FMO DATABASE

FMODB ID: 94N52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-599873.371513
FMO2-HF: Nuclear repulsion	564550.106844
FMO2-HF: Total energy	-35323.264669
FMO2-MP2: Total energy	-35424.664568

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.
-0.632	1.094	0.028	-0.811	-0.944	0.001

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 : -0.010 / q_NPA : -0.019

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	-0.004	0.001	3.591	-1.930	-0.204	0.028	-0.811	-0.944	0.001
4	A	116	LYS	1	0.991	1.003	5.735	1.202	1.202	0.000	0.000	0.000	0.000
5	A	117	ASP	-1	-0.874	-0.960	7.426	-0.512	-0.512	0.000	0.000	0.000	0.000
6	A	118	GLN	0	-0.106	-0.054	9.645	0.086	0.086	0.000	0.000	0.000	0.000
7	A	119	ILE	0	0.059	0.033	7.617	0.129	0.129	0.000	0.000	0.000	0.000
8	A	120	ALA	0	0.017	0.015	11.128	0.119	0.119	0.000	0.000	0.000	0.000
9	A	121	LYS	1	0.907	0.943	13.334	0.591	0.591	0.000	0.000	0.000	0.000
10	A	122	ASP	-1	-0.825	-0.902	13.968	-0.287	-0.287	0.000	0.000	0.000	0.000
11	A	123	VAL	0	-0.011	0.000	14.366	0.056	0.056	0.000	0.000	0.000	0.000
12	A	124	LYS	1	0.794	0.892	16.857	0.341	0.341	0.000	0.000	0.000	0.000
13	A	125	GLN	0	0.041	0.040	18.884	0.016	0.016	0.000	0.000	0.000	0.000
14	A	126	PHE	0	-0.029	-0.020	19.441	0.027	0.027	0.000	0.000	0.000	0.000
15	A	127	TYR	0	-0.030	-0.031	20.960	0.017	0.017	0.000	0.000	0.000	0.000
16	A	128	ASP	-1	-0.788	-0.873	22.897	-0.138	-0.138	0.000	0.000	0.000	0.000
17	A	129	GLN	0	-0.043	-0.028	23.547	0.008	0.008	0.000	0.000	0.000	0.000
18	A	130	ALA	0	0.024	0.020	25.416	0.012	0.012	0.000	0.000	0.000	0.000
19	A	131	LEU	0	-0.012	-0.014	26.981	0.009	0.009	0.000	0.000	0.000	0.000
20	A	132	GLN	0	-0.026	-0.028	28.147	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	133	GLN	0	0.007	0.009	29.638	0.002	0.002	0.000	0.000	0.000	0.000
22	A	134	ALA	0	-0.015	-0.008	31.230	0.006	0.006	0.000	0.000	0.000	0.000
23	A	135	VAL	0	-0.069	-0.040	32.960	0.005	0.005	0.000	0.000	0.000	0.000
24	A	136	VAL	0	-0.048	-0.020	33.953	0.003	0.003	0.000	0.000	0.000	0.000
25	A	137	ASP	-1	-0.904	-0.956	34.371	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	138	ASP	-1	-0.962	-0.975	36.441	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	139	ASP	-1	-0.970	-0.988	37.453	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	140	ALA	0	0.113	0.082	32.375	0.002	0.002	0.000	0.000	0.000	0.000
29	A	141	ASN	0	-0.027	-0.043	33.652	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	142	ASN	0	-0.005	-0.011	27.328	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	143	ALA	0	0.028	0.029	28.948	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	144	LYS	1	0.930	0.958	29.596	0.028	0.028	0.000	0.000	0.000	0.000
33	A	145	ALA	0	-0.047	-0.018	30.399	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	146	VAL	0	0.013	0.005	24.502	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	147	VAL	0	0.015	0.008	26.302	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	148	LYS	1	0.936	0.977	28.028	0.029	0.029	0.000	0.000	0.000	0.000
37	A	149	THR	0	0.000	0.007	24.092	0.000	0.000	0.000	0.000	0.000	0.000
38	A	150	PHE	0	-0.009	-0.005	19.957	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	151	HIS	0	0.005	0.015	24.479	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	152	GLU	-1	-0.907	-0.955	27.218	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	153	THR	0	-0.084	-0.047	21.602	0.002	0.002	0.000	0.000	0.000	0.000
42	A	154	LEU	0	-0.072	-0.052	19.522	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	155	ASP	-1	-0.927	-0.937	23.505	-0.082	-0.082	0.000	0.000	0.000	0.000
