FMO DATABASE

FMODB ID: Z911N

Calculation Name: 1LK2-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-l-fucopyranose | phosphate ion | (4s)-2-methyl-2,4-pentanediol | (4r)-2-methylpentane-2,4-diol

Ligand 3-letter code: NAG | FUC | PO4 | MPD | MRD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LK2

Chain ID: B

ChEMBL ID:

UniProt ID: P01887

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-775119.767889
FMO2-HF: Nuclear repulsion	733136.171005
FMO2-HF: Total energy	-41983.596884
FMO2-MP2: Total energy	-42102.447033

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(B:1:ILE)

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

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.
-29.631	-19.513	3.868	-5.372	-8.615	-0.062

Interaction energy analysis for fragmet #1(B:1:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.893

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	B	3	LYS	1	0.799	0.880	2.297	20.537	26.310	2.145	-3.761	-4.156	-0.047
4	B	4	THR	0	0.066	0.027	4.660	2.906	2.982	-0.001	-0.017	-0.058	0.000
31	B	31	HIS	0	0.042	0.000	2.822	-8.512	-5.527	1.666	-1.225	-3.427	-0.013
32	B	32	PRO	0	0.062	0.035	4.949	-5.755	-5.681	-0.001	-0.020	-0.053	0.000
60	B	60	TRP	0	-0.019	-0.012	3.303	-6.877	-5.936	0.060	-0.299	-0.702	-0.002
61	B	61	SER	0	-0.086	-0.034	4.026	-1.475	-1.260	0.000	-0.046	-0.169	0.000
62	B	62	PHE	0	0.039	0.007	5.080	4.105	4.159	-0.001	-0.004	-0.050	0.000
5	B	5	PRO	0	-0.025	0.001	8.388	0.120	0.120	0.000	0.000	0.000	0.000
6	B	6	GLN	0	-0.013	0.002	10.968	2.954	2.954	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.024	-0.020	13.124	0.238	0.238	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.021	0.013	16.319	1.001	1.001	0.000	0.000	0.000	0.000
9	B	9	VAL	0	-0.002	-0.013	19.168	0.072	0.072	0.000	0.000	0.000	0.000
10	B	10	TYR	0	0.055	0.031	20.444	0.092	0.092	0.000	0.000	0.000	0.000
11	B	11	SER	0	0.018	0.002	25.376	-0.100	-0.100	0.000	0.000	0.000	0.000
12	B	12	ARG	1	0.893	0.947	28.247	9.730	9.730	0.000	0.000	0.000	0.000
13	B	13	HIS	0	-0.006	0.001	29.207	0.015	0.015	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.082	0.037	32.151	-0.188	-0.188	0.000	0.000	0.000	0.000
15	B	15	PRO	0	-0.017	0.004	32.519	0.184	0.184	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.828	-0.903	34.970	-7.425	-7.425	0.000	0.000	0.000	0.000
17	B	17	ASN	0	-0.020	-0.028	38.536	-0.270	-0.270	0.000	0.000	0.000	0.000
18	B	18	GLY	0	-0.016	-0.009	39.829	0.194	0.194	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.855	0.931	38.598	7.921	7.921	0.000	0.000	0.000	0.000
20	B	20	PRO	0	-0.010	-0.008	37.151	-0.245	-0.245	0.000	0.000	0.000	0.000
21	B	21	ASN	0	-0.008	-0.006	32.219	-0.193	-0.193	0.000	0.000	0.000	0.000
