FMO DATABASE

FMODB ID: LG5J9

Calculation Name: 1B10-A-Other547

Preferred Name: Major prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1B10

Chain ID: A

ChEMBL ID: CHEMBL1293203

UniProt ID: P04273

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-863715.420663
FMO2-HF: Nuclear repulsion	818158.905356
FMO2-HF: Total energy	-45556.515307
FMO2-MP2: Total energy	-45683.258114

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.
-59.795	-50.188	4.974	-5.223	-9.361	-0.047

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 : 0.828 / q_NPA : 0.906

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	0.030	0.025	3.562	3.597	6.628	-0.021	-1.523	-1.487	-0.006
4	A	128	TYR	0	-0.022	-0.010	2.373	1.681	3.086	0.902	-0.589	-1.719	-0.002
5	A	129	MET	0	0.013	0.005	2.851	-8.720	-6.808	0.276	-1.097	-1.091	-0.013
6	A	130	LEU	0	-0.032	-0.013	4.956	1.157	1.221	-0.001	-0.003	-0.060	0.000
38	A	162	TYR	0	-0.010	-0.011	2.508	-3.082	-2.230	0.552	-0.296	-1.108	-0.002
58	A	182	ILE	0	-0.073	-0.030	2.828	-3.238	-2.412	0.139	-0.192	-0.774	-0.001
62	A	186	GLN	0	-0.001	-0.008	2.562	-8.111	-6.594	3.127	-1.523	-3.122	-0.023
7	A	131	GLY	0	0.041	0.038	6.696	1.138	1.138	0.000	0.000	0.000	0.000
8	A	132	SER	0	-0.007	-0.022	10.050	1.910	1.910	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.008	0.001	12.447	-0.779	-0.779	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.029	0.020	13.686	0.705	0.705	0.000	0.000	0.000	0.000
11	A	135	SER	0	0.023	0.005	17.425	0.115	0.115	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.895	0.927	19.843	11.978	11.978	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.032	0.008	19.627	0.473	0.473	0.000	0.000	0.000	0.000
14	A	138	MET	0	-0.049	0.007	22.542	0.304	0.304	0.000	0.000	0.000	0.000
15	A	139	MET	0	0.005	0.029	20.792	0.051	0.051	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.080	0.033	25.256	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.049	-0.027	21.919	-0.336	-0.336	0.000	0.000	0.000	0.000
18	A	142	GLY	0	-0.009	0.020	26.678	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	143	ASN	0	-0.060	-0.036	27.285	0.552	0.552	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.919	-0.955	30.364	-8.914	-8.914	0.000	0.000	0.000	0.000
21	A	145	TRP	0	0.028	-0.005	28.203	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.775	-0.888	24.630	-11.386	-11.386	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.805	-0.894	25.460	-10.491	-10.491	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.882	0.912	26.860	9.580	9.580	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.040	-0.031	23.065	0.215	0.215	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.055	-0.011	21.067	-0.521	-0.521	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.870	0.926	23.153	9.321	9.321	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.881	-0.918	25.612	-9.586	-9.586	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.066	-0.038	21.766	0.022	0.022	0.000	0.000	0.000	0.000
30	A	154	MET	0	-0.039	-0.003	19.605	-0.630	-0.630	0.000	0.000	0.000	0.000
31	A	155	ASN	0	-0.058	-0.029	18.813	-0.419	-0.419	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.883	0.957	18.248	11.842	11.842	0.000	0.000	0.000	0.000
33	A	157	TYR	0	0.006	-0.028	16.124	-0.724	-0.724	0.000	0.000	0.000	0.000
34	A	158	PRO	0	-0.009	0.003	11.178	0.098	0.098	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.046	-0.014	13.102	0.194	0.194	0.000	0.000	0.000	0.000
36	A	160	GLN	0	0.048	-0.001	10.293	-0.306	-0.306	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.020	0.007	9.545	-0.258	-0.258	0.000	0.000	0.000	0.000
39	A	163	TYR	0	-0.010	-0.036	6.609	0.701	0.701	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.892	0.961	6.799	24.680	24.680	0.000	0.000	0.000	0.000
41	A	165	PRO	0	0.066	0.037	8.811	1.062	1.062	0.000	0.000	0.000	0.000
42	A	166	VAL	0	0.026	-0.008	11.660	-0.160	-0.160	0.000	0.000	0.000	0.000
43	A	167	ASP	-1	-0.896	-0.946	14.917	-16.483	-16.483	0.000	0.000	0.000	0.000
44	A	168	GLN	0	-0.040	-0.012	12.475	-0.807	-0.807	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.090	-0.070	11.712	-0.654	-0.654	0.000	0.000	0.000	0.000
46	A	170	ASN	0	0.008	0.006	17.498	-0.053	-0.053	0.000	0.000	0.000	0.000
