FMO DATABASE

FMODB ID: 3GN9L

Calculation Name: 6CRQ-C-Other547

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG | BMA | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6CRQ

Chain ID: C

ChEMBL ID:

UniProt ID: Q2N0S7

Base Structure: ElectronMicroscopy

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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-906967.180557
FMO2-HF: Nuclear repulsion	857886.931815
FMO2-HF: Total energy	-49080.248742
FMO2-MP2: Total energy	-49220.842998

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(C:520:LEU)

Summations of interaction energy for fragment #1(C:520:LEU)

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.
-36.273	-30.789	4.182	-2.798	-6.87	-0.02

Interaction energy analysis for fragmet #1(C:520:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.930

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	C	522	PHE	0	0.050	0.016	3.772	-1.971	-0.093	-0.008	-0.942	-0.929	0.001
5	C	524	GLY	0	0.015	0.016	2.722	1.781	2.165	0.244	-0.178	-0.451	-0.002
6	C	525	ALA	0	-0.010	-0.012	2.309	-4.829	-2.744	2.536	-1.933	-2.688	-0.011
7	C	526	ALA	0	-0.004	0.010	3.232	4.886	3.948	0.040	1.158	-0.260	-0.001
8	C	527	GLY	0	-0.024	-0.002	4.796	3.447	3.479	-0.001	-0.002	-0.029	0.000
9	C	528	SER	0	-0.096	-0.059	3.002	-2.234	-1.338	0.137	-0.337	-0.697	-0.002
10	C	529	THR	0	0.066	0.036	4.997	0.658	0.656	-0.001	-0.005	0.008	0.000
13	C	532	ALA	0	-0.014	0.003	4.030	-1.235	-1.155	-0.001	-0.013	-0.066	0.000
14	C	533	ALA	0	0.000	0.000	3.627	-4.906	-4.670	0.003	-0.043	-0.196	0.000
15	C	534	SER	0	-0.017	-0.003	4.681	-1.283	-1.273	-0.001	-0.001	-0.007	0.000
17	C	536	THR	0	-0.090	-0.069	2.392	-6.048	-5.346	1.235	-0.483	-1.454	-0.005
20	C	539	VAL	0	-0.068	-0.023	4.231	0.521	0.642	-0.001	-0.019	-0.101	0.000
4	C	523	LEU	0	0.010	-0.001	6.240	-0.022	-0.022	0.000	0.000	0.000	0.000
11	C	530	MET	0	0.014	0.014	6.787	-2.380	-2.380	0.000	0.000	0.000	0.000
12	C	531	GLY	0	0.044	0.026	8.594	-0.628	-0.628	0.000	0.000	0.000	0.000
16	C	535	MET	0	0.003	0.001	5.232	1.135	1.135	0.000	0.000	0.000	0.000
18	C	537	LEU	0	0.053	0.034	5.558	0.568	0.568	0.000	0.000	0.000	0.000
19	C	538	THR	0	0.048	0.006	8.998	1.657	1.657	0.000	0.000	0.000	0.000
21	C	540	GLN	0	0.044	0.020	6.702	-1.469	-1.469	0.000	0.000	0.000	0.000
22	C	541	ALA	0	0.025	0.015	8.993	1.884	1.884	0.000	0.000	0.000	0.000
23	C	542	ARG	1	0.932	0.970	9.730	26.090	26.090	0.000	0.000	0.000	0.000
