FMO DATABASE

FMODB ID: 6RY2Z

Calculation Name: 4F2M-F-Xray549

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | acetic acid

Ligand 3-letter code: NAG | ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4F2M

Chain ID: F

ChEMBL ID:

UniProt ID: Q0PKZ5

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1339529.039869
FMO2-HF: Nuclear repulsion	1280123.313229
FMO2-HF: Total energy	-59405.72664
FMO2-MP2: Total energy	-59575.393085

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(F:507:PRO)

Summations of interaction energy for fragment #1(F:507:PRO)

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.
-77.502	-68.548	4.204	-4.848	-8.311	-0.05

Interaction energy analysis for fragmet #1(F:507:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.905

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	F	509	PHE	0	0.024	0.001	2.826	-9.175	-6.003	0.302	-1.703	-1.770	-0.013
51	F	557	GLN	0	-0.022	-0.012	2.346	-11.913	-9.411	1.188	-1.501	-2.188	-0.016
97	F	604	TYR	0	0.008	-0.007	2.520	-15.243	-13.164	2.521	-1.345	-3.256	-0.019
141	F	650	VAL	0	-0.001	0.001	2.804	-0.802	-0.299	0.099	-0.131	-0.472	-0.001
143	F	652	VAL	0	-0.047	-0.039	3.057	-5.949	-5.251	0.094	-0.168	-0.625	-0.001
4	F	510	TYR	0	-0.051	-0.013	5.671	2.878	2.878	0.000	0.000	0.000	0.000
5	F	511	THR	0	-0.060	-0.059	9.015	2.401	2.401	0.000	0.000	0.000	0.000
6	F	512	HIS	0	0.033	0.021	4.953	2.167	2.167	0.000	0.000	0.000	0.000
7	F	513	THR	0	-0.027	-0.011	8.718	2.536	2.536	0.000	0.000	0.000	0.000
8	F	514	ILE	0	0.008	0.003	10.368	-1.344	-1.344	0.000	0.000	0.000	0.000
9	F	515	VAL	0	-0.024	-0.004	12.361	1.849	1.849	0.000	0.000	0.000	0.000
10	F	516	ASN	0	0.001	-0.004	15.260	-0.334	-0.334	0.000	0.000	0.000	0.000
11	F	517	ILE	0	0.000	-0.002	17.947	0.759	0.759	0.000	0.000	0.000	0.000
12	F	518	THR	0	0.039	0.020	20.273	-0.127	-0.127	0.000	0.000	0.000	0.000
13	F	519	ILE	0	-0.011	-0.025	22.270	0.259	0.259	0.000	0.000	0.000	0.000
14	F	520	ASP	-1	-0.869	-0.888	25.695	-10.921	-10.921	0.000	0.000	0.000	0.000
15	F	521	LEU	0	-0.007	-0.020	28.013	0.345	0.345	0.000	0.000	0.000	0.000
16	F	522	GLY	0	0.044	0.009	30.910	0.174	0.174	0.000	0.000	0.000	0.000
17	F	523	MET	0	-0.006	0.003	33.452	0.029	0.029	0.000	0.000	0.000	0.000
18	F	524	LYS	1	0.939	0.953	36.073	7.745	7.745	0.000	0.000	0.000	0.000
19	F	525	ARG	1	0.923	0.966	39.468	7.337	7.337	0.000	0.000	0.000	0.000
20	F	526	SER	0	0.005	-0.001	42.143	0.158	0.158	0.000	0.000	0.000	0.000
21	F	527	GLY	0	0.025	0.006	44.208	0.069	0.069	0.000	0.000	0.000	0.000
22	F	528	TYR	0	0.000	0.003	46.688	0.102	0.102	0.000	0.000	0.000	0.000
23	F	529	GLY	0	0.007	0.007	45.624	-0.011	-0.011	0.000	0.000	0.000	0.000
24	F	530	GLN	0	0.025	0.017	39.514	-0.010	-0.010	0.000	0.000	0.000	0.000
25	F	531	PRO	0	-0.012	-0.012	37.481	0.019	0.019	0.000	0.000	0.000	0.000