22	B	22	ILE	0	0.025	0.009	27.718	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	23	LEU	0	0.000	0.015	26.341	-0.107	-0.107	0.000	0.000	0.000	0.000
24	B	24	ASN	0	-0.031	-0.033	22.746	-0.152	-0.152	0.000	0.000	0.000	0.000
25	B	25	CYS	0	-0.073	-0.036	19.663	-0.204	-0.204	0.000	0.000	0.000	0.000
26	B	26	TYR	0	0.031	0.035	15.896	-0.543	-0.543	0.000	0.000	0.000	0.000
27	B	27	VAL	0	-0.007	-0.009	12.932	-0.391	-0.391	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.006	-0.012	11.345	-0.571	-0.571	0.000	0.000	0.000	0.000
29	B	29	GLN	0	0.002	0.000	7.580	-2.017	-2.017	0.000	0.000	0.000	0.000
30	B	30	PHE	0	0.011	0.019	6.437	-4.772	-4.772	0.000	0.000	0.000	0.000
33	B	33	PRO	0	0.001	-0.005	5.909	1.237	1.237	0.000	0.000	0.000	0.000
34	B	34	HIS	0	0.011	0.024	8.709	2.256	2.256	0.000	0.000	0.000	0.000
35	B	35	ILE	0	0.000	-0.010	11.234	-1.390	-1.390	0.000	0.000	0.000	0.000
36	B	36	GLU	-1	-0.883	-0.906	13.613	-14.152	-14.152	0.000	0.000	0.000	0.000
37	B	37	ILE	0	0.033	0.002	15.269	-0.364	-0.364	0.000	0.000	0.000	0.000
38	B	38	GLN	0	-0.037	-0.017	19.117	0.900	0.900	0.000	0.000	0.000	0.000
39	B	39	MET	0	0.028	0.037	22.754	-0.186	-0.186	0.000	0.000	0.000	0.000
40	B	40	LEU	0	-0.039	-0.024	24.934	0.353	0.353	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.928	0.964	27.889	8.758	8.758	0.000	0.000	0.000	0.000
42	B	42	ASN	0	-0.005	-0.011	31.471	-0.011	-0.011	0.000	0.000	0.000	0.000
43	B	43	GLY	0	0.016	0.017	29.591	0.162	0.162	0.000	0.000	0.000	0.000
44	B	44	LYS	1	0.945	0.980	29.937	8.730	8.730	0.000	0.000	0.000	0.000
45	B	45	LYS	1	0.965	0.977	25.732	11.720	11.720	0.000	0.000	0.000	0.000
46	B	46	ILE	0	0.010	0.012	28.285	0.424	0.424	0.000	0.000	0.000	0.000
47	B	47	PRO	0	-0.048	-0.028	28.873	-0.330	-0.330	0.000	0.000	0.000	0.000
48	B	48	LYS	1	0.944	0.942	29.886	9.420	9.420	0.000	0.000	0.000	0.000
49	B	49	VAL	0	0.006	0.028	24.153	0.028	0.028	0.000	0.000	0.000	0.000
50	B	50	GLU	-1	-0.896	-0.937	25.214	-10.991	-10.991	0.000	0.000	0.000	0.000
51	B	51	MET	0	-0.048	-0.022	18.385	-0.294	-0.294	0.000	0.000	0.000	0.000
52	B	52	SER	0	-0.018	-0.041	20.391	0.444	0.444	0.000	0.000	0.000	0.000
53	B	53	ASP	-1	-0.827	-0.900	18.386	-14.339	-14.339	0.000	0.000	0.000	0.000
54	B	54	MET	0	-0.031	-0.009	12.148	-0.523	-0.523	0.000	0.000	0.000	0.000
55	B	55	SER	0	-0.039	-0.011	12.758	0.412	0.412	0.000	0.000	0.000	0.000
56	B	56	PHE	0	0.025	-0.004	7.399	-1.323	-1.323	0.000	0.000	0.000	0.000
57	B	57	SER	0	-0.009	-0.004	7.375	1.903	1.903	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.960	0.953	7.817	17.409	17.409	0.000	0.000	0.000	0.000
59	B	59	ASP	-1	-0.792	-0.849	4.849	-37.179	-37.179	0.000	0.000	0.000	0.000
