FMO DATABASE

FMODB ID: MV63Z

Calculation Name: 3HJ5-B-Xray372

Preferred Name: Prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HJ5

Chain ID: B

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	OptAll
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	-678419.18675
FMO2-HF: Nuclear repulsion	633843.569431
FMO2-HF: Total energy	-44575.61732
FMO2-MP2: Total energy	-44700.085873

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(B:126:GLY)

Summations of interaction energy for fragment #1(B:126:GLY)

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.
-0.971	1.575	2.061	-1.728	-2.879	0.005

Interaction energy analysis for fragmet #1(B:126:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.010

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	B	128	TYR	0	-0.090	-0.064	1.980	-3.855	-1.750	2.061	-1.566	-2.600	0.005
4	B	129	VAL	0	0.000	-0.007	4.465	1.440	1.527	-0.001	-0.011	-0.075	0.000
5	B	130	LEU	0	-0.030	0.001	7.451	-0.285	-0.285	0.000	0.000	0.000	0.000
6	B	131	GLY	0	-0.014	-0.003	9.555	0.011	0.011	0.000	0.000	0.000	0.000
7	B	132	SER	0	0.002	-0.016	13.031	0.013	0.013	0.000	0.000	0.000	0.000
8	B	133	ALA	0	-0.019	-0.018	16.338	-0.027	-0.027	0.000	0.000	0.000	0.000
9	B	134	MET	0	0.007	0.017	15.801	-0.006	-0.006	0.000	0.000	0.000	0.000
10	B	135	SER	0	-0.008	-0.016	20.132	0.004	0.004	0.000	0.000	0.000	0.000
11	B	136	ARG	1	0.890	0.950	19.916	-0.035	-0.035	0.000	0.000	0.000	0.000
12	B	137	PRO	0	0.000	0.019	22.853	0.003	0.003	0.000	0.000	0.000	0.000
13	B	138	ILE	0	0.024	0.011	25.878	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	139	ILE	0	-0.047	-0.020	24.808	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	140	HIS	0	0.013	0.017	29.391	0.001	0.001	0.000	0.000	0.000	0.000
16	B	141	PHE	0	-0.047	-0.030	26.412	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	142	GLY	0	-0.009	0.005	32.379	0.002	0.002	0.000	0.000	0.000	0.000
18	B	143	SER	0	-0.047	-0.056	34.732	0.003	0.003	0.000	0.000	0.000	0.000
19	B	144	ASP	-1	-0.853	-0.941	35.346	-0.020	-0.020	0.000	0.000	0.000	0.000
20	B	145	TYR	0	-0.035	-0.010	31.457	0.003	0.003	0.000	0.000	0.000	0.000
21	B	146	GLU	-1	-0.816	-0.890	31.078	-0.040	-0.040	0.000	0.000	0.000	0.000
22	B	147	ASP	-1	-0.760	-0.857	31.120	-0.018	-0.018	0.000	0.000	0.000	0.000
23	B	148	ARG	1	0.802	0.859	32.689	0.012	0.012	0.000	0.000	0.000	0.000
24	B	149	TYR	0	0.018	0.022	25.893	0.004	0.004	0.000	0.000	0.000	0.000
25	B	150	TYR	0	0.015	-0.019	24.341	0.001	0.001	0.000	0.000	0.000	0.000
26	B	151	ARG	1	0.818	0.891	28.178	0.014	0.014	0.000	0.000	0.000	0.000
27	B	152	GLU	-1	-0.794	-0.849	30.441	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	153	ASN	0	-0.024	-0.014	26.011	0.005	0.005	0.000	0.000	0.000	0.000
