FMO DATABASE

FMODB ID: 4QZ5N

Calculation Name: 1UW3-A-Xray547

Preferred Name: Major prion protein

Target Type: SINGLE PROTEIN

Ligand Name: glutathione | phosphate ion

Ligand 3-letter code: GSH | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1UW3

Chain ID: A

ChEMBL ID: CHEMBL2406893

UniProt ID: P23907

Base Structure: X-ray

Registration Date: 2025-10-03

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
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-866619.515069
FMO2-HF: Nuclear repulsion	820890.31961
FMO2-HF: Total energy	-45729.195459
FMO2-MP2: Total energy	-45857.516369

3D Structure Molmil

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:125:LEU)

Summations of interaction energy for fragment #1(A:125:LEU)

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.
-32.503	-21.855	6.837	-5.633	-11.852	-0.048

Interaction energy analysis for fragmet #1(A:125:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.910

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	127	GLY	0	0.019	0.025	3.670	7.950	10.499	-0.026	-1.234	-1.290	-0.004
4	A	128	TYR	0	-0.108	-0.087	2.490	-9.218	-6.785	0.856	-1.201	-2.088	-0.009
5	A	129	MET	0	0.010	0.022	4.578	-0.918	-0.848	-0.001	-0.011	-0.058	0.000
38	A	162	TYR	0	0.013	-0.003	2.543	-5.329	-3.575	3.764	-1.499	-4.018	-0.020
39	A	163	TYR	0	-0.024	-0.051	4.875	1.052	1.098	-0.001	-0.006	-0.039	0.000
58	A	182	ILE	0	-0.081	-0.036	2.635	-6.548	-5.271	0.883	-0.501	-1.659	-0.003
59	A	183	THR	0	0.003	-0.007	4.673	-3.767	-3.654	-0.001	-0.006	-0.105	0.000
61	A	185	LYS	1	0.955	1.004	3.997	53.927	54.068	-0.001	-0.011	-0.129	0.000
62	A	186	GLN	0	-0.021	-0.019	2.502	-10.149	-7.914	1.365	-1.163	-2.438	-0.012
63	A	187	HIS	0	0.015	0.011	5.217	0.272	0.302	-0.001	-0.001	-0.028	0.000
6	A	130	LEU	0	-0.020	-0.019	4.870	-3.672	-3.672	0.000	0.000	0.000	0.000
7	A	131	GLY	0	0.010	0.023	6.124	2.234	2.234	0.000	0.000	0.000	0.000
8	A	132	SER	0	0.010	-0.020	9.409	-0.750	-0.750	0.000	0.000	0.000	0.000
9	A	133	ALA	0	0.008	0.011	12.106	-0.246	-0.246	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.040	-0.010	13.363	1.330	1.330	0.000	0.000	0.000	0.000
11	A	135	SER	0	-0.028	-0.014	16.066	0.080	0.080	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.927	0.962	17.739	13.849	13.849	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.004	0.004	18.381	0.594	0.594	0.000	0.000	0.000	0.000
14	A	138	LEU	0	-0.009	-0.005	21.069	-0.318	-0.318	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.028	-0.017	19.058	0.306	0.306	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.050	0.028	22.880	0.153	0.153	0.000	0.000	0.000	0.000
17	A	141	PHE	0	0.002	-0.006	20.487	-0.435	-0.435	0.000	0.000	0.000	0.000
18	A	142	GLY	0	-0.006	0.001	26.581	0.271	0.271	0.000	0.000	0.000	0.000
19	A	143	ASN	0	0.014	0.017	28.067	0.383	0.383	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.815	-0.919	28.915	-9.151	-9.151	0.000	0.000	0.000	0.000
21	A	145	TYR	0	-0.016	-0.004	26.865	0.049	0.049	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.841	-0.906	24.815	-11.931	-11.931	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.835	-0.891	25.159	-10.598	-10.598	0.000	0.000	0.000	0.000
24	A	148	CYS	0	-0.016	-0.006	26.743	-0.175	-0.175	0.000	0.000	0.000	0.000
25	A	149	TYR	0	0.018	-0.008	21.741	0.075	0.075	0.000	0.000	0.000	0.000
26	A	150	TYR	0	-0.004	0.001	20.030	-0.341	-0.341	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.811	0.860	22.909	9.784	9.784	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.932	-0.951	25.260	-10.282	-10.282	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.036	-0.022	21.174	-0.201	-0.201	0.000	0.000	0.000	0.000
30	A	154	MET	0	-0.029	0.005	20.276	-0.730	-0.730	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.003	-0.019	18.282	-0.999	-0.999	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.867	0.946	16.701	14.214	14.214	0.000	0.000	0.000	0.000
33	A	157	TYR	0	-0.029	-0.025	14.326	-0.955	-0.955	0.000	0.000	0.000	0.000
34	A	158	PRO	0	-0.010	-0.008	9.843	0.227	0.227	0.000	0.000	0.000	0.000
35	A	159	ASN	0	0.012	0.003	11.685	1.653	1.653	0.000	0.000	0.000	0.000
36	A	160	GLN	0	0.011	0.003	8.172	1.311	1.311	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.010	0.005	7.470	-0.773	-0.773	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.928	0.970	5.907	35.325	35.325	0.000	0.000	0.000	0.000
41	A	165	PRO	0	0.005	0.009	8.411	1.684	1.684	0.000	0.000	0.000	0.000
42	A	166	VAL	0	0.049	0.008	11.744	-0.055	-0.055	0.000	0.000	0.000	0.000
43	A	167	ASP	-1	-0.864	-0.933	14.464	-19.531	-19.531	0.000	0.000	0.000	0.000
