FMO DATABASE

FMODB ID: LZMJ9

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	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	-676975.536313
FMO2-HF: Nuclear repulsion	632401.225534
FMO2-HF: Total energy	-44574.310779
FMO2-MP2: Total energy	-44698.897403

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.
0.333	3.407	0.467	-1.41	-2.131	0

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 : 0.027 / q_NPA : 0.006

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].
3	B	128	TYR	0	-0.071	-0.035	2.352	-2.254	0.614	0.470	-1.360	-1.979
4	B	129	VAL	0	0.020	-0.003	4.572	1.706	1.774	-0.001	-0.011	-0.056
5	B	130	LEU	0	-0.029	-0.012	7.004	-0.327	-0.327	0.000	0.000	0.000
6	B	131	GLY	0	-0.016	0.006	9.013	0.038	0.038	0.000	0.000	0.000
7	B	132	SER	0	-0.006	-0.012	12.543	0.009	0.009	0.000	0.000	0.000
8	B	133	ALA	0	-0.015	-0.010	15.801	-0.025	-0.025	0.000	0.000	0.000
9	B	134	MET	0	0.001	0.007	16.719	-0.001	-0.001	0.000	0.000	0.000
10	B	135	SER	0	-0.018	-0.013	19.832	0.001	0.001	0.000	0.000	0.000
11	B	136	ARG	1	0.872	0.935	19.468	-0.006	-0.006	0.000	0.000	0.000
12	B	137	PRO	0	0.002	0.016	22.780	0.005	0.005	0.000	0.000	0.000
13	B	138	ILE	0	0.027	-0.003	25.871	-0.001	-0.001	0.000	0.000	0.000
14	B	139	ILE	0	-0.044	-0.016	24.682	-0.001	-0.001	0.000	0.000	0.000
15	B	140	HIS	0	-0.022	-0.002	29.234	0.000	0.000	0.000	0.000	0.000
16	B	141	PHE	0	-0.018	-0.022	26.383	-0.004	-0.004	0.000	0.000	0.000
17	B	142	GLY	0	0.010	0.005	32.065	0.002	0.002	0.000	0.000	0.000
18	B	143	SER	0	-0.023	-0.006	34.475	0.003	0.003	0.000	0.000	0.000
19	B	144	ASP	-1	-0.818	-0.920	35.584	-0.021	-0.021	0.000	0.000	0.000
20	B	145	TYR	0	-0.069	-0.037	31.319	0.003	0.003	0.000	0.000	0.000
21	B	146	GLU	-1	-0.888	-0.957	30.463	-0.044	-0.044	0.000	0.000	0.000
22	B	147	ASP	-1	-0.801	-0.887	31.083	-0.028	-0.028	0.000	0.000	0.000
23	B	148	ARG	1	0.792	0.872	32.434	0.017	0.017	0.000	0.000	0.000
24	B	149	TYR	0	0.003	0.021	26.401	0.001	0.001	0.000	0.000	0.000
25	B	150	TYR	0	0.020	0.008	24.213	0.000	0.000	0.000	0.000	0.000
26	B	151	ARG	1	0.958	0.972	28.099	0.015	0.015	0.000	0.000	0.000
27	B	152	GLU	-1	-0.829	-0.904	30.082	-0.009	-0.009	0.000	0.000	0.000
28	B	153	ASN	0	-0.010	-0.010	25.622	0.003	0.003	0.000	0.000	0.000
29	B	154	MET	0	0.010	0.018	24.346	-0.001	-0.001	0.000	0.000	0.000
30	B	155	HIS	0	-0.082	-0.040	22.818	0.000	0.000	0.000	0.000	0.000
31	B	156	ARG	1	0.935	0.963	21.567	0.035	0.035	0.000	0.000	0.000