29	B	154	MET	0	-0.003	0.009	24.237	0.002	0.002	0.000	0.000	0.000	0.000
30	B	155	HIS	0	-0.023	-0.031	22.724	0.003	0.003	0.000	0.000	0.000	0.000
31	B	156	ARG	1	0.854	0.929	21.883	0.016	0.016	0.000	0.000	0.000	0.000
32	B	157	TYR	0	-0.011	0.008	18.819	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	158	PRO	0	0.012	0.017	14.440	0.017	0.017	0.000	0.000	0.000	0.000
34	B	159	ASN	0	-0.014	-0.012	16.544	-0.010	-0.010	0.000	0.000	0.000	0.000
35	B	160	GLN	0	0.032	0.008	13.632	0.006	0.006	0.000	0.000	0.000	0.000
36	B	161	VAL	0	-0.002	0.007	11.330	-0.013	-0.013	0.000	0.000	0.000	0.000
37	B	162	TYR	0	0.026	0.011	5.696	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	163	TYR	0	0.008	-0.012	8.040	-0.197	-0.197	0.000	0.000	0.000	0.000
39	B	164	ARG	1	0.955	0.984	3.809	3.061	3.282	0.000	-0.116	-0.104	0.000
40	B	165	PRO	0	-0.010	-0.016	8.303	0.053	0.053	0.000	0.000	0.000	0.000
41	B	166	MET	0	-0.027	-0.017	11.318	-0.090	-0.090	0.000	0.000	0.000	0.000
42	B	167	ASP	-1	-0.931	-0.945	11.312	-0.312	-0.312	0.000	0.000	0.000	0.000
43	B	168	GLU	-1	-0.894	-0.956	14.567	-0.119	-0.119	0.000	0.000	0.000	0.000
44	B	169	TYR	0	-0.055	-0.035	15.124	-0.004	-0.004	0.000	0.000	0.000	0.000
45	B	170	SER	0	-0.042	-0.008	12.751	-0.015	-0.015	0.000	0.000	0.000	0.000
46	B	171	ASN	0	0.025	0.008	15.654	0.039	0.039	0.000	0.000	0.000	0.000
47	B	172	GLN	0	0.061	0.019	17.298	-0.020	-0.020	0.000	0.000	0.000	0.000
48	B	173	ASN	0	0.016	0.012	17.553	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	174	ASN	0	0.022	0.005	14.527	0.010	0.010	0.000	0.000	0.000	0.000
50	B	175	PHE	0	0.038	0.023	12.842	-0.073	-0.073	0.000	0.000	0.000	0.000
51	B	176	VAL	0	0.009	-0.013	12.812	-0.033	-0.033	0.000	0.000	0.000	0.000
52	B	177	HIS	0	0.009	0.005	13.523	-0.034	-0.034	0.000	0.000	0.000	0.000
53	B	178	ASP	-1	-0.833	-0.883	8.459	-1.111	-1.111	0.000	0.000	0.000	0.000
54	B	179	CYS	0	0.015	0.010	9.308	-0.054	-0.054	0.000	0.000	0.000	0.000
55	B	180	VAL	0	-0.020	0.004	10.387	0.033	0.033	0.000	0.000	0.000	0.000
56	B	181	ASN	0	-0.054	-0.029	10.540	0.041	0.041	0.000	0.000	0.000	0.000
57	B	182	ILE	0	-0.043	-0.008	3.743	-0.138	-0.005	0.001	-0.035	-0.100	0.000
58	B	183	THR	0	0.010	-0.004	8.099	0.122	0.122	0.000	0.000	0.000	0.000
59	B	184	ILE	0	0.034	0.020	10.112	0.062	0.062	0.000	0.000	0.000	0.000
60	B	185	LYS	1	0.954	0.995	9.727	0.443	0.443	0.000	0.000	0.000	0.000
61	B	186	GLN	0	0.007	0.009	7.415	-0.081	-0.081	0.000	0.000	0.000	0.000
62	B	187	HIS	0	-0.008	-0.018	9.550	0.084	0.084	0.000	0.000	0.000	0.000
63	B	188	THR	0	-0.060	-0.050	13.032	0.028	0.028	0.000	0.000	0.000	0.000
64	B	189	VAL	0	-0.049	-0.016	10.128	0.011	0.011	0.000	0.000	0.000	0.000
65	B	190	THR	0	-0.062	-0.018	12.568	0.052	0.052	0.000	0.000	0.000	0.000
66	B	191	THR	0	-0.040	-0.023	14.263	-0.010	-0.010	0.000	0.000	0.000	0.000
