FMO DATABASE

FMODB ID: JKMM9

Calculation Name: 6ZRK-D-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG | BMA | MAN | FUC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6ZRK

Chain ID: D

ChEMBL ID:

UniProt ID:

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1336370.138133
FMO2-HF: Nuclear repulsion	1270425.526005
FMO2-HF: Total energy	-65944.612128
FMO2-MP2: Total energy	-66132.968999

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(D:328:GLY)

Summations of interaction energy for fragment #1(D:328:GLY)

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.
-284.995	-279.353	8.969	-7.534	-7.076	-0.093

Interaction energy analysis for fragmet #1(D:328:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.894

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	D	330	PHE	0	-0.027	-0.020	3.456	12.916	14.132	-0.005	-0.552	-0.658	-0.002
4	D	331	GLY	0	-0.018	-0.009	2.532	11.031	11.788	0.118	-0.368	-0.506	-0.001
5	D	332	ALA	0	0.008	0.011	3.694	10.108	10.277	0.000	0.007	-0.176	0.000
6	D	333	ILE	0	-0.004	-0.018	3.951	5.253	5.438	-0.001	-0.040	-0.144	0.000
7	D	334	ALA	0	-0.043	-0.020	2.693	-25.131	-23.311	0.391	-1.126	-1.085	-0.013
8	D	335	GLY	0	-0.023	-0.006	4.594	-6.146	-6.081	-0.001	-0.015	-0.049	0.000
109	D	436	ASP	-1	-0.832	-0.923	3.068	-69.287	-67.976	0.126	-0.750	-0.688	-0.006
110	D	437	GLU	-1	-0.863	-0.927	4.982	-23.642	-23.671	-0.001	-0.002	0.033	0.000
112	D	439	ASP	-1	-0.741	-0.866	1.911	-116.361	-116.220	8.343	-4.687	-3.798	-0.071
113	D	440	SER	0	-0.042	-0.010	5.299	4.046	4.053	-0.001	-0.001	-0.005	0.000
9	D	336	PHE	0	-0.056	-0.017	5.465	5.745	5.745	0.000	0.000	0.000	0.000
10	D	337	ILE	0	-0.014	-0.006	7.432	4.739	4.739	0.000	0.000	0.000	0.000
11	D	338	GLU	-1	-0.940	-0.970	7.646	-29.391	-29.391	0.000	0.000	0.000	0.000
12	D	339	GLY	0	-0.014	-0.015	8.765	-1.235	-1.235	0.000	0.000	0.000	0.000
13	D	340	GLY	0	-0.003	0.008	10.350	0.496	0.496	0.000	0.000	0.000	0.000
14	D	341	TRP	0	0.010	-0.010	12.199	1.204	1.204	0.000	0.000	0.000	0.000
15	D	342	SER	0	0.007	-0.007	16.036	0.102	0.102	0.000	0.000	0.000	0.000
16	D	343	GLY	0	0.015	0.012	18.070	0.560	0.560	0.000	0.000	0.000	0.000
17	D	344	MET	0	-0.080	-0.023	14.703	0.963	0.963	0.000	0.000	0.000	0.000
18	D	345	ILE	0	-0.009	0.004	18.004	-0.707	-0.707	0.000	0.000	0.000	0.000
19	D	346	ASP	-1	-0.914	-0.951	20.298	-13.367	-13.367	0.000	0.000	0.000	0.000
20	D	347	GLY	0	0.007	-0.021	18.524	0.383	0.383	0.000	0.000	0.000	0.000
21	D	348	TRP	0	-0.010	0.001	12.936	-0.486	-0.486	0.000	0.000	0.000	0.000