44	A	156	CYS	0	-0.063	-0.027	23.190	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	157	CYS	0	-0.019	-0.029	27.385	0.004	0.004	0.000	0.000	0.000	0.000
46	A	158	GLY	0	0.083	0.040	28.769	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	159	SER	0	-0.001	-0.016	26.152	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	160	SER	0	-0.044	-0.039	26.412	0.009	0.009	0.000	0.000	0.000	0.000
49	A	161	THR	0	-0.025	-0.021	25.139	0.004	0.004	0.000	0.000	0.000	0.000
50	A	162	LEU	0	-0.015	-0.001	27.211	0.007	0.007	0.000	0.000	0.000	0.000
51	A	163	THR	0	0.021	-0.005	30.572	0.007	0.007	0.000	0.000	0.000	0.000
52	A	164	ALA	0	0.037	0.014	33.107	0.005	0.005	0.000	0.000	0.000	0.000
53	A	165	LEU	0	0.039	0.008	32.296	0.004	0.004	0.000	0.000	0.000	0.000
54	A	166	THR	0	0.019	0.038	31.504	0.005	0.005	0.000	0.000	0.000	0.000
55	A	167	THR	0	-0.017	-0.001	33.249	0.003	0.003	0.000	0.000	0.000	0.000
56	A	168	SER	0	-0.009	-0.016	36.890	0.003	0.003	0.000	0.000	0.000	0.000
57	A	169	VAL	0	-0.002	0.008	31.835	0.004	0.004	0.000	0.000	0.000	0.000
58	A	170	LEU	0	-0.010	-0.005	35.241	0.003	0.003	0.000	0.000	0.000	0.000
59	A	171	LYS	1	0.896	0.949	36.115	0.050	0.050	0.000	0.000	0.000	0.000
60	A	172	ASN	0	-0.014	0.009	37.210	0.005	0.005	0.000	0.000	0.000	0.000
61	A	173	ASN	0	-0.054	-0.023	37.624	0.001	0.001	0.000	0.000	0.000	0.000
62	A	174	LEU	0	-0.014	-0.013	32.423	0.002	0.002	0.000	0.000	0.000	0.000
63	A	176	PRO	0	0.097	0.071	30.341	0.005	0.005	0.000	0.000	0.000	0.000
64	A	177	SER	0	0.040	0.008	33.043	0.001	0.001	0.000	0.000	0.000	0.000
65	A	178	GLY	0	0.003	0.046	36.743	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	179	SER	0	-0.095	-0.073	37.868	0.001	0.001	0.000	0.000	0.000	0.000
67	A	180	ASN	0	-0.018	0.003	33.798	0.003	0.003	0.000	0.000	0.000	0.000
68	A	181	ILE	0	-0.002	-0.023	37.885	0.002	0.002	0.000	0.000	0.000	0.000
69	A	182	ILE	0	0.025	-0.009	37.835	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	183	SER	0	0.038	0.017	36.169	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	184	ASN	0	-0.045	-0.030	35.236	0.001	0.001	0.000	0.000	0.000	0.000
72	A	185	LEU	0	0.096	0.056	32.786	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	186	PHE	0	-0.008	0.006	31.143	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.824	0.926	30.191	0.068	0.068	0.000	0.000	0.000	0.000
75	A	188	GLU	-1	-0.903	-0.960	28.737	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	189	ASP	-1	-0.772	-0.875	25.621	-0.148	-0.148	0.000	0.000	0.000	0.000
77	A	191	HIS	1	0.779	0.853	20.825	0.157	0.157	0.000	0.000	0.000	0.000
78	A	192	GLN	0	0.031	0.020	19.758	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	193	LYS	1	0.983	0.999	20.037	0.105	0.105	0.000	0.000	0.000	0.000
80	A	194	ILE	0	-0.017	-0.008	16.132	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	195	ASP	-1	-0.824	-0.904	15.538	-0.351	-0.351	0.000	0.000	0.000	0.000
82	A	196	ASP	-1	-0.888	-0.960	15.132	-0.225	-0.225	0.000	0.000	0.000	0.000
83	A	197	LEU	0	-0.048	-0.008	14.563	0.008	0.008	0.000	0.000	0.000	0.000
84	A	198	PHE	0	0.002	-0.012	9.830	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	199	SER	0	-0.108	-0.057	10.877	-0.070	-0.070	0.000	0.000	0.000	0.000
86	A	200	GLY	0	-0.027	0.002	13.245	0.019	0.019	0.000	0.000	0.000	0.000
87	A	201	LYS	1	0.887	0.950	14.721	0.243	0.243	0.000	0.000	0.000	0.000
88	A	202	HIS	0	0.026	0.024	18.350	0.025	0.025	0.000	0.000	0.000	0.000

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