FMO DATABASE

FMODB ID: ZLN6N

Calculation Name: 3MB3-A-Xray547

Preferred Name: PH-interacting protein

Target Type: SINGLE PROTEIN

Ligand Name: 1-methylpyrrolidin-2-one

Ligand 3-letter code: MB3

Ligand of Interest (LOI):

PDB ID: 3MB3

Chain ID: A

ChEMBL ID: CHEMBL2176773

UniProt ID: Q8WWQ0

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-995462.689253
FMO2-HF: Nuclear repulsion	946750.181732
FMO2-HF: Total energy	-48712.507521
FMO2-MP2: Total energy	-48852.30288

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:1316:TYR)

Summations of interaction energy for fragment #1(A:1316:TYR)

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.
-114.573	-111.34	26.709	-12.323	-17.616	-0.059

Interaction energy analysis for fragmet #1(A:1316:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.878

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

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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	1318	ILE	0	0.042	0.021	3.232	-1.107	1.983	1.079	-1.629	-2.540	0.000
5	A	1320	ALA	0	-0.010	-0.004	2.401	1.683	1.651	3.619	-1.205	-2.382	0.006
6	A	1321	TRP	0	0.000	0.001	3.655	0.437	1.501	0.069	-0.238	-0.896	0.001
7	A	1322	LYS	1	0.955	0.981	4.437	23.947	24.054	0.000	-0.025	-0.083	0.000
9	A	1324	GLN	0	0.089	0.051	1.698	-19.368	-25.504	16.222	-5.957	-4.128	-0.047
106	A	1421	VAL	0	-0.002	0.011	4.952	-2.990	-2.841	-0.001	-0.003	-0.144	0.000
107	A	1422	LEU	0	-0.029	-0.015	5.074	-1.979	-1.910	-0.001	-0.001	-0.067	0.000
109	A	1424	ASP	-1	-0.898	-0.946	2.482	-39.500	-39.072	2.863	-0.869	-2.421	0.003
110	A	1425	TYR	0	0.017	-0.004	2.725	-11.751	-9.297	1.472	-1.372	-2.554	-0.019
111	A	1426	LYS	1	0.912	0.943	3.762	21.346	21.423	0.001	0.018	-0.096	0.000
112	A	1427	SER	0	-0.060	-0.030	4.444	-0.819	-0.585	-0.001	-0.030	-0.202	0.000
113	A	1428	ALA	0	-0.009	-0.002	2.204	-3.620	-2.937	1.298	-0.626	-1.355	0.000
114	A	1429	LEU	0	-0.063	-0.020	3.924	2.222	2.401	0.004	-0.052	-0.131	0.000
116	A	1431	PHE	-1	-0.928	-0.946	3.046	-42.351	-41.484	0.085	-0.334	-0.617	-0.003
4	A	1319	GLN	0	0.022	0.011	5.727	5.004	5.004	0.000	0.000	0.000	0.000
8	A	1323	LYS	1	0.878	0.939	6.391	21.128	21.128	0.000	0.000	0.000	0.000
10	A	1325	CYS	0	-0.050	-0.018	6.208	1.904	1.904	0.000	0.000	0.000	0.000
11	A	1326	GLU	-1	-0.835	-0.906	9.145	-15.752	-15.752	0.000	0.000	0.000	0.000