26	F	532	ILE	0	-0.018	-0.007	36.764	-0.031	-0.031	0.000	0.000	0.000	0.000
27	F	533	ALA	0	0.058	0.017	32.748	0.001	0.001	0.000	0.000	0.000	0.000
28	F	534	SER	0	-0.047	-0.021	34.704	0.224	0.224	0.000	0.000	0.000	0.000
29	F	535	THR	0	0.050	0.025	34.351	-0.334	-0.334	0.000	0.000	0.000	0.000
30	F	536	LEU	0	-0.012	-0.007	33.910	-0.205	-0.205	0.000	0.000	0.000	0.000
31	F	537	SER	0	0.008	0.002	30.997	0.042	0.042	0.000	0.000	0.000	0.000
32	F	538	ASN	0	-0.049	-0.023	30.487	-0.071	-0.071	0.000	0.000	0.000	0.000
33	F	539	ILE	0	0.032	0.008	23.229	-0.181	-0.181	0.000	0.000	0.000	0.000
34	F	540	THR	0	-0.025	0.004	25.041	0.335	0.335	0.000	0.000	0.000	0.000
35	F	541	LEU	0	0.007	0.003	20.754	-0.504	-0.504	0.000	0.000	0.000	0.000
36	F	542	PRO	0	0.001	0.001	18.508	0.523	0.523	0.000	0.000	0.000	0.000
37	F	543	MET	0	-0.005	0.000	21.835	0.129	0.129	0.000	0.000	0.000	0.000
38	F	544	GLN	0	0.002	-0.015	19.041	-0.253	-0.253	0.000	0.000	0.000	0.000
39	F	545	ASP	-1	-0.809	-0.876	23.698	-12.502	-12.502	0.000	0.000	0.000	0.000
40	F	546	ASN	0	-0.042	-0.020	26.497	0.328	0.328	0.000	0.000	0.000	0.000
41	F	547	ASN	0	-0.013	-0.013	27.113	0.162	0.162	0.000	0.000	0.000	0.000
42	F	548	THR	0	0.050	0.042	25.745	-0.687	-0.687	0.000	0.000	0.000	0.000
43	F	549	ASP	-1	-0.914	-0.977	26.298	-10.438	-10.438	0.000	0.000	0.000	0.000
44	F	550	VAL	0	0.014	0.002	22.971	-0.045	-0.045	0.000	0.000	0.000	0.000
45	F	551	TYR	0	-0.005	0.012	16.218	-0.364	-0.364	0.000	0.000	0.000	0.000
46	F	552	CYS	0	-0.037	-0.011	15.638	-0.557	-0.557	0.000	0.000	0.000	0.000
47	F	553	ILE	0	-0.012	0.010	11.255	0.295	0.295	0.000	0.000	0.000	0.000
48	F	554	ARG	1	0.797	0.861	14.999	14.866	14.866	0.000	0.000	0.000	0.000
49	F	555	SER	0	-0.010	0.001	10.487	0.410	0.410	0.000	0.000	0.000	0.000
50	F	556	ASP	-1	-0.696	-0.807	7.184	-32.788	-32.788	0.000	0.000	0.000	0.000
52	F	558	PHE	0	0.005	-0.006	7.019	4.300	4.300	0.000	0.000	0.000	0.000
53	F	559	SER	0	0.034	0.015	7.635	-1.731	-1.731	0.000	0.000	0.000	0.000
54	F	560	VAL	0	-0.020	-0.018	9.399	2.199	2.199	0.000	0.000	0.000	0.000
55	F	561	TYR	0	-0.031	-0.002	13.057	-0.194	-0.194	0.000	0.000	0.000	0.000
56	F	562	VAL	0	0.008	0.001	15.636	0.696	0.696	0.000	0.000	0.000	0.000
57	F	563	HIS	0	0.005	0.002	18.769	-0.297	-0.297	0.000	0.000	0.000	0.000
58	F	564	SER	0	0.021	0.018	21.762	0.572	0.572	0.000	0.000	0.000	0.000
59	F	565	THR	0	-0.077	-0.060	24.448	0.277	0.277	0.000	0.000	0.000	0.000
60	F	566	CYS	0	-0.015	0.009	28.033	0.394	0.394	0.000	0.000	0.000	0.000
61	F	567	LYS	1	0.881	0.948	31.315	8.953	8.953	0.000	0.000	0.000	0.000
62	F	568	SER	0	0.006	0.002	34.969	0.046	0.046	0.000	0.000	0.000	0.000
63	F	569	SER	0	-0.064	-0.044	38.094	0.083	0.083	0.000	0.000	0.000	0.000
64	F	570	LEU	0	-0.041	-0.027	41.291	0.019	0.019	0.000	0.000	0.000	0.000
65	F	571	TRP	0	0.032	0.019	44.836	-0.025	-0.025	0.000	0.000	0.000	0.000