44	A	168	GLN	0	-0.077	-0.033	10.718	-1.333	-1.333	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.091	-0.085	9.529	-0.213	-0.213	0.000	0.000	0.000	0.000
46	A	170	SER	0	0.007	0.009	16.237	0.439	0.439	0.000	0.000	0.000	0.000
47	A	171	ASN	0	-0.014	-0.010	18.564	0.233	0.233	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.071	0.034	17.512	-0.668	-0.668	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.023	0.003	16.443	-1.060	-1.060	0.000	0.000	0.000	0.000
50	A	174	ASN	0	-0.010	-0.002	15.921	-0.506	-0.506	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.029	0.024	11.828	-1.543	-1.543	0.000	0.000	0.000	0.000
52	A	176	VAL	0	-0.009	-0.019	11.682	-1.738	-1.738	0.000	0.000	0.000	0.000
53	A	177	HIS	0	0.016	0.019	12.614	-1.519	-1.519	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.764	-0.822	8.202	-36.293	-36.293	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.019	-0.002	7.885	-3.270	-3.270	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.037	0.018	8.296	-1.699	-1.699	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.020	0.016	9.215	-0.296	-0.296	0.000	0.000	0.000	0.000
60	A	184	VAL	0	0.056	0.035	6.226	0.207	0.207	0.000	0.000	0.000	0.000
64	A	188	THR	0	0.019	0.004	8.300	2.604	2.604	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.040	-0.024	6.873	1.245	1.245	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.037	-0.029	6.285	1.000	1.000	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.033	-0.017	8.618	2.019	2.019	0.000	0.000	0.000	0.000
68	A	192	THR	0	0.002	-0.003	11.681	1.325	1.325	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.065	-0.049	10.110	0.965	0.965	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.826	0.923	12.631	18.303	18.303	0.000	0.000	0.000	0.000
71	A	195	GLY	0	0.003	0.012	14.829	0.997	0.997	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.858	-0.913	15.753	-14.919	-14.919	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.035	-0.036	16.420	-0.334	-0.334	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.005	-0.009	12.698	0.061	0.061	0.000	0.000	0.000	0.000
75	A	199	THR	0	0.007	-0.003	18.330	0.164	0.164	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.900	-0.964	19.770	-13.113	-13.113	0.000	0.000	0.000	0.000
77	A	201	THR	0	0.010	0.000	20.896	-0.166	-0.166	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.737	-0.835	17.717	-14.270	-14.270	0.000	0.000	0.000	0.000
79	A	203	ILE	0	-0.012	0.006	14.700	-0.652	-0.652	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.858	0.918	16.932	11.860	11.860	0.000	0.000	0.000	0.000
81	A	205	ILE	0	-0.024	-0.004	18.745	0.072	0.072	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.020	-0.003	12.443	-0.763	-0.763	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.935	-0.975	13.766	-19.362	-19.362	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.924	0.954	14.976	12.414	12.414	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.020	-0.016	14.788	0.316	0.316	0.000	0.000	0.000	0.000
86	A	210	VAL	0	-0.020	-0.011	10.216	-0.294	-0.294	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.910	-0.955	13.209	-15.614	-15.614	0.000	0.000	0.000	0.000
88	A	212	GLN	0	0.028	0.011	15.427	-0.051	-0.051	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.042	0.004	11.977	0.392	0.392	0.000	0.000	0.000	0.000
90	A	215	ILE	0	-0.006	0.004	13.105	0.003	0.003	0.000	0.000	0.000	0.000
91	A	216	THR	0	-0.040	-0.033	16.168	0.606	0.606	0.000	0.000	0.000	0.000
92	A	217	GLN	0	-0.022	-0.015	10.946	1.239	1.239	0.000	0.000	0.000	0.000
93	A	218	TYR	0	0.035	0.019	14.302	0.184	0.184	0.000	0.000	0.000	0.000
94	A	219	GLN	0	-0.027	-0.022	15.720	0.612	0.612	0.000	0.000	0.000	0.000
95	A	220	ARG	1	0.918	0.970	15.835	15.660	15.660	0.000	0.000	0.000	0.000
96	A	221	GLU	-1	-0.815	-0.899	13.023	-19.694	-19.694	0.000	0.000	0.000	0.000
97	A	222	SER	0	-0.010	-0.009	16.495	0.671	0.671	0.000	0.000	0.000	0.000
98	A	223	GLN	0	-0.024	-0.011	19.033	0.330	0.330	0.000	0.000	0.000	0.000
99	A	224	ALA	0	-0.025	-0.023	18.602	0.522	0.522	0.000	0.000	0.000	0.000
100	A	225	TYR	0	-0.034	-0.006	18.309	0.156	0.156	0.000	0.000	0.000	0.000
101	A	226	TYR	0	-0.020	-0.015	20.382	0.457	0.457	0.000	0.000	0.000	0.000
102	A	227	GLN	0	-0.030	-0.011	23.541	0.845	0.845	0.000	0.000	0.000	0.000
103	A	228	ARG	1	0.904	0.959	25.565	10.294	10.294	0.000	0.000	0.000	0.000
104	A	229	GLY	0	-0.039	-0.018	28.495	-0.071	-0.071	0.000	0.000	0.000	0.000
105	A	230	ALA	-1	-0.915	-0.945	30.307	-8.908	-8.908	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:125:LEU)