22	D	349	TYR	0	0.001	-0.030	10.797	-1.617	-1.617	0.000	0.000	0.000	0.000
23	D	350	GLY	0	0.030	0.008	14.242	1.523	1.523	0.000	0.000	0.000	0.000
24	D	351	PHE	0	0.007	0.004	15.988	-0.874	-0.874	0.000	0.000	0.000	0.000
25	D	352	HIS	0	0.012	0.009	18.634	0.139	0.139	0.000	0.000	0.000	0.000
26	D	353	HIS	0	0.031	0.005	20.452	-0.544	-0.544	0.000	0.000	0.000	0.000
27	D	354	SER	0	-0.007	-0.003	23.555	0.331	0.331	0.000	0.000	0.000	0.000
28	D	355	ASN	0	0.047	0.010	26.356	0.038	0.038	0.000	0.000	0.000	0.000
29	D	356	SER	0	-0.037	-0.038	29.639	0.166	0.166	0.000	0.000	0.000	0.000
30	D	357	GLU	-1	-0.886	-0.922	32.488	-9.218	-9.218	0.000	0.000	0.000	0.000
31	D	358	GLY	0	0.010	0.021	31.253	0.088	0.088	0.000	0.000	0.000	0.000
32	D	359	THR	0	-0.023	-0.038	25.376	-0.449	-0.449	0.000	0.000	0.000	0.000
33	D	360	GLY	0	-0.013	0.011	25.670	0.441	0.441	0.000	0.000	0.000	0.000
34	D	361	MET	0	-0.034	-0.013	19.904	-0.649	-0.649	0.000	0.000	0.000	0.000
35	D	362	ALA	0	-0.010	-0.001	21.117	0.547	0.547	0.000	0.000	0.000	0.000
36	D	363	ALA	0	0.047	0.029	18.626	-0.688	-0.688	0.000	0.000	0.000	0.000
37	D	364	ASP	-1	-0.812	-0.889	17.579	-15.499	-15.499	0.000	0.000	0.000	0.000
38	D	365	GLN	0	0.004	-0.017	18.807	-0.672	-0.672	0.000	0.000	0.000	0.000
39	D	366	LYS	1	0.851	0.941	20.118	15.403	15.403	0.000	0.000	0.000	0.000
40	D	367	SER	0	0.003	-0.038	15.271	-0.501	-0.501	0.000	0.000	0.000	0.000
41	D	368	THR	0	-0.003	-0.006	16.401	-1.205	-1.205	0.000	0.000	0.000	0.000
42	D	369	GLN	0	-0.035	-0.026	17.573	-0.243	-0.243	0.000	0.000	0.000	0.000
43	D	370	GLU	-1	-0.854	-0.922	17.759	-16.694	-16.694	0.000	0.000	0.000	0.000
44	D	371	ALA	0	-0.035	-0.015	14.015	-0.344	-0.344	0.000	0.000	0.000	0.000
45	D	372	ILE	0	0.012	0.009	15.772	-0.164	-0.164	0.000	0.000	0.000	0.000
46	D	373	ASP	-1	-0.837	-0.898	18.506	-13.676	-13.676	0.000	0.000	0.000	0.000
47	D	374	LYS	1	0.893	0.947	14.776	20.280	20.280	0.000	0.000	0.000	0.000
48	D	375	ILE	0	0.013	0.008	14.072	0.230	0.230	0.000	0.000	0.000	0.000
49	D	376	THR	0	-0.010	-0.012	16.733	0.645	0.645	0.000	0.000	0.000	0.000
50	D	377	ASN	0	-0.024	-0.019	20.187	0.990	0.990	0.000	0.000	0.000	0.000
51	D	378	LYS	1	0.773	0.875	12.510	22.679	22.679	0.000	0.000	0.000	0.000
52	D	379	VAL	0	0.025	0.009	18.175	0.442	0.442	0.000	0.000	0.000	0.000
53	D	380	ASN	0	0.016	0.001	20.388	0.596	0.596	0.000	0.000	0.000	0.000
54	D	381	ASN	0	-0.044	-0.021	21.459	1.018	1.018	0.000	0.000	0.000	0.000
55	D	382	ILE	0	0.013	0.009	17.544	0.339	0.339	0.000	0.000	0.000	0.000
