FMO DATABASE

FMODB ID: MV6KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-599944.569221
FMO2-HF: Nuclear repulsion	564620.682827
FMO2-HF: Total energy	-35323.886394
FMO2-MP2: Total energy	-35425.243893

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.
-0.577	1.14	0.023	-0.795	-0.946	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 : -0.019 / q_NPA : -0.021

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	0.003	0.008	3.567	-1.835	-0.118	0.023	-0.795	-0.946	0.001
4	A	116	LYS	1	0.935	0.958	5.829	1.113	1.113	0.000	0.000	0.000	0.000
5	A	117	ASP	-1	-0.828	-0.926	7.442	-0.454	-0.454	0.000	0.000	0.000	0.000
6	A	118	GLN	0	-0.077	-0.043	9.739	0.095	0.095	0.000	0.000	0.000	0.000
7	A	119	ILE	0	0.077	0.040	8.124	0.122	0.122	0.000	0.000	0.000	0.000
8	A	120	ALA	0	0.009	0.010	11.119	0.106	0.106	0.000	0.000	0.000	0.000
9	A	121	LYS	1	0.908	0.947	13.321	0.535	0.535	0.000	0.000	0.000	0.000
10	A	122	ASP	-1	-0.826	-0.898	13.979	-0.218	-0.218	0.000	0.000	0.000	0.000
11	A	123	VAL	0	-0.018	-0.004	14.437	0.048	0.048	0.000	0.000	0.000	0.000
12	A	124	LYS	1	0.760	0.869	16.741	0.296	0.296	0.000	0.000	0.000	0.000
13	A	125	GLN	0	0.008	0.015	18.878	0.011	0.011	0.000	0.000	0.000	0.000
14	A	126	PHE	0	-0.033	-0.025	19.423	0.023	0.023	0.000	0.000	0.000	0.000
15	A	127	TYR	0	-0.033	-0.047	20.956	0.014	0.014	0.000	0.000	0.000	0.000
16	A	128	ASP	-1	-0.793	-0.891	22.897	-0.114	-0.114	0.000	0.000	0.000	0.000
17	A	129	GLN	0	-0.003	0.004	23.176	0.005	0.005	0.000	0.000	0.000	0.000
18	A	130	ALA	0	0.020	0.016	25.415	0.010	0.010	0.000	0.000	0.000	0.000
19	A	131	LEU	0	-0.011	-0.014	26.982	0.007	0.007	0.000	0.000	0.000	0.000
20	A	132	GLN	0	-0.032	-0.028	28.175	0.001	0.001	0.000	0.000	0.000	0.000
21	A	133	GLN	0	-0.060	-0.029	29.954	0.002	0.002	0.000	0.000	0.000	0.000
22	A	134	ALA	0	-0.010	-0.005	31.233	0.005	0.005	0.000	0.000	0.000	0.000
23	A	135	VAL	0	-0.065	-0.035	32.964	0.004	0.004	0.000	0.000	0.000	0.000
24	A	136	VAL	0	-0.050	-0.028	33.939	0.002	0.002	0.000	0.000	0.000	0.000
25	A	137	ASP	-1	-0.856	-0.916	34.346	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	138	ASP	-1	-0.933	-0.957	36.444	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	139	ASP	-1	-0.940	-0.984	37.406	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	140	ALA	0	0.106	0.082	32.386	0.003	0.003	0.000	0.000	0.000	0.000
29	A	141	ASN	0	-0.075	-0.074	33.663	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	142	ASN	0	-0.008	-0.008	27.290	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	143	ALA	0	0.035	0.030	28.957	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	144	LYS	1	0.907	0.954	29.605	0.019	0.019	0.000	0.000	0.000	0.000
33	A	145	ALA	0	-0.025	-0.007	30.495	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	146	VAL	0	0.015	0.008	24.450	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	147	VAL	0	0.019	0.011	26.314	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	148	LYS	1	0.940	0.984	28.036	0.022	0.022	0.000	0.000	0.000	0.000
37	A	149	THR	0	-0.015	-0.013	24.437	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	150	PHE	0	-0.002	0.003	19.910	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	151	HIS	0	0.003	0.022	24.488	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	152	GLU	-1	-0.885	-0.946	27.224	-0.049	-0.049	0.000	0.000	0.000	0.000
41	A	153	THR	0	-0.085	-0.048	21.615	0.001	0.001	0.000	0.000	0.000	0.000
42	A	154	LEU	0	-0.059	-0.039	19.600	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	155	ASP	-1	-0.874	-0.925	23.511	-0.081	-0.081	0.000	0.000	0.000	0.000