12	A	1327	GLU	-1	-0.937	-0.977	8.326	-21.652	-21.652	0.000	0.000	0.000	0.000
13	A	1328	LEU	0	-0.041	-0.014	10.298	1.084	1.084	0.000	0.000	0.000	0.000
14	A	1329	LEU	0	0.042	0.012	12.020	1.059	1.059	0.000	0.000	0.000	0.000
15	A	1330	ASN	0	0.009	0.017	14.133	1.358	1.358	0.000	0.000	0.000	0.000
16	A	1331	LEU	0	-0.017	-0.009	12.997	0.776	0.776	0.000	0.000	0.000	0.000
17	A	1332	ILE	0	-0.010	-0.004	15.500	0.710	0.710	0.000	0.000	0.000	0.000
18	A	1333	PHE	0	0.005	-0.001	18.121	0.665	0.665	0.000	0.000	0.000	0.000
19	A	1334	GLN	0	-0.057	-0.025	18.328	0.168	0.168	0.000	0.000	0.000	0.000
20	A	1335	CYS	0	-0.070	-0.010	20.639	0.457	0.457	0.000	0.000	0.000	0.000
21	A	1336	GLU	-1	-0.884	-0.959	22.444	-9.236	-9.236	0.000	0.000	0.000	0.000
22	A	1337	ASP	-1	-0.782	-0.864	23.614	-9.916	-9.916	0.000	0.000	0.000	0.000
23	A	1338	SER	0	-0.001	-0.027	21.625	0.204	0.204	0.000	0.000	0.000	0.000
24	A	1339	GLU	-1	-0.972	-0.975	23.677	-8.805	-8.805	0.000	0.000	0.000	0.000
25	A	1340	PRO	0	0.025	-0.005	26.911	0.016	0.016	0.000	0.000	0.000	0.000
26	A	1341	PHE	0	-0.011	-0.009	23.955	0.104	0.104	0.000	0.000	0.000	0.000
27	A	1342	ARG	1	0.865	0.931	23.253	9.915	9.915	0.000	0.000	0.000	0.000
28	A	1343	GLN	0	-0.010	-0.005	24.331	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	1344	PRO	0	0.009	0.016	26.420	0.061	0.061	0.000	0.000	0.000	0.000
30	A	1345	VAL	0	-0.017	-0.003	28.501	0.180	0.180	0.000	0.000	0.000	0.000
31	A	1346	ASP	-1	-0.806	-0.899	31.364	-7.467	-7.467	0.000	0.000	0.000	0.000
32	A	1347	LEU	0	-0.022	-0.021	34.740	0.070	0.070	0.000	0.000	0.000	0.000
33	A	1348	LEU	0	-0.063	-0.039	37.445	0.222	0.222	0.000	0.000	0.000	0.000
34	A	1349	GLU	-1	-0.980	-0.975	35.646	-7.491	-7.491	0.000	0.000	0.000	0.000
35	A	1350	TYR	0	-0.061	-0.034	34.745	0.122	0.122	0.000	0.000	0.000	0.000
36	A	1351	PRO	0	-0.008	-0.006	37.603	-0.122	-0.122	0.000	0.000	0.000	0.000
37	A	1352	ASP	-1	-0.828	-0.891	39.430	-7.211	-7.211	0.000	0.000	0.000	0.000
38	A	1353	TYR	0	0.012	-0.004	29.732	-0.198	-0.198	0.000	0.000	0.000	0.000
39	A	1354	ARG	1	0.828	0.894	33.196	8.117	8.117	0.000	0.000	0.000	0.000
40	A	1355	ASP	-1	-0.898	-0.932	36.631	-6.953	-6.953	0.000	0.000	0.000	0.000
41	A	1356	ILE	0	-0.109	-0.048	34.638	0.009	0.009	0.000	0.000	0.000	0.000
42	A	1357	ILE	0	-0.054	-0.014	30.298	-0.222	-0.222	0.000	0.000	0.000	0.000
43	A	1358	ASP	-1	-0.875	-0.934	31.663	-8.328	-8.328	0.000	0.000	0.000	0.000
