FMO DATABASE

FMODB ID: KQR13

Calculation Name: 6E7D-U-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | sulfate ion

Ligand 3-letter code: NAG | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6E7D

Chain ID: U

ChEMBL ID:

UniProt ID: Q91V08

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1028964.958121
FMO2-HF: Nuclear repulsion	980240.405977
FMO2-HF: Total energy	-48724.552144
FMO2-MP2: Total energy	-48863.240001

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(U:94:CYS)

Summations of interaction energy for fragment #1(U:94:CYS)

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.
-172.879	-163.556	32.445	-17.939	-23.828	-0.034

Interaction energy analysis for fragmet #1(U:94:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.754 / q_NPA : 0.879

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	U	96	GLN	0	0.000	0.000	3.570	-4.367	-3.094	0.023	-0.618	-0.678	0.000
5	U	98	TRP	0	-0.039	-0.029	2.235	-1.405	0.564	2.742	-1.364	-3.346	-0.011
6	U	99	LEU	0	0.024	0.026	3.698	-4.498	-3.737	0.015	-0.249	-0.528	-0.001
7	U	100	SER	0	-0.050	-0.050	1.965	-25.623	-22.570	14.687	-8.916	-8.824	0.012
8	U	101	HIS	0	-0.015	-0.018	2.236	-7.810	-8.082	1.958	0.307	-1.993	0.024
9	U	102	ARG	1	0.792	0.882	3.427	17.896	18.337	0.113	-0.132	-0.422	-0.001
10	U	103	ASP	-1	-0.898	-0.944	3.888	-30.268	-28.317	-0.023	-0.956	-0.972	-0.004
13	U	107	HIS	0	-0.015	-0.004	3.861	-0.266	1.995	-0.022	-1.172	-1.067	0.005
115	U	211	GLN	0	0.058	0.010	4.113	0.023	0.358	-0.002	-0.086	-0.247	0.000
116	U	212	LYS	0	0.020	0.010	1.783	-30.340	-32.789	12.954	-4.753	-5.751	-0.058
4	U	97	ASP	-1	-0.919	-0.949	6.238	-26.190	-26.190	0.000	0.000	0.000	0.000
14	U	108	VAL	0	0.012	0.007	6.573	1.180	1.180	0.000	0.000	0.000	0.000
15	U	109	SER	0	-0.002	0.010	10.325	0.150	0.150	0.000	0.000	0.000	0.000
16	U	110	GLN	0	0.028	-0.004	13.207	0.045	0.045	0.000	0.000	0.000	0.000
17	U	111	VAL	0	-0.015	-0.002	16.110	0.892	0.892	0.000	0.000	0.000	0.000
18	U	112	SER	0	0.003	0.006	17.325	-0.580	-0.580	0.000	0.000	0.000	0.000
19	U	113	ASN	0	-0.002	0.001	19.997	0.459	0.459	0.000	0.000	0.000	0.000
20	U	114	THR	0	0.069	0.043	20.732	-0.311	-0.311	0.000	0.000	0.000	0.000
21	U	115	TRP	0	0.002	-0.007	16.875	-0.368	-0.368	0.000	0.000	0.000	0.000
22	U	116	LYS	1	0.876	0.926	18.152	11.495	11.495	0.000	0.000	0.000	0.000
23	U	117	GLU	-1	-0.864	-0.936	18.674	-13.758	-13.758	0.000	0.000	0.000	0.000
24	U	118	GLY	0	0.050	0.033	15.655	-0.643	-0.643	0.000	0.000	0.000	0.000
25	U	119	ARG	1	0.921	0.960	13.955	15.061	15.061	0.000	0.000	0.000	0.000
26	U	120	ILE	0	0.021	0.017	14.023	-0.873	-0.873	0.000	0.000	0.000	0.000
27	U	121	ASP	-1	-0.833	-0.895	12.713	-20.735	-20.735	0.000	0.000	0.000	0.000
28	U	122	CYS	0	-0.064	-0.009	7.370	-0.105	-0.105	0.000	0.000	0.000	0.000
29	U	123	ASP	-1	-0.883	-0.939	10.224	-19.937	-19.937	0.000	0.000	0.000	0.000
30	U	124	LYS	1	0.894	0.942	12.580	15.199	15.199	0.000	0.000	0.000	0.000
31	U	125	LYS	1	0.818	0.911	8.210	22.177	22.177	0.000	0.000	0.000	0.000
32	U	126	GLY	0	-0.012	-0.004	8.297	-2.807	-2.807	0.000	0.000	0.000	0.000
