FMO DATABASE

FMODB ID: 2G7GR

Calculation Name: 1D9K-E-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG | NDG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D9K

Chain ID: E

ChEMBL ID:

UniProt ID: P01910

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-866948.912794
FMO2-HF: Nuclear repulsion	823940.57587
FMO2-HF: Total energy	-43008.336925
FMO2-MP2: Total energy	-43135.401376

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(E:2:GLN)

Summations of interaction energy for fragment #1(E: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.
-14.04	-5.009	6.86	-7.271	-8.62	0.009

Interaction energy analysis for fragmet #1(E:2:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.939

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

Sort

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	E	4	ARG	1	0.909	0.950	2.007	13.594	18.218	6.526	-5.074	-6.075	0.030
4	E	5	GLN	0	0.067	0.011	4.796	0.133	0.165	-0.001	-0.008	-0.023	0.000
23	E	24	TYR	0	-0.001	-0.003	4.644	-4.587	-4.482	-0.001	-0.046	-0.059	0.000
24	E	25	GLU	-1	-0.929	-0.958	2.939	-35.467	-34.230	0.036	-0.390	-0.883	-0.003
25	E	26	ASP	-1	-0.803	-0.901	2.745	-66.655	-63.976	0.297	-1.636	-1.341	-0.018
26	E	27	SER	0	-0.012	-0.014	5.188	5.004	5.012	-0.001	0.000	-0.006	0.000
28	E	29	PHE	0	-0.079	-0.034	3.928	-2.476	-2.314	-0.001	-0.071	-0.090	0.000
97	E	105	THR	0	-0.039	-0.015	3.629	-2.001	-1.817	0.005	-0.046	-0.143	0.000
5	E	6	SER	0	-0.004	0.003	8.492	-0.005	-0.005	0.000	0.000	0.000	0.000
6	E	7	PRO	0	-0.029	-0.002	11.005	0.658	0.658	0.000	0.000	0.000	0.000
7	E	8	GLN	0	-0.006	-0.009	11.578	0.954	0.954	0.000	0.000	0.000	0.000
8	E	9	SER	0	-0.029	-0.003	13.730	0.774	0.774	0.000	0.000	0.000	0.000
9	E	10	LEU	0	0.005	0.018	17.312	0.168	0.168	0.000	0.000	0.000	0.000
10	E	11	THR	0	-0.028	-0.028	19.724	0.137	0.137	0.000	0.000	0.000	0.000
11	E	12	VAL	0	-0.017	-0.002	22.638	-0.151	-0.151	0.000	0.000	0.000	0.000
12	E	13	TRP	0	0.061	0.036	25.501	-0.024	-0.024	0.000	0.000	0.000	0.000
13	E	14	GLU	-1	-0.899	-0.974	28.430	-9.498	-9.498	0.000	0.000	0.000	0.000
14	E	15	GLY	0	-0.015	-0.003	29.930	0.204	0.204	0.000	0.000	0.000	0.000
15	E	16	GLU	-1	-0.933	-0.973	27.361	-10.764	-10.764	0.000	0.000	0.000	0.000
16	E	17	THR	0	-0.053	-0.019	24.544	-0.223	-0.223	0.000	0.000	0.000	0.000
17	E	18	THR	0	0.003	0.006	19.605	-0.173	-0.173	0.000	0.000	0.000	0.000
18	E	19	ILE	0	0.003	0.002	17.534	-0.407	-0.407	0.000	0.000	0.000	0.000
19	E	20	LEU	0	0.000	0.000	14.907	-0.474	-0.474	0.000	0.000	0.000	0.000
20	E	21	ASN	0	-0.029	-0.014	12.905	0.007	0.007	0.000	0.000	0.000	0.000
21	E	22	CYS	0	-0.057	-0.021	8.615	-1.479	-1.479	0.000	0.000	0.000	0.000
22	E	23	SER	0	0.003	0.011	7.547	1.717	1.717	0.000	0.000	0.000	0.000
27	E	28	THR	0	-0.048	-0.003	7.536	4.918	4.918	0.000	0.000	0.000	0.000
29	E	30	ASP	-1	-0.882	-0.951	8.883	-21.220	-21.220	0.000	0.000	0.000	0.000
