FMO DATABASE

FMODB ID: KK913

Calculation Name: 3BT2-B-Xray540

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BT2

Chain ID: B

ChEMBL ID:

UniProt ID: P01837

Base Structure: X-ray

Registration Date: 2025-07-14

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-172108.29638
FMO2-HF: Nuclear repulsion	153902.738638
FMO2-HF: Total energy	-18205.557742
FMO2-MP2: Total energy	-18250.775007

3D Structure Molmil

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.
-3.705	-1.205	-0.007	-1.276	-1.218	0.003

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 : 0.112 / q_NPA : 0.018

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

Sort

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].
4	B	3	GLU	-1	-1.052	-0.849	4.279	-0.883	-0.451	0.002	-0.192	-0.242	0.000
5	B	4	SER	0	0.065	-0.096	3.821	-1.377	0.465	-0.005	-1.040	-0.797	0.003
6	B	4	SER	0	-0.052	0.081	5.763	0.531	0.531	0.000	0.000	0.000	0.000
7	B	5	CYS	0	0.028	-0.064	4.529	-1.243	-1.137	-0.001	-0.035	-0.071	0.000
8	B	5	CYS	0	-0.230	0.109	6.334	0.173	0.173	0.000	0.000	0.000	0.000
9	B	6	LYS	0	0.196	-0.062	5.930	0.432	0.475	-0.002	0.000	-0.042	0.000
10	B	6	LYS	1	0.749	0.982	7.528	1.036	1.036	0.000	0.000	0.000	0.000
11	B	7	GLY	0	-0.079	-0.140	7.163	0.372	0.372	0.000	0.000	0.000	0.000
12	B	8	ARG	0	0.020	0.037	8.723	-0.073	-0.073	0.000	0.000	0.000	0.000
13	B	8	ARG	1	0.904	1.043	10.501	0.445	0.445	0.000	0.000	0.000	0.000
14	B	9	CYS	0	0.091	-0.088	10.642	0.092	0.092	0.000	0.000	0.000	0.000
15	B	9	CYS	0	-0.222	0.205	12.332	-0.060	-0.060	0.000	0.000	0.000	0.000
16	B	10	THR	0	0.062	-0.068	12.128	0.025	0.025	0.000	0.000	0.000	0.000
17	B	10	THR	0	-0.008	0.073	15.704	0.037	0.037	0.000	0.000	0.000	0.000
18	B	11	GLU	0	0.054	-0.117	11.334	0.162	0.162	0.000	0.000	0.000	0.000
19	B	11	GLU	-1	-0.949	-0.817	8.705	-1.216	-1.216	0.000	0.000	0.000	0.000
20	B	12	GLY	0	0.018	-0.078	12.850	0.114	0.114	0.000	0.000	0.000	0.000
21	B	13	PHE	0	0.147	0.023	12.069	-0.192	-0.192	0.000	0.000	0.000	0.000
22	B	13	PHE	0	-0.105	0.085	13.832	-0.007	-0.007	0.000	0.000	0.000	0.000
23	B	14	ASN	0	0.080	-0.072	8.921	0.193	0.193	0.000	0.000	0.000	0.000
24	B	14	ASN	0	-0.137	0.037	8.382	0.049	0.049	0.000	0.000	0.000	0.000
25	B	15	VAL	0	0.077	-0.079	10.413	-0.086	-0.086	0.000	0.000	0.000	0.000
26	B	15	VAL	0	-0.078	0.094	11.727	0.013	0.013	0.000	0.000	0.000	0.000
27	B	16	ASP	0	0.044	-0.121	9.943	-0.035	-0.035	0.000	0.000	0.000	0.000
28	B	16	ASP	-1	-1.009	-0.863	9.749	0.070	0.070	0.000	0.000	0.000	0.000
29	B	17	LYS	0	0.035	-0.147	6.114	0.373	0.373	0.000	0.000	0.000	0.000
30	B	17	LYS	1	0.898	1.063	4.140	1.216	1.293	-0.001	-0.009	-0.066	0.000
31	B	18	LYS	0	0.038	-0.081	6.199	0.184	0.184	0.000	0.000	0.000	0.000
32	B	18	LYS	1	0.858	1.036	6.883	0.453	0.453	0.000	0.000	0.000	0.000
33	B	19	CYS	0	0.070	-0.053	6.623	-0.597	-0.597	0.000	0.000	0.000	0.000
34	B	19	CYS	0	-0.157	0.240	8.009	-0.254	-0.254	0.000	0.000	0.000	0.000