33	U	127	ALA	0	-0.078	-0.027	6.407	-3.188	-3.188	0.000	0.000	0.000	0.000
34	U	128	THR	0	0.032	0.017	7.575	3.262	3.262	0.000	0.000	0.000	0.000
35	U	129	LEU	0	0.011	0.002	8.563	-1.921	-1.921	0.000	0.000	0.000	0.000
36	U	130	LEU	0	-0.033	-0.016	7.816	-0.449	-0.449	0.000	0.000	0.000	0.000
37	U	131	LEU	0	-0.015	-0.005	8.628	2.609	2.609	0.000	0.000	0.000	0.000
38	U	132	ILE	0	-0.039	-0.025	8.921	-1.555	-1.555	0.000	0.000	0.000	0.000
39	U	133	GLN	0	-0.038	-0.027	5.961	2.270	2.270	0.000	0.000	0.000	0.000
40	U	134	ASP	-1	-0.767	-0.864	10.444	-18.293	-18.293	0.000	0.000	0.000	0.000
41	U	135	GLN	0	0.029	-0.004	12.184	-0.282	-0.282	0.000	0.000	0.000	0.000
42	U	136	GLU	-1	-0.843	-0.899	10.749	-18.449	-18.449	0.000	0.000	0.000	0.000
43	U	137	GLU	-1	-0.745	-0.863	6.036	-28.370	-28.370	0.000	0.000	0.000	0.000
44	U	138	LEU	0	-0.006	-0.007	9.563	-0.206	-0.206	0.000	0.000	0.000	0.000
45	U	139	ARG	1	0.780	0.866	12.428	15.095	15.095	0.000	0.000	0.000	0.000
46	U	140	PHE	0	0.039	0.021	6.447	0.469	0.469	0.000	0.000	0.000	0.000
47	U	141	LEU	0	-0.012	0.010	7.317	-0.073	-0.073	0.000	0.000	0.000	0.000
48	U	142	LEU	0	-0.078	-0.037	10.728	0.348	0.348	0.000	0.000	0.000	0.000
49	U	143	ASP	-1	-0.839	-0.890	13.837	-14.249	-14.249	0.000	0.000	0.000	0.000
50	U	144	SER	0	-0.078	-0.052	9.826	-0.258	-0.258	0.000	0.000	0.000	0.000
51	U	145	ILE	0	-0.011	0.011	11.892	-0.484	-0.484	0.000	0.000	0.000	0.000
52	U	146	LYS	1	0.984	1.001	13.041	15.336	15.336	0.000	0.000	0.000	0.000
53	U	147	GLU	-1	-0.844	-0.906	16.130	-13.724	-13.724	0.000	0.000	0.000	0.000
54	U	148	LYS	1	0.896	0.915	18.070	13.352	13.352	0.000	0.000	0.000	0.000
55	U	149	TYR	0	-0.050	-0.023	18.956	0.345	0.345	0.000	0.000	0.000	0.000
56	U	150	ASN	0	-0.050	-0.010	19.070	0.810	0.810	0.000	0.000	0.000	0.000
57	U	151	SER	0	0.039	0.025	19.493	-0.190	-0.190	0.000	0.000	0.000	0.000
58	U	152	PHE	0	-0.035	-0.019	14.282	-0.228	-0.228	0.000	0.000	0.000	0.000
59	U	153	TRP	0	-0.053	-0.035	15.696	-0.196	-0.196	0.000	0.000	0.000	0.000
60	U	154	ILE	0	0.020	0.001	13.027	-1.360	-1.360	0.000	0.000	0.000	0.000
61	U	155	GLY	0	0.019	0.011	12.731	0.912	0.912	0.000	0.000	0.000	0.000
62	U	156	LEU	0	-0.050	-0.022	13.939	0.181	0.181	0.000	0.000	0.000	0.000
63	U	157	SER	0	-0.008	-0.007	17.304	0.097	0.097	0.000	0.000	0.000	0.000
64	U	158	TYR	0	0.007	0.011	20.888	0.041	0.041	0.000	0.000	0.000	0.000
65	U	159	THR	0	-0.014	-0.029	24.190	0.051	0.051	0.000	0.000	0.000	0.000
66	U	160	LEU	0	0.042	0.004	26.655	0.127	0.127	0.000	0.000	0.000	0.000
67	U	161	THR	0	-0.053	-0.039	27.540	0.240	0.240	0.000	0.000	0.000	0.000
68	U	162	ASP	-1	-0.820	-0.877	26.387	-10.709	-10.709	0.000	0.000	0.000	0.000
69	U	163	MET	0	-0.049	-0.012	28.760	0.064	0.064	0.000	0.000	0.000	0.000
70	U	164	ASN	0	0.009	0.012	25.316	-0.136	-0.136	0.000	0.000	0.000	0.000
71	U	165	TRP	0	-0.018	-0.018	21.401	-0.366	-0.366	0.000	0.000	0.000	0.000
72	U	166	LYS	1	0.850	0.909	20.609	11.615	11.615	0.000	0.000	0.000	0.000
73	U	167	TRP	0	0.067	0.028	13.586	-0.516	-0.516	0.000	0.000	0.000	0.000
