FMO DATABASE

FMODB ID: 76K2K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-170144.005145
FMO2-HF: Nuclear repulsion	152220.218302
FMO2-HF: Total energy	-17923.786842
FMO2-MP2: Total energy	-17974.578827

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.
-1.224	2.134	2.305	-2.15	-3.513	0.009

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 : -0.040 / q_NPA : -0.033

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	-0.063	-0.031	2.641	-4.853	-1.782	0.437	-1.545	-1.963	0.013
4	A	53	TRP	0	-0.072	-0.028	2.754	4.224	4.479	1.869	-0.602	-1.522	-0.004
5	A	54	ILE	0	-0.022	-0.013	5.121	-0.327	-0.295	-0.001	-0.003	-0.028	0.000
6	A	55	GLU	-1	-0.842	-0.919	8.671	-0.193	-0.193	0.000	0.000	0.000	0.000
7	A	56	ARG	1	0.749	0.856	11.749	-0.293	-0.293	0.000	0.000	0.000	0.000
8	A	57	THR	0	0.058	0.020	15.034	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	58	ALA	0	0.053	0.004	17.780	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	59	ASP	-1	-0.876	-0.913	20.029	0.249	0.249	0.000	0.000	0.000	0.000
11	A	60	ILE	0	-0.039	-0.024	20.515	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	61	SER	0	-0.048	-0.020	23.984	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	62	TRP	0	-0.042	-0.022	27.704	0.007	0.007	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.837	-0.918	29.314	0.118	0.118	0.000	0.000	0.000	0.000
15	A	64	SER	0	0.014	-0.011	32.039	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	65	ASP	-1	-0.850	-0.926	34.314	0.063	0.063	0.000	0.000	0.000	0.000
17	A	66	ALA	0	-0.037	-0.019	32.117	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	67	GLU	-1	-0.941	-0.945	34.280	0.087	0.087	0.000	0.000	0.000	0.000
19	A	68	ILE	0	-0.061	-0.029	37.004	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	69	THR	0	-0.038	-0.025	36.791	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	70	GLY	0	-0.039	-0.013	36.177	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	71	SER	0	-0.065	-0.042	31.914	0.009	0.009	0.000	0.000	0.000	0.000
23	A	72	SER	0	0.000	0.000	31.409	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	73	GLU	-1	-0.971	-0.971	27.504	0.041	0.041	0.000	0.000	0.000	0.000
25	A	74	ARG	1	0.784	0.861	24.193	-0.152	-0.152	0.000	0.000	0.000	0.000
26	A	75	VAL	0	0.044	0.024	27.648	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	76	ASP	-1	-0.759	-0.843	23.860	0.162	0.162	0.000	0.000	0.000	0.000
28	A	77	VAL	0	-0.016	-0.016	24.594	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.823	0.906	21.914	-0.143	-0.143	0.000	0.000	0.000	0.000
30	A	79	LEU	0	-0.007	-0.002	25.143	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	80	ASP	-1	-0.865	-0.928	25.987	0.013	0.013	0.000	0.000	0.000	0.000
32	A	81	ASP	-1	-0.913	-0.973	27.241	0.042	0.042	0.000	0.000	0.000	0.000
33	A	82	ASP	-1	-1.001	-0.989	30.052	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	83	GLY	0	-0.056	-0.020	31.136	0.000	0.000	0.000	0.000	0.000	0.000
35	A	84	ASN	0	-0.051	-0.020	29.247	0.002	0.002	0.000	0.000	0.000	0.000
36	A	85	PHE	0	0.010	-0.006	27.969	0.009	0.009	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.020	-0.012	19.698	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	87	LEU	0	-0.004	-0.009	24.043	0.019	0.019	0.000	0.000	0.000	0.000
39	A	88	MET	0	-0.041	0.011	18.474	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	89	ASN	0	0.005	-0.034	19.640	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	90	ASP	-1	-0.859	-0.904	21.702	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	91	PRO	0	-0.037	-0.023	18.632	0.004	0.004	0.000	0.000	0.000	0.000
43	A	92	GLY	0	-0.042	-0.025	18.002	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	93	ALA	0	-0.074	-0.019	17.237	-0.036	-0.036	0.000	0.000	0.000	0.000

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