FMO DATABASE

FMODB ID: 7238K

Calculation Name: 5DFV-A-Xray372

Preferred Name: CD81 antigen

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DFV

Chain ID: A

ChEMBL ID: CHEMBL1075180

UniProt ID: P60033

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601828.651915
FMO2-HF: Nuclear repulsion	566504.356625
FMO2-HF: Total energy	-35324.295291
FMO2-MP2: Total energy	-35425.632585

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:113:PHE)

Summations of interaction energy for fragment #1(A:113:PHE)

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.
-0.341	1.101	0.001	-0.619	-0.825	0.002

Interaction energy analysis for fragmet #1(A:113:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.015

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	115	ASN	0	0.018	0.006	3.744	-1.484	-0.042	0.001	-0.619	-0.825	0.002
4	A	116	LYS	1	0.890	0.947	5.555	1.038	1.038	0.000	0.000	0.000	0.000
5	A	117	ASP	-1	-0.768	-0.886	7.351	-0.422	-0.422	0.000	0.000	0.000	0.000
6	A	118	GLN	0	-0.070	-0.010	9.600	0.082	0.082	0.000	0.000	0.000	0.000
7	A	119	ILE	0	0.075	0.039	8.387	0.117	0.117	0.000	0.000	0.000	0.000
8	A	120	ALA	0	0.002	0.005	11.322	0.090	0.090	0.000	0.000	0.000	0.000
9	A	121	LYS	1	0.809	0.882	13.188	0.481	0.481	0.000	0.000	0.000	0.000
10	A	122	ASP	-1	-0.821	-0.905	13.873	-0.167	-0.167	0.000	0.000	0.000	0.000
11	A	123	VAL	0	-0.010	-0.016	14.539	0.040	0.040	0.000	0.000	0.000	0.000
12	A	124	LYS	1	0.744	0.871	16.541	0.264	0.264	0.000	0.000	0.000	0.000
13	A	125	GLN	0	0.002	0.001	19.043	0.007	0.007	0.000	0.000	0.000	0.000
14	A	126	PHE	0	-0.033	-0.018	19.777	0.019	0.019	0.000	0.000	0.000	0.000
15	A	127	TYR	0	0.008	-0.023	21.226	0.010	0.010	0.000	0.000	0.000	0.000
16	A	128	ASP	-1	-0.772	-0.861	23.155	-0.095	-0.095	0.000	0.000	0.000	0.000
17	A	129	GLN	0	0.022	0.019	23.566	0.003	0.003	0.000	0.000	0.000	0.000
18	A	130	ALA	0	0.012	0.012	25.607	0.008	0.008	0.000	0.000	0.000	0.000
19	A	131	LEU	0	-0.025	-0.023	27.175	0.005	0.005	0.000	0.000	0.000	0.000
20	A	132	GLN	0	-0.029	-0.022	28.789	0.004	0.004	0.000	0.000	0.000	0.000
21	A	133	GLN	0	-0.050	-0.035	30.253	0.002	0.002	0.000	0.000	0.000	0.000
22	A	134	ALA	0	-0.018	-0.007	31.405	0.004	0.004	0.000	0.000	0.000	0.000
23	A	135	VAL	0	-0.062	-0.043	33.099	0.002	0.002	0.000	0.000	0.000	0.000
24	A	136	VAL	0	-0.059	-0.023	33.987	0.001	0.001	0.000	0.000	0.000	0.000
25	A	137	ASP	-1	-0.818	-0.898	34.840	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	138	ASP	-1	-0.929	-0.948	37.069	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	139	ASP	-1	-0.923	-0.979	37.437	0.000	0.000	0.000	0.000	0.000	0.000
28	A	140	ALA	0	0.109	0.075	32.704	0.003	0.003	0.000	0.000	0.000	0.000
29	A	141	ASN	0	-0.112	-0.096	33.504	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	142	ASN	0	-0.017	-0.009	27.683	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	143	ALA	0	0.032	0.030	29.023	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	144	LYS	1	0.901	0.956	29.746	0.009	0.009	0.000	0.000	0.000	0.000
33	A	145	ALA	0	-0.020	-0.001	30.749	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	146	VAL	0	0.009	0.015	24.597	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	147	VAL	0	0.014	0.010	26.461	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	148	LYS	1	0.953	0.989	28.036	0.013	0.013	0.000	0.000	0.000	0.000
37	A	149	THR	0	-0.015	-0.012	24.710	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	150	PHE	0	-0.006	-0.007	20.036	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	151	HIS	0	0.008	-0.004	24.750	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	152	GLU	-1	-0.859	-0.940	27.638	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	153	THR	0	-0.086	-0.052	22.059	0.000	0.000	0.000	0.000	0.000	0.000
