FMO DATABASE

FMODB ID: 723GK

Calculation Name: 3HJ5-A-Xray372

Preferred Name: Prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HJ5

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-669661.739925
FMO2-HF: Nuclear repulsion	625727.253771
FMO2-HF: Total energy	-43934.486154
FMO2-MP2: Total energy	-44057.224352

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.
-7.538	-4.085	7.816	-4.364	-6.905	-0.017

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 : -0.020 / q_NPA : -0.008

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	-0.012	-0.015	3.234	-3.015	-0.475	0.060	-1.308	-1.292	-0.002
4	A	128	TYR	0	-0.047	-0.020	2.077	0.711	-1.535	6.984	-1.826	-2.912	-0.002
5	A	129	VAL	0	0.039	0.024	2.914	-2.447	-1.290	0.592	-0.656	-1.093	-0.008
6	A	130	LEU	0	-0.028	-0.022	5.347	0.053	0.053	0.000	0.000	0.000	0.000
7	A	131	GLY	0	-0.035	-0.017	6.612	0.151	0.151	0.000	0.000	0.000	0.000
8	A	132	SER	0	0.026	0.004	9.983	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.034	-0.026	12.972	0.029	0.029	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.039	-0.016	14.633	0.031	0.031	0.000	0.000	0.000	0.000
11	A	135	SER	0	-0.029	-0.013	17.182	0.011	0.011	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.934	0.959	17.409	0.155	0.155	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.027	0.011	18.890	0.010	0.010	0.000	0.000	0.000	0.000
14	A	138	ILE	0	0.018	0.025	21.899	0.005	0.005	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.048	-0.031	21.648	0.001	0.001	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.004	0.020	26.147	0.004	0.004	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.018	-0.012	23.664	0.003	0.003	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.019	0.013	29.213	0.000	0.000	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.020	-0.008	32.038	0.000	0.000	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.847	-0.942	32.863	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	145	TYR	0	-0.018	-0.005	29.014	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.895	-0.956	28.151	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.792	-0.900	28.574	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.826	0.915	29.903	0.018	0.018	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.035	-0.012	24.066	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	150	TYR	0	-0.004	-0.022	22.066	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.936	0.970	25.362	0.034	0.034	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.897	-0.943	27.080	-0.039	-0.039	0.000	0.000	0.000	0.000
29	A	153	ASN	0	0.002	-0.019	23.193	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	154	MET	0	0.035	0.040	21.317	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.069	-0.028	19.824	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.921	0.973	18.855	0.030	0.030	0.000	0.000	0.000	0.000
33	A	157	TYR	0	-0.030	-0.014	16.186	0.000	0.000	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.031	0.020	11.834	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	159	ASN	0	0.004	-0.003	13.621	0.003	0.003	0.000	0.000	0.000	0.000
36	A	160	GLN	0	-0.002	0.009	9.725	0.023	0.023	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.044	0.020	9.350	0.000	0.000	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.029	0.022	3.149	-1.385	-0.169	0.152	-0.423	-0.946	-0.004
39	A	163	TYR	0	-0.010	-0.003	5.921	0.219	0.219	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.961	0.971	6.231	-0.048	-0.048	0.000	0.000	0.000	0.000
41	A	165	PRO	0	-0.031	-0.017	7.574	0.096	0.096	0.000	0.000	0.000	0.000
42	A	166	MET	0	-0.002	-0.003	10.830	0.039	0.039	0.000	0.000	0.000	0.000
43	A	167	ASP	-1	-0.815	-0.911	14.095	-0.147	-0.147	0.000	0.000	0.000	0.000
44	A	168	GLU	-1	-0.943	-0.976	16.417	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.026	-0.004	16.686	0.029	0.029	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.048	-0.021	15.078	0.006	0.006	0.000	0.000	0.000	0.000
