FMO DATABASE

FMODB ID: N1JLQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1423681.119531
FMO2-HF: Nuclear repulsion	1364769.808569
FMO2-HF: Total energy	-58911.310963
FMO2-MP2: Total energy	-59084.320266

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.
-30.862	-20.088	3.335	-6.468	-7.641	0.021

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 : 0.059 / q_NPA : 0.016

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	-0.009	0.006	2.297	-10.124	-5.560	2.003	-3.165	-3.402	0.026
4	A	1248	LEU	0	-0.014	0.010	4.088	-2.602	-2.333	0.002	-0.091	-0.179	0.000
5	A	1249	THR	0	0.042	-0.002	5.275	0.307	0.307	0.000	0.000	0.000	0.000
6	A	1250	PRO	0	0.064	0.008	8.042	0.149	0.149	0.000	0.000	0.000	0.000
7	A	1251	MET	0	0.001	0.001	8.662	0.292	0.292	0.000	0.000	0.000	0.000
8	A	1252	HIS	0	0.030	0.019	4.451	0.838	0.891	-0.001	-0.003	-0.049	0.000
9	A	1253	LEU	0	0.010	0.012	10.035	0.191	0.191	0.000	0.000	0.000	0.000
10	A	1254	ARG	1	0.951	0.969	13.139	0.968	0.968	0.000	0.000	0.000	0.000
11	A	1255	LYS	1	0.892	0.949	10.412	1.381	1.381	0.000	0.000	0.000	0.000
12	A	1256	ALA	0	0.009	-0.002	13.637	0.096	0.096	0.000	0.000	0.000	0.000
13	A	1257	LYS	1	0.798	0.901	15.309	0.478	0.478	0.000	0.000	0.000	0.000
14	A	1258	LEU	0	0.016	0.018	17.261	0.050	0.050	0.000	0.000	0.000	0.000
15	A	1259	MET	0	0.013	0.012	14.485	0.002	0.002	0.000	0.000	0.000	0.000
16	A	1260	PHE	0	0.011	0.024	19.012	0.055	0.055	0.000	0.000	0.000	0.000
17	A	1261	PHE	0	-0.029	-0.016	21.584	0.039	0.039	0.000	0.000	0.000	0.000
18	A	1262	TRP	0	0.020	0.002	21.758	0.006	0.006	0.000	0.000	0.000	0.000
19	A	1263	VAL	0	-0.029	-0.013	19.053	0.025	0.025	0.000	0.000	0.000	0.000
20	A	1264	ARG	1	0.810	0.893	21.665	0.194	0.194	0.000	0.000	0.000	0.000
21	A	1265	TYR	0	-0.080	-0.075	22.740	0.010	0.010	0.000	0.000	0.000	0.000
22	A	1266	PRO	0	0.041	0.050	17.785	0.020	0.020	0.000	0.000	0.000	0.000
23	A	1267	SER	0	0.041	0.018	19.339	0.010	0.010	0.000	0.000	0.000	0.000
24	A	1268	SER	0	0.048	-0.009	15.197	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	1269	ALA	0	-0.014	-0.001	14.475	-0.039	-0.039	0.000	0.000	0.000	0.000
26	A	1270	VAL	0	0.034	0.026	15.307	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	1271	LEU	0	0.002	-0.007	12.694	-0.064	-0.064	0.000	0.000	0.000	0.000
28	A	1272	LYS	1	0.936	0.960	10.461	-0.260	-0.260	0.000	0.000	0.000	0.000
29	A	1273	MET	0	-0.004	0.017	10.665	-0.096	-0.096	0.000	0.000	0.000	0.000
30	A	1274	TYR	0	0.016	-0.020	12.802	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	1275	PHE	0	-0.047	-0.014	8.003	-0.086	-0.086	0.000	0.000	0.000	0.000
32	A	1276	PRO	0	0.050	0.019	7.291	-0.252	-0.252	0.000	0.000	0.000	0.000
33	A	1277	ASP	-1	-0.855	-0.909	4.897	-3.019	-3.019	0.000	0.000	0.000	0.000
