FMO DATABASE

FMODB ID: YVY62

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

Total energy (hartree)

FMO2-HF: Electronic energy	-300546.748446
FMO2-HF: Nuclear repulsion	276848.720954
FMO2-HF: Total energy	-23698.027492
FMO2-MP2: Total energy	-23764.633514

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.
-1.872	0.23	-0.031	-0.856	-1.217	0.004

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 : -0.029 / 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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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	-0.004	0.013	3.793	-1.914	-0.087	-0.030	-0.813	-0.985	0.004
4	B	11	CYS	0	-0.026	0.023	6.752	0.463	0.463	0.000	0.000	0.000	0.000
5	B	12	PHE	0	0.038	0.007	8.957	0.097	0.097	0.000	0.000	0.000	0.000
6	B	13	SER	0	-0.012	-0.014	12.685	0.087	0.087	0.000	0.000	0.000	0.000
7	B	14	TYR	0	0.005	0.026	14.763	-0.018	-0.018	0.000	0.000	0.000	0.000
8	B	15	THR	0	-0.064	-0.031	16.393	0.016	0.016	0.000	0.000	0.000	0.000
9	B	16	SER	0	0.024	0.000	18.925	0.002	0.002	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.938	0.973	22.265	0.060	0.060	0.000	0.000	0.000	0.000
11	B	18	GLN	0	0.061	0.050	21.164	0.017	0.017	0.000	0.000	0.000	0.000
12	B	19	ILE	0	-0.004	-0.003	21.280	0.006	0.006	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.044	-0.016	20.986	0.009	0.009	0.000	0.000	0.000	0.000
14	B	21	GLN	0	0.085	0.014	24.093	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	22	ASN	0	-0.048	-0.028	20.656	0.006	0.006	0.000	0.000	0.000	0.000
16	B	23	PHE	0	0.065	0.028	22.620	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	24	ILE	0	-0.034	-0.014	20.614	0.010	0.010	0.000	0.000	0.000	0.000
18	B	25	ALA	0	-0.014	0.002	16.551	0.013	0.013	0.000	0.000	0.000	0.000
19	B	26	ASP	-1	-0.783	-0.849	12.218	0.558	0.558	0.000	0.000	0.000	0.000
20	B	27	TYR	0	0.006	-0.018	12.055	-0.011	-0.011	0.000	0.000	0.000	0.000
21	B	28	PHE	0	-0.011	-0.005	4.199	0.209	0.404	0.000	-0.039	-0.157	0.000
22	B	29	GLU	-1	-0.757	-0.858	8.146	-0.493	-0.493	0.000	0.000	0.000	0.000
23	B	30	THR	0	-0.046	-0.042	6.714	-0.113	-0.113	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.040	-0.036	7.559	-0.334	-0.334	0.000	0.000	0.000	0.000
25	B	32	SER	0	-0.061	-0.026	5.044	-0.052	0.028	-0.001	-0.004	-0.075	0.000
26	B	33	GLN	0	-0.026	-0.024	6.599	-0.227	-0.227	0.000	0.000	0.000	0.000
27	B	35	SER	0	0.002	-0.017	8.192	0.195	0.195	0.000	0.000	0.000	0.000
28	B	36	LYS	1	0.867	0.910	10.583	0.842	0.842	0.000	0.000	0.000	0.000
29	B	37	PRO	0	0.057	0.045	10.565	-0.171	-0.171	0.000	0.000	0.000	0.000
30	B	38	GLY	0	0.022	-0.003	11.453	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	39	VAL	0	0.036	0.041	10.797	-0.011	-0.011	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.037	-0.015	7.467	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	41	PHE	0	0.045	0.012	10.089	0.072	0.072	0.000	0.000	0.000	0.000
34	B	42	LEU	0	0.005	0.003	9.789	0.024	0.024	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.024	-0.031	13.428	-0.100	-0.100	0.000	0.000	0.000	0.000
36	B	44	LYS	1	0.980	0.997	16.930	-0.201	-0.201	0.000	0.000	0.000	0.000
37	B	45	ARG	1	0.857	0.904	11.985	-0.618	-0.618	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.020	-0.035	15.149	-0.019	-0.019	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.928	0.978	14.715	-0.180	-0.180	0.000	0.000	0.000	0.000
40	B	48	GLN	0	0.025	0.011	7.547	0.266	0.266	0.000	0.000	0.000	0.000
41	B	49	VAL	0	-0.015	0.007	12.237	-0.073	-0.073	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.021	0.009	13.281	0.017	0.017	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.881	-0.960	14.545	-0.254	-0.254	0.000	0.000	0.000	0.000
44	B	53	PRO	0	-0.048	-0.010	16.928	0.022	0.022	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.028	-0.028	19.042	0.002	0.002	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.877	-0.966	22.248	-0.040	-0.040	0.000	0.000	0.000	0.000
47	B	56	GLU	-1	-0.782	-0.878	18.802	-0.090	-0.090	0.000	0.000	0.000	0.000
48	B	57	TRP	0	-0.049	-0.020	19.394	0.023	0.023	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.104	0.033	20.413	0.015	0.015	0.000	0.000	0.000	0.000
50	B	59	GLN	0	0.010	0.023	19.391	0.012	0.012	0.000	0.000	0.000	0.000
51	B	60	LYS	1	0.812	0.892	15.100	-0.028	-0.028	0.000	0.000	0.000	0.000
52	B	61	TYR	0	-0.045	-0.048	18.417	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	62	VAL	0	-0.081	-0.001	21.046	0.001	0.001	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.101	-0.056	22.122	0.000	0.000	0.000	0.000	0.000	0.000
55	B	64	ASP	-1	-1.008	-0.955	19.629	0.062	0.062	0.000	0.000	0.000	0.000

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