FMO DATABASE

FMODB ID: 3Z1QL

Calculation Name: 6E7D-A-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: A

ChEMBL ID:

UniProt ID: Q91V08

Base Structure: X-ray

Registration Date: 2025-10-04

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1125239.837557
FMO2-HF: Nuclear repulsion	1073865.043368
FMO2-HF: Total energy	-51374.794189
FMO2-MP2: Total energy	-51521.802442

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(A:76:THR)

Summations of interaction energy for fragment #1(A:76:THR)

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.
-57.477	-55.491	-0.01	-0.958	-1.018	-0.003

Interaction energy analysis for fragmet #1(A:76:THR)

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 : 0.904

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	A	78	ALA	0	0.069	0.046	3.699	-1.641	0.345	-0.010	-0.958	-1.018	-0.003
4	A	79	ALA	0	-0.003	0.003	6.277	1.564	1.564	0.000	0.000	0.000	0.000
5	A	80	CYS	0	-0.009	0.020	9.454	-0.195	-0.195	0.000	0.000	0.000	0.000
6	A	81	PRO	0	0.034	0.013	12.694	0.340	0.340	0.000	0.000	0.000	0.000
7	A	82	GLN	0	0.026	-0.001	15.305	0.805	0.805	0.000	0.000	0.000	0.000
8	A	83	ASN	0	-0.019	-0.022	18.248	0.499	0.499	0.000	0.000	0.000	0.000
9	A	84	TRP	0	-0.006	0.005	17.014	0.473	0.473	0.000	0.000	0.000	0.000
10	A	85	ILE	0	-0.028	-0.010	17.171	-0.583	-0.583	0.000	0.000	0.000	0.000
11	A	86	GLY	0	-0.003	-0.005	13.325	0.056	0.056	0.000	0.000	0.000	0.000
12	A	87	VAL	0	-0.018	-0.020	14.317	0.292	0.292	0.000	0.000	0.000	0.000
13	A	88	GLU	-1	-0.887	-0.948	11.615	-21.321	-21.321	0.000	0.000	0.000	0.000
14	A	89	ASN	0	-0.036	-0.010	10.877	-1.794	-1.794	0.000	0.000	0.000	0.000
15	A	90	LYS	1	0.807	0.890	11.992	16.659	16.659	0.000	0.000	0.000	0.000
16	A	92	PHE	0	0.005	-0.009	16.136	1.094	1.094	0.000	0.000	0.000	0.000
17	A	93	TYR	0	0.029	0.026	19.756	-0.240	-0.240	0.000	0.000	0.000	0.000
18	A	94	PHE	0	0.019	-0.008	22.100	0.340	0.340	0.000	0.000	0.000	0.000
19	A	95	SER	0	-0.030	-0.013	25.735	-0.080	-0.080	0.000	0.000	0.000	0.000
20	A	96	GLU	-1	-0.888	-0.944	28.217	-10.748	-10.748	0.000	0.000	0.000	0.000
21	A	97	TYR	0	-0.011	-0.003	30.790	0.548	0.548	0.000	0.000	0.000	0.000
22	A	98	PRO	0	0.007	0.002	32.905	-0.217	-0.217	0.000	0.000	0.000	0.000
23	A	99	SER	0	-0.021	-0.018	34.131	0.054	0.054	0.000	0.000	0.000	0.000
24	A	100	ASN	0	0.042	0.033	36.194	-0.104	-0.104	0.000	0.000	0.000	0.000
25	A	101	TRP	0	0.050	0.025	32.852	-0.126	-0.126	0.000	0.000	0.000	0.000
26	A	102	THR	0	0.024	0.000	33.720	-0.282	-0.282	0.000	0.000	0.000	0.000
27	A	103	PHE	0	-0.010	-0.003	32.242	-0.157	-0.157	0.000	0.000	0.000	0.000
28	A	104	ALA	0	0.030	0.029	30.789	-0.255	-0.255	0.000	0.000	0.000	0.000
29	A	105	GLN	0	0.077	0.024	28.092	-0.521	-0.521	0.000	0.000	0.000	0.000
30	A	106	ALA	0	-0.008	-0.007	29.156	-0.312	-0.312	0.000	0.000	0.000	0.000
31	A	107	PHE	0	0.006	-0.003	25.285	-0.200	-0.200	0.000	0.000	0.000	0.000