34	A	1278	ILE	0	-0.041	-0.017	2.568	-8.110	-5.328	0.633	-1.646	-1.769	-0.020
35	A	1279	LYS	1	0.953	0.973	2.949	-10.037	-6.933	0.699	-1.557	-2.247	0.015
36	A	1280	PHE	0	-0.008	-0.024	4.935	0.171	0.173	-0.001	-0.006	0.005	0.000
37	A	1281	ASN	0	0.019	0.016	7.337	0.114	0.114	0.000	0.000	0.000	0.000
38	A	1282	LYS	1	1.022	1.017	10.546	-0.482	-0.482	0.000	0.000	0.000	0.000
39	A	1283	ASN	0	0.034	0.015	11.178	-0.151	-0.151	0.000	0.000	0.000	0.000
40	A	1284	ASN	0	0.049	0.015	6.389	-0.200	-0.200	0.000	0.000	0.000	0.000
41	A	1285	THR	0	0.008	-0.011	10.302	-0.252	-0.252	0.000	0.000	0.000	0.000
42	A	1286	ALA	0	-0.004	-0.002	12.422	-0.083	-0.083	0.000	0.000	0.000	0.000
43	A	1287	GLN	0	-0.010	0.000	10.294	0.004	0.004	0.000	0.000	0.000	0.000
44	A	1288	LEU	0	0.015	0.006	10.079	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	1289	VAL	0	-0.001	-0.010	13.291	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	1290	LYS	1	0.901	0.952	16.589	0.101	0.101	0.000	0.000	0.000	0.000
47	A	1291	TRP	0	0.023	0.011	10.321	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	1292	PHE	0	0.079	0.030	15.482	0.011	0.011	0.000	0.000	0.000	0.000
49	A	1293	SER	0	-0.026	-0.013	19.593	0.028	0.028	0.000	0.000	0.000	0.000
50	A	1294	ASN	0	0.018	0.013	19.835	0.038	0.038	0.000	0.000	0.000	0.000
51	A	1295	PHE	0	-0.033	-0.014	16.663	0.010	0.010	0.000	0.000	0.000	0.000
52	A	1296	ARG	1	0.934	0.963	21.888	0.164	0.164	0.000	0.000	0.000	0.000
53	A	1297	GLU	-1	-0.963	-0.959	25.187	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	1298	PHE	0	0.011	-0.003	25.628	0.008	0.008	0.000	0.000	0.000	0.000
55	A	1299	TYR	0	-0.013	-0.025	26.833	0.003	0.003	0.000	0.000	0.000	0.000
56	A	1300	TYR	0	0.035	0.001	28.504	0.009	0.009	0.000	0.000	0.000	0.000
57	A	1301	ILE	0	-0.009	0.021	29.617	0.009	0.009	0.000	0.000	0.000	0.000
58	A	1302	GLN	0	0.009	0.001	30.393	0.012	0.012	0.000	0.000	0.000	0.000
59	A	1303	MET	0	-0.052	-0.014	31.556	0.007	0.007	0.000	0.000	0.000	0.000
60	A	1304	GLU	-1	-0.748	-0.865	34.692	-0.068	-0.068	0.000	0.000	0.000	0.000
61	A	1305	LYS	1	0.912	0.957	34.641	0.131	0.131	0.000	0.000	0.000	0.000
62	A	1306	TYR	0	0.034	0.005	37.091	0.003	0.003	0.000	0.000	0.000	0.000
63	A	1307	ALA	0	0.015	0.012	38.857	0.003	0.003	0.000	0.000	0.000	0.000
64	A	1308	ARG	1	0.815	0.869	40.252	0.069	0.069	0.000	0.000	0.000	0.000
65	A	1309	GLN	0	-0.042	0.004	40.023	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	1310	ALA	0	0.029	0.008	43.101	0.003	0.003	0.000	0.000	0.000	0.000
67	A	1311	VAL	0	-0.045	-0.017	44.963	0.003	0.003	0.000	0.000	0.000	0.000
68	A	1312	THR	0	-0.084	-0.055	46.052	0.004	0.004	0.000	0.000	0.000	0.000
69	A	1313	GLU	-1	-1.006	-0.978	46.915	-0.071	-0.071	0.000	0.000	0.000	0.000
