FMO DATABASE

FMODB ID: 6NL6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-671395.69599
FMO2-HF: Nuclear repulsion	627459.757075
FMO2-HF: Total energy	-43935.938915
FMO2-MP2: Total energy	-44058.58237

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.
-7.446	-1.009	4.719	-3.642	-7.515	-0.018

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 : -0.019 / q_NPA : -0.011

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	-0.014	-0.014	3.200	-2.350	-0.034	0.080	-1.245	-1.151	-0.002
4	A	128	TYR	0	-0.109	-0.075	2.464	-0.824	-0.166	1.983	-0.666	-1.976	-0.001
5	A	129	VAL	0	0.026	0.017	3.092	-1.664	-0.567	0.263	-0.551	-0.808	-0.005
6	A	130	LEU	0	-0.023	-0.006	5.135	0.001	0.001	0.000	0.000	0.000	0.000
7	A	131	GLY	0	-0.005	-0.008	6.654	0.102	0.102	0.000	0.000	0.000	0.000
8	A	132	SER	0	0.001	-0.006	10.114	0.007	0.007	0.000	0.000	0.000	0.000
9	A	133	ALA	0	-0.030	-0.017	13.106	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	134	MET	0	-0.033	-0.009	14.001	0.008	0.008	0.000	0.000	0.000	0.000
11	A	135	SER	0	0.003	0.002	17.577	0.007	0.007	0.000	0.000	0.000	0.000
12	A	136	ARG	1	0.867	0.926	16.694	0.113	0.113	0.000	0.000	0.000	0.000
13	A	137	PRO	0	0.029	0.010	18.606	0.008	0.008	0.000	0.000	0.000	0.000
14	A	138	ILE	0	0.016	0.024	21.642	0.004	0.004	0.000	0.000	0.000	0.000
15	A	139	ILE	0	-0.066	-0.031	21.297	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	140	HIS	0	0.001	0.008	25.881	0.006	0.006	0.000	0.000	0.000	0.000
17	A	141	PHE	0	-0.051	-0.031	23.330	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	142	GLY	0	0.006	0.013	29.109	0.004	0.004	0.000	0.000	0.000	0.000
19	A	143	SER	0	-0.077	-0.072	31.763	0.005	0.005	0.000	0.000	0.000	0.000
20	A	144	ASP	-1	-0.890	-0.953	32.273	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	145	TYR	0	0.008	0.008	28.863	0.000	0.000	0.000	0.000	0.000	0.000
22	A	146	GLU	-1	-0.831	-0.895	28.056	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	147	ASP	-1	-0.775	-0.885	28.019	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	148	ARG	1	0.798	0.864	29.203	0.048	0.048	0.000	0.000	0.000	0.000
25	A	149	TYR	0	-0.001	0.002	23.893	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	150	TYR	0	0.016	-0.019	21.154	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	151	ARG	1	0.865	0.916	25.130	0.051	0.051	0.000	0.000	0.000	0.000
28	A	152	GLU	-1	-0.786	-0.840	27.239	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	153	ASN	0	-0.006	-0.011	23.046	0.003	0.003	0.000	0.000	0.000	0.000
30	A	154	MET	0	0.002	0.016	21.254	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	155	HIS	0	-0.045	-0.021	19.677	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	156	ARG	1	0.862	0.932	18.530	0.075	0.075	0.000	0.000	0.000	0.000
33	A	157	TYR	0	0.015	0.022	15.825	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	158	PRO	0	0.040	0.032	11.316	0.012	0.012	0.000	0.000	0.000	0.000
35	A	159	ASN	0	-0.020	-0.017	13.201	0.001	0.001	0.000	0.000	0.000	0.000
36	A	160	GLN	0	0.017	0.013	9.154	0.039	0.039	0.000	0.000	0.000	0.000
37	A	161	VAL	0	0.029	0.007	9.104	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	162	TYR	0	0.038	0.017	2.465	-1.674	-0.247	1.036	-0.671	-1.792	-0.008
39	A	163	TYR	0	0.006	0.007	5.754	0.081	0.081	0.000	0.000	0.000	0.000
40	A	164	ARG	1	0.903	0.927	6.747	0.186	0.186	0.000	0.000	0.000	0.000
41	A	165	PRO	0	-0.025	-0.019	7.724	0.069	0.069	0.000	0.000	0.000	0.000
42	A	166	MET	0	-0.006	0.006	10.924	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	167	ASP	-1	-0.768	-0.852	14.479	-0.162	-0.162	0.000	0.000	0.000	0.000
44	A	168	GLU	-1	-0.879	-0.928	16.528	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	169	TYR	0	-0.070	-0.042	16.679	0.005	0.005	0.000	0.000	0.000	0.000
46	A	170	SER	0	-0.070	-0.047	14.610	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	171	ASN	0	-0.012	-0.005	16.305	0.015	0.015	0.000	0.000	0.000	0.000