47	A	171	ASN	0	-0.027	-0.030	19.570	1.023	1.023	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.018	0.023	18.453	-0.549	-0.549	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.042	0.023	17.449	-0.562	-0.562	0.000	0.000	0.000	0.000
50	A	174	ASN	0	0.041	0.013	16.942	0.050	0.050	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.049	0.034	11.965	-1.048	-1.048	0.000	0.000	0.000	0.000
52	A	176	VAL	0	-0.022	-0.013	12.698	-1.547	-1.547	0.000	0.000	0.000	0.000
53	A	177	HIS	0	-0.013	0.001	13.005	-0.920	-0.920	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.855	-0.907	9.403	-26.104	-26.104	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.040	-0.002	8.764	-3.235	-3.235	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.040	0.039	8.802	-1.690	-1.690	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.053	0.040	8.184	-1.055	-1.055	0.000	0.000	0.000	0.000
59	A	183	THR	0	0.012	-0.004	5.459	-2.741	-2.741	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.032	0.025	7.171	-0.322	-0.322	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.874	0.963	6.024	31.657	31.657	0.000	0.000	0.000	0.000
63	A	187	HIS	0	0.036	0.028	5.639	0.378	0.378	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.015	-0.031	8.988	1.360	1.360	0.000	0.000	0.000	0.000
65	A	189	VAL	0	0.017	0.025	7.938	1.612	1.612	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.005	-0.019	6.794	0.891	0.891	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.073	-0.065	9.295	1.488	1.488	0.000	0.000	0.000	0.000
68	A	192	THR	0	0.006	0.000	12.605	1.553	1.553	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.090	-0.056	11.576	0.480	0.480	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.874	0.940	11.775	19.170	19.170	0.000	0.000	0.000	0.000
71	A	195	GLY	0	0.007	0.013	15.131	0.813	0.813	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.922	-0.929	15.898	-15.633	-15.633	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.015	-0.025	17.535	-0.537	-0.537	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.014	0.006	14.249	0.429	0.429	0.000	0.000	0.000	0.000
75	A	199	THR	0	0.009	-0.029	19.001	0.248	0.248	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.891	-0.964	20.155	-12.339	-12.339	0.000	0.000	0.000	0.000
77	A	201	THR	0	0.020	-0.001	21.434	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.795	-0.822	19.081	-13.229	-13.229	0.000	0.000	0.000	0.000
79	A	203	ILE	0	0.018	0.013	15.134	-0.518	-0.518	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.929	0.945	17.529	11.357	11.357	0.000	0.000	0.000	0.000
81	A	205	ILE	0	-0.060	-0.008	19.251	0.262	0.262	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.053	-0.022	13.040	-0.097	-0.097	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.864	-0.948	14.937	-18.557	-18.557	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.909	0.968	16.295	12.071	12.071	0.000	0.000	0.000	0.000
85	A	209	VAL	0	0.001	-0.033	17.208	0.206	0.206	0.000	0.000	0.000	0.000
86	A	210	VAL	0	-0.002	-0.006	11.235	-0.155	-0.155	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.901	-0.953	14.399	-14.840	-14.840	0.000	0.000	0.000	0.000
88	A	212	GLN	0	-0.009	-0.012	16.332	-0.117	-0.117	0.000	0.000	0.000	0.000
89	A	213	MET	0	0.010	0.008	15.420	0.609	0.609	0.000	0.000	0.000	0.000
90	A	215	THR	0	0.000	0.009	14.315	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	216	THR	0	-0.019	-0.020	17.895	0.487	0.487	0.000	0.000	0.000	0.000
92	A	217	GLN	0	-0.030	-0.028	13.571	1.179	1.179	0.000	0.000	0.000	0.000
93	A	218	TYR	0	0.028	0.019	15.577	0.235	0.235	0.000	0.000	0.000	0.000
94	A	219	GLN	0	0.006	-0.014	16.581	0.278	0.278	0.000	0.000	0.000	0.000
95	A	220	LYS	1	0.895	0.962	17.024	13.267	13.267	0.000	0.000	0.000	0.000
96	A	221	GLU	-1	-0.823	-0.904	13.079	-19.498	-19.498	0.000	0.000	0.000	0.000
97	A	222	SER	0	-0.030	-0.014	16.599	0.356	0.356	0.000	0.000	0.000	0.000
98	A	223	GLN	0	-0.029	-0.032	19.851	0.316	0.316	0.000	0.000	0.000	0.000
99	A	224	ALA	0	0.043	0.025	17.942	0.400	0.400	0.000	0.000	0.000	0.000
100	A	225	TYR	0	-0.108	-0.038	18.396	0.172	0.172	0.000	0.000	0.000	0.000
101	A	226	TYR	0	-0.116	-0.061	20.488	0.481	0.481	0.000	0.000	0.000	0.000
102	A	227	ASP	-1	-0.952	-0.971	22.083	-12.314	-12.314	0.000	0.000	0.000	0.000
103	A	228	GLY	-1	-0.987	-0.976	23.860	-10.585	-10.585	0.000	0.000	0.000	0.000

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