FMO DATABASE

FMODB ID: 947K2

Calculation Name: 3BT2-B-Xray372

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

Total energy (hartree)

FMO2-HF: Electronic energy	-171546.112197
FMO2-HF: Nuclear repulsion	153332.708045
FMO2-HF: Total energy	-18213.404151
FMO2-MP2: Total energy	-18258.817044

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.
-13.312	-6.025	2.093	-3.714	-5.669	-0.021

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 : -0.089 / q_NPA : -0.067

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	0.039	0.026	2.378	-0.762	2.178	0.401	-1.324	-2.018	-0.006
4	B	5	CYS	0	-0.101	-0.062	2.574	-6.478	-3.084	1.686	-2.187	-2.893	-0.016
5	B	6	LYS	1	1.024	0.998	3.888	-1.161	-0.900	0.000	-0.006	-0.255	0.000
6	B	7	GLY	0	-0.077	-0.038	4.242	-1.068	-0.873	-0.001	-0.034	-0.160	0.000
7	B	8	ARG	1	0.923	0.962	5.927	-1.388	-1.388	0.000	0.000	0.000	0.000
8	B	9	CYS	0	-0.065	-0.011	8.063	-0.369	-0.369	0.000	0.000	0.000	0.000
9	B	10	THR	0	0.042	0.019	9.682	-0.282	-0.282	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.981	-0.991	8.756	1.889	1.889	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.029	0.021	11.171	-0.157	-0.157	0.000	0.000	0.000	0.000
12	B	13	PHE	0	0.009	-0.007	11.359	0.113	0.113	0.000	0.000	0.000	0.000
13	B	14	ASN	0	0.010	0.007	6.999	-0.247	-0.247	0.000	0.000	0.000	0.000
14	B	15	VAL	0	-0.025	-0.004	10.480	-0.158	-0.158	0.000	0.000	0.000	0.000
15	B	16	ASP	-1	-0.934	-0.972	9.611	0.739	0.739	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.921	0.960	3.409	-2.372	-1.875	0.007	-0.163	-0.343	0.001
17	B	18	LYS	1	0.908	0.949	6.008	-0.507	-0.507	0.000	0.000	0.000	0.000
18	B	19	CYS	0	0.059	0.062	6.463	-0.599	-0.599	0.000	0.000	0.000	0.000
19	B	20	GLN	0	0.026	0.022	7.496	-0.041	-0.041	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.856	-0.922	10.085	0.540	0.540	0.000	0.000	0.000	0.000
21	B	23	GLU	-1	-0.880	-0.956	13.328	0.359	0.359	0.000	0.000	0.000	0.000
22	B	24	LEU	0	-0.055	-0.022	16.600	-0.077	-0.077	0.000	0.000	0.000	0.000
23	B	25	CYS	0	0.013	0.032	11.604	-0.131	-0.131	0.000	0.000	0.000	0.000
24	B	26	SER	0	0.018	-0.010	15.306	-0.058	-0.058	0.000	0.000	0.000	0.000
25	B	27	TYR	0	-0.124	-0.050	17.846	-0.033	-0.033	0.000	0.000	0.000	0.000
26	B	28	TYR	0	-0.010	-0.013	16.856	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	29	GLN	0	-0.070	-0.030	17.564	-0.022	-0.022	0.000	0.000	0.000	0.000
28	B	30	SER	0	0.019	0.006	13.018	-0.039	-0.039	0.000	0.000	0.000	0.000
29	B	33	THR	0	-0.009	-0.023	9.401	0.111	0.111	0.000	0.000	0.000	0.000
30	B	34	ASP	-1	-0.820	-0.922	6.921	-1.074	-1.074	0.000	0.000	0.000	0.000
31	B	35	TYR	0	0.092	0.024	9.729	0.117	0.117	0.000	0.000	0.000	0.000
32	B	36	THR	0	-0.107	-0.057	11.028	0.109	0.109	0.000	0.000	0.000	0.000
33	B	37	ALA	0	-0.053	-0.035	12.985	0.043	0.043	0.000	0.000	0.000	0.000
34	B	38	GLU	-1	-0.875	-0.928	8.343	-0.418	-0.418	0.000	0.000	0.000	0.000
35	B	40	LYS	1	0.933	0.968	13.598	0.080	0.080	0.000	0.000	0.000	0.000
36	B	41	PRO	0	0.018	0.023	16.833	0.043	0.043	0.000	0.000	0.000	0.000

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