56	D	383	VAL	0	0.002	0.002	22.215	0.417	0.417	0.000	0.000	0.000	0.000
57	D	384	ASP	-1	-0.806	-0.879	25.474	-10.284	-10.284	0.000	0.000	0.000	0.000
58	D	385	LYS	1	0.754	0.843	24.630	12.179	12.179	0.000	0.000	0.000	0.000
59	D	386	MET	0	-0.008	0.010	23.306	0.199	0.199	0.000	0.000	0.000	0.000
60	D	387	ASN	0	-0.042	-0.014	27.592	0.287	0.287	0.000	0.000	0.000	0.000
61	D	388	ARG	1	0.809	0.897	30.067	10.305	10.305	0.000	0.000	0.000	0.000
62	D	389	GLU	-1	-0.949	-0.969	33.043	-7.987	-7.987	0.000	0.000	0.000	0.000
63	D	390	PHE	0	-0.003	-0.012	34.758	-0.013	-0.013	0.000	0.000	0.000	0.000
64	D	391	GLU	-1	-0.973	-0.985	36.770	-7.323	-7.323	0.000	0.000	0.000	0.000
65	D	392	VAL	0	0.010	0.009	38.316	0.023	0.023	0.000	0.000	0.000	0.000
66	D	393	VAL	0	-0.022	-0.001	41.101	0.073	0.073	0.000	0.000	0.000	0.000
67	D	394	ASN	0	-0.011	0.000	44.861	-0.057	-0.057	0.000	0.000	0.000	0.000
68	D	395	HIS	0	0.001	-0.002	46.161	0.265	0.265	0.000	0.000	0.000	0.000
69	D	396	GLU	-1	-0.964	-0.975	49.278	-5.943	-5.943	0.000	0.000	0.000	0.000
70	D	397	PHE	0	0.004	-0.009	48.552	0.070	0.070	0.000	0.000	0.000	0.000
71	D	398	SER	0	-0.034	-0.048	53.984	0.057	0.057	0.000	0.000	0.000	0.000
72	D	399	GLU	-1	-0.865	-0.950	56.177	-5.692	-5.692	0.000	0.000	0.000	0.000
73	D	400	VAL	0	-0.067	-0.037	57.899	-0.004	-0.004	0.000	0.000	0.000	0.000
74	D	401	GLU	-1	-0.850	-0.895	54.514	-5.673	-5.673	0.000	0.000	0.000	0.000
75	D	402	LYS	1	0.883	0.948	52.631	5.627	5.627	0.000	0.000	0.000	0.000
76	D	403	ARG	1	0.939	0.966	50.926	5.623	5.623	0.000	0.000	0.000	0.000
77	D	404	ILE	0	0.011	0.006	49.880	-0.102	-0.102	0.000	0.000	0.000	0.000
78	D	405	ASN	0	0.048	0.030	48.866	-0.181	-0.181	0.000	0.000	0.000	0.000
79	D	406	MET	0	0.039	0.019	45.902	-0.104	-0.104	0.000	0.000	0.000	0.000
80	D	407	ILE	0	-0.108	-0.060	45.135	-0.155	-0.155	0.000	0.000	0.000	0.000
81	D	408	ASN	0	-0.008	-0.005	44.414	-0.080	-0.080	0.000	0.000	0.000	0.000
82	D	409	ASP	-1	-0.848	-0.922	42.990	-7.142	-7.142	0.000	0.000	0.000	0.000
83	D	410	LYS	1	0.912	0.964	40.681	7.095	7.095	0.000	0.000	0.000	0.000
84	D	411	ILE	0	-0.066	-0.032	39.473	-0.197	-0.197	0.000	0.000	0.000	0.000
85	D	412	ASP	-1	-0.839	-0.923	38.474	-7.791	-7.791	0.000	0.000	0.000	0.000
86	D	413	ASP	-1	-0.901	-0.950	36.872	-8.375	-8.375	0.000	0.000	0.000	0.000
87	D	414	GLN	0	-0.080	-0.058	35.013	-0.201	-0.201	0.000	0.000	0.000	0.000
88	D	415	ILE	0	-0.028	-0.013	33.877	-0.280	-0.280	0.000	0.000	0.000	0.000
89	D	416	GLU	-1	-0.942	-0.963	32.475	-9.419	-9.419	0.000	0.000	0.000	0.000
90	D	417	ASP	-1	-0.946	-0.971	30.694	-10.503	-10.503	0.000	0.000	0.000	0.000