30	E	31	TYR	0	0.045	0.019	11.642	1.847	1.847	0.000	0.000	0.000	0.000
31	E	32	PHE	0	-0.008	-0.022	8.620	-2.967	-2.967	0.000	0.000	0.000	0.000
32	E	33	PRO	0	-0.002	0.006	11.774	1.668	1.668	0.000	0.000	0.000	0.000
33	E	34	TRP	0	0.049	-0.001	12.942	-1.987	-1.987	0.000	0.000	0.000	0.000
34	E	35	TYR	0	0.029	0.006	14.125	1.517	1.517	0.000	0.000	0.000	0.000
35	E	36	ARG	1	0.898	0.967	15.742	12.684	12.684	0.000	0.000	0.000	0.000
36	E	37	GLN	0	-0.025	-0.014	17.026	-0.328	-0.328	0.000	0.000	0.000	0.000
37	E	38	PHE	0	0.034	0.025	19.464	-0.093	-0.093	0.000	0.000	0.000	0.000
38	E	39	PRO	0	0.030	0.002	22.275	-0.292	-0.292	0.000	0.000	0.000	0.000
39	E	40	GLY	0	0.026	0.012	22.563	0.464	0.464	0.000	0.000	0.000	0.000
40	E	41	LYS	1	0.905	0.967	22.833	11.529	11.529	0.000	0.000	0.000	0.000
41	E	42	SER	0	0.060	0.026	20.758	-0.345	-0.345	0.000	0.000	0.000	0.000
42	E	43	PRO	0	-0.027	-0.015	16.464	0.363	0.363	0.000	0.000	0.000	0.000
43	E	44	ALA	0	0.009	0.003	18.876	0.170	0.170	0.000	0.000	0.000	0.000
44	E	45	LEU	0	-0.025	-0.011	17.136	-0.602	-0.602	0.000	0.000	0.000	0.000
45	E	46	LEU	0	-0.045	-0.015	18.727	0.739	0.739	0.000	0.000	0.000	0.000
46	E	47	ILE	0	0.040	0.017	18.051	0.656	0.656	0.000	0.000	0.000	0.000
47	E	48	ALA	0	0.002	0.002	16.768	-1.285	-1.285	0.000	0.000	0.000	0.000
48	E	49	ILE	0	-0.027	-0.002	14.983	1.052	1.052	0.000	0.000	0.000	0.000
49	E	50	SER	0	0.021	0.010	15.253	-0.915	-0.915	0.000	0.000	0.000	0.000
50	E	51	LEU	0	-0.006	-0.025	12.625	0.961	0.961	0.000	0.000	0.000	0.000
51	E	52	VAL	0	-0.045	-0.005	15.563	0.378	0.378	0.000	0.000	0.000	0.000
52	E	53	SER	0	-0.004	0.011	18.842	0.799	0.799	0.000	0.000	0.000	0.000
53	E	54	ASN	0	0.014	0.001	18.211	-0.810	-0.810	0.000	0.000	0.000	0.000
54	E	55	LYS	1	0.884	0.937	19.591	11.846	11.846	0.000	0.000	0.000	0.000
55	E	56	LYS	1	0.878	0.947	20.842	13.735	13.735	0.000	0.000	0.000	0.000
56	E	57	GLU	-1	-0.834	-0.897	22.366	-11.971	-11.971	0.000	0.000	0.000	0.000
57	E	58	ASP	-1	-0.903	-0.975	24.576	-12.481	-12.481	0.000	0.000	0.000	0.000
58	E	59	GLY	0	0.025	0.024	25.941	-0.206	-0.206	0.000	0.000	0.000	0.000
59	E	61	ARG	1	0.838	0.917	26.284	11.008	11.008	0.000	0.000	0.000	0.000
60	E	62	PHE	0	-0.018	0.007	21.590	-0.372	-0.372	0.000	0.000	0.000	0.000
61	E	63	THR	0	-0.021	-0.026	21.830	0.492	0.492	0.000	0.000	0.000	0.000
62	E	64	ILE	0	-0.036	0.005	15.925	-0.653	-0.653	0.000	0.000	0.000	0.000
63	E	65	PHE	0	0.041	0.014	18.299	0.765	0.765	0.000	0.000	0.000	0.000
64	E	66	PHE	0	-0.030	-0.029	11.529	-1.296	-1.296	0.000	0.000	0.000	0.000
65	E	67	ASN	0	0.027	0.006	15.085	0.404	0.404	0.000	0.000	0.000	0.000
66	E	68	LYS	1	1.010	1.000	13.696	17.219	17.219	0.000	0.000	0.000	0.000
67	E	69	ARG	1	0.905	0.929	12.587	18.341	18.341	0.000	0.000	0.000	0.000
68	E	70	GLU	-1	-0.813	-0.872	13.176	-18.095	-18.095	0.000	0.000	0.000	0.000
69	E	71	LYS	1	0.786	0.882	7.581	33.341	33.341	0.000	0.000	0.000	0.000
