FMO DATABASE

FMODB ID: 6Y4NZ

Calculation Name: 2GGV-A-Xray372

Preferred Name: Genome polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GGV

Chain ID: A

ChEMBL ID: CHEMBL5419

UniProt ID: P06935

Base Structure: X-ray

Registration Date: 2023-09-23

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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-170348.40347
FMO2-HF: Nuclear repulsion	152424.167592
FMO2-HF: Total energy	-17924.235878
FMO2-MP2: Total energy	-17975.001302

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:50:THR)

Summations of interaction energy for fragment #1(A:50:THR)

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.
-19.464	-15.839	7.593	-5.408	-5.81	-0.005

Interaction energy analysis for fragmet #1(A:50:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.022

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	52	MET	0	-0.064	-0.027	2.250	-5.374	-1.887	2.228	-2.703	-3.012	0.027
4	A	53	TRP	0	-0.064	-0.039	2.006	-13.084	-13.007	5.366	-2.694	-2.750	-0.032
5	A	54	ILE	0	-0.026	-0.016	4.706	1.088	1.149	-0.001	-0.011	-0.048	0.000
6	A	55	GLU	-1	-0.828	-0.904	8.328	-1.268	-1.268	0.000	0.000	0.000	0.000
7	A	56	ARG	1	0.759	0.864	11.689	0.237	0.237	0.000	0.000	0.000	0.000
8	A	57	THR	0	0.051	0.025	14.870	0.009	0.009	0.000	0.000	0.000	0.000
9	A	58	ALA	0	0.017	0.006	17.461	0.022	0.022	0.000	0.000	0.000	0.000
10	A	59	ASP	-1	-0.813	-0.859	19.563	-0.092	-0.092	0.000	0.000	0.000	0.000
11	A	60	ILE	0	-0.042	-0.033	19.738	0.000	0.000	0.000	0.000	0.000	0.000
12	A	61	SER	0	-0.061	-0.050	23.778	0.011	0.011	0.000	0.000	0.000	0.000
13	A	62	TRP	0	-0.071	-0.039	27.522	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.723	-0.847	28.675	-0.074	-0.074	0.000	0.000	0.000	0.000
15	A	64	SER	0	0.018	-0.016	31.555	0.001	0.001	0.000	0.000	0.000	0.000
16	A	65	ASP	-1	-0.891	-0.936	33.797	-0.061	-0.061	0.000	0.000	0.000	0.000
17	A	66	ALA	0	-0.007	0.005	31.637	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	67	GLU	-1	-0.918	-0.934	33.769	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	68	ILE	0	-0.063	-0.033	36.226	0.003	0.003	0.000	0.000	0.000	0.000
20	A	69	THR	0	-0.051	-0.046	36.063	0.000	0.000	0.000	0.000	0.000	0.000
21	A	70	GLY	0	-0.049	-0.008	35.805	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	71	SER	0	-0.072	-0.052	31.079	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	72	SER	0	-0.007	0.001	31.144	0.001	0.001	0.000	0.000	0.000	0.000
24	A	73	GLU	-1	-0.972	-0.969	26.930	-0.169	-0.169	0.000	0.000	0.000	0.000
25	A	74	ARG	1	0.750	0.848	23.684	0.112	0.112	0.000	0.000	0.000	0.000
26	A	75	VAL	0	0.048	0.013	27.380	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	76	ASP	-1	-0.709	-0.789	23.330	-0.122	-0.122	0.000	0.000	0.000	0.000
28	A	77	VAL	0	-0.021	-0.021	24.261	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.779	0.854	22.116	0.134	0.134	0.000	0.000	0.000	0.000
30	A	79	LEU	0	-0.018	-0.001	25.249	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	80	ASP	-1	-0.797	-0.876	25.872	-0.135	-0.135	0.000	0.000	0.000	0.000
32	A	81	ASP	-1	-0.954	-0.991	27.152	-0.078	-0.078	0.000	0.000	0.000	0.000
33	A	82	ASP	-1	-0.963	-0.968	29.991	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	83	GLY	0	-0.056	-0.022	30.702	0.006	0.006	0.000	0.000	0.000	0.000
35	A	84	ASN	0	-0.115	-0.075	28.453	0.002	0.002	0.000	0.000	0.000	0.000
36	A	85	PHE	0	-0.016	-0.026	27.955	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.006	0.003	19.932	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	87	LEU	0	0.003	-0.002	24.186	0.016	0.016	0.000	0.000	0.000	0.000
39	A	88	MET	0	-0.038	-0.011	18.166	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	89	ASN	0	-0.028	-0.049	19.624	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	90	ASP	-1	-0.863	-0.912	21.637	-0.315	-0.315	0.000	0.000	0.000	0.000
42	A	91	PRO	0	-0.027	-0.021	18.748	-0.039	-0.039	0.000	0.000	0.000	0.000
43	A	92	GLY	0	-0.041	-0.017	18.050	-0.066	-0.066	0.000	0.000	0.000	0.000
44	A	93	ALA	0	-0.085	-0.030	16.881	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:50:THR)