44	A	156	CYS	0	-0.009	0.013	23.275	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	157	CYS	0	-0.033	-0.019	27.383	0.004	0.004	0.000	0.000	0.000	0.000
46	A	158	GLY	0	0.071	0.030	28.701	0.000	0.000	0.000	0.000	0.000	0.000
47	A	159	SER	0	-0.001	-0.005	25.715	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	160	SER	0	-0.026	-0.044	26.321	0.008	0.008	0.000	0.000	0.000	0.000
49	A	161	THR	0	-0.059	-0.044	25.366	0.001	0.001	0.000	0.000	0.000	0.000
50	A	162	LEU	0	-0.001	0.004	27.503	0.006	0.006	0.000	0.000	0.000	0.000
51	A	163	THR	0	0.031	0.014	30.556	0.005	0.005	0.000	0.000	0.000	0.000
52	A	164	ALA	0	0.004	-0.001	33.091	0.004	0.004	0.000	0.000	0.000	0.000
53	A	165	LEU	0	0.051	0.015	32.134	0.003	0.003	0.000	0.000	0.000	0.000
54	A	166	THR	0	0.035	0.031	31.334	0.004	0.004	0.000	0.000	0.000	0.000
55	A	167	THR	0	-0.015	-0.001	33.240	0.003	0.003	0.000	0.000	0.000	0.000
56	A	168	SER	0	-0.014	-0.013	36.590	0.002	0.002	0.000	0.000	0.000	0.000
57	A	169	VAL	0	-0.008	-0.006	31.728	0.003	0.003	0.000	0.000	0.000	0.000
58	A	170	LEU	0	-0.003	0.001	35.240	0.003	0.003	0.000	0.000	0.000	0.000
59	A	171	LYS	1	0.896	0.950	36.113	0.041	0.041	0.000	0.000	0.000	0.000
60	A	172	ASN	0	-0.026	0.001	37.323	0.004	0.004	0.000	0.000	0.000	0.000
61	A	173	ASN	0	-0.059	-0.025	37.590	0.001	0.001	0.000	0.000	0.000	0.000
62	A	174	LEU	0	-0.001	-0.003	32.509	0.002	0.002	0.000	0.000	0.000	0.000
63	A	176	PRO	0	0.097	0.067	30.124	0.004	0.004	0.000	0.000	0.000	0.000
64	A	177	SER	0	0.026	0.006	33.048	0.001	0.001	0.000	0.000	0.000	0.000
65	A	178	GLY	0	0.002	0.046	36.749	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	179	SER	0	-0.092	-0.072	37.870	0.001	0.001	0.000	0.000	0.000	0.000
67	A	180	ASN	0	-0.030	-0.011	33.841	0.003	0.003	0.000	0.000	0.000	0.000
68	A	181	ILE	0	0.005	-0.027	37.882	0.003	0.003	0.000	0.000	0.000	0.000
69	A	182	ILE	0	0.012	-0.013	37.808	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	183	SER	0	0.030	0.024	36.165	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	184	ASN	0	-0.031	-0.035	35.198	0.002	0.002	0.000	0.000	0.000	0.000
72	A	185	LEU	0	0.100	0.059	32.791	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	186	PHE	0	-0.005	0.008	31.130	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.796	0.905	30.173	0.059	0.059	0.000	0.000	0.000	0.000
75	A	188	GLU	-1	-0.846	-0.916	28.703	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	189	ASP	-1	-0.760	-0.858	25.231	-0.129	-0.129	0.000	0.000	0.000	0.000
77	A	191	HIS	1	0.797	0.868	20.814	0.132	0.132	0.000	0.000	0.000	0.000
78	A	192	GLN	0	-0.001	-0.005	19.742	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	193	LYS	1	0.876	0.932	20.023	0.087	0.087	0.000	0.000	0.000	0.000
80	A	194	ILE	0	-0.019	-0.011	16.200	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	195	ASP	-1	-0.799	-0.884	15.509	-0.312	-0.312	0.000	0.000	0.000	0.000
82	A	196	ASP	-1	-0.852	-0.918	15.117	-0.201	-0.201	0.000	0.000	0.000	0.000
83	A	197	LEU	0	-0.057	-0.009	14.653	0.007	0.007	0.000	0.000	0.000	0.000
84	A	198	PHE	0	-0.004	-0.012	10.156	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	199	SER	0	-0.093	-0.056	10.866	-0.058	-0.058	0.000	0.000	0.000	0.000
86	A	200	GLY	0	-0.021	0.001	13.231	0.017	0.017	0.000	0.000	0.000	0.000
87	A	201	LYS	1	0.858	0.934	14.717	0.224	0.224	0.000	0.000	0.000	0.000
88	A	202	HIS	0	0.013	0.019	18.312	0.023	0.023	0.000	0.000	0.000	0.000

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