48	A	172	GLN	0	0.029	0.001	16.813	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	173	ASN	0	0.036	0.018	16.853	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	174	ASN	0	0.038	0.008	14.268	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	175	PHE	0	0.026	0.027	12.449	-0.051	-0.051	0.000	0.000	0.000	0.000
52	A	176	VAL	0	0.006	-0.016	11.815	-0.046	-0.046	0.000	0.000	0.000	0.000
53	A	177	HIS	0	-0.042	-0.016	12.795	0.004	0.004	0.000	0.000	0.000	0.000
54	A	178	ASP	-1	-0.823	-0.885	8.304	-0.579	-0.579	0.000	0.000	0.000	0.000
55	A	179	CYS	0	-0.075	-0.035	8.188	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	180	VAL	0	0.026	0.018	8.809	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	181	ASN	0	0.016	0.007	10.103	0.034	0.034	0.000	0.000	0.000	0.000
58	A	182	ILE	0	-0.018	-0.008	3.509	-0.354	-0.001	0.022	-0.062	-0.313	0.000
59	A	183	THR	0	-0.008	-0.013	6.549	0.026	0.026	0.000	0.000	0.000	0.000
60	A	184	ILE	0	0.026	0.018	7.842	0.046	0.046	0.000	0.000	0.000	0.000
61	A	185	LYS	1	0.952	0.996	7.087	0.586	0.586	0.000	0.000	0.000	0.000
62	A	186	GLN	0	0.007	-0.004	2.278	-0.819	-0.233	1.335	-0.447	-1.475	-0.002
63	A	187	HIS	0	-0.004	-0.009	6.897	0.035	0.035	0.000	0.000	0.000	0.000
64	A	188	THR	0	-0.058	-0.044	10.228	0.038	0.038	0.000	0.000	0.000	0.000
65	A	189	VAL	0	-0.061	-0.024	7.568	0.019	0.019	0.000	0.000	0.000	0.000
66	A	190	THR	0	-0.048	-0.011	9.424	0.028	0.028	0.000	0.000	0.000	0.000
67	A	191	THR	0	-0.038	-0.017	11.250	0.007	0.007	0.000	0.000	0.000	0.000
68	A	192	THR	0	-0.046	-0.046	14.193	0.002	0.002	0.000	0.000	0.000	0.000
69	A	193	THR	0	-0.051	-0.065	17.314	0.002	0.002	0.000	0.000	0.000	0.000
70	A	194	LYS	1	0.958	0.952	21.089	0.038	0.038	0.000	0.000	0.000	0.000
71	A	195	GLY	0	0.021	0.029	23.473	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	196	GLU	-1	-0.779	-0.834	19.462	-0.044	-0.044	0.000	0.000	0.000	0.000
73	A	197	ASN	0	-0.039	-0.015	18.516	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	198	PHE	0	-0.034	-0.008	22.541	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	199	THR	0	-0.010	-0.028	26.310	0.002	0.002	0.000	0.000	0.000	0.000
76	A	200	GLU	-1	-0.790	-0.919	28.148	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	201	THR	0	-0.034	-0.035	30.921	0.003	0.003	0.000	0.000	0.000	0.000
78	A	202	ASP	-1	-0.833	-0.880	27.737	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	203	VAL	0	-0.013	-0.004	30.587	0.002	0.002	0.000	0.000	0.000	0.000
80	A	204	LYS	1	0.787	0.908	32.815	0.032	0.032	0.000	0.000	0.000	0.000
81	A	205	MET	0	-0.046	-0.016	33.625	0.001	0.001	0.000	0.000	0.000	0.000
82	A	206	MET	0	-0.025	-0.012	29.970	0.003	0.003	0.000	0.000	0.000	0.000
83	A	207	GLU	-1	-0.831	-0.930	34.491	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	208	ARG	1	0.975	0.997	37.417	0.028	0.028	0.000	0.000	0.000	0.000
85	A	209	VAL	0	-0.001	-0.003	36.632	0.001	0.001	0.000	0.000	0.000	0.000
86	A	210	VAL	0	0.022	-0.002	35.556	0.001	0.001	0.000	0.000	0.000	0.000
87	A	211	GLU	-1	-0.923	-0.941	38.724	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	212	GLN	0	0.026	0.007	41.982	0.000	0.000	0.000	0.000	0.000	0.000
89	A	213	MET	0	-0.043	-0.008	37.485	0.000	0.000	0.000	0.000	0.000	0.000
90	A	214	CYS	0	-0.038	-0.023	40.985	0.002	0.002	0.000	0.000	0.000	0.000
91	A	215	ILE	0	-0.019	-0.006	43.751	0.001	0.001	0.000	0.000	0.000	0.000
92	A	216	THR	0	-0.005	-0.014	45.351	0.001	0.001	0.000	0.000	0.000	0.000
93	A	217	GLN	0	-0.041	-0.029	43.772	0.000	0.000	0.000	0.000	0.000	0.000
94	A	218	TYR	0	-0.007	0.005	46.690	0.001	0.001	0.000	0.000	0.000	0.000
95	A	219	GLU	-1	-0.914	-0.952	49.198	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	220	ARG	1	0.837	0.912	46.801	0.012	0.012	0.000	0.000	0.000	0.000
97	A	221	GLU	-1	-0.865	-0.923	48.271	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	222	SER	0	-0.055	-0.043	51.298	0.001	0.001	0.000	0.000	0.000	0.000
99	A	223	GLN	0	-0.050	-0.031	53.471	0.001	0.001	0.000	0.000	0.000	0.000
100	A	224	ALA	0	-0.052	-0.009	54.207	0.000	0.000	0.000	0.000	0.000	0.000
101	A	225	TYR	0	-0.052	-0.015	55.974	0.001	0.001	0.000	0.000	0.000	0.000

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