FMO DATABASE

FMODB ID: 2J72R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-670147.018686
FMO2-HF: Nuclear repulsion	626211.612142
FMO2-HF: Total energy	-43935.406543
FMO2-MP2: Total energy	-44058.100272

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.
-7.184	-1.031	3.902	-3.341	-6.713	-0.015

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 : -0.013 / q_NPA : -0.013

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

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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	-0.010	-0.012	3.625	-2.037	0.101	-0.006	-1.071	-1.061	0.000
4	A	128	TYR	0	-0.108	-0.074	2.378	-0.664	-0.324	2.643	-0.843	-2.139	-0.003
5	A	129	VAL	0	0.023	0.021	3.042	-1.821	-0.712	0.202	-0.533	-0.778	-0.005
6	A	130	LEU	0	-0.028	-0.017	5.474	0.001	0.001	0.000	0.000	0.000	0.000
7	A	131	GLY	0	-0.036	-0.023	6.815	0.111	0.111	0.000	0.000	0.000	0.000
8	A	132	SER	0	0.014	0.004	10.150	0.006	0.006	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.033	-0.032	13.135	0.000	0.000	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.030	-0.012	14.434	0.019	0.019	0.000	0.000	0.000	0.000
11	A	135	SER	0	0.000	-0.001	17.189	0.008	0.008	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.876	0.927	16.947	0.132	0.132	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.034	0.008	18.706	0.010	0.010	0.000	0.000	0.000	0.000
14	A	138	ILE	0	-0.005	0.014	21.730	0.004	0.004	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.050	-0.029	21.250	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.002	0.016	25.902	0.006	0.006	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.025	-0.019	23.166	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.011	0.010	28.891	0.004	0.004	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.082	-0.067	31.592	0.005	0.005	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.865	-0.951	32.508	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	145	TYR	0	0.003	0.005	28.592	0.001	0.001	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.840	-0.893	27.871	-0.081	-0.081	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.782	-0.894	28.208	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.807	0.891	29.625	0.050	0.050	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.026	-0.016	23.985	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.004	-0.020	21.394	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.879	0.937	25.160	0.055	0.055	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.829	-0.894	26.889	-0.055	-0.055	0.000	0.000	0.000	0.000
29	A	153	ASN	0	0.016	0.000	22.937	0.001	0.001	0.000	0.000	0.000	0.000
30	A	154	MET	0	0.037	0.041	21.108	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.062	-0.025	19.640	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.875	0.930	18.618	0.081	0.081	0.000	0.000	0.000	0.000
33	A	157	TYR	0	-0.022	-0.004	15.982	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.035	0.031	11.541	0.012	0.012	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.004	-0.003	13.449	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	160	GLN	0	-0.009	0.008	9.699	0.038	0.038	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.052	0.024	9.193	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.052	0.025	2.680	-1.624	-0.216	0.483	-0.544	-1.347	-0.006
39	A	163	TYR	0	0.003	0.007	5.869	0.082	0.082	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.918	0.932	6.493	0.234	0.234	0.000	0.000	0.000	0.000
41	A	165	PRO	0	-0.031	-0.016	7.800	0.077	0.077	0.000	0.000	0.000	0.000
42	A	166	MET	0	-0.003	0.000	10.968	0.000	0.000	0.000	0.000	0.000	0.000
43	A	167	ASP	-1	-0.787	-0.865	14.523	-0.215	-0.215	0.000	0.000	0.000	0.000
44	A	168	GLU	-1	-0.882	-0.937	16.574	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.066	-0.033	16.821	0.011	0.011	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.061	-0.042	15.116	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	171	ASN	0	0.009	0.009	16.756	0.013	0.013	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.033	0.002	17.086	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.026	0.005	16.590	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	174	ASN	0	0.018	0.008	14.595	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.023	0.021	12.347	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	176	VAL	0	0.005	-0.012	11.717	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	177	HIS	0	-0.032	-0.002	12.803	0.005	0.005	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.832	-0.891	8.361	-0.575	-0.575	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.038	-0.020	8.193	0.001	0.001	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.014	0.017	9.067	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.025	-0.002	10.278	0.032	0.032	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.049	-0.016	3.581	-0.303	0.006	0.013	-0.049	-0.273	0.000
59	A	183	THR	0	-0.001	-0.018	6.777	0.004	0.004	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.025	0.025	7.881	0.033	0.033	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.961	0.998	7.317	0.449	0.449	0.000	0.000	0.000	0.000
62	A	186	GLN	0	-0.005	-0.019	2.581	-0.857	-0.008	0.567	-0.301	-1.115	-0.001
63	A	187	HIS	0	0.008	0.006	6.883	0.015	0.015	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.081	-0.052	10.139	0.040	0.040	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.049	-0.021	7.487	0.025	0.025	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.046	0.002	9.257	0.030	0.030	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.011	0.000	11.102	0.012	0.012	0.000	0.000	0.000	0.000
68	A	192	THR	0	-0.052	-0.062	14.301	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.052	-0.050	17.495	0.004	0.004	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.964	0.952	21.292	0.026	0.026	0.000	0.000	0.000	0.000
71	A	195	GLY	0	0.029	0.030	23.224	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.785	-0.832	19.070	-0.051	-0.051	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.038	-0.017	18.274	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.049	-0.020	22.263	0.000	0.000	0.000	0.000	0.000	0.000
75	A	199	THR	0	-0.027	-0.029	26.015	0.001	0.001	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.812	-0.931	27.914	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.065	-0.051	31.020	0.004	0.004	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.818	-0.879	27.752	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.013	0.003	30.733	0.003	0.003	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.815	0.899	32.919	0.032	0.032	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.024	-0.007	33.580	0.002	0.002	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.013	-0.007	29.848	0.003	0.003	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.828	-0.902	34.448	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.972	0.994	37.357	0.027	0.027	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.029	-0.023	36.462	0.002	0.002	0.000	0.000	0.000	0.000
86	A	210	VAL	0	0.017	-0.022	35.290	0.002	0.002	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.918	-0.932	38.546	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	212	GLN	0	-0.004	-0.015	41.820	0.000	0.000	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.026	0.002	37.420	0.000	0.000	0.000	0.000	0.000	0.000
90	A	214	CYS	0	-0.032	-0.013	41.049	0.002	0.002	0.000	0.000	0.000	0.000
91	A	215	ILE	0	0.018	0.011	43.747	0.001	0.001	0.000	0.000	0.000	0.000
92	A	216	THR	0	-0.006	-0.002	45.459	0.001	0.001	0.000	0.000	0.000	0.000
93	A	217	GLN	0	-0.026	-0.037	43.644	0.001	0.001	0.000	0.000	0.000	0.000
94	A	218	TYR	0	-0.010	0.014	46.478	0.001	0.001	0.000	0.000	0.000	0.000
95	A	219	GLU	-1	-0.894	-0.942	49.148	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	220	ARG	1	0.890	0.934	47.147	0.007	0.007	0.000	0.000	0.000	0.000
97	A	221	GLU	-1	-0.946	-0.974	47.900	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	222	SER	0	-0.063	-0.027	50.898	0.001	0.001	0.000	0.000	0.000	0.000
99	A	223	GLN	0	-0.090	-0.041	53.471	0.000	0.000	0.000	0.000	0.000	0.000
100	A	224	ALA	0	-0.065	-0.017	54.504	0.000	0.000	0.000	0.000	0.000	0.000
101	A	225	TYR	0	-0.001	0.003	55.501	0.000	0.000	0.000	0.000	0.000	0.000

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