67	B	192	THR	0	-0.027	-0.025	17.372	0.011	0.011	0.000	0.000	0.000	0.000
68	B	193	THR	0	-0.030	-0.025	20.614	-0.007	-0.007	0.000	0.000	0.000	0.000
69	B	194	LYS	1	0.974	0.962	24.407	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	195	GLY	0	0.007	0.008	26.811	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	196	GLU	-1	-0.820	-0.881	22.646	0.058	0.058	0.000	0.000	0.000	0.000
72	B	197	ASN	0	-0.001	0.005	21.543	-0.008	-0.008	0.000	0.000	0.000	0.000
73	B	198	PHE	0	-0.065	-0.017	25.622	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	199	THR	0	0.014	-0.021	29.067	0.004	0.004	0.000	0.000	0.000	0.000
75	B	200	GLU	-1	-0.906	-0.970	31.077	0.011	0.011	0.000	0.000	0.000	0.000
76	B	201	THR	0	-0.021	-0.024	33.815	0.000	0.000	0.000	0.000	0.000	0.000
77	B	202	ASP	-1	-0.851	-0.894	30.602	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	203	VAL	0	-0.001	-0.003	33.447	0.000	0.000	0.000	0.000	0.000	0.000
79	B	204	LYS	1	0.897	0.940	35.688	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	205	MET	0	-0.042	-0.011	36.468	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	206	MET	0	-0.020	-0.023	32.370	0.000	0.000	0.000	0.000	0.000	0.000
82	B	207	GLU	-1	-0.858	-0.915	37.723	0.005	0.005	0.000	0.000	0.000	0.000
83	B	208	ARG	1	0.982	0.989	40.600	0.004	0.004	0.000	0.000	0.000	0.000
84	B	209	VAL	0	-0.010	-0.004	38.616	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	210	VAL	0	0.023	-0.003	38.695	0.000	0.000	0.000	0.000	0.000	0.000
86	B	211	GLU	-1	-0.867	-0.907	41.613	0.000	0.000	0.000	0.000	0.000	0.000
87	B	212	GLN	0	-0.026	-0.027	44.849	0.000	0.000	0.000	0.000	0.000	0.000
88	B	213	MET	0	-0.050	-0.011	39.044	0.000	0.000	0.000	0.000	0.000	0.000
89	B	214	CYS	0	-0.049	-0.030	43.790	0.001	0.001	0.000	0.000	0.000	0.000
90	B	215	ILE	0	0.014	0.018	46.256	0.000	0.000	0.000	0.000	0.000	0.000
91	B	216	THR	0	-0.009	-0.018	46.773	0.000	0.000	0.000	0.000	0.000	0.000
92	B	217	GLN	0	-0.012	0.002	44.094	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	218	TYR	0	0.027	0.014	48.164	0.001	0.001	0.000	0.000	0.000	0.000
94	B	219	GLU	-1	-0.919	-0.949	51.434	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	220	ARG	1	0.873	0.938	45.898	0.003	0.003	0.000	0.000	0.000	0.000
96	B	221	GLU	-1	-0.927	-0.966	50.443	0.002	0.002	0.000	0.000	0.000	0.000
97	B	222	SER	0	-0.059	-0.056	52.680	0.000	0.000	0.000	0.000	0.000	0.000
98	B	223	GLN	0	-0.061	-0.031	55.211	0.000	0.000	0.000	0.000	0.000	0.000
99	B	224	ALA	0	0.012	0.009	54.908	0.000	0.000	0.000	0.000	0.000	0.000
100	B	225	TYR	0	-0.056	-0.031	56.440	0.000	0.000	0.000	0.000	0.000	0.000
101	B	226	TYR	0	-0.041	-0.012	58.171	0.001	0.001	0.000	0.000	0.000	0.000
102	B	227	GLN	0	-0.046	-0.007	58.339	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:126:GLY)