FMO DATABASE

FMODB ID: J36N9

Calculation Name: 1VIT-L-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	37
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-131578.167403
FMO2-HF: Nuclear repulsion	116908.528029
FMO2-HF: Total energy	-14669.639374
FMO2-MP2: Total energy	-14712.264732

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:0:ACE )

Summations of interaction energy for fragment #1(L:0:ACE )

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.
1.068	1.707	-0.005	-0.28	-0.354	0.001

Interaction energy analysis for fragmet #1(L:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.006

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	PHE	0	0.001	0.003	3.840	0.892	1.531	-0.005	-0.280	-0.354	0.001
4	L	1	GLY	0	0.125	0.063	6.918	0.372	0.372	0.000	0.000	0.000	0.000
5	L	1	ALA	0	-0.060	-0.025	8.008	-0.172	-0.172	0.000	0.000	0.000	0.000
6	L	1	GLY	0	-0.004	-0.008	10.014	0.095	0.095	0.000	0.000	0.000	0.000
7	L	1	GLU	-1	-1.009	-1.007	9.761	-0.153	-0.153	0.000	0.000	0.000	0.000
8	L	1	ALA	0	0.063	0.032	13.170	0.047	0.047	0.000	0.000	0.000	0.000
9	L	1	ASP	-1	-0.892	-0.953	11.774	-0.449	-0.449	0.000	0.000	0.000	0.000
10	L	1	CYS	0	-0.030	-0.010	14.348	-0.009	-0.009	0.000	0.000	0.000	0.000
11	L	2	GLY	0	-0.006	-0.005	17.203	0.018	0.018	0.000	0.000	0.000	0.000
12	L	3	LEU	0	0.024	0.010	15.985	0.016	0.016	0.000	0.000	0.000	0.000
13	L	4	ARG	1	0.838	0.907	17.496	0.095	0.095	0.000	0.000	0.000	0.000
14	L	5	PRO	0	0.001	-0.009	16.337	0.008	0.008	0.000	0.000	0.000	0.000
15	L	6	LEU	0	-0.041	-0.028	18.159	0.008	0.008	0.000	0.000	0.000	0.000
16	L	7	PHE	0	-0.016	-0.020	21.072	0.017	0.017	0.000	0.000	0.000	0.000
17	L	8	GLU	-1	-0.729	-0.836	20.189	-0.149	-0.149	0.000	0.000	0.000	0.000
18	L	9	LYS	1	0.832	0.939	12.769	0.472	0.472	0.000	0.000	0.000	0.000
19	L	10	LYS	1	0.885	0.943	18.092	0.146	0.146	0.000	0.000	0.000	0.000
20	L	11	GLN	0	-0.027	-0.017	20.673	0.021	0.021	0.000	0.000	0.000	0.000
21	L	12	VAL	0	-0.048	0.004	23.184	0.014	0.014	0.000	0.000	0.000	0.000
22	L	13	GLN	0	0.046	0.022	25.404	-0.003	-0.003	0.000	0.000	0.000	0.000
23	L	14	ASP	-1	-0.849	-0.939	28.034	-0.100	-0.100	0.000	0.000	0.000	0.000
24	L	14	GLN	0	-0.064	-0.053	29.926	0.009	0.009	0.000	0.000	0.000	0.000
25	L	14	THR	0	0.027	0.011	33.026	0.004	0.004	0.000	0.000	0.000	0.000
26	L	14	GLU	-1	-0.850	-0.920	27.606	-0.102	-0.102	0.000	0.000	0.000	0.000
27	L	14	LYS	1	0.875	0.925	31.613	0.078	0.078	0.000	0.000	0.000	0.000
28	L	14	GLU	-1	-0.884	-0.929	34.451	-0.055	-0.055	0.000	0.000	0.000	0.000
29	L	14	LEU	0	0.003	0.005	31.094	0.003	0.003	0.000	0.000	0.000	0.000
30	L	14	PHE	0	-0.019	0.018	28.127	0.003	0.003	0.000	0.000	0.000	0.000
31	L	14	GLU	-1	-0.944	-0.951	34.281	-0.041	-0.041	0.000	0.000	0.000	0.000
32	L	14	SER	0	-0.072	-0.081	36.773	0.003	0.003	0.000	0.000	0.000	0.000
33	L	14	TYR	0	-0.063	-0.042	31.364	0.000	0.000	0.000	0.000	0.000	0.000
34	L	14	ILE	0	-0.008	0.015	37.110	0.003	0.003	0.000	0.000	0.000	0.000
35	L	14	GLU	-1	-0.966	-0.985	36.076	-0.028	-0.028	0.000	0.000	0.000	0.000
36	L	14	GLY	0	0.022	0.028	35.581	-0.004	-0.004	0.000	0.000	0.000	0.000
37	L	15	ARG	0	-0.102	-0.062	31.029	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:0:ACE )