FMO DATABASE

FMODB ID: 94NG2

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	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	-676946.309149
FMO2-HF: Nuclear repulsion	632371.295094
FMO2-HF: Total energy	-44575.014055
FMO2-MP2: Total energy	-44699.524033

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.
0.667	3.91	0.254	-1.381	-2.115	-0.001

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 : 0.038 / 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	-0.095	-0.061	2.595	-2.089	0.847	0.257	-1.265	-1.929	-0.001
4	B	129	VAL	0	0.006	-0.010	4.467	1.637	1.711	-0.001	-0.013	-0.059	0.000
5	B	130	LEU	0	-0.034	-0.009	6.911	-0.313	-0.313	0.000	0.000	0.000	0.000
6	B	131	GLY	0	-0.019	0.002	8.955	0.053	0.053	0.000	0.000	0.000	0.000
7	B	132	SER	0	0.023	0.001	12.476	0.016	0.016	0.000	0.000	0.000	0.000
8	B	133	ALA	0	-0.040	-0.023	15.744	-0.028	-0.028	0.000	0.000	0.000	0.000
9	B	134	MET	0	-0.005	0.006	16.021	-0.001	-0.001	0.000	0.000	0.000	0.000
10	B	135	SER	0	-0.014	-0.011	19.795	0.004	0.004	0.000	0.000	0.000	0.000
11	B	136	ARG	1	0.884	0.936	19.691	0.008	0.008	0.000	0.000	0.000	0.000
12	B	137	PRO	0	0.001	0.014	22.841	0.006	0.006	0.000	0.000	0.000	0.000
13	B	138	ILE	0	0.021	0.007	25.858	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	139	ILE	0	-0.050	-0.018	24.616	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	140	HIS	0	0.004	0.010	29.235	0.000	0.000	0.000	0.000	0.000	0.000
16	B	141	PHE	0	-0.018	-0.016	26.265	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	142	GLY	0	0.003	0.001	32.082	0.003	0.003	0.000	0.000	0.000	0.000
18	B	143	SER	0	-0.050	-0.057	34.579	0.004	0.004	0.000	0.000	0.000	0.000
19	B	144	ASP	-1	-0.842	-0.933	35.612	-0.027	-0.027	0.000	0.000	0.000	0.000
20	B	145	TYR	0	-0.053	-0.026	31.187	0.003	0.003	0.000	0.000	0.000	0.000
21	B	146	GLU	-1	-0.855	-0.905	30.763	-0.052	-0.052	0.000	0.000	0.000	0.000
22	B	147	ASP	-1	-0.812	-0.901	31.114	-0.035	-0.035	0.000	0.000	0.000	0.000
23	B	148	ARG	1	0.761	0.836	32.459	0.022	0.022	0.000	0.000	0.000	0.000
24	B	149	TYR	0	0.004	0.022	26.470	0.000	0.000	0.000	0.000	0.000	0.000
25	B	150	TYR	0	0.027	-0.001	24.316	0.000	0.000	0.000	0.000	0.000	0.000
26	B	151	ARG	1	0.937	0.971	28.125	0.023	0.023	0.000	0.000	0.000	0.000
27	B	152	GLU	-1	-0.806	-0.874	30.105	-0.016	-0.016	0.000	0.000	0.000	0.000
28	B	153	ASN	0	-0.018	-0.017	25.734	0.002	0.002	0.000	0.000	0.000	0.000
29	B	154	MET	0	0.022	0.024	24.354	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	155	HIS	0	-0.089	-0.043	22.839	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	156	ARG	1	0.888	0.930	21.590	0.040	0.040	0.000	0.000	0.000	0.000