32	A	108	CYS	0	-0.083	-0.018	23.218	0.043	0.043	0.000	0.000	0.000	0.000
33	A	109	MET	0	0.024	0.022	24.457	-0.341	-0.341	0.000	0.000	0.000	0.000
34	A	110	ALA	0	-0.021	-0.005	25.264	-0.294	-0.294	0.000	0.000	0.000	0.000
35	A	111	GLN	0	-0.069	-0.025	21.790	-0.516	-0.516	0.000	0.000	0.000	0.000
36	A	112	GLU	-1	-0.941	-0.959	18.973	-16.713	-16.713	0.000	0.000	0.000	0.000
37	A	113	ALA	0	-0.045	-0.018	20.374	-0.762	-0.762	0.000	0.000	0.000	0.000
38	A	114	GLN	0	-0.063	-0.029	22.405	0.262	0.262	0.000	0.000	0.000	0.000
39	A	115	LEU	0	0.015	-0.014	24.779	-0.361	-0.361	0.000	0.000	0.000	0.000
40	A	116	ALA	0	-0.071	-0.034	24.439	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	117	ARG	1	0.871	0.909	23.145	13.409	13.409	0.000	0.000	0.000	0.000
42	A	118	PHE	0	-0.020	-0.009	22.438	-0.650	-0.650	0.000	0.000	0.000	0.000
43	A	119	ASP	-1	-0.813	-0.893	20.815	-13.843	-13.843	0.000	0.000	0.000	0.000
44	A	120	ASN	0	-0.050	-0.029	18.525	0.436	0.436	0.000	0.000	0.000	0.000
45	A	121	GLN	0	0.063	0.007	22.535	0.255	0.255	0.000	0.000	0.000	0.000
46	A	122	ASP	-1	-0.894	-0.929	19.267	-14.740	-14.740	0.000	0.000	0.000	0.000
47	A	123	GLU	-1	-0.749	-0.863	18.368	-16.364	-16.364	0.000	0.000	0.000	0.000
48	A	124	LEU	0	-0.011	0.003	20.939	0.295	0.295	0.000	0.000	0.000	0.000
49	A	125	ASN	0	-0.012	-0.013	23.031	0.816	0.816	0.000	0.000	0.000	0.000
50	A	126	PHE	0	-0.013	-0.003	20.271	0.251	0.251	0.000	0.000	0.000	0.000
51	A	127	LEU	0	-0.004	-0.001	22.402	0.449	0.449	0.000	0.000	0.000	0.000
52	A	128	MET	0	-0.012	-0.007	24.811	0.446	0.446	0.000	0.000	0.000	0.000
53	A	129	ARG	1	0.934	0.983	24.023	13.257	13.257	0.000	0.000	0.000	0.000
54	A	130	TYR	0	-0.008	-0.009	22.896	0.206	0.206	0.000	0.000	0.000	0.000
55	A	131	LYS	1	0.847	0.939	25.654	10.434	10.434	0.000	0.000	0.000	0.000
56	A	132	ALA	0	0.027	0.008	28.655	0.460	0.460	0.000	0.000	0.000	0.000
57	A	133	ASN	0	-0.046	-0.025	30.713	0.388	0.388	0.000	0.000	0.000	0.000
58	A	134	PHE	0	0.016	0.021	30.642	0.362	0.362	0.000	0.000	0.000	0.000
59	A	135	ASP	-1	-0.844	-0.920	32.546	-9.035	-9.035	0.000	0.000	0.000	0.000
60	A	136	SER	0	-0.054	-0.053	30.286	0.013	0.013	0.000	0.000	0.000	0.000
61	A	137	TRP	0	-0.114	-0.076	31.823	-0.075	-0.075	0.000	0.000	0.000	0.000
62	A	138	ILE	0	0.039	0.016	28.333	-0.396	-0.396	0.000	0.000	0.000	0.000
63	A	139	GLY	0	0.026	0.026	28.745	0.416	0.416	0.000	0.000	0.000	0.000
64	A	140	LEU	0	-0.039	-0.024	29.942	0.041	0.041	0.000	0.000	0.000	0.000
65	A	141	HIS	0	-0.035	-0.022	32.857	0.518	0.518	0.000	0.000	0.000	0.000
66	A	142	ARG	1	0.884	0.947	36.310	7.809	7.809	0.000	0.000	0.000	0.000
67	A	143	GLU	-1	-0.787	-0.884	39.640	-8.131	-8.131	0.000	0.000	0.000	0.000
68	A	144	SER	0	-0.073	-0.071	42.555	0.130	0.130	0.000	0.000	0.000	0.000
69	A	145	SER	0	0.026	0.013	43.544	-0.274	-0.274	0.000	0.000	0.000	0.000
70	A	146	GLU	-1	-0.840	-0.891	44.674	-6.871	-6.871	0.000	0.000	0.000	0.000