70	E	72	LYS	1	0.886	0.937	9.336	17.326	17.326	0.000	0.000	0.000	0.000
71	E	73	LEU	0	-0.017	-0.016	11.331	1.310	1.310	0.000	0.000	0.000	0.000
72	E	74	SER	0	-0.001	-0.013	13.054	-0.613	-0.613	0.000	0.000	0.000	0.000
73	E	75	LEU	0	-0.023	0.012	15.597	0.532	0.532	0.000	0.000	0.000	0.000
74	E	76	HIS	0	-0.002	-0.007	17.347	0.334	0.334	0.000	0.000	0.000	0.000
75	E	77	ILE	0	0.023	0.001	19.826	-0.047	-0.047	0.000	0.000	0.000	0.000
76	E	78	THR	0	0.036	0.005	23.044	0.245	0.245	0.000	0.000	0.000	0.000
77	E	79	ASP	-1	-0.895	-0.954	26.478	-9.851	-9.851	0.000	0.000	0.000	0.000
78	E	80	SER	0	-0.023	-0.007	25.293	0.055	0.055	0.000	0.000	0.000	0.000
79	E	81	GLN	0	0.105	0.074	27.166	0.296	0.296	0.000	0.000	0.000	0.000
80	E	82	PRO	0	0.029	0.031	27.411	-0.521	-0.521	0.000	0.000	0.000	0.000
81	E	83	GLY	0	-0.043	-0.030	27.488	0.220	0.220	0.000	0.000	0.000	0.000
82	E	84	ASP	-1	-0.786	-0.891	23.875	-12.259	-12.259	0.000	0.000	0.000	0.000
83	E	85	SER	0	0.004	0.016	22.758	-0.716	-0.716	0.000	0.000	0.000	0.000
84	E	86	ALA	0	-0.026	-0.009	20.397	0.248	0.248	0.000	0.000	0.000	0.000
85	E	87	THR	0	-0.027	-0.010	14.552	-0.173	-0.173	0.000	0.000	0.000	0.000
86	E	88	TYR	0	0.006	-0.033	15.454	-0.242	-0.242	0.000	0.000	0.000	0.000
87	E	89	PHE	0	-0.013	0.002	10.696	-0.993	-0.993	0.000	0.000	0.000	0.000
88	E	91	ALA	0	-0.002	-0.006	8.678	-3.315	-3.315	0.000	0.000	0.000	0.000
89	E	92	ALA	0	-0.022	-0.020	7.164	1.460	1.460	0.000	0.000	0.000	0.000
90	E	93	THR	0	-0.025	-0.050	7.562	-4.330	-4.330	0.000	0.000	0.000	0.000
91	E	99	GLY	0	0.105	0.067	8.903	1.880	1.880	0.000	0.000	0.000	0.000
92	E	100	SER	0	-0.117	-0.067	10.567	-1.123	-1.123	0.000	0.000	0.000	0.000
93	E	101	PHE	0	0.049	0.034	12.828	0.676	0.676	0.000	0.000	0.000	0.000
94	E	102	ASN	0	0.041	0.027	16.017	0.148	0.148	0.000	0.000	0.000	0.000
95	E	103	LYS	1	0.967	0.992	9.011	31.266	31.266	0.000	0.000	0.000	0.000
96	E	104	LEU	0	-0.009	0.016	10.459	-0.538	-0.538	0.000	0.000	0.000	0.000
98	E	106	PHE	0	0.024	0.003	6.763	-0.657	-0.657	0.000	0.000	0.000	0.000
99	E	107	GLY	0	0.002	0.005	5.127	-6.549	-6.549	0.000	0.000	0.000	0.000
100	E	108	ALA	0	-0.036	-0.036	6.198	2.657	2.657	0.000	0.000	0.000	0.000
101	E	109	GLY	0	0.036	0.034	7.659	2.294	2.294	0.000	0.000	0.000	0.000
102	E	110	THR	0	-0.039	-0.033	11.169	0.031	0.031	0.000	0.000	0.000	0.000
103	E	111	ARG	1	0.943	0.978	13.666	15.434	15.434	0.000	0.000	0.000	0.000
104	E	112	LEU	0	0.017	0.019	17.274	-0.179	-0.179	0.000	0.000	0.000	0.000
105	E	113	ALA	0	-0.039	-0.029	20.059	0.207	0.207	0.000	0.000	0.000	0.000
106	E	114	VAL	0	0.006	0.003	23.670	-0.073	-0.073	0.000	0.000	0.000	0.000
107	E	115	SER	0	-0.033	-0.021	26.214	0.097	0.097	0.000	0.000	0.000	0.000
108	E	116	PRO	0	-0.003	0.001	29.265	-0.021	-0.021	0.000	0.000	0.000	0.000
109	E	117	TYR	-1	-0.927	-0.959	32.785	-8.500	-8.500	0.000	0.000	0.000	0.000

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