91	D	418	LEU	0	-0.026	-0.019	29.005	-0.479	-0.479	0.000	0.000	0.000	0.000
92	D	419	TRP	0	0.002	-0.002	27.216	-0.666	-0.666	0.000	0.000	0.000	0.000
93	D	420	ALA	0	0.013	0.015	26.772	-0.467	-0.467	0.000	0.000	0.000	0.000
94	D	421	TYR	0	-0.016	-0.008	22.982	-0.828	-0.828	0.000	0.000	0.000	0.000
95	D	422	ASN	0	-0.047	-0.036	23.049	-0.868	-0.868	0.000	0.000	0.000	0.000
96	D	423	ALA	0	-0.013	-0.002	22.431	-0.598	-0.598	0.000	0.000	0.000	0.000
97	D	424	GLU	-1	-0.931	-0.968	20.464	-14.462	-14.462	0.000	0.000	0.000	0.000
98	D	425	LEU	0	-0.032	-0.008	17.851	-1.183	-1.183	0.000	0.000	0.000	0.000
99	D	426	LEU	0	0.020	0.004	17.441	-1.050	-1.050	0.000	0.000	0.000	0.000
100	D	427	VAL	0	0.015	0.006	16.512	-1.158	-1.158	0.000	0.000	0.000	0.000
101	D	428	LEU	0	-0.019	-0.007	14.245	-1.606	-1.606	0.000	0.000	0.000	0.000
102	D	429	LEU	0	0.002	0.000	12.485	-2.056	-2.056	0.000	0.000	0.000	0.000
103	D	430	GLU	-1	-0.768	-0.875	11.919	-21.848	-21.848	0.000	0.000	0.000	0.000
104	D	431	ASN	0	-0.018	0.017	11.471	-1.333	-1.333	0.000	0.000	0.000	0.000
105	D	432	GLN	0	-0.023	-0.002	7.400	-0.081	-0.081	0.000	0.000	0.000	0.000
106	D	433	LYS	1	0.832	0.896	7.092	17.531	17.531	0.000	0.000	0.000	0.000
107	D	434	THR	0	0.028	-0.004	8.474	-1.010	-1.010	0.000	0.000	0.000	0.000
108	D	435	LEU	0	-0.039	-0.007	5.186	-0.708	-0.708	0.000	0.000	0.000	0.000
111	D	438	HIS	0	0.028	0.045	7.239	1.187	1.187	0.000	0.000	0.000	0.000
114	D	441	ASN	0	-0.034	-0.028	8.132	3.565	3.565	0.000	0.000	0.000	0.000
115	D	442	VAL	0	0.011	0.013	7.550	2.415	2.415	0.000	0.000	0.000	0.000
116	D	443	LYS	1	0.868	0.922	7.182	32.733	32.733	0.000	0.000	0.000	0.000
117	D	444	ASN	0	-0.030	-0.017	9.025	2.897	2.897	0.000	0.000	0.000	0.000
118	D	445	LEU	0	0.020	0.017	12.399	1.738	1.738	0.000	0.000	0.000	0.000
119	D	446	PHE	0	0.007	0.014	11.438	1.294	1.294	0.000	0.000	0.000	0.000
120	D	447	ASP	-1	-0.808	-0.907	12.228	-23.631	-23.631	0.000	0.000	0.000	0.000
121	D	448	GLU	-1	-0.977	-0.976	14.630	-14.836	-14.836	0.000	0.000	0.000	0.000
122	D	449	VAL	0	0.026	0.012	17.034	1.193	1.193	0.000	0.000	0.000	0.000
123	D	450	LYS	1	0.870	0.932	15.754	20.209	20.209	0.000	0.000	0.000	0.000
124	D	451	ARG	1	0.868	0.928	15.512	19.305	19.305	0.000	0.000	0.000	0.000
125	D	452	ARG	1	0.823	0.928	20.699	14.920	14.920	0.000	0.000	0.000	0.000
126	D	453	LEU	0	0.026	0.009	20.590	0.714	0.714	0.000	0.000	0.000	0.000
127	D	454	SER	0	-0.025	-0.005	22.551	0.626	0.626	0.000	0.000	0.000	0.000
128	D	455	THR	0	-0.043	-0.037	23.720	-0.249	-0.249	0.000	0.000	0.000	0.000
