FMO DATABASE

FMODB ID: 5J39Z

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	OptH
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	-300603.546759
FMO2-HF: Nuclear repulsion	276905.736837
FMO2-HF: Total energy	-23697.809923
FMO2-MP2: Total energy	-23764.444013

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.
-1.065	1.125	-0.032	-0.871	-1.289	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 : -0.024 / q_NPA : -0.065

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	-0.006	0.022	3.793	-1.392	0.536	-0.031	-0.830	-1.067	0.004
4	B	11	CYS	0	0.029	0.023	6.115	0.293	0.293	0.000	0.000	0.000	0.000
5	B	12	PHE	0	0.036	0.011	8.242	0.099	0.099	0.000	0.000	0.000	0.000
6	B	13	SER	0	-0.041	-0.030	12.138	0.061	0.061	0.000	0.000	0.000	0.000
7	B	14	TYR	0	0.018	0.034	14.515	-0.017	-0.017	0.000	0.000	0.000	0.000
8	B	15	THR	0	-0.059	-0.024	16.385	0.005	0.005	0.000	0.000	0.000	0.000
9	B	16	SER	0	0.019	-0.004	18.919	0.002	0.002	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.941	0.973	22.258	0.015	0.015	0.000	0.000	0.000	0.000
11	B	18	GLN	0	0.059	0.051	21.149	0.011	0.011	0.000	0.000	0.000	0.000
12	B	19	ILE	0	-0.008	-0.011	21.277	0.000	0.000	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.019	0.010	20.985	0.008	0.008	0.000	0.000	0.000	0.000
14	B	21	GLN	0	0.061	-0.004	24.092	0.001	0.001	0.000	0.000	0.000	0.000
15	B	22	ASN	0	-0.050	-0.030	20.798	0.005	0.005	0.000	0.000	0.000	0.000
16	B	23	PHE	0	0.065	0.028	22.738	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	24	ILE	0	-0.029	-0.011	20.551	0.006	0.006	0.000	0.000	0.000	0.000
18	B	25	ALA	0	-0.014	0.000	16.516	0.006	0.006	0.000	0.000	0.000	0.000
19	B	26	ASP	-1	-0.789	-0.851	12.139	0.416	0.416	0.000	0.000	0.000	0.000
20	B	27	TYR	0	0.003	-0.021	12.065	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	28	PHE	0	-0.013	-0.006	4.237	0.123	0.316	0.000	-0.038	-0.156	0.000
22	B	29	GLU	-1	-0.753	-0.848	8.132	-0.199	-0.199	0.000	0.000	0.000	0.000
23	B	30	THR	0	-0.032	-0.046	6.702	-0.106	-0.106	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.047	-0.042	7.695	-0.112	-0.112	0.000	0.000	0.000	0.000
25	B	32	SER	0	-0.061	-0.024	5.053	-0.155	-0.086	-0.001	-0.003	-0.066	0.000
26	B	33	GLN	0	-0.025	-0.023	6.719	0.116	0.116	0.000	0.000	0.000	0.000
27	B	35	SER	0	0.000	-0.015	8.516	0.056	0.056	0.000	0.000	0.000	0.000
28	B	36	LYS	1	0.857	0.907	10.424	0.353	0.353	0.000	0.000	0.000	0.000
29	B	37	PRO	0	0.069	0.049	10.752	-0.082	-0.082	0.000	0.000	0.000	0.000
30	B	38	GLY	0	0.018	-0.006	11.435	-0.018	-0.018	0.000	0.000	0.000	0.000
31	B	39	VAL	0	0.032	0.036	10.788	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.038	-0.018	7.312	-0.021	-0.021	0.000	0.000	0.000	0.000
33	B	41	PHE	0	0.039	0.010	10.086	0.051	0.051	0.000	0.000	0.000	0.000
34	B	42	LEU	0	0.017	0.006	9.712	0.004	0.004	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.036	-0.035	13.432	-0.075	-0.075	0.000	0.000	0.000	0.000
36	B	44	LYS	1	0.988	1.000	16.930	-0.133	-0.133	0.000	0.000	0.000	0.000
37	B	45	ARG	1	0.861	0.909	12.190	-0.413	-0.413	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.022	-0.033	15.202	-0.024	-0.024	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.931	0.979	14.675	-0.129	-0.129	0.000	0.000	0.000	0.000
40	B	48	GLN	0	0.023	0.005	7.668	0.311	0.311	0.000	0.000	0.000	0.000
41	B	49	VAL	0	-0.018	0.007	12.237	-0.056	-0.056	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.000	0.013	13.276	0.003	0.003	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.881	-0.957	14.536	-0.095	-0.095	0.000	0.000	0.000	0.000
44	B	53	PRO	0	-0.054	-0.015	16.919	0.013	0.013	0.000	0.000	0.000	0.000
45	B	54	SER	0	-0.028	-0.022	19.033	0.000	0.000	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.879	-0.956	22.249	0.002	0.002	0.000	0.000	0.000	0.000
47	B	56	GLU	-1	-0.791	-0.898	18.829	-0.010	-0.010	0.000	0.000	0.000	0.000
48	B	57	TRP	0	-0.036	-0.018	19.391	0.014	0.014	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.137	-0.016	20.407	0.007	0.007	0.000	0.000	0.000	0.000
50	B	59	GLN	0	-0.008	0.012	19.352	0.012	0.012	0.000	0.000	0.000	0.000
51	B	60	LYS	1	0.837	0.911	15.085	-0.065	-0.065	0.000	0.000	0.000	0.000
52	B	61	TYR	0	-0.051	-0.060	18.414	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	62	VAL	0	-0.087	0.059	21.042	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.128	-0.060	22.217	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	64	ASP	-1	-1.013	-0.953	19.630	0.057	0.057	0.000	0.000	0.000	0.000

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