44	A	1359	THR	0	-0.043	-0.026	26.793	0.034	0.034	0.000	0.000	0.000	0.000
45	A	1360	PRO	0	-0.002	-0.003	27.835	-0.236	-0.236	0.000	0.000	0.000	0.000
46	A	1361	MET	0	-0.015	0.010	22.058	-0.230	-0.230	0.000	0.000	0.000	0.000
47	A	1362	ASP	-1	-0.763	-0.861	23.427	-10.422	-10.422	0.000	0.000	0.000	0.000
48	A	1363	PHE	0	0.038	-0.017	17.707	-0.414	-0.414	0.000	0.000	0.000	0.000
49	A	1364	ALA	0	-0.022	0.011	19.606	-0.516	-0.516	0.000	0.000	0.000	0.000
50	A	1365	THR	0	0.027	-0.011	20.971	-0.306	-0.306	0.000	0.000	0.000	0.000
51	A	1366	VAL	0	-0.014	-0.004	16.133	-0.394	-0.394	0.000	0.000	0.000	0.000
52	A	1367	ARG	1	0.865	0.935	15.743	12.435	12.435	0.000	0.000	0.000	0.000
53	A	1368	GLU	-1	-0.908	-0.948	17.208	-11.346	-11.346	0.000	0.000	0.000	0.000
54	A	1369	THR	0	-0.043	-0.030	17.626	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	1370	LEU	0	-0.071	-0.043	10.822	-0.656	-0.656	0.000	0.000	0.000	0.000
56	A	1371	GLU	-1	-0.929	-0.970	14.712	-13.887	-13.887	0.000	0.000	0.000	0.000
57	A	1372	ALA	0	-0.058	-0.024	16.551	-0.055	-0.055	0.000	0.000	0.000	0.000
58	A	1373	GLY	0	-0.050	-0.023	14.963	0.049	0.049	0.000	0.000	0.000	0.000
59	A	1374	ASN	0	-0.036	-0.017	16.027	-0.365	-0.365	0.000	0.000	0.000	0.000
60	A	1375	TYR	0	-0.087	-0.071	13.351	-0.123	-0.123	0.000	0.000	0.000	0.000
61	A	1376	GLU	-1	-0.889	-0.934	13.425	-19.524	-19.524	0.000	0.000	0.000	0.000
62	A	1377	SER	0	-0.006	-0.028	10.240	-1.415	-1.415	0.000	0.000	0.000	0.000
63	A	1378	PRO	0	0.027	0.009	6.847	1.254	1.254	0.000	0.000	0.000	0.000
64	A	1379	MET	0	-0.025	-0.015	10.130	0.298	0.298	0.000	0.000	0.000	0.000
65	A	1380	GLU	-1	-0.821	-0.878	12.813	-13.993	-13.993	0.000	0.000	0.000	0.000
66	A	1381	LEU	0	0.070	0.041	11.567	0.624	0.624	0.000	0.000	0.000	0.000
67	A	1382	CYS	0	-0.076	-0.043	12.290	0.422	0.422	0.000	0.000	0.000	0.000
68	A	1383	LYS	1	0.781	0.872	15.094	14.806	14.806	0.000	0.000	0.000	0.000
69	A	1384	ASP	-1	-0.753	-0.844	18.154	-12.391	-12.391	0.000	0.000	0.000	0.000
70	A	1385	VAL	0	0.008	-0.005	15.549	0.518	0.518	0.000	0.000	0.000	0.000
71	A	1386	ARG	1	0.751	0.824	14.966	15.466	15.466	0.000	0.000	0.000	0.000
72	A	1387	LEU	0	0.007	0.022	20.365	0.453	0.453	0.000	0.000	0.000	0.000
73	A	1388	ILE	0	0.002	0.027	20.132	0.503	0.503	0.000	0.000	0.000	0.000
74	A	1389	PHE	0	0.017	0.001	18.629	0.478	0.478	0.000	0.000	0.000	0.000
75	A	1390	SER	0	-0.040	-0.028	24.108	0.286	0.286	0.000	0.000	0.000	0.000