24	C	543	ASN	0	-0.037	-0.021	8.438	-1.680	-1.680	0.000	0.000	0.000	0.000
25	C	544	LEU	0	0.024	0.006	11.737	0.012	0.012	0.000	0.000	0.000	0.000
26	C	545	LEU	0	-0.004	0.013	12.590	1.182	1.182	0.000	0.000	0.000	0.000
27	C	546	SER	0	0.002	0.000	15.146	1.030	1.030	0.000	0.000	0.000	0.000
28	C	547	GLY	0	0.011	0.005	17.639	0.882	0.882	0.000	0.000	0.000	0.000
29	C	548	ILE	0	-0.070	-0.028	18.827	0.798	0.798	0.000	0.000	0.000	0.000
30	C	549	VAL	0	-0.087	-0.053	19.431	-0.546	-0.546	0.000	0.000	0.000	0.000
31	C	550	GLN	-1	-0.902	-0.939	19.715	-14.378	-14.378	0.000	0.000	0.000	0.000
32	C	573	ILE	0	0.057	0.012	34.760	-0.044	-0.044	0.000	0.000	0.000	0.000
33	C	574	LYS	1	1.014	1.014	30.723	9.831	9.831	0.000	0.000	0.000	0.000
34	C	575	GLN	0	0.037	0.006	28.724	-0.311	-0.311	0.000	0.000	0.000	0.000
35	C	576	LEU	0	-0.018	-0.006	28.662	-0.333	-0.333	0.000	0.000	0.000	0.000
36	C	577	GLN	0	0.039	0.007	29.716	-0.278	-0.278	0.000	0.000	0.000	0.000
37	C	578	ALA	0	0.015	0.005	25.437	-0.161	-0.161	0.000	0.000	0.000	0.000
38	C	579	ARG	1	0.937	0.972	25.199	11.049	11.049	0.000	0.000	0.000	0.000
39	C	580	VAL	0	0.015	0.021	25.981	-0.225	-0.225	0.000	0.000	0.000	0.000
40	C	581	LEU	0	0.029	0.020	24.974	-0.245	-0.245	0.000	0.000	0.000	0.000
41	C	582	ALA	0	-0.035	-0.013	21.583	-0.320	-0.320	0.000	0.000	0.000	0.000
42	C	583	VAL	0	0.024	0.011	22.383	-0.430	-0.430	0.000	0.000	0.000	0.000
43	C	584	GLU	-1	-0.912	-0.965	24.668	-10.595	-10.595	0.000	0.000	0.000	0.000
44	C	585	ARG	1	0.925	0.956	21.051	13.185	13.185	0.000	0.000	0.000	0.000
45	C	586	TYR	0	0.020	0.021	18.292	-0.367	-0.367	0.000	0.000	0.000	0.000
46	C	587	LEU	0	-0.016	-0.019	21.664	-0.039	-0.039	0.000	0.000	0.000	0.000
47	C	588	ARG	1	0.861	0.911	21.790	13.196	13.196	0.000	0.000	0.000	0.000
48	C	589	ASP	-1	-0.816	-0.881	20.065	-14.105	-14.105	0.000	0.000	0.000	0.000
49	C	590	GLN	0	-0.012	-0.008	21.573	-0.395	-0.395	0.000	0.000	0.000	0.000
50	C	591	GLN	0	-0.007	0.002	23.087	0.124	0.124	0.000	0.000	0.000	0.000
51	C	592	LEU	0	-0.010	0.003	22.437	0.287	0.287	0.000	0.000	0.000	0.000
52	C	593	LEU	0	0.014	0.003	18.828	0.112	0.112	0.000	0.000	0.000	0.000
53	C	594	GLY	0	-0.037	-0.024	23.191	0.165	0.165	0.000	0.000	0.000	0.000
54	C	595	ILE	0	-0.025	-0.008	26.701	0.272	0.272	0.000	0.000	0.000	0.000
55	C	596	TRP	0	-0.010	-0.022	20.540	-0.051	-0.051	0.000	0.000	0.000	0.000
56	C	597	GLY	0	0.025	0.030	26.331	0.058	0.058	0.000	0.000	0.000	0.000