66	F	572	ASP	-1	-0.810	-0.897	46.176	-6.867	-6.867	0.000	0.000	0.000	0.000
67	F	573	ASN	0	-0.018	0.000	41.042	-0.180	-0.180	0.000	0.000	0.000	0.000
68	F	574	ILE	0	-0.007	-0.007	40.958	-0.204	-0.204	0.000	0.000	0.000	0.000
69	F	575	PHE	0	-0.012	-0.003	36.695	0.029	0.029	0.000	0.000	0.000	0.000
70	F	576	LYS	1	0.965	0.986	37.898	7.045	7.045	0.000	0.000	0.000	0.000
71	F	577	ARG	1	0.933	0.972	39.699	7.166	7.166	0.000	0.000	0.000	0.000
72	F	578	ASN	0	0.049	0.020	35.905	-0.348	-0.348	0.000	0.000	0.000	0.000
73	F	580	THR	0	0.046	0.031	34.883	-0.169	-0.169	0.000	0.000	0.000	0.000
74	F	581	ASP	-1	-0.845	-0.944	37.420	-7.838	-7.838	0.000	0.000	0.000	0.000
75	F	582	VAL	0	-0.032	-0.019	36.440	-0.188	-0.188	0.000	0.000	0.000	0.000
76	F	583	LEU	0	-0.058	-0.022	35.867	-0.138	-0.138	0.000	0.000	0.000	0.000
77	F	584	ASP	-1	-0.875	-0.922	31.859	-9.957	-9.957	0.000	0.000	0.000	0.000
78	F	585	ALA	0	0.020	-0.002	30.421	0.016	0.016	0.000	0.000	0.000	0.000
79	F	586	THR	0	-0.055	-0.019	23.934	-0.243	-0.243	0.000	0.000	0.000	0.000
80	F	587	ALA	0	0.012	0.010	24.359	0.117	0.117	0.000	0.000	0.000	0.000
81	F	588	VAL	0	-0.023	-0.017	20.708	-0.572	-0.572	0.000	0.000	0.000	0.000
82	F	589	ILE	0	0.014	0.009	18.577	0.562	0.562	0.000	0.000	0.000	0.000
83	F	590	LYS	1	0.863	0.925	19.672	11.216	11.216	0.000	0.000	0.000	0.000
84	F	591	THR	0	0.029	0.005	18.349	0.018	0.018	0.000	0.000	0.000	0.000
85	F	592	GLY	0	0.022	0.026	20.885	0.461	0.461	0.000	0.000	0.000	0.000
86	F	593	THR	0	-0.028	-0.023	24.042	0.082	0.082	0.000	0.000	0.000	0.000
87	F	594	CYS	0	-0.076	-0.013	18.734	0.124	0.124	0.000	0.000	0.000	0.000
88	F	595	PRO	0	0.029	0.011	18.106	-0.068	-0.068	0.000	0.000	0.000	0.000
89	F	596	PHE	0	0.028	0.021	13.751	-0.400	-0.400	0.000	0.000	0.000	0.000
90	F	597	SER	0	0.008	-0.008	13.360	0.893	0.893	0.000	0.000	0.000	0.000
91	F	598	PHE	0	0.003	-0.015	12.805	-1.242	-1.242	0.000	0.000	0.000	0.000
92	F	599	ASP	-1	-0.960	-0.971	12.746	-17.784	-17.784	0.000	0.000	0.000	0.000
93	F	600	LYS	1	0.853	0.893	10.604	22.673	22.673	0.000	0.000	0.000	0.000
94	F	601	LEU	0	-0.006	0.027	11.218	1.617	1.617	0.000	0.000	0.000	0.000
95	F	602	ASN	0	-0.001	-0.003	9.711	-1.140	-1.140	0.000	0.000	0.000	0.000
96	F	603	ASN	0	-0.020	-0.020	7.107	1.054	1.054	0.000	0.000	0.000	0.000
98	F	605	LEU	0	0.010	0.018	6.353	2.421	2.421	0.000	0.000	0.000	0.000
99	F	606	THR	0	0.002	0.010	7.221	-3.193	-3.193	0.000	0.000	0.000	0.000
100	F	607	PHE	0	-0.017	-0.011	9.238	2.300	2.300	0.000	0.000	0.000	0.000
101	F	608	ASN	0	0.033	0.011	11.701	-2.046	-2.046	0.000	0.000	0.000	0.000
102	F	609	LYS	1	0.899	0.960	14.447	13.992	13.992	0.000	0.000	0.000	0.000
103	F	610	PHE	0	0.013	0.002	13.635	0.174	0.174	0.000	0.000	0.000	0.000
104	F	612	LEU	0	0.024	0.021	16.667	0.229	0.229	0.000	0.000	0.000	0.000
105	F	613	SER	0	-0.003	-0.027	19.879	0.462	0.462	0.000	0.000	0.000	0.000