63	B	63	TYR	0	-0.015	-0.021	8.346	0.144	0.144	0.000	0.000	0.000	0.000
64	B	64	ILE	0	-0.013	0.000	11.942	0.530	0.530	0.000	0.000	0.000	0.000
65	B	65	LEU	0	-0.010	0.013	15.251	-0.191	-0.191	0.000	0.000	0.000	0.000
66	B	66	ALA	0	0.040	0.021	18.857	0.389	0.389	0.000	0.000	0.000	0.000
67	B	67	HIS	1	0.892	0.927	21.144	12.122	12.122	0.000	0.000	0.000	0.000
68	B	68	THR	0	-0.018	-0.029	24.725	0.125	0.125	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.902	-0.928	28.397	-9.020	-9.020	0.000	0.000	0.000	0.000
70	B	70	PHE	0	-0.050	-0.033	31.313	-0.114	-0.114	0.000	0.000	0.000	0.000
71	B	71	THR	0	0.010	0.001	33.308	0.254	0.254	0.000	0.000	0.000	0.000
72	B	72	PRO	0	-0.030	0.019	34.294	-0.018	-0.018	0.000	0.000	0.000	0.000
73	B	73	THR	0	0.026	0.000	36.010	0.255	0.255	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.846	-0.912	37.547	-8.286	-8.286	0.000	0.000	0.000	0.000
75	B	75	THR	0	0.006	-0.007	37.759	-0.167	-0.167	0.000	0.000	0.000	0.000
76	B	76	ASP	-1	-0.870	-0.908	35.136	-8.678	-8.678	0.000	0.000	0.000	0.000
77	B	77	THR	0	0.002	0.002	31.388	-0.290	-0.290	0.000	0.000	0.000	0.000
78	B	78	TYR	0	0.019	-0.007	28.800	0.054	0.054	0.000	0.000	0.000	0.000
79	B	79	ALA	0	0.000	0.007	25.204	-0.132	-0.132	0.000	0.000	0.000	0.000
80	B	81	ARG	1	0.941	0.975	20.817	13.187	13.187	0.000	0.000	0.000	0.000
81	B	82	VAL	0	0.007	-0.005	14.737	0.065	0.065	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.834	0.900	16.112	15.340	15.340	0.000	0.000	0.000	0.000
83	B	84	HIS	0	0.063	0.026	7.111	1.191	1.191	0.000	0.000	0.000	0.000
84	B	85	ASP	-1	-0.848	-0.916	9.728	-25.456	-25.456	0.000	0.000	0.000	0.000
85	B	86	SER	0	-0.081	-0.048	7.559	-0.407	-0.407	0.000	0.000	0.000	0.000
86	B	87	MET	0	-0.102	-0.050	9.497	1.069	1.069	0.000	0.000	0.000	0.000
87	B	88	ALA	0	0.026	0.019	13.160	0.567	0.567	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-0.917	-0.948	15.988	-13.555	-13.555	0.000	0.000	0.000	0.000
89	B	90	PRO	0	-0.085	-0.059	17.186	-0.794	-0.794	0.000	0.000	0.000	0.000
90	B	91	LYS	1	1.012	1.027	14.765	20.520	20.520	0.000	0.000	0.000	0.000
91	B	92	THR	0	-0.039	-0.035	18.399	0.159	0.159	0.000	0.000	0.000	0.000
92	B	93	VAL	0	-0.005	0.001	18.952	-0.044	-0.044	0.000	0.000	0.000	0.000
93	B	94	TYR	0	0.021	-0.008	22.098	0.082	0.082	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.011	-0.023	25.099	-0.196	-0.196	0.000	0.000	0.000	0.000
95	B	96	ASP	-1	-0.868	-0.930	26.588	-10.551	-10.551	0.000	0.000	0.000	0.000
96	B	97	ARG	1	0.794	0.877	28.492	8.740	8.740	0.000	0.000	0.000	0.000
97	B	98	ASP	-1	-0.924	-0.966	31.297	-8.965	-8.965	0.000	0.000	0.000	0.000
98	B	99	MET	-1	-0.996	-0.977	23.266	-10.902	-10.902	0.000	0.000	0.000	0.000

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