32	B	157	TYR	0	-0.002	0.005	18.552	-0.007	-0.007	0.000	0.000	0.000
33	B	158	PRO	0	0.016	0.021	14.306	0.018	0.018	0.000	0.000	0.000
34	B	159	ASN	0	0.007	-0.008	16.297	-0.004	-0.004	0.000	0.000	0.000
35	B	160	GLN	0	0.035	0.020	12.900	0.006	0.006	0.000	0.000	0.000
36	B	161	VAL	0	0.027	0.024	11.011	-0.019	-0.019	0.000	0.000	0.000
37	B	162	TYR	0	0.000	0.010	5.420	-0.029	-0.029	0.000	0.000	0.000
38	B	163	TYR	0	0.026	0.003	7.897	-0.163	-0.163	0.000	0.000	0.000
39	B	164	ARG	1	1.001	1.009	4.622	2.181	2.248	-0.001	-0.028	-0.037
40	B	165	PRO	0	-0.025	-0.020	8.199	-0.008	-0.008	0.000	0.000	0.000
41	B	166	MET	0	-0.053	-0.021	11.412	-0.062	-0.062	0.000	0.000	0.000
42	B	167	ASP	-1	-0.910	-0.922	12.226	-0.109	-0.109	0.000	0.000	0.000
43	B	168	GLU	-1	-0.922	-1.007	15.179	-0.073	-0.073	0.000	0.000	0.000
44	B	169	TYR	0	-0.024	-0.008	15.621	-0.008	-0.008	0.000	0.000	0.000
45	B	170	SER	0	-0.046	-0.002	13.329	-0.017	-0.017	0.000	0.000	0.000
46	B	171	ASN	0	0.043	0.026	16.373	0.035	0.035	0.000	0.000	0.000
47	B	172	GLN	0	0.070	0.014	17.673	-0.016	-0.016	0.000	0.000	0.000
48	B	173	ASN	0	0.047	0.025	17.299	-0.024	-0.024	0.000	0.000	0.000
49	B	174	ASN	0	-0.002	-0.008	15.140	-0.018	-0.018	0.000	0.000	0.000
50	B	175	PHE	0	0.034	0.029	12.185	-0.068	-0.068	0.000	0.000	0.000
51	B	176	VAL	0	-0.005	-0.009	13.111	-0.041	-0.041	0.000	0.000	0.000
52	B	177	HIS	0	-0.010	-0.001	14.579	-0.029	-0.029	0.000	0.000	0.000
53	B	178	ASP	-1	-0.865	-0.932	9.043	-0.915	-0.915	0.000	0.000	0.000
54	B	179	CYS	0	-0.039	-0.035	9.786	-0.041	-0.041	0.000	0.000	0.000
55	B	180	VAL	0	-0.007	0.010	10.628	0.001	0.001	0.000	0.000	0.000
56	B	181	ASN	0	-0.025	-0.010	10.416	0.029	0.029	0.000	0.000	0.000
57	B	182	ILE	0	-0.014	0.006	4.296	-0.062	0.009	-0.001	-0.011	-0.059
58	B	183	THR	0	0.025	-0.025	8.612	0.092	0.092	0.000	0.000	0.000
59	B	184	ILE	0	0.041	0.022	9.967	0.058	0.058	0.000	0.000	0.000
60	B	185	LYS	1	0.945	0.988	9.914	0.445	0.445	0.000	0.000	0.000
61	B	186	GLN	0	-0.023	-0.002	7.129	-0.138	-0.138	0.000	0.000	0.000
62	B	187	HIS	0	-0.031	-0.004	9.303	0.069	0.069	0.000	0.000	0.000
63	B	188	THR	0	-0.055	-0.046	12.693	0.032	0.032	0.000	0.000	0.000
64	B	189	VAL	0	-0.030	-0.009	10.376	0.021	0.021	0.000	0.000	0.000
65	B	190	THR	0	-0.049	-0.026	13.040	0.029	0.029	0.000	0.000	0.000
66	B	191	THR	0	-0.040	-0.016	14.123	-0.003	-0.003	0.000	0.000	0.000
67	B	192	THR	0	0.018	0.019	17.292	0.011	0.011	0.000	0.000	0.000
68	B	193	THR	0	-0.021	-0.022	20.312	0.001	0.001	0.000	0.000	0.000
69	B	194	LYS	1	0.964	0.967	24.036	0.019	0.019	0.000	0.000	0.000
70	B	195	GLY	0	0.022	0.002	26.517	-0.002	-0.002	0.000	0.000	0.000
71	B	196	GLU	-1	-0.880	-0.934	22.091	0.027	0.027	0.000	0.000	0.000
72	B	197	ASN	0	-0.026	-0.020	21.621	0.003	0.003	0.000	0.000	0.000
73	B	198	PHE	0	-0.109	-0.040	25.428	-0.004	-0.004	0.000	0.000	0.000
74	B	199	THR	0	0.025	0.012	28.461	0.004	0.004	0.000	0.000	0.000
75	B	200	GLU	-1	-0.898	-0.975	30.654	0.001	0.001	0.000	0.000	0.000
76	B	201	THR	0	-0.052	-0.019	33.538	0.001	0.001	0.000	0.000	0.000
77	B	202	ASP	-1	-0.815	-0.911	30.795	-0.018	-0.018	0.000	0.000	0.000
78	B	203	VAL	0	0.004	0.015	33.298	0.000	0.000	0.000	0.000	0.000
79	B	204	LYS	1	1.019	1.016	35.446	0.006	0.006	0.000	0.000	0.000
80	B	205	MET	0	-0.108	-0.046	36.239	-0.001	-0.001	0.000	0.000	0.000
81	B	206	MET	0	-0.026	-0.042	32.460	-0.001	-0.001	0.000	0.000	0.000
82	B	207	GLU	-1	-0.888	-0.923	37.517	-0.002	-0.002	0.000	0.000	0.000
83	B	208	ARG	1	0.979	0.985	40.229	0.010	0.010	0.000	0.000	0.000
84	B	209	VAL	0	-0.053	-0.024	37.967	0.000	0.000	0.000	0.000	0.000
85	B	210	VAL	0	0.013	-0.026	38.317	0.000	0.000	0.000	0.000	0.000
86	B	211	GLU	-1	-0.918	-0.938	41.311	-0.004	-0.004	0.000	0.000	0.000
87	B	212	GLN	0	0.008	0.002	44.448	0.000	0.000	0.000	0.000	0.000
88	B	213	MET	0	-0.025	-0.012	39.283	0.000	0.000	0.000	0.000	0.000
89	B	214	CYS	0	-0.067	-0.031	43.352	0.000	0.000	0.000	0.000	0.000
90	B	215	ILE	0	0.011	0.017	45.896	0.001	0.001	0.000	0.000	0.000
91	B	216	THR	0	-0.013	-0.013	46.955	0.000	0.000	0.000	0.000	0.000
92	B	217	GLN	0	-0.046	-0.029	45.306	0.000	0.000	0.000	0.000	0.000
93	B	218	TYR	0	0.057	0.039	48.225	0.001	0.001	0.000	0.000	0.000
94	B	219	GLU	-1	-0.895	-0.940	51.276	-0.006	-0.006	0.000	0.000	0.000
95	B	220	ARG	1	0.876	0.950	45.241	0.010	0.010	0.000	0.000	0.000
96	B	221	GLU	-1	-0.944	-0.979	50.058	-0.004	-0.004	0.000	0.000	0.000
97	B	222	SER	0	-0.044	-0.057	52.317	0.000	0.000	0.000	0.000	0.000
98	B	223	GLN	0	-0.051	-0.014	55.450	0.000	0.000	0.000	0.000	0.000
99	B	224	ALA	0	0.010	-0.008	54.922	0.000	0.000	0.000	0.000	0.000
100	B	225	TYR	0	-0.079	-0.022	56.252	0.001	0.001	0.000	0.000	0.000
101	B	226	TYR	0	-0.064	-0.022	57.916	0.001	0.001	0.000	0.000	0.000
102	B	227	GLN	0	-0.007	0.009	58.398	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)