32	B	157	TYR	0	-0.004	0.007	18.596	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	158	PRO	0	0.016	0.018	14.170	0.019	0.019	0.000	0.000	0.000	0.000
34	B	159	ASN	0	0.018	0.001	16.314	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	160	GLN	0	0.023	0.013	13.378	0.013	0.013	0.000	0.000	0.000	0.000
36	B	161	VAL	0	0.001	0.007	11.020	-0.016	-0.016	0.000	0.000	0.000	0.000
37	B	162	TYR	0	0.026	0.012	5.093	-0.016	-0.016	0.000	0.000	0.000	0.000
38	B	163	TYR	0	0.003	-0.012	7.805	-0.171	-0.171	0.000	0.000	0.000	0.000
39	B	164	ARG	1	0.975	0.989	4.294	2.511	2.673	-0.001	-0.093	-0.067	0.000
40	B	165	PRO	0	-0.014	-0.011	8.128	0.027	0.027	0.000	0.000	0.000	0.000
41	B	166	MET	0	-0.041	-0.024	11.311	-0.057	-0.057	0.000	0.000	0.000	0.000
42	B	167	ASP	-1	-0.923	-0.931	12.005	-0.185	-0.185	0.000	0.000	0.000	0.000
43	B	168	GLU	-1	-0.945	-1.007	15.179	-0.093	-0.093	0.000	0.000	0.000	0.000
44	B	169	TYR	0	-0.002	0.000	15.563	-0.008	-0.008	0.000	0.000	0.000	0.000
45	B	170	SER	0	-0.061	-0.004	13.213	-0.012	-0.012	0.000	0.000	0.000	0.000
46	B	171	ASN	0	0.037	0.021	16.377	0.034	0.034	0.000	0.000	0.000	0.000
47	B	172	GLN	0	0.076	0.013	17.624	-0.019	-0.019	0.000	0.000	0.000	0.000
48	B	173	ASN	0	0.036	0.025	17.259	-0.029	-0.029	0.000	0.000	0.000	0.000
49	B	174	ASN	0	0.018	0.001	15.127	-0.006	-0.006	0.000	0.000	0.000	0.000
50	B	175	PHE	0	0.048	0.033	12.394	-0.075	-0.075	0.000	0.000	0.000	0.000
51	B	176	VAL	0	-0.010	-0.015	13.081	-0.047	-0.047	0.000	0.000	0.000	0.000
52	B	177	HIS	0	0.000	0.004	14.568	-0.032	-0.032	0.000	0.000	0.000	0.000
53	B	178	ASP	-1	-0.840	-0.895	8.975	-1.009	-1.009	0.000	0.000	0.000	0.000
54	B	179	CYS	0	-0.008	-0.028	9.738	-0.054	-0.054	0.000	0.000	0.000	0.000
55	B	180	VAL	0	-0.035	-0.009	10.628	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	181	ASN	0	-0.047	-0.018	10.547	0.016	0.016	0.000	0.000	0.000	0.000
57	B	182	ILE	0	-0.021	0.002	4.235	-0.049	0.022	-0.001	-0.010	-0.060	0.000
58	B	183	THR	0	0.045	0.004	8.658	0.099	0.099	0.000	0.000	0.000	0.000
59	B	184	ILE	0	0.058	0.031	9.996	0.064	0.064	0.000	0.000	0.000	0.000
60	B	185	LYS	1	0.941	0.994	10.073	0.462	0.462	0.000	0.000	0.000	0.000
61	B	186	GLN	0	-0.024	-0.002	6.872	-0.142	-0.142	0.000	0.000	0.000	0.000
62	B	187	HIS	0	-0.013	-0.005	9.378	0.077	0.077	0.000	0.000	0.000	0.000
63	B	188	THR	0	-0.059	-0.059	12.756	0.036	0.036	0.000	0.000	0.000	0.000
64	B	189	VAL	0	-0.034	-0.012	10.250	0.024	0.024	0.000	0.000	0.000	0.000
65	B	190	THR	0	-0.043	-0.009	12.484	0.041	0.041	0.000	0.000	0.000	0.000
66	B	191	THR	0	-0.048	-0.021	14.061	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	192	THR	0	-0.024	-0.032	17.241	0.010	0.010	0.000	0.000	0.000	0.000
