FMO DATABASE

FMODB ID: VQR81

Calculation Name: 4ZKB-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4ZKB

Chain ID: B

ChEMBL ID:

UniProt ID: P10147

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-301122.846983
FMO2-HF: Nuclear repulsion	277424.114943
FMO2-HF: Total energy	-23698.73204
FMO2-MP2: Total energy	-23765.2546

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:8:THR)

Summations of interaction energy for fragment #1(B:8:THR)

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.
-1.659	0.095	-0.012	-0.693	-1.049	0.003

Interaction energy analysis for fragmet #1(B:8:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.019

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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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	10	CYS	0	-0.016	0.027	3.843	-1.818	-0.323	-0.013	-0.628	-0.854	0.003
4	B	11	CYS	0	-0.011	0.017	6.367	0.680	0.680	0.000	0.000	0.000	0.000
5	B	12	PHE	0	0.034	0.020	8.961	0.176	0.176	0.000	0.000	0.000	0.000
6	B	13	SER	0	-0.045	-0.025	12.407	0.122	0.122	0.000	0.000	0.000	0.000
7	B	14	TYR	0	-0.026	-0.008	14.121	-0.049	-0.049	0.000	0.000	0.000	0.000
8	B	15	THR	0	-0.034	-0.013	16.224	0.022	0.022	0.000	0.000	0.000	0.000
9	B	16	SER	0	0.005	-0.002	18.982	0.007	0.007	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.928	0.958	21.688	0.087	0.087	0.000	0.000	0.000	0.000
11	B	18	GLN	0	0.062	0.053	20.984	0.019	0.019	0.000	0.000	0.000	0.000
12	B	19	ILE	0	-0.012	0.001	21.310	0.005	0.005	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.037	-0.020	21.041	0.010	0.010	0.000	0.000	0.000	0.000
14	B	21	GLN	0	0.100	0.032	23.925	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	22	ASN	0	-0.066	-0.044	20.616	0.009	0.009	0.000	0.000	0.000	0.000
16	B	23	PHE	0	0.105	0.054	22.508	-0.009	-0.009	0.000	0.000	0.000	0.000
17	B	24	ILE	0	-0.030	-0.011	20.844	0.011	0.011	0.000	0.000	0.000	0.000
18	B	25	ALA	0	-0.014	0.002	17.092	0.015	0.015	0.000	0.000	0.000	0.000
19	B	26	ASP	-1	-0.737	-0.825	12.561	0.722	0.722	0.000	0.000	0.000	0.000
20	B	27	TYR	0	-0.003	-0.018	11.670	0.000	0.000	0.000	0.000	0.000	0.000
21	B	28	PHE	0	-0.024	-0.009	4.088	0.347	0.606	0.001	-0.065	-0.195	0.000
22	B	29	GLU	-1	-0.765	-0.859	8.060	-0.614	-0.614	0.000	0.000	0.000	0.000
23	B	30	THR	0	-0.023	-0.047	6.521	-0.171	-0.171	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.039	-0.058	7.602	-0.371	-0.371	0.000	0.000	0.000	0.000
25	B	32	SER	0	-0.043	0.000	5.177	0.116	0.116	0.000	0.000	0.000	0.000
26	B	33	GLN	0	-0.037	-0.027	6.436	-0.417	-0.417	0.000	0.000	0.000	0.000
27	B	35	SER	0	0.009	-0.029	7.723	0.242	0.242	0.000	0.000	0.000	0.000
28	B	36	LYS	1	0.853	0.902	10.284	0.994	0.994	0.000	0.000	0.000	0.000
29	B	37	PRO	0	0.053	0.042	10.369	-0.206	-0.206	0.000	0.000	0.000	0.000
30	B	38	GLY	0	0.010	-0.001	11.549	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	39	VAL	0	0.026	0.040	10.359	-0.056	-0.056	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.018	-0.005	7.319	-0.007	-0.007	0.000	0.000	0.000	0.000
33	B	41	PHE	0	0.032	0.003	10.087	0.094	0.094	0.000	0.000	0.000	0.000
34	B	42	LEU	0	0.014	0.009	10.039	0.017	0.017	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.028	-0.024	13.677	-0.117	-0.117	0.000	0.000	0.000	0.000
36	B	44	LYS	1	0.976	0.985	17.083	-0.228	-0.228	0.000	0.000	0.000	0.000
37	B	45	ARG	1	0.844	0.884	12.110	-0.769	-0.769	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.030	-0.033	15.423	-0.027	-0.027	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.936	0.977	14.941	-0.189	-0.189	0.000	0.000	0.000	0.000
40	B	48	GLN	0	0.001	0.010	7.541	0.064	0.064	0.000	0.000	0.000	0.000
41	B	49	VAL	0	-0.015	0.001	12.373	-0.106	-0.106	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.004	0.004	13.015	0.010	0.010	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.813	-0.911	14.355	-0.279	-0.279	0.000	0.000	0.000	0.000
44	B	53	PRO	0	-0.031	-0.011	16.574	0.032	0.032	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.044	-0.039	18.652	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.882	-0.968	22.194	-0.043	-0.043	0.000	0.000	0.000	0.000
47	B	56	GLU	-1	-0.811	-0.891	18.420	-0.100	-0.100	0.000	0.000	0.000	0.000
48	B	57	TRP	0	-0.025	-0.004	19.198	0.036	0.036	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.042	0.020	20.213	0.022	0.022	0.000	0.000	0.000	0.000
50	B	59	GLN	0	-0.042	-0.036	19.295	0.020	0.020	0.000	0.000	0.000	0.000
51	B	60	LYS	1	0.808	0.895	15.186	-0.052	-0.052	0.000	0.000	0.000	0.000
52	B	61	TYR	0	-0.058	-0.016	18.494	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	62	VAL	0	-0.012	0.013	21.165	-0.012	-0.012	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.098	-0.041	22.263	0.000	0.000	0.000	0.000	0.000	0.000
55	B	64	ASP	-1	-0.972	-0.972	19.799	0.121	0.121	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:THR)