FMO DATABASE

FMODB ID: K3YJ3

Calculation Name: 1VIT-L-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 1VIT

Chain ID: L

ChEMBL ID:

UniProt ID: P28507

Base Structure: X-ray

Registration Date: 2023-06-20

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-130231.884942
FMO2-HF: Nuclear repulsion	115712.881546
FMO2-HF: Total energy	-14519.003396
FMO2-MP2: Total energy	-14561.155839

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(L:1:THR)

Summations of interaction energy for fragment #1(L:1: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.
-6.745	-3.135	2.824	-2.845	-3.588	0.011

Interaction energy analysis for fragmet #1(L:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.002

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	L	1	GLY	0	0.076	0.046	2.184	-6.330	-3.296	2.797	-2.835	-2.996	0.011
4	L	1	ALA	0	-0.056	-0.036	3.684	-0.522	0.008	0.028	-0.009	-0.548	0.000
5	L	1	GLY	0	-0.002	-0.009	5.576	-0.862	-0.816	-0.001	-0.001	-0.044	0.000
6	L	1	GLU	-1	-0.919	-0.958	6.173	1.272	1.272	0.000	0.000	0.000	0.000
7	L	1	ALA	0	0.013	0.004	9.315	-0.159	-0.159	0.000	0.000	0.000	0.000
8	L	1	ASP	-1	-0.849	-0.903	7.917	0.109	0.109	0.000	0.000	0.000	0.000
9	L	1	CYS	0	0.005	-0.005	10.065	-0.062	-0.062	0.000	0.000	0.000	0.000
10	L	2	GLY	0	-0.012	0.001	12.002	-0.057	-0.057	0.000	0.000	0.000	0.000
11	L	3	LEU	0	0.008	0.004	11.485	-0.040	-0.040	0.000	0.000	0.000	0.000
12	L	4	ARG	1	0.825	0.874	12.677	-0.010	-0.010	0.000	0.000	0.000	0.000
13	L	5	PRO	0	-0.008	-0.020	10.915	-0.038	-0.038	0.000	0.000	0.000	0.000
14	L	6	LEU	0	-0.009	-0.004	13.105	-0.034	-0.034	0.000	0.000	0.000	0.000
15	L	7	PHE	0	-0.010	-0.007	16.491	-0.005	-0.005	0.000	0.000	0.000	0.000
16	L	8	GLU	-1	-0.721	-0.848	15.390	-0.013	-0.013	0.000	0.000	0.000	0.000
17	L	9	LYS	1	0.737	0.864	8.168	-0.075	-0.075	0.000	0.000	0.000	0.000
18	L	10	LYS	1	0.812	0.902	14.000	0.013	0.013	0.000	0.000	0.000	0.000
19	L	11	GLN	0	-0.020	0.003	16.877	0.030	0.030	0.000	0.000	0.000	0.000
20	L	12	VAL	0	-0.030	-0.005	19.789	0.006	0.006	0.000	0.000	0.000	0.000
21	L	13	GLN	0	0.046	0.028	21.072	0.004	0.004	0.000	0.000	0.000	0.000
22	L	14	ASP	-1	-0.834	-0.908	23.128	0.028	0.028	0.000	0.000	0.000	0.000
23	L	14	GLN	0	-0.030	-0.030	24.730	-0.008	-0.008	0.000	0.000	0.000	0.000
24	L	14	THR	0	0.041	0.015	27.869	-0.003	-0.003	0.000	0.000	0.000	0.000
25	L	14	GLU	-1	-0.805	-0.881	23.046	-0.007	-0.007	0.000	0.000	0.000	0.000
26	L	14	LYS	1	0.841	0.907	26.863	0.008	0.008	0.000	0.000	0.000	0.000
27	L	14	GLU	-1	-0.879	-0.932	29.687	0.018	0.018	0.000	0.000	0.000	0.000
28	L	14	LEU	0	-0.024	-0.005	25.844	0.001	0.001	0.000	0.000	0.000	0.000
29	L	14	PHE	0	-0.003	-0.001	23.466	-0.001	-0.001	0.000	0.000	0.000	0.000
30	L	14	GLU	-1	-0.959	-0.967	29.551	-0.007	-0.007	0.000	0.000	0.000	0.000
31	L	14	SER	0	-0.072	-0.051	31.726	0.001	0.001	0.000	0.000	0.000	0.000
32	L	14	TYR	0	-0.019	-0.016	26.938	0.001	0.001	0.000	0.000	0.000	0.000
33	L	14	ILE	0	-0.021	0.012	32.828	-0.002	-0.002	0.000	0.000	0.000	0.000
34	L	14	GLU	-1	-0.950	-0.968	32.579	-0.021	-0.021	0.000	0.000	0.000	0.000
35	L	14	GLY	0	0.040	0.027	31.759	-0.001	-0.001	0.000	0.000	0.000	0.000
36	L	15	ARG	1	0.828	0.902	28.338	0.021	0.021	0.000	0.000	0.000	0.000

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