57	C	598	CYS	0	-0.109	-0.049	16.083	0.580	0.580	0.000	0.000	0.000	0.000
58	C	599	SER	0	0.010	0.004	21.264	-0.913	-0.913	0.000	0.000	0.000	0.000
59	C	600	GLY	0	0.010	0.003	21.297	0.181	0.181	0.000	0.000	0.000	0.000
60	C	601	LYS	1	0.917	0.963	18.456	12.991	12.991	0.000	0.000	0.000	0.000
61	C	602	LEU	0	-0.011	-0.004	11.930	-0.132	-0.132	0.000	0.000	0.000	0.000
62	C	603	ILE	0	0.003	-0.001	12.045	-0.522	-0.522	0.000	0.000	0.000	0.000
63	C	605	CYS	0	-0.025	-0.012	19.669	-0.409	-0.409	0.000	0.000	0.000	0.000
64	C	606	THR	0	0.050	0.022	22.174	0.345	0.345	0.000	0.000	0.000	0.000
65	C	607	ASN	0	-0.020	-0.022	25.536	-0.053	-0.053	0.000	0.000	0.000	0.000
66	C	608	VAL	0	-0.011	0.004	26.789	0.304	0.304	0.000	0.000	0.000	0.000
67	C	609	PRO	0	-0.010	0.002	26.349	-0.405	-0.405	0.000	0.000	0.000	0.000
68	C	610	TRP	0	0.009	-0.002	20.877	-0.202	-0.202	0.000	0.000	0.000	0.000
69	C	611	ASN	0	0.042	0.035	25.270	0.365	0.365	0.000	0.000	0.000	0.000
70	C	612	SER	0	0.026	0.004	25.522	-0.213	-0.213	0.000	0.000	0.000	0.000
71	C	613	SER	0	-0.012	-0.021	26.095	-0.233	-0.233	0.000	0.000	0.000	0.000
72	C	614	TRP	0	-0.011	-0.015	24.067	-0.014	-0.014	0.000	0.000	0.000	0.000
73	C	615	SER	0	0.012	-0.002	21.371	-0.160	-0.160	0.000	0.000	0.000	0.000
74	C	616	ASN	0	-0.063	-0.027	23.733	0.336	0.336	0.000	0.000	0.000	0.000
75	C	617	ARG	1	0.769	0.871	19.301	13.423	13.423	0.000	0.000	0.000	0.000
76	C	618	ASN	0	0.005	-0.013	20.863	0.064	0.064	0.000	0.000	0.000	0.000
77	C	619	LEU	0	0.026	0.013	18.597	-0.562	-0.562	0.000	0.000	0.000	0.000
78	C	620	SER	0	0.043	0.005	16.211	-0.521	-0.521	0.000	0.000	0.000	0.000
79	C	621	GLU	-1	-0.859	-0.910	15.424	-14.006	-14.006	0.000	0.000	0.000	0.000
80	C	622	ILE	0	0.022	0.001	15.182	-0.692	-0.692	0.000	0.000	0.000	0.000
81	C	623	TRP	0	-0.015	-0.013	11.532	-1.421	-1.421	0.000	0.000	0.000	0.000
82	C	624	ASP	-1	-0.918	-0.967	10.838	-21.293	-21.293	0.000	0.000	0.000	0.000
83	C	625	ASN	0	-0.051	-0.029	11.582	-1.133	-1.133	0.000	0.000	0.000	0.000
84	C	626	MET	0	-0.047	0.001	12.810	0.562	0.562	0.000	0.000	0.000	0.000
85	C	627	THR	0	0.017	-0.001	8.481	-1.226	-1.226	0.000	0.000	0.000	0.000
86	C	628	TRP	0	0.035	-0.006	7.915	1.974	1.974	0.000	0.000	0.000	0.000
87	C	629	LEU	0	-0.013	-0.001	10.525	1.202	1.202	0.000	0.000	0.000	0.000
88	C	630	GLN	0	-0.013	0.007	12.863	0.225	0.225	0.000	0.000	0.000	0.000
89	C	631	TRP	0	0.083	0.024	14.064	1.009	1.009	0.000	0.000	0.000	0.000