70	A	1327	SER	0	0.076	0.023	37.694	0.002	0.002	0.000	0.000	0.000	0.000
71	A	1328	GLU	-1	-0.765	-0.844	35.969	-0.161	-0.161	0.000	0.000	0.000	0.000
72	A	1329	LEU	0	0.025	0.015	33.523	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	1330	TYR	0	-0.021	-0.057	31.961	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	1331	ARG	1	0.855	0.911	31.135	0.151	0.151	0.000	0.000	0.000	0.000
75	A	1332	VAL	0	-0.011	-0.005	30.542	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	1333	LEU	0	-0.029	-0.020	28.274	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	1334	ASN	0	0.019	0.002	26.641	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	1335	LEU	0	0.038	0.032	25.961	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	1336	HIS	0	-0.030	0.002	22.803	-0.040	-0.040	0.000	0.000	0.000	0.000
80	A	1337	TYR	0	-0.039	-0.040	21.654	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	1338	ASN	0	0.003	-0.016	21.413	-0.075	-0.075	0.000	0.000	0.000	0.000
82	A	1339	ARG	1	0.907	0.957	21.998	0.328	0.328	0.000	0.000	0.000	0.000
83	A	1340	ASN	0	-0.044	-0.039	21.527	0.013	0.013	0.000	0.000	0.000	0.000
84	A	1341	ASN	0	0.007	0.011	23.814	0.016	0.016	0.000	0.000	0.000	0.000
85	A	1342	HIS	0	-0.029	-0.006	19.408	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	1343	ILE	0	-0.003	0.011	21.795	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1344	GLU	-1	-0.887	-0.928	24.664	-0.211	-0.211	0.000	0.000	0.000	0.000
88	A	1345	VAL	0	-0.058	-0.038	27.181	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	1346	PRO	0	0.042	0.033	25.842	0.018	0.018	0.000	0.000	0.000	0.000
90	A	1347	GLN	0	0.092	0.026	28.961	0.002	0.002	0.000	0.000	0.000	0.000
91	A	1348	ASN	0	0.006	-0.025	28.980	0.018	0.018	0.000	0.000	0.000	0.000
92	A	1349	PHE	0	-0.007	0.002	27.075	0.005	0.005	0.000	0.000	0.000	0.000
93	A	1350	ARG	1	0.963	0.982	29.591	0.192	0.192	0.000	0.000	0.000	0.000
94	A	1351	PHE	0	0.030	0.029	33.131	0.010	0.010	0.000	0.000	0.000	0.000
95	A	1352	VAL	0	0.028	0.026	29.521	0.012	0.012	0.000	0.000	0.000	0.000
96	A	1353	VAL	0	0.014	0.025	31.037	0.009	0.009	0.000	0.000	0.000	0.000
97	A	1354	GLU	-1	-0.848	-0.913	33.466	-0.114	-0.114	0.000	0.000	0.000	0.000
98	A	1355	SER	0	-0.044	-0.039	35.303	0.012	0.012	0.000	0.000	0.000	0.000
99	A	1356	THR	0	-0.042	-0.031	33.014	0.006	0.006	0.000	0.000	0.000	0.000
100	A	1357	LEU	0	0.013	0.007	35.686	0.007	0.007	0.000	0.000	0.000	0.000
101	A	1358	ARG	1	0.958	0.985	38.075	0.104	0.104	0.000	0.000	0.000	0.000
102	A	1359	GLU	-1	-0.876	-0.908	37.843	-0.065	-0.065	0.000	0.000	0.000	0.000
103	A	1360	PHE	0	-0.045	-0.033	34.661	0.004	0.004	0.000	0.000	0.000	0.000
104	A	1361	PHE	0	0.010	0.012	39.917	0.004	0.004	0.000	0.000	0.000	0.000
105	A	1362	ARG	1	0.873	0.912	41.759	0.072	0.072	0.000	0.000	0.000	0.000
