FMO DATABASE

FMODB ID: MV8JZ

Calculation Name: 3BT2-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3BT2

Chain ID: B

ChEMBL ID:

UniProt ID: P01837

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	36
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-172116.434804
FMO2-HF: Nuclear repulsion	153902.738638
FMO2-HF: Total energy	-18213.696166
FMO2-MP2: Total energy	-18259.109027

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(B:2:GLN)

Summations of interaction energy for fragment #1(B:2:GLN)

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.
-14.24	-7.515	3.411	-4.036	-6.101	-0.015

Interaction energy analysis for fragmet #1(B:2:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.029

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	B	4	SER	0	0.043	0.022	2.639	-1.298	2.118	0.441	-1.619	-2.238	-0.001
4	B	5	CYS	0	-0.100	-0.068	2.474	-6.742	-4.090	2.972	-2.354	-3.271	-0.014
5	B	6	LYS	1	0.913	0.924	3.971	-1.663	-1.397	0.001	0.001	-0.268	0.000
6	B	7	GLY	0	-0.061	-0.033	4.097	-1.204	-0.971	-0.001	-0.055	-0.177	0.000
7	B	8	ARG	1	0.929	0.964	5.704	-2.496	-2.496	-0.001	0.000	0.001	0.000
8	B	9	CYS	0	-0.073	-0.020	7.820	-0.471	-0.471	0.000	0.000	0.000	0.000
9	B	10	THR	0	0.039	0.015	9.461	-0.360	-0.360	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.921	-0.932	7.520	3.413	3.413	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.053	0.030	10.823	-0.189	-0.189	0.000	0.000	0.000	0.000
12	B	13	PHE	0	-0.005	-0.012	11.215	0.119	0.119	0.000	0.000	0.000	0.000
13	B	14	ASN	0	-0.029	-0.028	8.382	-0.159	-0.159	0.000	0.000	0.000	0.000
14	B	15	VAL	0	-0.004	-0.001	10.413	-0.282	-0.282	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.934	-0.964	9.749	0.621	0.621	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.887	0.946	4.140	-3.811	-3.653	-0.001	-0.009	-0.148	0.000
17	B	18	LYS	1	0.900	0.943	6.199	1.751	1.751	0.000	0.000	0.000	0.000
18	B	19	CYS	0	0.048	0.057	6.623	-0.969	-0.969	0.000	0.000	0.000	0.000
19	B	20	GLN	0	0.012	0.014	7.572	0.005	0.005	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.829	-0.910	9.914	0.567	0.567	0.000	0.000	0.000	0.000
21	B	23	GLU	-1	-0.879	-0.956	13.100	0.511	0.511	0.000	0.000	0.000	0.000
22	B	24	LEU	0	-0.046	-0.014	16.394	-0.094	-0.094	0.000	0.000	0.000	0.000
23	B	25	CYS	0	-0.016	0.020	11.023	-0.234	-0.234	0.000	0.000	0.000	0.000
24	B	26	SER	0	0.028	-0.001	15.010	-0.097	-0.097	0.000	0.000	0.000	0.000
25	B	27	TYR	0	-0.117	-0.047	17.238	-0.035	-0.035	0.000	0.000	0.000	0.000
26	B	28	TYR	0	-0.010	-0.015	16.781	-0.022	-0.022	0.000	0.000	0.000	0.000
27	B	29	GLN	0	-0.070	-0.027	16.966	-0.076	-0.076	0.000	0.000	0.000	0.000
28	B	30	SER	0	0.031	0.008	13.056	-0.069	-0.069	0.000	0.000	0.000	0.000
29	B	33	THR	0	0.002	-0.020	8.881	0.219	0.219	0.000	0.000	0.000	0.000
30	B	34	ASP	-1	-0.813	-0.917	6.537	-1.595	-1.595	0.000	0.000	0.000	0.000
31	B	35	TYR	0	0.065	0.001	9.417	0.198	0.198	0.000	0.000	0.000	0.000
32	B	36	THR	0	-0.091	-0.056	10.575	0.157	0.157	0.000	0.000	0.000	0.000
33	B	37	ALA	0	-0.040	-0.021	12.711	0.064	0.064	0.000	0.000	0.000	0.000
34	B	38	GLU	-1	-0.794	-0.868	8.274	-0.082	-0.082	0.000	0.000	0.000	0.000
35	B	40	LYS	1	0.897	0.957	13.526	0.039	0.039	0.000	0.000	0.000	0.000
36	B	41	PRO	0	0.021	0.029	16.792	0.044	0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLN)