FMO DATABASE

FMODB ID: 8G4RY

Calculation Name: 1LMQ-A-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: 1LMQ

Chain ID: A

ChEMBL ID:

UniProt ID: P11941

Base Structure: X-ray

Registration Date: 2025-10-03

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1121145.647176
FMO2-HF: Nuclear repulsion	1069384.79864
FMO2-HF: Total energy	-51760.848536
FMO2-MP2: Total energy	-51906.507373

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(A:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
-277.722	-271.248	55.614	-29.251	-32.837	-0.342

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.606 / q_NPA : 1.791

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	A	3	TYR	0	-0.058	-0.048	2.572	-27.875	-22.328	10.267	-4.573	-11.241	-0.046
4	A	4	ASP	-1	-0.786	-0.897	3.574	-46.989	-46.680	0.025	0.037	-0.370	-0.001
7	A	7	GLU	-1	-0.854	-0.910	1.760	-170.525	-174.640	18.924	-8.908	-5.901	-0.106
39	A	39	ASN	0	0.040	0.021	3.896	-29.065	-28.923	0.000	-0.108	-0.034	0.000
40	A	40	THR	0	0.031	0.008	1.911	-12.366	-11.308	6.275	-3.628	-3.705	-0.042
41	A	41	GLN	0	-0.002	-0.012	2.218	-13.174	-10.488	2.638	-2.516	-2.808	-0.034
42	A	42	ALA	0	-0.006	0.018	4.773	8.350	8.417	-0.001	-0.006	-0.060	0.000
84	A	85	THR	0	-0.041	-0.020	4.425	-10.983	-10.878	-0.001	-0.013	-0.091	0.000
85	A	86	ASP	-1	-0.799	-0.906	1.765	-173.736	-173.863	17.444	-9.329	-7.989	-0.108
86	A	87	ASP	-1	-0.827	-0.875	3.298	-61.618	-60.816	0.043	-0.207	-0.638	-0.005
5	A	5	ARG	1	0.854	0.912	5.814	40.041	40.041	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.082	-0.045	8.629	2.234	2.234	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.010	0.007	6.002	1.833	1.833	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.014	-0.002	6.845	4.327	4.327	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.981	0.992	7.002	58.069	58.069	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.032	0.027	6.650	3.160	3.160	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.002	-0.004	8.807	3.906	3.906	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.861	0.932	11.383	34.787	34.787	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.007	0.005	11.508	2.409	2.409	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.032	-0.016	11.106	1.442	1.442	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.007	0.010	13.788	1.554	1.554	0.000	0.000	0.000	0.000
17	A	17	MET	0	-0.019	-0.018	13.303	1.686	1.686	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.882	-0.935	16.355	-29.265	-29.265	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.040	0.019	18.228	0.938	0.938	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.029	-0.005	19.198	1.122	1.122	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.007	-0.008	21.122	-0.420	-0.420	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.041	0.028	24.111	0.492	0.492	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.060	-0.029	20.296	0.452	0.452	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.060	0.031	19.831	-1.329	-1.329	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.019	-0.008	12.954	-0.683	-0.683	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.023	-0.020	15.476	-2.083	-2.083	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.019	0.021	16.864	-0.352	-0.352	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.045	0.025	13.682	-1.607	-1.607	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.006	0.020	11.358	-2.836	-2.836	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.071	-0.012	12.914	-2.540	-2.540	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.024	0.006	14.194	-0.712	-0.712	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.001	-0.017	9.859	-1.782	-1.782	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.878	0.959	11.125	36.611	36.611	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.060	-0.070	12.646	0.181	0.181	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.822	-0.908	13.185	-33.421	-33.421	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.035	-0.037	8.376	-1.597	-1.597	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.059	-0.021	9.116	-2.737	-2.737	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.005	-0.009	6.386	-1.347	-1.347	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.047	-0.032	7.943	2.358	2.358	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.021	0.017	11.175	0.894	0.894	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.888	0.952	14.844	29.025	29.025	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.008	-0.007	18.184	0.872	0.872	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.041	-0.002	21.298	0.162	0.162	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.865	-0.897	23.385	-23.951	-23.951	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.003	0.001	23.457	0.426	0.426	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.085	-0.058	20.514	-1.167	-1.167	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.025	-0.017	14.567	-0.035	-0.035	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.796	-0.853	14.557	-32.062	-32.062	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.018	-0.067	10.820	-2.121	-2.121	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.072	0.048	7.373	1.628	1.628	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.016	-0.002	5.470	2.883	2.883	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.013	0.001	8.097	2.209	2.209	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.013	-0.017	10.148	5.589	5.589	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.007	0.009	12.721	3.032	3.032	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.016	-0.017	14.693	0.336	0.336	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.022	-0.038	17.347	0.628	0.628	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.926	0.980	18.625	23.260	23.260	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.031	-0.016	21.197	1.332	1.332	0.000	0.000	0.000	0.000