74	U	168	ILE	0	-0.069	-0.040	12.386	0.669	0.669	0.000	0.000	0.000	0.000
75	U	169	ASN	0	0.016	0.029	12.512	0.712	0.712	0.000	0.000	0.000	0.000
76	U	170	GLY	0	-0.024	0.004	15.143	-0.164	-0.164	0.000	0.000	0.000	0.000
77	U	171	THR	0	-0.035	-0.040	16.171	0.841	0.841	0.000	0.000	0.000	0.000
78	U	172	ALA	0	0.019	0.006	18.654	-0.143	-0.143	0.000	0.000	0.000	0.000
79	U	173	PHE	0	0.001	-0.010	18.178	-0.332	-0.332	0.000	0.000	0.000	0.000
80	U	174	ASN	0	0.041	0.022	19.844	0.753	0.753	0.000	0.000	0.000	0.000
81	U	175	SER	0	-0.016	-0.024	19.495	-0.445	-0.445	0.000	0.000	0.000	0.000
82	U	176	ASP	-1	-0.971	-0.979	20.373	-11.970	-11.970	0.000	0.000	0.000	0.000
83	U	177	VAL	0	0.028	0.028	15.126	-0.055	-0.055	0.000	0.000	0.000	0.000
84	U	178	LEU	0	-0.014	0.003	15.318	-0.857	-0.857	0.000	0.000	0.000	0.000
85	U	179	LYS	1	0.882	0.951	17.458	14.030	14.030	0.000	0.000	0.000	0.000
86	U	180	ILE	0	-0.009	-0.019	19.583	0.408	0.408	0.000	0.000	0.000	0.000
87	U	181	THR	0	0.102	0.058	21.705	-0.400	-0.400	0.000	0.000	0.000	0.000
88	U	182	GLY	0	0.002	-0.009	23.283	0.166	0.166	0.000	0.000	0.000	0.000
89	U	183	VAL	0	-0.039	-0.005	25.543	-0.065	-0.065	0.000	0.000	0.000	0.000
90	U	184	THR	0	0.018	0.009	28.137	0.306	0.306	0.000	0.000	0.000	0.000
91	U	185	GLU	-1	-0.816	-0.892	27.020	-10.300	-10.300	0.000	0.000	0.000	0.000
92	U	186	ASN	0	-0.075	-0.033	28.572	0.566	0.566	0.000	0.000	0.000	0.000
93	U	187	GLY	0	0.035	0.001	28.010	0.168	0.168	0.000	0.000	0.000	0.000
94	U	188	SER	0	-0.044	0.001	25.242	0.047	0.047	0.000	0.000	0.000	0.000
95	U	189	CYS	0	-0.022	-0.019	20.197	-0.378	-0.378	0.000	0.000	0.000	0.000
96	U	190	ALA	0	0.059	0.027	18.086	0.338	0.338	0.000	0.000	0.000	0.000
97	U	191	ALA	0	-0.012	-0.001	17.360	-0.839	-0.839	0.000	0.000	0.000	0.000
98	U	192	ILE	0	-0.016	0.001	13.442	0.451	0.451	0.000	0.000	0.000	0.000
99	U	193	SER	0	0.036	0.006	17.526	0.044	0.044	0.000	0.000	0.000	0.000
100	U	194	GLY	0	0.034	0.022	20.520	0.445	0.445	0.000	0.000	0.000	0.000
101	U	195	GLU	-1	-0.855	-0.936	19.051	-14.273	-14.273	0.000	0.000	0.000	0.000
102	U	196	LYS	1	0.796	0.884	20.092	11.403	11.403	0.000	0.000	0.000	0.000
103	U	197	VAL	0	0.017	0.018	16.848	-0.314	-0.314	0.000	0.000	0.000	0.000
104	U	198	THR	0	-0.059	-0.051	19.728	0.795	0.795	0.000	0.000	0.000	0.000
105	U	199	SER	0	-0.005	-0.006	21.233	-0.594	-0.594	0.000	0.000	0.000	0.000
106	U	200	GLU	-1	-0.762	-0.875	22.343	-11.866	-11.866	0.000	0.000	0.000	0.000
107	U	201	GLY	0	0.049	0.022	24.762	-0.099	-0.099	0.000	0.000	0.000	0.000
108	U	203	SER	0	-0.034	-0.021	23.491	-0.447	-0.447	0.000	0.000	0.000	0.000
109	U	204	SER	0	-0.004	-0.007	24.336	0.321	0.321	0.000	0.000	0.000	0.000
110	U	205	ASP	-1	-0.883	-0.952	23.069	-12.264	-12.264	0.000	0.000	0.000	0.000
111	U	206	ASN	0	-0.028	-0.008	19.395	0.359	0.359	0.000	0.000	0.000	0.000
112	U	207	ARG	1	0.838	0.916	15.873	14.116	14.116	0.000	0.000	0.000	0.000
113	U	208	TRP	0	-0.025	-0.037	11.729	0.900	0.900	0.000	0.000	0.000	0.000
114	U	209	ILE	0	0.017	0.015	8.101	-0.627	-0.627	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(U:94:CYS)