76	A	1391	ASN	0	0.023	0.003	26.416	0.475	0.475	0.000	0.000	0.000	0.000
77	A	1392	SER	0	-0.008	0.010	26.906	0.461	0.461	0.000	0.000	0.000	0.000
78	A	1393	LYS	1	0.891	0.937	28.180	9.780	9.780	0.000	0.000	0.000	0.000
79	A	1394	ALA	0	-0.016	-0.012	29.976	0.257	0.257	0.000	0.000	0.000	0.000
80	A	1395	TYR	0	0.024	-0.005	31.957	0.155	0.155	0.000	0.000	0.000	0.000
81	A	1396	THR	0	-0.083	-0.043	32.354	0.238	0.238	0.000	0.000	0.000	0.000
82	A	1397	PRO	0	0.056	0.033	32.916	-0.157	-0.157	0.000	0.000	0.000	0.000
83	A	1398	SER	0	-0.063	-0.033	34.438	0.009	0.009	0.000	0.000	0.000	0.000
84	A	1399	LYS	1	1.002	0.981	33.880	8.093	8.093	0.000	0.000	0.000	0.000
85	A	1400	ARG	1	0.933	0.971	35.339	6.748	6.748	0.000	0.000	0.000	0.000
86	A	1401	SER	0	0.007	0.023	34.244	0.077	0.077	0.000	0.000	0.000	0.000
87	A	1402	ARG	1	0.995	0.986	33.079	7.443	7.443	0.000	0.000	0.000	0.000
88	A	1403	ILE	0	0.115	0.057	30.135	-0.213	-0.213	0.000	0.000	0.000	0.000
89	A	1404	TYR	0	0.038	0.022	29.177	-0.311	-0.311	0.000	0.000	0.000	0.000
90	A	1405	SER	0	-0.055	-0.042	28.732	-0.255	-0.255	0.000	0.000	0.000	0.000
91	A	1406	MET	0	-0.061	-0.011	26.858	-0.100	-0.100	0.000	0.000	0.000	0.000
92	A	1407	SER	0	0.035	0.028	24.964	-0.533	-0.533	0.000	0.000	0.000	0.000
93	A	1408	LEU	0	-0.035	-0.026	23.800	-0.385	-0.385	0.000	0.000	0.000	0.000
94	A	1409	ARG	1	0.779	0.860	23.324	9.359	9.359	0.000	0.000	0.000	0.000
95	A	1410	LEU	0	0.030	0.021	20.036	-0.482	-0.482	0.000	0.000	0.000	0.000
96	A	1411	SER	0	-0.004	0.010	19.156	-0.764	-0.764	0.000	0.000	0.000	0.000
97	A	1412	ALA	0	-0.005	-0.008	18.606	-0.615	-0.615	0.000	0.000	0.000	0.000
98	A	1413	PHE	0	0.038	0.026	15.766	-0.727	-0.727	0.000	0.000	0.000	0.000
99	A	1414	PHE	0	0.067	0.032	13.185	-0.993	-0.993	0.000	0.000	0.000	0.000
100	A	1415	GLU	-1	-0.747	-0.850	13.756	-16.101	-16.101	0.000	0.000	0.000	0.000
101	A	1416	GLU	-1	-0.946	-0.965	14.146	-15.152	-15.152	0.000	0.000	0.000	0.000
102	A	1417	HIS	1	0.809	0.898	10.735	15.811	15.811	0.000	0.000	0.000	0.000
103	A	1418	ILE	0	0.018	0.009	9.297	-1.993	-1.993	0.000	0.000	0.000	0.000
104	A	1419	SER	0	-0.010	-0.016	9.572	-1.138	-1.138	0.000	0.000	0.000	0.000
105	A	1420	SER	0	-0.002	0.011	7.472	-0.324	-0.324	0.000	0.000	0.000	0.000
108	A	1423	SER	0	-0.021	-0.023	6.651	-0.600	-0.600	0.000	0.000	0.000	0.000
115	A	1430	ARG	1	0.868	0.930	6.858	29.942	29.942	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1316:TYR)