106	A	1363	ALA	0	-0.015	-0.001	41.998	0.004	0.004	0.000	0.000	0.000	0.000
107	A	1364	ILE	0	-0.002	-0.007	40.747	0.003	0.003	0.000	0.000	0.000	0.000
108	A	1365	GLN	0	0.015	0.020	44.857	0.003	0.003	0.000	0.000	0.000	0.000
109	A	1366	GLY	0	-0.039	-0.013	47.335	0.003	0.003	0.000	0.000	0.000	0.000
110	A	1367	GLY	0	0.020	0.009	48.105	0.003	0.003	0.000	0.000	0.000	0.000
111	A	1368	LYS	1	0.830	0.885	44.961	0.040	0.040	0.000	0.000	0.000	0.000
112	A	1369	ASP	-1	-0.843	-0.919	42.394	-0.051	-0.051	0.000	0.000	0.000	0.000
113	A	1370	THR	0	-0.025	-0.006	43.362	0.001	0.001	0.000	0.000	0.000	0.000
114	A	1371	GLU	-1	-0.821	-0.884	44.573	-0.030	-0.030	0.000	0.000	0.000	0.000
115	A	1372	GLN	0	0.019	-0.008	42.133	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	1373	SER	0	-0.080	-0.059	38.595	0.001	0.001	0.000	0.000	0.000	0.000
117	A	1374	TRP	0	0.076	0.062	39.488	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	1375	LYS	1	0.880	0.940	34.727	0.070	0.070	0.000	0.000	0.000	0.000
119	A	1376	LYS	1	0.921	0.961	32.488	0.032	0.032	0.000	0.000	0.000	0.000
120	A	1377	SER	0	0.014	0.007	35.258	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	1378	ILE	0	0.065	0.036	34.803	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	1379	TYR	0	-0.010	-0.011	31.020	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	1380	LYS	1	0.954	0.981	31.495	0.028	0.028	0.000	0.000	0.000	0.000
124	A	1381	ILE	0	0.001	0.013	32.756	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	1382	ILE	0	0.030	0.000	29.403	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	1383	SER	0	-0.088	-0.043	28.058	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	1384	ARG	1	0.935	0.972	28.040	0.060	0.060	0.000	0.000	0.000	0.000
128	A	1385	MET	0	-0.056	-0.010	29.887	0.002	0.002	0.000	0.000	0.000	0.000
129	A	1386	ASP	-1	-0.749	-0.851	23.582	-0.214	-0.214	0.000	0.000	0.000	0.000
130	A	1387	ASP	-1	-0.868	-0.925	25.109	-0.188	-0.188	0.000	0.000	0.000	0.000
131	A	1388	PRO	0	0.010	-0.001	22.785	-0.020	-0.020	0.000	0.000	0.000	0.000
132	A	1389	VAL	0	-0.022	-0.009	17.210	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	1390	PRO	0	0.017	0.018	20.287	0.002	0.002	0.000	0.000	0.000	0.000
134	A	1391	GLU	-1	-0.706	-0.841	18.476	-0.381	-0.381	0.000	0.000	0.000	0.000
135	A	1392	TYR	0	0.034	0.020	17.227	-0.037	-0.037	0.000	0.000	0.000	0.000
136	A	1393	PHE	0	-0.021	-0.017	15.311	-0.082	-0.082	0.000	0.000	0.000	0.000
137	A	1394	LYS	1	0.737	0.852	12.821	0.209	0.209	0.000	0.000	0.000	0.000
138	A	1395	SER	0	-0.039	-0.002	12.184	-0.064	-0.064	0.000	0.000	0.000	0.000
139	A	1396	PRO	0	-0.016	0.002	10.203	-0.097	-0.097	0.000	0.000	0.000	0.000

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