FMO DATABASE

FMODB ID: YZ6Q2

Calculation Name: 3HAK-A-Xray372

Preferred Name: Prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HAK

Chain ID: A

ChEMBL ID: CHEMBL4869

UniProt ID: P04156

Base Structure: X-ray

Registration Date: 2023-06-21

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-847599.807746
FMO2-HF: Nuclear repulsion	802662.031216
FMO2-HF: Total energy	-44937.776529
FMO2-MP2: Total energy	-45063.800969

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: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.
-6.239	-1.641	0.784	-1.981	-3.403	0.001

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 : 0 / q_Mulliken : 0.032 / q_NPA : 0.009

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	-0.004	0.010	2.958	-2.738	0.404	0.006	-1.560	-1.589	0.003
4	A	128	TYR	0	0.046	0.014	4.773	-0.992	-0.954	-0.001	-0.008	-0.029	0.000
5	A	129	VAL	0	-0.020	-0.005	6.914	0.055	0.055	0.000	0.000	0.000	0.000
6	A	130	LEU	0	-0.014	-0.006	9.474	0.033	0.033	0.000	0.000	0.000	0.000
7	A	131	GLY	0	0.020	0.035	13.247	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	132	SER	0	-0.021	-0.022	15.365	0.036	0.036	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.003	-0.001	18.632	0.008	0.008	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.043	-0.020	19.632	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	135	SER	0	-0.029	-0.016	24.054	0.011	0.011	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.911	0.935	26.641	0.020	0.020	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.016	0.033	26.569	0.000	0.000	0.000	0.000	0.000	0.000
14	A	138	ILE	0	0.010	-0.002	29.409	0.007	0.007	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.036	-0.017	28.076	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.016	0.015	32.205	0.006	0.006	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.018	-0.022	31.605	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.017	0.018	36.388	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.027	-0.036	39.226	0.001	0.001	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.814	-0.908	40.762	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	145	TYR	0	-0.081	-0.045	39.234	0.000	0.000	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.862	-0.924	36.915	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.801	-0.897	37.395	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.793	0.892	38.216	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.024	-0.033	34.121	0.000	0.000	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.081	0.020	29.093	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.932	0.964	34.401	0.012	0.012	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.912	-0.952	36.235	0.000	0.000	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.021	-0.013	33.215	0.007	0.007	0.000	0.000	0.000	0.000
30	A	154	MET	0	0.012	0.029	30.801	0.001	0.001	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.071	-0.030	29.586	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.874	0.938	29.383	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	157	TYR	0	-0.020	-0.012	26.347	0.006	0.006	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.051	0.019	21.217	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.022	-0.012	22.720	0.000	0.000	0.000	0.000	0.000	0.000
36	A	160	GLN	0	-0.013	-0.004	17.299	0.006	0.006	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.016	0.009	16.263	0.024	0.024	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.007	-0.004	11.706	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	163	TYR	0	0.033	-0.005	9.869	0.055	0.055	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.893	0.932	5.857	-0.222	-0.222	0.000	0.000	0.000	0.000
41	A	165	PRO	0	0.043	0.023	4.836	-0.057	-0.057	0.000	0.000	0.000	0.000
42	A	166	MET	0	0.010	0.001	2.664	-1.946	-0.528	0.779	-0.413	-1.785	-0.002
43	A	167	ASP	-1	-0.791	-0.875	5.616	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	168	GLH	0	-0.111	-0.077	8.626	0.106	0.106	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.050	-0.015	5.924	0.037	0.037	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.072	-0.036	9.465	0.142	0.142	0.000	0.000	0.000	0.000
47	A	171	ASN	0	0.018	-0.003	12.018	0.003	0.003	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.063	0.022	14.919	0.006	0.006	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.052	0.018	17.055	0.008	0.008	0.000	0.000	0.000	0.000
50	A	174	ASN	0	-0.055	-0.023	12.116	0.071	0.071	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.034	0.034	11.118	0.030	0.030	0.000	0.000	0.000	0.000
52	A	176	VAL	0	0.007	0.000	13.900	0.023	0.023	0.000	0.000	0.000	0.000
53	A	177	HIS	0	0.008	0.003	17.391	0.040	0.040	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.883	-0.931	12.184	0.063	0.063	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.082	-0.041	14.896	0.025	0.025	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.042	0.022	15.808	0.029	0.029	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.001	-0.001	17.401	0.012	0.012	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.050	-0.023	12.577	0.033	0.033	0.000	0.000	0.000	0.000
59	A	183	THR	0	0.003	-0.006	15.826	0.009	0.009	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.032	0.023	17.600	0.009	0.009	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.945	0.980	18.122	-0.177	-0.177	0.000	0.000	0.000	0.000
62	A	186	GLN	0	0.017	0.015	13.920	0.018	0.018	0.000	0.000	0.000	0.000
63	A	187	HIS	0	-0.007	-0.015	18.131	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.004	-0.012	21.191	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.021	-0.007	19.542	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	190	THR	0	0.001	-0.001	20.022	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.050	-0.034	22.534	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	192	THR	0	0.013	0.012	25.276	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.076	-0.037	23.969	0.001	0.001	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.873	0.944	26.633	-0.049	-0.049	0.000	0.000	0.000	0.000
71	A	195	GLY	0	-0.003	0.004	29.272	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.991	-0.982	30.050	0.036	0.036	0.000	0.000	0.000	0.000
73	A	197	ASN	0	0.010	-0.008	29.706	0.013	0.013	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.045	-0.020	25.422	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	199	THR	0	0.002	-0.004	30.287	0.004	0.004	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.858	-0.950	31.332	0.043	0.043	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.042	-0.019	31.981	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.726	-0.846	30.018	0.024	0.024	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.011	0.002	26.305	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	204	LYS	1	1.008	1.014	27.704	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.042	-0.011	29.675	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.045	-0.022	25.004	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.890	-0.953	24.833	0.017	0.017	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.887	0.959	25.521	0.019	0.019	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.020	-0.014	25.834	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	210	VAL	0	-0.003	-0.016	20.516	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.875	-0.926	21.770	-0.072	-0.072	0.000	0.000	0.000	0.000
88	A	212	GLN	0	-0.018	-0.016	22.227	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.053	-0.021	21.471	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	215	ILE	0	0.029	0.026	17.925	-0.040	-0.040	0.000	0.000	0.000	0.000
91	A	216	THR	0	-0.004	0.006	19.785	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	217	GLN	0	-0.049	-0.027	14.307	0.027	0.027	0.000	0.000	0.000	0.000
93	A	218	TYR	0	0.015	0.005	13.891	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	219	GLU	-1	-0.933	-0.974	16.306	-0.198	-0.198	0.000	0.000	0.000	0.000
95	A	220	ARG	1	0.921	0.955	17.763	0.173	0.173	0.000	0.000	0.000	0.000
96	A	221	GLU	-1	-0.846	-0.902	11.272	-0.611	-0.611	0.000	0.000	0.000	0.000
97	A	222	SER	0	-0.026	-0.013	14.584	-0.031	-0.031	0.000	0.000	0.000	0.000
98	A	223	GLN	0	-0.018	-0.025	16.424	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	224	ALA	0	-0.007	-0.001	15.045	0.011	0.011	0.000	0.000	0.000	0.000
100	A	225	TYR	0	-0.051	-0.015	11.427	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	226	TYR	0	-0.047	-0.028	14.862	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	227	GLN	0	-0.080	-0.012	18.146	0.032	0.032	0.000	0.000	0.000	0.000

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