129	D	456	ASN	0	-0.025	-0.008	26.129	0.206	0.206	0.000	0.000	0.000	0.000
130	D	457	ALA	0	-0.001	-0.004	22.636	0.227	0.227	0.000	0.000	0.000	0.000
131	D	458	ILE	0	-0.021	0.004	21.810	-0.155	-0.155	0.000	0.000	0.000	0.000
132	D	459	ASP	-1	-0.819	-0.898	15.987	-20.400	-20.400	0.000	0.000	0.000	0.000
133	D	460	ALA	0	0.008	0.004	18.077	0.302	0.302	0.000	0.000	0.000	0.000
134	D	461	GLY	0	-0.047	-0.023	14.545	-0.061	-0.061	0.000	0.000	0.000	0.000
135	D	462	ASN	0	0.017	-0.001	12.795	-1.771	-1.771	0.000	0.000	0.000	0.000
136	D	463	GLY	0	0.023	0.008	12.721	-0.467	-0.467	0.000	0.000	0.000	0.000
137	D	464	CYS	0	-0.065	-0.019	13.198	0.994	0.994	0.000	0.000	0.000	0.000
138	D	465	PHE	0	0.001	-0.022	15.896	-0.138	-0.138	0.000	0.000	0.000	0.000
139	D	466	ASP	-1	-0.902	-0.930	20.015	-13.503	-13.503	0.000	0.000	0.000	0.000
140	D	467	ILE	0	-0.036	-0.029	23.589	0.174	0.174	0.000	0.000	0.000	0.000
141	D	468	LEU	0	-0.027	-0.014	26.139	0.370	0.370	0.000	0.000	0.000	0.000
142	D	469	HIS	0	0.019	0.022	29.125	0.235	0.235	0.000	0.000	0.000	0.000
143	D	470	LYS	1	0.924	0.955	30.307	8.827	8.827	0.000	0.000	0.000	0.000
144	D	471	CYS	0	0.029	0.030	28.267	-0.275	-0.275	0.000	0.000	0.000	0.000
145	D	472	ASN	0	0.031	0.016	30.254	-0.376	-0.376	0.000	0.000	0.000	0.000
146	D	473	ASN	0	0.025	-0.017	30.090	-0.651	-0.651	0.000	0.000	0.000	0.000
147	D	474	GLU	-1	-0.924	-0.948	30.086	-9.217	-9.217	0.000	0.000	0.000	0.000
148	D	476	MET	0	-0.018	-0.006	25.857	-0.558	-0.558	0.000	0.000	0.000	0.000
149	D	477	GLU	-1	-0.867	-0.932	25.606	-12.329	-12.329	0.000	0.000	0.000	0.000
150	D	478	THR	0	-0.031	-0.013	26.654	-0.203	-0.203	0.000	0.000	0.000	0.000
151	D	479	ILE	0	-0.022	-0.019	22.228	-0.223	-0.223	0.000	0.000	0.000	0.000
152	D	480	LYS	1	0.782	0.907	21.911	12.385	12.385	0.000	0.000	0.000	0.000
153	D	481	ASN	0	0.020	0.018	22.494	-0.468	-0.468	0.000	0.000	0.000	0.000
154	D	482	GLY	0	0.013	0.006	24.055	0.114	0.114	0.000	0.000	0.000	0.000
155	D	483	THR	0	-0.069	-0.047	24.916	0.272	0.272	0.000	0.000	0.000	0.000
156	D	484	TYR	0	-0.056	-0.037	25.951	0.297	0.297	0.000	0.000	0.000	0.000
157	D	485	ASN	0	-0.007	0.000	27.363	-0.512	-0.512	0.000	0.000	0.000	0.000
158	D	486	HIS	0	0.044	0.009	27.340	0.148	0.148	0.000	0.000	0.000	0.000
159	D	487	LYS	1	0.807	0.902	29.417	9.824	9.824	0.000	0.000	0.000	0.000
160	D	488	GLU	-1	-0.864	-0.929	33.018	-9.114	-9.114	0.000	0.000	0.000	0.000
161	D	489	TYR	-1	-0.959	-0.963	31.171	-9.524	-9.524	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:328:GLY)