FMO DATABASE

FMODB ID: 172JZ

Calculation Name: 3HAK-A-Xray372

Preferred Name: Prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HAK

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	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	-850311.169005
FMO2-HF: Nuclear repulsion	805372.737729
FMO2-HF: Total energy	-44938.431276
FMO2-MP2: Total energy	-45064.426515

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.
-4.643	-0.954	2.586	-2.176	-4.098	-0.004

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 : 0.028 / q_NPA : 0.002

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	-0.004	0.011	3.347	-1.732	1.160	-0.010	-1.504	-1.378	0.001
4	A	128	TYR	0	0.018	-0.003	5.064	-0.724	-0.696	-0.001	-0.007	-0.019	0.000
5	A	129	VAL	0	-0.010	-0.007	6.600	0.081	0.081	0.000	0.000	0.000	0.000
6	A	130	LEU	0	-0.016	-0.002	9.300	0.039	0.039	0.000	0.000	0.000	0.000
7	A	131	GLY	0	0.043	0.031	13.060	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	132	SER	0	-0.041	-0.008	14.770	0.046	0.046	0.000	0.000	0.000	0.000
9	A	133	ALA	0	0.012	0.000	18.093	0.008	0.008	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.045	-0.018	19.571	0.000	0.000	0.000	0.000	0.000	0.000
11	A	135	SER	0	0.027	0.021	23.988	0.010	0.010	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.850	0.896	26.316	0.070	0.070	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.013	0.030	26.346	0.003	0.003	0.000	0.000	0.000	0.000
14	A	138	ILE	0	0.022	-0.007	29.171	0.007	0.007	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.059	-0.020	27.789	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.065	0.040	31.903	0.007	0.007	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.063	-0.037	31.402	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.017	0.024	36.117	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.028	-0.046	38.989	0.003	0.003	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.851	-0.929	40.602	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	145	TYR	0	-0.055	-0.025	39.530	0.000	0.000	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.807	-0.890	36.802	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.775	-0.893	37.072	-0.050	-0.050	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.760	0.856	38.005	0.022	0.022	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.036	-0.047	33.862	0.001	0.001	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.064	0.012	29.856	0.000	0.000	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.851	0.924	34.151	0.035	0.035	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.767	-0.864	36.110	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.006	0.008	33.014	0.006	0.006	0.000	0.000	0.000	0.000
30	A	154	MET	0	-0.030	0.000	30.557	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.068	-0.037	29.334	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.837	0.901	29.134	0.013	0.013	0.000	0.000	0.000	0.000
33	A	157	TYR	0	0.005	-0.004	26.174	0.003	0.003	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.057	0.032	21.070	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.033	-0.023	22.748	0.006	0.006	0.000	0.000	0.000	0.000
36	A	160	GLN	0	-0.021	-0.019	16.958	0.015	0.015	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.024	0.006	15.877	0.024	0.024	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.023	0.010	11.463	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	163	TYR	0	-0.030	-0.041	9.790	0.035	0.035	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.877	0.918	6.810	0.051	0.051	0.000	0.000	0.000	0.000
41	A	165	PRO	0	0.041	0.023	4.572	-0.096	0.010	-0.001	-0.005	-0.100	0.000
42	A	166	MET	0	-0.001	0.001	2.795	-1.733	-1.070	2.598	-0.660	-2.601	-0.005
43	A	167	ASP	-1	-0.801	-0.884	5.638	-0.250	-0.250	0.000	0.000	0.000	0.000
44	A	168	GLH	0	-0.062	-0.058	8.494	0.135	0.135	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.052	-0.007	5.008	0.104	0.104	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.064	-0.050	9.472	0.132	0.132	0.000	0.000	0.000	0.000
47	A	171	ASN	0	0.011	0.004	12.336	0.000	0.000	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.071	0.031	15.114	0.000	0.000	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.033	0.009	16.921	0.003	0.003	0.000	0.000	0.000	0.000
50	A	174	ASN	0	-0.046	-0.010	12.666	0.054	0.054	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.014	0.016	10.697	0.019	0.019	0.000	0.000	0.000	0.000
52	A	176	VAL	0	-0.003	-0.001	13.828	0.008	0.008	0.000	0.000	0.000	0.000
53	A	177	HIS	0	0.008	-0.010	17.255	0.027	0.027	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.871	-0.922	12.980	-0.053	-0.053	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.079	-0.028	14.395	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.016	0.021	15.567	0.028	0.028	0.000	0.000	0.000	0.000
57	A	181	ASN	0	-0.006	-0.001	17.326	0.050	0.050	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.005	-0.002	12.206	0.034	0.034	0.000	0.000	0.000	0.000
59	A	183	THR	0	0.003	-0.006	15.514	0.011	0.011	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.028	0.016	17.388	0.017	0.017	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.870	0.948	18.010	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	186	GLN	0	0.030	0.013	14.444	0.042	0.042	0.000	0.000	0.000	0.000
63	A	187	HIS	0	-0.008	-0.004	18.018	0.002	0.002	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.007	-0.012	21.124	0.002	0.002	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.004	0.018	19.774	0.003	0.003	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.021	-0.016	20.190	0.002	0.002	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.022	-0.028	22.609	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	192	THR	0	-0.019	-0.024	25.347	0.001	0.001	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.071	-0.039	23.780	0.006	0.006	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.758	0.876	26.303	0.006	0.006	0.000	0.000	0.000	0.000
71	A	195	GLY	0	-0.008	0.007	28.987	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.871	-0.912	29.775	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.004	-0.016	29.668	0.010	0.010	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.023	-0.022	25.304	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	199	THR	0	0.014	-0.005	30.400	0.005	0.005	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.797	-0.908	31.496	0.002	0.002	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.005	0.006	32.393	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.719	-0.798	30.011	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.027	0.003	26.486	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.913	0.950	27.662	0.002	0.002	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.062	-0.008	29.688	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.039	-0.014	24.779	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.899	-0.965	24.684	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.858	0.924	25.322	0.053	0.053	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.006	0.001	25.498	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	210	VAL	0	-0.011	-0.022	20.263	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.823	-0.911	21.239	-0.127	-0.127	0.000	0.000	0.000	0.000
88	A	212	GLN	0	0.006	0.005	21.505	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.045	0.003	21.009	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	215	ILE	0	0.012	0.014	17.359	-0.042	-0.042	0.000	0.000	0.000	0.000
91	A	216	THR	0	-0.008	-0.015	19.127	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	217	GLN	0	-0.065	-0.040	13.713	0.039	0.039	0.000	0.000	0.000	0.000
93	A	218	TYR	0	0.038	0.008	13.663	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	219	GLU	-1	-0.922	-0.967	15.764	-0.226	-0.226	0.000	0.000	0.000	0.000
95	A	220	ARG	1	0.900	0.945	17.021	0.236	0.236	0.000	0.000	0.000	0.000
96	A	221	GLU	-1	-0.797	-0.853	10.675	-0.723	-0.723	0.000	0.000	0.000	0.000
97	A	222	SER	0	-0.010	-0.008	14.015	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	223	GLN	0	-0.024	-0.016	15.860	0.018	0.018	0.000	0.000	0.000	0.000
99	A	224	ALA	0	-0.030	-0.018	14.385	0.015	0.015	0.000	0.000	0.000	0.000
100	A	225	TYR	0	-0.051	-0.021	10.388	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	226	TYR	0	-0.031	-0.014	14.332	0.005	0.005	0.000	0.000	0.000	0.000
102	A	227	GLN	0	-0.064	-0.012	17.863	0.040	0.040	0.000	0.000	0.000	0.000

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