FMO DATABASE

FMODB ID: 2NMJR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-170089.072797
FMO2-HF: Nuclear repulsion	152164.98398
FMO2-HF: Total energy	-17924.088816
FMO2-MP2: Total energy	-17974.845727

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.
-9.678	-4.81	1.665	-2.846	-3.687	0.011

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 : -0.029 / 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

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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	-0.058	-0.032	2.554	-5.578	-1.942	0.598	-1.971	-2.263	0.019
4	A	53	TRP	0	-0.085	-0.044	2.562	-2.945	-1.756	1.068	-0.871	-1.386	-0.008
5	A	54	ILE	0	-0.025	-0.017	5.033	0.564	0.607	-0.001	-0.004	-0.038	0.000
6	A	55	GLU	-1	-0.831	-0.903	8.527	-1.054	-1.054	0.000	0.000	0.000	0.000
7	A	56	ARG	1	0.755	0.853	11.742	0.148	0.148	0.000	0.000	0.000	0.000
8	A	57	THR	0	0.060	0.025	14.969	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	58	ALA	0	0.050	0.017	17.718	0.007	0.007	0.000	0.000	0.000	0.000
10	A	59	ASP	-1	-0.828	-0.864	19.866	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	60	ILE	0	-0.028	-0.019	20.045	0.000	0.000	0.000	0.000	0.000	0.000
12	A	61	SER	0	-0.046	-0.038	23.720	0.006	0.006	0.000	0.000	0.000	0.000
13	A	62	TRP	0	-0.068	-0.035	27.445	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.783	-0.888	29.059	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	64	SER	0	0.014	-0.009	31.819	0.001	0.001	0.000	0.000	0.000	0.000
16	A	65	ASP	-1	-0.865	-0.935	34.148	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	66	ALA	0	-0.018	-0.012	31.913	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	67	GLU	-1	-0.941	-0.941	34.059	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	68	ILE	0	-0.058	-0.025	36.759	0.001	0.001	0.000	0.000	0.000	0.000
20	A	69	THR	0	-0.044	-0.029	36.603	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	70	GLY	0	-0.036	-0.011	35.967	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	71	SER	0	-0.065	-0.044	31.673	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	72	SER	0	-0.006	-0.002	31.226	0.000	0.000	0.000	0.000	0.000	0.000
24	A	73	GLU	-1	-0.974	-0.969	27.384	-0.123	-0.123	0.000	0.000	0.000	0.000
25	A	74	ARG	1	0.767	0.848	24.032	0.064	0.064	0.000	0.000	0.000	0.000
26	A	75	VAL	0	0.028	0.011	27.605	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	76	ASP	-1	-0.735	-0.806	23.732	-0.068	-0.068	0.000	0.000	0.000	0.000
28	A	77	VAL	0	-0.011	-0.015	24.626	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.771	0.859	22.071	0.088	0.088	0.000	0.000	0.000	0.000
30	A	79	LEU	0	-0.003	0.002	25.272	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	80	ASP	-1	-0.827	-0.898	25.913	-0.103	-0.103	0.000	0.000	0.000	0.000
32	A	81	ASP	-1	-0.931	-0.982	27.116	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	82	ASP	-1	-0.981	-0.978	29.862	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	83	GLY	0	-0.054	-0.019	31.010	0.004	0.004	0.000	0.000	0.000	0.000
35	A	84	ASN	0	-0.093	-0.056	28.739	0.003	0.003	0.000	0.000	0.000	0.000
36	A	85	PHE	0	-0.010	-0.014	28.041	0.000	0.000	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.017	-0.008	19.874	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	87	LEU	0	-0.004	-0.011	24.103	0.015	0.015	0.000	0.000	0.000	0.000
39	A	88	MET	0	-0.040	-0.006	18.403	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	89	ASN	0	-0.021	-0.051	19.680	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	90	ASP	-1	-0.864	-0.910	21.694	-0.244	-0.244	0.000	0.000	0.000	0.000
42	A	91	PRO	0	-0.033	-0.023	18.682	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	92	GLY	0	-0.038	-0.017	18.049	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	93	ALA	0	-0.068	-0.018	16.982	-0.018	-0.018	0.000	0.000	0.000	0.000

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