47	A	171	ASN	0	0.030	0.019	16.616	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.057	0.006	17.051	0.014	0.014	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.032	0.002	16.599	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	174	ASN	0	-0.017	0.001	14.486	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.011	0.016	11.900	0.000	0.000	0.000	0.000	0.000	0.000
52	A	176	VAL	0	-0.016	-0.023	11.747	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	177	HIS	0	-0.013	0.009	12.983	0.001	0.001	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.904	-0.945	8.387	0.076	0.076	0.000	0.000	0.000	0.000
55	A	179	CYS	0	0.019	0.005	8.359	0.002	0.002	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.001	0.048	9.344	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.028	-0.001	10.557	-0.041	-0.041	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.051	-0.020	3.801	-0.115	0.122	0.003	-0.030	-0.210	0.000
59	A	183	THR	0	-0.016	-0.061	6.941	-0.099	-0.099	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.013	0.020	8.262	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.956	0.991	7.377	-0.971	-0.971	0.000	0.000	0.000	0.000
62	A	186	GLN	0	-0.012	-0.028	3.373	-0.516	0.033	0.025	-0.121	-0.452	-0.001
63	A	187	HIS	0	0.011	0.015	7.063	-0.080	-0.080	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.081	-0.040	10.446	0.028	0.028	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.057	-0.028	7.789	0.022	0.022	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.040	0.001	9.805	-0.046	-0.046	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.007	-0.004	11.186	0.027	0.027	0.000	0.000	0.000	0.000
68	A	192	THR	0	-0.005	-0.011	14.392	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.054	-0.037	17.579	0.024	0.024	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.975	0.954	21.378	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	195	GLY	0	0.029	0.030	23.340	0.002	0.002	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.821	-0.882	19.593	-0.102	-0.102	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.094	-0.053	18.707	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.047	-0.019	22.533	0.008	0.008	0.000	0.000	0.000	0.000
75	A	199	THR	0	-0.007	0.012	26.147	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.823	-0.931	28.160	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.090	-0.066	31.456	0.003	0.003	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.843	-0.926	27.787	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.012	0.006	31.071	0.004	0.004	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.959	0.977	33.189	0.025	0.025	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.052	-0.020	33.855	0.004	0.004	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.004	-0.006	29.975	0.004	0.004	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.912	-0.956	34.748	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.973	0.993	37.645	0.006	0.006	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.049	-0.030	36.364	0.002	0.002	0.000	0.000	0.000	0.000
86	A	210	VAL	0	0.008	-0.021	35.510	0.002	0.002	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.904	-0.924	38.705	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	212	GLN	0	-0.024	-0.027	42.028	0.002	0.002	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.011	0.004	37.786	0.002	0.002	0.000	0.000	0.000	0.000
90	A	214	CYS	0	-0.035	-0.019	41.290	0.001	0.001	0.000	0.000	0.000	0.000
91	A	215	ILE	0	0.027	0.016	43.835	0.000	0.000	0.000	0.000	0.000	0.000
92	A	216	THR	0	0.007	0.008	45.447	0.001	0.001	0.000	0.000	0.000	0.000
93	A	217	GLN	0	-0.023	-0.034	43.700	0.002	0.002	0.000	0.000	0.000	0.000
94	A	218	TYR	0	-0.024	0.009	46.571	0.000	0.000	0.000	0.000	0.000	0.000
95	A	219	GLU	-1	-0.900	-0.948	49.239	0.006	0.006	0.000	0.000	0.000	0.000
96	A	220	ARG	1	0.938	0.960	48.055	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	221	GLU	-1	-1.016	-1.020	48.044	0.006	0.006	0.000	0.000	0.000	0.000
98	A	222	SER	0	-0.043	-0.001	50.994	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	223	GLN	0	-0.091	-0.048	53.657	0.000	0.000	0.000	0.000	0.000	0.000
100	A	224	ALA	0	-0.062	-0.016	54.643	0.000	0.000	0.000	0.000	0.000	0.000
101	A	225	TYR	0	-0.007	0.001	55.599	-0.001	-0.001	0.000	0.000	0.000	0.000

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