42	A	154	LEU	0	-0.048	-0.026	19.872	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	155	ASP	-1	-0.873	-0.913	23.715	-0.076	-0.076	0.000	0.000	0.000	0.000
44	A	156	CYS	0	-0.027	-0.001	22.869	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	157	CYS	0	-0.023	0.004	27.614	0.004	0.004	0.000	0.000	0.000	0.000
46	A	158	GLY	0	0.080	0.021	28.154	0.004	0.004	0.000	0.000	0.000	0.000
47	A	159	SER	0	-0.003	-0.005	25.984	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	160	SER	0	-0.050	-0.062	25.530	0.006	0.006	0.000	0.000	0.000	0.000
49	A	161	THR	0	-0.016	-0.010	25.782	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	162	LEU	0	-0.024	-0.002	27.689	0.006	0.006	0.000	0.000	0.000	0.000
51	A	163	THR	0	0.027	0.014	30.701	0.006	0.006	0.000	0.000	0.000	0.000
52	A	164	ALA	0	0.021	0.013	33.051	0.003	0.003	0.000	0.000	0.000	0.000
53	A	165	LEU	0	0.050	0.030	32.144	0.003	0.003	0.000	0.000	0.000	0.000
54	A	166	THR	0	0.028	0.014	31.420	0.004	0.004	0.000	0.000	0.000	0.000
55	A	167	THR	0	-0.031	-0.013	33.373	0.002	0.002	0.000	0.000	0.000	0.000
56	A	168	SER	0	-0.056	-0.043	36.651	0.003	0.003	0.000	0.000	0.000	0.000
57	A	169	VAL	0	0.030	0.021	31.804	0.003	0.003	0.000	0.000	0.000	0.000
58	A	170	LEU	0	0.011	-0.002	35.286	0.002	0.002	0.000	0.000	0.000	0.000
59	A	171	LYS	1	0.918	0.951	36.312	0.033	0.033	0.000	0.000	0.000	0.000
60	A	172	ASN	0	-0.048	-0.020	37.410	0.004	0.004	0.000	0.000	0.000	0.000
61	A	173	ASN	0	-0.063	-0.027	38.124	0.001	0.001	0.000	0.000	0.000	0.000
62	A	174	LEU	0	-0.026	-0.010	33.033	0.002	0.002	0.000	0.000	0.000	0.000
63	A	176	PRO	0	0.083	0.063	30.309	0.004	0.004	0.000	0.000	0.000	0.000
64	A	177	SER	0	-0.016	-0.018	33.224	0.000	0.000	0.000	0.000	0.000	0.000
65	A	178	GLY	0	0.010	0.018	36.813	0.000	0.000	0.000	0.000	0.000	0.000
66	A	179	SER	0	-0.051	-0.020	38.577	0.001	0.001	0.000	0.000	0.000	0.000
67	A	180	ASN	0	-0.048	-0.024	33.754	0.002	0.002	0.000	0.000	0.000	0.000
68	A	181	ILE	0	-0.024	-0.033	37.620	0.002	0.002	0.000	0.000	0.000	0.000
69	A	182	ILE	0	0.029	0.007	37.713	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	183	SER	0	0.002	0.003	36.077	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	184	ASN	0	-0.041	-0.029	34.854	0.002	0.002	0.000	0.000	0.000	0.000
72	A	185	LEU	0	0.084	0.034	32.780	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	186	PHE	0	-0.024	0.001	31.038	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.838	0.915	29.779	0.052	0.052	0.000	0.000	0.000	0.000
75	A	188	GLU	-1	-0.792	-0.882	28.557	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	189	ASP	-1	-0.751	-0.845	25.089	-0.113	-0.113	0.000	0.000	0.000	0.000
77	A	191	HIS	1	0.743	0.840	20.677	0.108	0.108	0.000	0.000	0.000	0.000
78	A	192	GLN	0	0.020	0.008	19.539	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	193	LYS	1	0.860	0.916	19.643	0.076	0.076	0.000	0.000	0.000	0.000
80	A	194	ILE	0	0.006	0.003	16.101	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	195	ASP	-1	-0.796	-0.881	15.266	-0.290	-0.290	0.000	0.000	0.000	0.000
82	A	196	ASP	-1	-0.845	-0.921	15.081	-0.181	-0.181	0.000	0.000	0.000	0.000
83	A	197	LEU	0	-0.048	-0.007	14.843	0.001	0.001	0.000	0.000	0.000	0.000
84	A	198	PHE	0	-0.005	-0.015	10.591	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	199	SER	0	-0.052	-0.041	10.683	-0.081	-0.081	0.000	0.000	0.000	0.000
86	A	200	GLY	0	-0.027	0.006	12.923	0.020	0.020	0.000	0.000	0.000	0.000
87	A	201	LYS	1	0.880	0.941	14.546	0.215	0.215	0.000	0.000	0.000	0.000
88	A	202	HIS	0	-0.039	-0.010	18.215	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:113:PHE)