FMO DATABASE

FMODB ID: V5821

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

Total energy (hartree)

FMO2-HF: Electronic energy	-848421.635647
FMO2-HF: Nuclear repulsion	803483.313573
FMO2-HF: Total energy	-44938.322074
FMO2-MP2: Total energy	-45064.345474

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.
-5.428	-0.94	0.898	-1.957	-3.429	-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 : 0.030 / q_NPA : 0.004

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	-0.007	0.007	2.833	-2.274	0.821	0.012	-1.524	-1.583	0.002
4	A	128	TYR	0	0.039	0.005	4.646	-0.813	-0.779	-0.001	-0.009	-0.024	0.000
5	A	129	VAL	0	-0.017	-0.005	6.884	0.036	0.036	0.000	0.000	0.000	0.000
6	A	130	LEU	0	-0.011	-0.002	9.426	0.045	0.045	0.000	0.000	0.000	0.000
7	A	131	GLY	0	0.032	0.035	13.205	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	132	SER	0	-0.030	-0.021	15.354	0.036	0.036	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.010	-0.011	18.620	0.007	0.007	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.042	-0.019	19.581	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	135	SER	0	0.025	0.016	24.043	0.011	0.011	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.842	0.886	26.116	0.043	0.043	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.009	0.030	26.569	0.001	0.001	0.000	0.000	0.000	0.000
14	A	138	ILE	0	0.014	-0.005	29.406	0.007	0.007	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.045	-0.022	28.090	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.034	0.025	32.213	0.007	0.007	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.037	-0.021	31.426	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.020	0.024	36.408	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.024	-0.041	39.249	0.002	0.002	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.843	-0.923	40.663	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	145	TYR	0	-0.060	-0.035	39.525	0.000	0.000	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.836	-0.905	36.664	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.780	-0.892	37.297	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.764	0.864	38.128	0.008	0.008	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.022	-0.042	33.978	0.001	0.001	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.081	0.020	30.048	0.001	0.001	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.869	0.930	34.315	0.021	0.021	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.811	-0.886	36.159	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.004	0.003	33.120	0.006	0.006	0.000	0.000	0.000	0.000
30	A	154	MET	0	0.001	0.023	30.710	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.072	-0.032	29.510	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.842	0.905	29.331	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	157	TYR	0	-0.010	-0.012	26.263	0.005	0.005	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.072	0.043	21.118	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.030	-0.019	22.659	0.002	0.002	0.000	0.000	0.000	0.000
36	A	160	GLN	0	-0.020	-0.004	17.151	0.009	0.009	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.022	0.012	16.306	0.023	0.023	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.025	0.006	11.531	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	163	TYR	0	-0.040	-0.058	10.241	0.044	0.044	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.901	0.930	6.442	-0.190	-0.190	0.000	0.000	0.000	0.000
41	A	165	PRO	0	0.047	0.030	4.838	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	166	MET	0	0.005	-0.001	2.682	-1.874	-0.515	0.887	-0.424	-1.822	-0.003
43	A	167	ASP	-1	-0.803	-0.878	5.688	-0.094	-0.094	0.000	0.000	0.000	0.000
44	A	168	GLH	0	-0.088	-0.076	8.637	0.113	0.113	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.044	-0.013	5.292	0.076	0.076	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.078	-0.040	9.478	0.143	0.143	0.000	0.000	0.000	0.000
47	A	171	ASN	0	0.013	0.000	12.076	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.068	0.024	14.996	0.004	0.004	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.054	0.024	17.127	0.006	0.006	0.000	0.000	0.000	0.000
50	A	174	ASN	0	-0.056	-0.030	12.507	0.057	0.057	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.024	0.026	11.088	0.028	0.028	0.000	0.000	0.000	0.000
52	A	176	VAL	0	0.009	0.002	13.998	0.016	0.016	0.000	0.000	0.000	0.000
53	A	177	HIS	0	-0.006	-0.001	17.494	0.037	0.037	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.878	-0.924	12.773	0.039	0.039	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.069	-0.030	14.816	0.014	0.014	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.034	0.025	15.700	0.028	0.028	0.000	0.000	0.000	0.000
57	A	181	ASN	0	-0.002	-0.002	17.311	0.044	0.044	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.021	-0.011	12.373	0.029	0.029	0.000	0.000	0.000	0.000
59	A	183	THR	0	0.004	-0.006	15.704	0.007	0.007	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.021	0.016	17.495	0.011	0.011	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.884	0.948	18.019	-0.112	-0.112	0.000	0.000	0.000	0.000
62	A	186	GLN	0	0.012	0.012	14.225	0.035	0.035	0.000	0.000	0.000	0.000
63	A	187	HIS	0	0.004	-0.005	18.026	0.000	0.000	0.000	0.000	0.000	0.000
64	A	188	THR	0	0.001	-0.009	21.095	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.020	0.008	19.377	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.016	-0.020	20.077	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.029	-0.025	22.449	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	192	THR	0	-0.007	-0.015	25.319	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.074	-0.032	23.866	0.003	0.003	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.761	0.881	26.551	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	195	GLY	0	-0.007	0.001	29.194	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.877	-0.917	29.869	0.018	0.018	0.000	0.000	0.000	0.000
73	A	197	ASN	0	0.000	-0.012	29.605	0.011	0.011	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.031	-0.014	25.272	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	199	THR	0	0.001	-0.011	30.176	0.004	0.004	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.818	-0.929	31.212	0.026	0.026	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.025	-0.009	31.858	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.725	-0.814	29.935	0.007	0.007	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.014	0.000	26.122	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.968	0.993	27.586	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.056	-0.012	29.562	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.045	-0.021	24.902	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.883	-0.953	24.720	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.862	0.936	25.413	0.031	0.031	0.000	0.000	0.000	0.000
85	A	209	VAL	0	0.002	-0.003	25.810	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	210	VAL	0	-0.001	-0.020	20.448	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.863	-0.926	21.788	-0.091	-0.091	0.000	0.000	0.000	0.000
88	A	212	GLN	0	-0.018	-0.009	22.240	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.048	-0.015	21.460	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	215	ILE	0	0.025	0.027	17.928	-0.040	-0.040	0.000	0.000	0.000	0.000
91	A	216	THR	0	-0.007	-0.003	19.775	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	217	GLN	0	-0.045	-0.027	14.120	0.029	0.029	0.000	0.000	0.000	0.000
93	A	218	TYR	0	0.017	0.005	13.898	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	219	GLU	-1	-0.920	-0.968	16.293	-0.208	-0.208	0.000	0.000	0.000	0.000
95	A	220	ARG	1	0.911	0.955	17.620	0.200	0.200	0.000	0.000	0.000	0.000
96	A	221	GLU	-1	-0.793	-0.853	11.125	-0.662	-0.662	0.000	0.000	0.000	0.000
97	A	222	SER	0	-0.038	-0.012	14.546	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	223	GLN	0	-0.021	-0.027	16.384	0.003	0.003	0.000	0.000	0.000	0.000
99	A	224	ALA	0	-0.020	-0.012	15.029	0.013	0.013	0.000	0.000	0.000	0.000
100	A	225	TYR	0	-0.042	-0.010	10.946	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	226	TYR	0	-0.039	-0.025	14.797	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	227	GLN	0	-0.069	-0.005	18.080	0.037	0.037	0.000	0.000	0.000	0.000

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