63	A	63	TRP	0	0.048	0.022	17.944	0.387	0.387	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.070	-0.017	13.737	-1.925	-1.925	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.810	-0.899	17.998	-26.640	-26.640	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.744	-0.853	16.700	-31.563	-31.563	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.013	-0.001	18.155	0.098	0.098	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.857	0.925	16.471	32.059	32.059	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.008	0.008	20.254	0.418	0.418	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.021	0.018	22.889	0.489	0.489	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.002	-0.014	26.303	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.005	-0.001	22.791	0.046	0.046	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.876	0.933	24.078	21.679	21.679	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.015	0.007	20.228	-0.440	-0.440	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.043	0.013	22.144	0.173	0.173	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.104	-0.030	14.962	2.615	2.615	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.015	0.028	19.797	-0.580	-0.580	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.045	-0.022	14.422	-0.461	-0.461	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.931	0.948	15.253	29.399	29.399	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.047	0.019	10.881	-2.585	-2.585	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.001	-0.006	9.721	-2.707	-2.707	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.020	-0.007	9.668	-1.661	-1.661	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.027	-0.007	6.085	-3.050	-3.050	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.062	0.022	5.168	1.519	1.519	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.049	-0.030	7.928	6.205	6.205	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.029	-0.022	11.283	3.933	3.933	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.037	0.016	9.637	2.828	2.828	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.019	-0.002	9.935	3.000	3.000	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.949	0.981	13.283	37.598	37.598	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.042	0.013	14.666	1.999	1.999	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.851	0.913	16.214	35.518	35.518	0.000	0.000	0.000	0.000
95	A	97	ARG	1	0.824	0.883	19.121	26.301	26.301	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.009	0.002	18.054	1.517	1.517	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.052	-0.027	20.189	1.190	1.190	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.020	-0.006	22.840	0.835	0.835	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.801	-0.859	25.199	-22.177	-22.177	0.000	0.000	0.000	0.000
100	A	102	PRO	0	-0.002	-0.019	27.067	-0.410	-0.410	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.015	0.003	26.126	0.796	0.796	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.025	0.024	25.074	-0.296	-0.296	0.000	0.000	0.000	0.000
103	A	105	ILE	0	0.006	-0.009	18.714	-0.813	-0.813	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.027	0.018	21.995	-0.808	-0.808	0.000	0.000	0.000	0.000
105	A	107	ALA	0	-0.033	-0.008	21.560	0.506	0.506	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.058	-0.027	15.383	0.495	0.495	0.000	0.000	0.000	0.000
107	A	109	VAL	0	0.011	0.002	19.737	1.227	1.227	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.003	-0.001	17.452	1.083	1.083	0.000	0.000	0.000	0.000
109	A	111	TRP	0	0.023	-0.016	19.255	0.553	0.553	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.912	0.943	20.544	25.462	25.462	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.017	0.000	22.773	0.818	0.818	0.000	0.000	0.000	0.000
112	A	114	HIS	1	0.856	0.932	19.731	29.485	29.485	0.000	0.000	0.000	0.000
113	A	116	GLN	0	0.063	0.030	21.834	0.180	0.180	0.000	0.000	0.000	0.000
114	A	117	ASN	0	-0.041	-0.032	25.119	0.178	0.178	0.000	0.000	0.000	0.000
115	A	118	GLN	0	-0.002	0.027	23.697	1.244	1.244	0.000	0.000	0.000	0.000
116	A	119	ASP	-1	-0.860	-0.933	25.049	-24.521	-24.521	0.000	0.000	0.000	0.000
117	A	120	LEU	0	-0.033	-0.021	19.818	-1.194	-1.194	0.000	0.000	0.000	0.000
118	A	121	ARG	1	0.966	0.978	19.675	23.499	23.499	0.000	0.000	0.000	0.000
119	A	122	SER	0	0.029	0.010	19.874	-1.170	-1.170	0.000	0.000	0.000	0.000
120	A	123	TYR	0	0.051	0.035	15.100	-2.046	-2.046	0.000	0.000	0.000	0.000
121	A	124	VAL	0	0.044	0.021	14.577	-2.826	-2.826	0.000	0.000	0.000	0.000
122	A	125	ALA	0	0.000	0.011	16.104	0.100	0.100	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.027	0.005	16.042	-1.595	-1.595	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.005	0.010	13.401	-1.379	-1.379	0.000	0.000	0.000	0.000
125	A	129	VAL	-1	-0.900	-0.936	13.440	-31.994	-31.994	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)