35	B	20	GLN	0	0.148	-0.088	7.572	-0.536	-0.536	0.000	0.000	0.000	0.000
36	B	20	GLN	0	-0.121	0.069	8.919	-0.243	-0.243	0.000	0.000	0.000	0.000
37	B	21	CYS	0	0.015	-0.076	9.878	0.049	0.049	0.000	0.000	0.000	0.000
38	B	22	ASP	0	0.180	-0.035	11.302	0.022	0.022	0.000	0.000	0.000	0.000
39	B	22	ASP	-1	-0.916	-0.867	14.010	-0.748	-0.748	0.000	0.000	0.000	0.000
40	B	23	GLU	0	0.103	-0.103	14.597	-0.045	-0.045	0.000	0.000	0.000	0.000
41	B	23	GLU	-1	-0.993	-0.871	17.025	-0.570	-0.570	0.000	0.000	0.000	0.000
42	B	24	LEU	0	0.016	-0.085	18.034	0.016	0.016	0.000	0.000	0.000	0.000
43	B	24	LEU	0	-0.062	0.086	19.035	0.013	0.013	0.000	0.000	0.000	0.000
44	B	25	CYS	0	0.144	-0.080	14.730	0.076	0.076	0.000	0.000	0.000	0.000
45	B	25	CYS	0	-0.180	0.205	13.383	0.031	0.031	0.000	0.000	0.000	0.000
46	B	26	SER	0	0.094	-0.085	16.069	-0.017	-0.017	0.000	0.000	0.000	0.000
47	B	26	SER	0	-0.033	0.079	18.535	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	27	TYR	0	0.035	-0.103	18.701	0.037	0.037	0.000	0.000	0.000	0.000
49	B	27	TYR	0	-0.137	0.070	20.766	0.014	0.014	0.000	0.000	0.000	0.000
50	B	28	TYR	0	0.025	-0.109	17.850	0.054	0.054	0.000	0.000	0.000	0.000
51	B	28	TYR	0	-0.089	0.079	16.970	0.020	0.020	0.000	0.000	0.000	0.000
52	B	29	GLN	0	0.029	-0.095	17.998	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	29	GLN	0	-0.095	0.094	18.981	0.014	0.014	0.000	0.000	0.000	0.000
54	B	30	SER	0	0.065	-0.087	14.010	0.028	0.028	0.000	0.000	0.000	0.000
55	B	30	SER	0	-0.039	0.064	13.056	-0.020	-0.020	0.000	0.000	0.000	0.000
56	B	31	CYS	0	0.029	-0.127	12.159	-0.174	-0.174	0.000	0.000	0.000	0.000
57	B	32	CYS	0	0.063	-0.089	9.049	0.232	0.232	0.000	0.000	0.000	0.000
58	B	33	THR	0	0.045	-0.073	10.504	0.041	0.041	0.000	0.000	0.000	0.000
59	B	33	THR	0	-0.059	0.057	12.753	-0.041	-0.041	0.000	0.000	0.000	0.000
60	B	34	ASP	0	0.063	-0.102	10.263	0.271	0.271	0.000	0.000	0.000	0.000
61	B	34	ASP	-1	-0.829	-0.798	8.649	-2.293	-2.293	0.000	0.000	0.000	0.000
62	B	35	TYR	0	0.141	-0.078	11.485	0.103	0.103	0.000	0.000	0.000	0.000
63	B	35	TYR	0	-0.076	0.083	11.553	0.027	0.027	0.000	0.000	0.000	0.000
64	B	36	THR	0	-0.074	-0.112	12.602	0.092	0.092	0.000	0.000	0.000	0.000
65	B	36	THR	0	-0.061	0.047	16.359	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	37	ALA	0	0.112	-0.077	14.841	0.093	0.093	0.000	0.000	0.000	0.000
67	B	37	ALA	0	-0.099	0.082	15.173	0.011	0.011	0.000	0.000	0.000	0.000
68	B	38	GLU	0	0.065	-0.071	12.602	0.102	0.102	0.000	0.000	0.000	0.000
69	B	38	GLU	-1	-0.942	-0.833	10.523	-1.050	-1.050	0.000	0.000	0.000	0.000
70	B	39	CYS	0	0.088	-0.091	14.025	0.098	0.098	0.000	0.000	0.000	0.000
71	B	40	LYS	0	-0.041	-0.084	16.044	0.016	0.016	0.000	0.000	0.000	0.000
72	B	40	LYS	1	0.838	1.055	17.298	0.633	0.633	0.000	0.000	0.000	0.000
73	B	41	PRO	0	0.131	-0.102	19.059	0.018	0.018	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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