68	B	193	THR	0	-0.034	-0.021	20.261	0.001	0.001	0.000	0.000	0.000	0.000
69	B	194	LYS	1	0.974	0.972	23.984	0.016	0.016	0.000	0.000	0.000	0.000
70	B	195	GLY	0	0.028	0.013	26.453	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	196	GLU	-1	-0.824	-0.889	22.307	0.025	0.025	0.000	0.000	0.000	0.000
72	B	197	ASN	0	-0.023	-0.009	21.682	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	198	PHE	0	-0.081	-0.023	25.489	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	199	THR	0	0.022	0.002	28.517	0.004	0.004	0.000	0.000	0.000	0.000
75	B	200	GLU	-1	-0.906	-0.976	30.704	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	201	THR	0	-0.039	-0.012	33.543	0.001	0.001	0.000	0.000	0.000	0.000
77	B	202	ASP	-1	-0.799	-0.900	30.880	-0.021	-0.021	0.000	0.000	0.000	0.000
78	B	203	VAL	0	0.003	0.015	33.214	0.001	0.001	0.000	0.000	0.000	0.000
79	B	204	LYS	1	1.008	1.013	35.508	0.007	0.007	0.000	0.000	0.000	0.000
80	B	205	MET	0	-0.085	-0.040	36.332	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	206	MET	0	-0.027	-0.036	32.199	0.000	0.000	0.000	0.000	0.000	0.000
82	B	207	GLU	-1	-0.906	-0.936	37.566	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	208	ARG	1	0.978	0.985	40.218	0.012	0.012	0.000	0.000	0.000	0.000
84	B	209	VAL	0	-0.024	-0.015	38.336	0.000	0.000	0.000	0.000	0.000	0.000
85	B	210	VAL	0	0.006	-0.025	38.168	0.000	0.000	0.000	0.000	0.000	0.000
86	B	211	GLU	-1	-0.878	-0.917	41.237	-0.006	-0.006	0.000	0.000	0.000	0.000
87	B	212	GLN	0	-0.034	-0.026	44.525	0.000	0.000	0.000	0.000	0.000	0.000
88	B	213	MET	0	-0.039	-0.016	38.866	0.000	0.000	0.000	0.000	0.000	0.000
89	B	214	CYS	0	-0.050	-0.023	43.275	0.001	0.001	0.000	0.000	0.000	0.000
90	B	215	ILE	0	0.016	0.016	45.826	0.001	0.001	0.000	0.000	0.000	0.000
91	B	216	THR	0	-0.013	-0.012	46.807	0.000	0.000	0.000	0.000	0.000	0.000
92	B	217	GLN	0	0.001	0.009	44.008	0.000	0.000	0.000	0.000	0.000	0.000
93	B	218	TYR	0	0.040	0.029	48.155	0.001	0.001	0.000	0.000	0.000	0.000
94	B	219	GLU	-1	-0.922	-0.946	51.209	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	220	ARG	1	0.865	0.926	45.268	0.009	0.009	0.000	0.000	0.000	0.000
96	B	221	GLU	-1	-0.943	-0.976	50.099	-0.002	-0.002	0.000	0.000	0.000	0.000
97	B	222	SER	0	-0.051	-0.058	52.252	0.000	0.000	0.000	0.000	0.000	0.000
98	B	223	GLN	0	-0.052	-0.017	55.233	0.000	0.000	0.000	0.000	0.000	0.000
99	B	224	ALA	0	-0.005	-0.007	54.827	0.000	0.000	0.000	0.000	0.000	0.000
100	B	225	TYR	0	-0.064	-0.018	56.172	0.001	0.001	0.000	0.000	0.000	0.000
101	B	226	TYR	0	-0.059	-0.020	57.855	0.001	0.001	0.000	0.000	0.000	0.000
102	B	227	GLN	0	-0.008	0.006	58.449	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)