106	F	614	LEU	0	0.001	-0.007	23.736	-0.018	-0.018	0.000	0.000	0.000	0.000
107	F	615	SER	0	-0.020	0.005	26.884	0.472	0.472	0.000	0.000	0.000	0.000
108	F	616	PRO	0	-0.053	-0.024	25.747	0.045	0.045	0.000	0.000	0.000	0.000
109	F	617	VAL	0	0.029	0.019	27.812	0.206	0.206	0.000	0.000	0.000	0.000
110	F	618	GLY	0	-0.019	-0.023	27.698	-0.289	-0.289	0.000	0.000	0.000	0.000
111	F	619	ALA	0	-0.027	-0.006	24.244	-0.393	-0.393	0.000	0.000	0.000	0.000
112	F	620	ASN	0	0.003	0.006	21.465	0.462	0.462	0.000	0.000	0.000	0.000
113	F	622	LYS	1	0.893	0.949	22.921	10.366	10.366	0.000	0.000	0.000	0.000
114	F	623	PHE	0	0.037	0.006	16.883	-0.220	-0.220	0.000	0.000	0.000	0.000
115	F	624	ASP	-1	-0.836	-0.916	22.267	-10.969	-10.969	0.000	0.000	0.000	0.000
116	F	625	VAL	0	-0.040	-0.015	23.049	-0.459	-0.459	0.000	0.000	0.000	0.000
117	F	626	ALA	0	-0.007	-0.018	25.153	0.580	0.580	0.000	0.000	0.000	0.000
118	F	627	ALA	0	0.013	0.014	26.304	-0.336	-0.336	0.000	0.000	0.000	0.000
119	F	628	ARG	1	0.913	0.941	22.430	12.678	12.678	0.000	0.000	0.000	0.000
120	F	629	THR	0	0.015	-0.012	28.484	0.206	0.206	0.000	0.000	0.000	0.000
121	F	630	ARG	1	0.808	0.892	30.928	9.320	9.320	0.000	0.000	0.000	0.000
122	F	631	THR	0	0.006	-0.006	31.873	0.163	0.163	0.000	0.000	0.000	0.000
123	F	632	ASN	0	0.000	0.003	32.872	0.168	0.168	0.000	0.000	0.000	0.000
124	F	633	GLU	-1	-0.772	-0.852	27.359	-11.549	-11.549	0.000	0.000	0.000	0.000
125	F	634	GLN	0	0.015	0.010	30.565	0.395	0.395	0.000	0.000	0.000	0.000
126	F	635	VAL	0	0.011	0.013	27.971	-0.251	-0.251	0.000	0.000	0.000	0.000
127	F	636	VAL	0	-0.054	-0.015	29.092	0.360	0.360	0.000	0.000	0.000	0.000
128	F	637	ARG	1	0.911	0.953	28.729	10.543	10.543	0.000	0.000	0.000	0.000
129	F	638	SER	0	-0.009	-0.004	26.248	-0.040	-0.040	0.000	0.000	0.000	0.000
130	F	639	LEU	0	-0.042	-0.003	20.329	0.230	0.230	0.000	0.000	0.000	0.000
131	F	640	TYR	0	0.009	-0.006	22.414	-0.275	-0.275	0.000	0.000	0.000	0.000
132	F	641	VAL	0	0.028	0.000	17.921	-0.250	-0.250	0.000	0.000	0.000	0.000
133	F	642	ILE	0	0.011	0.014	20.304	0.443	0.443	0.000	0.000	0.000	0.000
134	F	643	TYR	0	-0.058	-0.037	16.398	-0.516	-0.516	0.000	0.000	0.000	0.000
135	F	644	GLU	-1	-0.853	-0.930	17.159	-13.445	-13.445	0.000	0.000	0.000	0.000
136	F	645	GLU	-1	-0.915	-0.967	15.129	-17.715	-17.715	0.000	0.000	0.000	0.000
137	F	646	GLY	0	-0.021	-0.023	14.075	0.885	0.885	0.000	0.000	0.000	0.000
138	F	647	ASP	-1	-0.905	-0.962	8.942	-28.810	-28.810	0.000	0.000	0.000	0.000
139	F	648	ASN	0	-0.043	0.001	9.699	-1.587	-1.587	0.000	0.000	0.000	0.000
140	F	649	ILE	0	-0.051	-0.020	8.679	-1.215	-1.215	0.000	0.000	0.000	0.000
142	F	651	LEU	0	-0.017	-0.004	5.903	-0.416	-0.416	0.000	0.000	0.000	0.000
144	F	653	PRO	0	-0.022	-0.013	5.799	3.710	3.710	0.000	0.000	0.000	0.000
145	F	654	ARG	0	0.135	0.086	8.709	-6.700	-6.700	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:507:PRO)