90	C	632	ASP	-1	-0.936	-0.964	15.135	-14.964	-14.964	0.000	0.000	0.000	0.000
91	C	633	LYS	1	0.929	0.943	16.927	15.058	15.058	0.000	0.000	0.000	0.000
92	C	634	GLU	-1	-0.854	-0.871	18.609	-12.597	-12.597	0.000	0.000	0.000	0.000
93	C	635	ILE	0	0.008	-0.007	18.555	0.666	0.666	0.000	0.000	0.000	0.000
94	C	636	SER	0	0.036	0.023	21.410	0.313	0.313	0.000	0.000	0.000	0.000
95	C	637	ASN	0	-0.050	-0.023	22.407	-0.022	-0.022	0.000	0.000	0.000	0.000
96	C	638	TYR	0	0.016	0.024	23.919	0.643	0.643	0.000	0.000	0.000	0.000
97	C	639	THR	0	-0.006	-0.001	22.603	-0.038	-0.038	0.000	0.000	0.000	0.000
98	C	640	GLN	0	-0.001	-0.006	24.521	-0.205	-0.205	0.000	0.000	0.000	0.000
99	C	641	ILE	0	0.000	0.002	28.123	0.199	0.199	0.000	0.000	0.000	0.000
100	C	642	ILE	0	0.003	0.001	22.553	0.080	0.080	0.000	0.000	0.000	0.000
101	C	643	TYR	0	-0.014	-0.027	20.873	-0.168	-0.168	0.000	0.000	0.000	0.000
102	C	644	GLY	0	0.062	0.046	26.295	0.058	0.058	0.000	0.000	0.000	0.000
103	C	645	LEU	0	0.035	0.010	28.516	0.118	0.118	0.000	0.000	0.000	0.000
104	C	646	LEU	0	-0.035	-0.011	23.143	0.088	0.088	0.000	0.000	0.000	0.000
105	C	647	GLU	-1	-0.935	-0.968	27.685	-9.455	-9.455	0.000	0.000	0.000	0.000
106	C	648	GLU	-1	-0.947	-0.979	30.417	-8.459	-8.459	0.000	0.000	0.000	0.000
107	C	649	SER	0	-0.037	-0.027	31.244	0.291	0.291	0.000	0.000	0.000	0.000
108	C	650	GLN	0	-0.005	0.011	27.620	-0.004	-0.004	0.000	0.000	0.000	0.000
109	C	651	ASN	0	0.003	0.017	28.981	0.187	0.187	0.000	0.000	0.000	0.000
110	C	652	GLN	0	-0.029	-0.032	30.876	0.246	0.246	0.000	0.000	0.000	0.000
111	C	653	GLN	0	-0.026	-0.006	34.258	0.178	0.178	0.000	0.000	0.000	0.000
112	C	654	GLU	-1	-0.868	-0.927	30.197	-9.959	-9.959	0.000	0.000	0.000	0.000
113	C	655	LYS	1	0.840	0.907	30.251	10.003	10.003	0.000	0.000	0.000	0.000
114	C	656	ASN	0	0.007	0.005	35.671	0.227	0.227	0.000	0.000	0.000	0.000
115	C	657	GLU	-1	-0.889	-0.935	37.450	-7.917	-7.917	0.000	0.000	0.000	0.000
116	C	658	GLN	0	-0.076	-0.047	35.438	-0.035	-0.035	0.000	0.000	0.000	0.000
117	C	659	ASP	-1	-0.945	-0.970	38.094	-7.368	-7.368	0.000	0.000	0.000	0.000
118	C	660	LEU	0	0.009	-0.002	40.733	0.169	0.169	0.000	0.000	0.000	0.000
119	C	661	LEU	0	-0.086	-0.038	38.854	0.142	0.142	0.000	0.000	0.000	0.000
120	C	662	ALA	0	-0.099	-0.045	41.088	0.019	0.019	0.000	0.000	0.000	0.000
121	C	663	LEU	-1	-0.989	-0.968	43.173	-6.520	-6.520	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:520:LEU)