1379	TYR	0	-0.024	-0.017	31.047	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	1380	LYS	1	0.937	0.974	31.466	0.038	0.038	0.000	0.000	0.000	0.000
124	A	1381	ILE	0	-0.003	0.017	32.716	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	1382	ILE	0	0.019	-0.001	29.369	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	1383	SER	0	-0.092	-0.052	28.010	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	1384	ARG	1	0.941	0.969	28.003	0.071	0.071	0.000	0.000	0.000	0.000
128	A	1385	MET	0	-0.060	-0.013	29.889	0.002	0.002	0.000	0.000	0.000	0.000
129	A	1386	ASP	-1	-0.776	-0.884	23.673	-0.225	-0.225	0.000	0.000	0.000	0.000
130	A	1387	ASP	-1	-0.863	-0.916	25.125	-0.191	-0.191	0.000	0.000	0.000	0.000
131	A	1388	PRO	0	-0.012	-0.015	22.784	-0.024	-0.024	0.000	0.000	0.000	0.000
132	A	1389	VAL	0	-0.011	0.003	17.269	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	1390	PRO	0	0.024	0.023	20.318	0.002	0.002	0.000	0.000	0.000	0.000
134	A	1391	GLU	-1	-0.762	-0.898	18.537	-0.401	-0.401	0.000	0.000	0.000	0.000
135	A	1392	TYR	0	0.034	0.019	17.293	-0.042	-0.042	0.000	0.000	0.000	0.000
136	A	1393	PHE	0	-0.044	-0.025	15.356	-0.084	-0.084	0.000	0.000	0.000	0.000
137	A	1394	LYS	1	0.787	0.881	12.887	0.242	0.242	0.000	0.000	0.000	0.000
138	A	1395	SER	0	-0.044	-0.003	12.268	-0.067	-0.067	0.000	0.000	0.000	0.000
139	A	1396	PRO	0	-0.008	0.005	10.235	-0.103	-0.103	0.000	0.000	0.000	0.000

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