FMO DATABASE

FMODB ID: 72N5K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-173080.691638
FMO2-HF: Nuclear repulsion	154866.760393
FMO2-HF: Total energy	-18213.931245
FMO2-MP2: Total energy	-18259.353406

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.
-19.362	-11.385	4.689	-4.945	-7.722	0.009

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 : -0.022 / q_NPA : -0.021

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	0.028	0.016	2.892	-0.533	2.610	0.135	-1.482	-1.796	0.000
4	B	5	CYS	0	-0.112	-0.063	2.534	-6.449	-3.823	4.229	-2.886	-3.970	-0.003
5	B	6	LYS	1	0.878	0.903	2.857	-5.471	-4.768	0.292	0.110	-1.105	0.006
6	B	7	GLY	0	-0.031	0.006	3.137	-5.160	-3.793	0.035	-0.676	-0.726	0.006
7	B	8	ARG	1	0.908	0.924	4.938	-4.001	-3.993	-0.001	-0.005	-0.002	0.000
8	B	9	CYS	0	-0.082	-0.021	6.981	-0.839	-0.839	0.000	0.000	0.000	0.000
9	B	10	THR	0	0.056	0.023	8.563	-0.482	-0.482	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.850	-0.906	6.874	3.875	3.875	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.046	0.032	10.111	-0.325	-0.325	0.000	0.000	0.000	0.000
12	B	13	PHE	0	-0.023	-0.019	11.070	0.155	0.155	0.000	0.000	0.000	0.000
13	B	14	ASN	0	-0.020	-0.019	8.724	-0.377	-0.377	0.000	0.000	0.000	0.000
14	B	15	VAL	0	-0.007	-0.007	10.625	-0.239	-0.239	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.920	-0.957	9.325	0.249	0.249	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.807	0.916	4.655	-3.445	-3.315	-0.001	-0.006	-0.123	0.000
17	B	18	LYS	1	0.913	0.951	5.916	1.980	1.980	0.000	0.000	0.000	0.000
18	B	19	CYS	0	0.027	0.035	6.147	-1.211	-1.211	0.000	0.000	0.000	0.000
19	B	20	GLN	0	0.009	0.013	8.226	0.335	0.335	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.782	-0.889	9.192	0.930	0.930	0.000	0.000	0.000	0.000
21	B	23	GLU	-1	-0.875	-0.941	12.545	0.877	0.877	0.000	0.000	0.000	0.000
22	B	24	LEU	0	-0.036	-0.011	15.964	-0.112	-0.112	0.000	0.000	0.000	0.000
23	B	25	CYS	0	-0.064	-0.003	10.673	-0.197	-0.197	0.000	0.000	0.000	0.000
24	B	26	SER	0	0.028	0.002	14.425	-0.104	-0.104	0.000	0.000	0.000	0.000
25	B	27	TYR	0	-0.091	-0.033	16.688	-0.062	-0.062	0.000	0.000	0.000	0.000
26	B	28	TYR	0	-0.025	-0.031	16.219	-0.058	-0.058	0.000	0.000	0.000	0.000
27	B	29	GLN	0	-0.060	-0.023	16.728	-0.099	-0.099	0.000	0.000	0.000	0.000
28	B	30	SER	0	0.030	0.016	13.006	-0.067	-0.067	0.000	0.000	0.000	0.000
29	B	33	THR	0	0.034	0.007	8.258	0.368	0.368	0.000	0.000	0.000	0.000
30	B	34	ASP	-1	-0.775	-0.902	6.247	-0.340	-0.340	0.000	0.000	0.000	0.000
31	B	35	TYR	0	0.044	-0.017	9.012	0.219	0.219	0.000	0.000	0.000	0.000
32	B	36	THR	0	-0.088	-0.048	10.354	0.049	0.049	0.000	0.000	0.000	0.000
33	B	37	ALA	0	-0.050	-0.037	12.343	-0.034	-0.034	0.000	0.000	0.000	0.000
34	B	38	GLU	-1	-0.779	-0.859	7.753	1.728	1.728	0.000	0.000	0.000	0.000
35	B	40	LYS	1	0.869	0.954	12.989	-0.504	-0.504	0.000	0.000	0.000	0.000
36	B	41	PRO	0	-0.013	-0.001	15.872	-0.018	-0.018	0.000	0.000	0.000	0.000

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