71	A	147	HIS	0	-0.070	-0.024	41.598	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	148	PRO	0	0.054	0.029	37.748	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	149	TRP	0	-0.030	-0.017	35.176	-0.080	-0.080	0.000	0.000	0.000	0.000
74	A	150	LYS	1	0.798	0.896	33.627	8.478	8.478	0.000	0.000	0.000	0.000
75	A	151	TRP	0	0.047	0.015	27.418	-0.048	-0.048	0.000	0.000	0.000	0.000
76	A	152	THR	0	0.006	0.006	27.482	0.265	0.265	0.000	0.000	0.000	0.000
77	A	153	ASP	-1	-0.877	-0.922	25.626	-12.241	-12.241	0.000	0.000	0.000	0.000
78	A	154	ASN	0	-0.019	-0.025	28.956	0.085	0.085	0.000	0.000	0.000	0.000
79	A	155	THR	0	-0.010	0.006	28.003	0.077	0.077	0.000	0.000	0.000	0.000
80	A	156	GLU	-1	-0.877	-0.951	31.092	-8.837	-8.837	0.000	0.000	0.000	0.000
81	A	157	TYR	0	-0.034	-0.025	29.745	-0.462	-0.462	0.000	0.000	0.000	0.000
82	A	158	ASN	0	0.029	0.016	28.160	0.482	0.482	0.000	0.000	0.000	0.000
83	A	159	ASN	0	-0.041	-0.033	32.010	0.298	0.298	0.000	0.000	0.000	0.000
84	A	160	THR	0	-0.036	-0.023	29.671	0.114	0.114	0.000	0.000	0.000	0.000
85	A	161	ILE	0	0.004	0.019	29.783	0.141	0.141	0.000	0.000	0.000	0.000
86	A	162	PRO	0	0.032	0.022	33.358	-0.077	-0.077	0.000	0.000	0.000	0.000
87	A	163	ILE	0	-0.031	-0.010	33.883	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	164	ARG	1	0.947	0.972	37.319	8.190	8.190	0.000	0.000	0.000	0.000
89	A	165	GLY	0	0.014	0.013	40.362	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	166	GLU	-1	-0.865	-0.939	42.656	-6.832	-6.832	0.000	0.000	0.000	0.000
91	A	167	GLU	-1	-0.885	-0.917	42.785	-7.053	-7.053	0.000	0.000	0.000	0.000
92	A	168	ARG	1	0.891	0.932	41.229	7.179	7.179	0.000	0.000	0.000	0.000
93	A	169	PHE	0	0.013	0.015	36.673	-0.094	-0.094	0.000	0.000	0.000	0.000
94	A	170	ALA	0	0.046	0.024	33.989	0.177	0.177	0.000	0.000	0.000	0.000
95	A	171	TYR	0	-0.033	-0.029	33.162	-0.181	-0.181	0.000	0.000	0.000	0.000
96	A	172	LEU	0	0.031	0.025	27.854	0.171	0.171	0.000	0.000	0.000	0.000
97	A	173	ASN	0	0.062	0.017	32.474	0.036	0.036	0.000	0.000	0.000	0.000
98	A	174	ASN	0	-0.003	-0.026	34.025	-0.432	-0.432	0.000	0.000	0.000	0.000
99	A	175	ASN	0	-0.099	-0.038	35.730	0.186	0.186	0.000	0.000	0.000	0.000
100	A	176	GLY	0	0.032	0.025	33.085	0.086	0.086	0.000	0.000	0.000	0.000
101	A	177	ILE	0	0.054	0.022	31.203	-0.180	-0.180	0.000	0.000	0.000	0.000
102	A	178	SER	0	-0.045	-0.012	34.661	0.360	0.360	0.000	0.000	0.000	0.000
103	A	179	SER	0	0.026	0.011	37.005	-0.161	-0.161	0.000	0.000	0.000	0.000
104	A	180	THR	0	-0.075	-0.051	39.572	0.151	0.151	0.000	0.000	0.000	0.000
105	A	181	ARG	1	0.876	0.921	41.186	6.704	6.704	0.000	0.000	0.000	0.000
106	A	182	ILE	0	0.033	0.030	39.634	-0.083	-0.083	0.000	0.000	0.000	0.000
107	A	183	TYR	0	0.017	0.002	40.504	-0.126	-0.126	0.000	0.000	0.000	0.000
108	A	184	SER	0	-0.071	-0.028	41.091	0.013	0.013	0.000	0.000	0.000	0.000
109	A	185	LEU	0	0.033	0.010	38.953	-0.155	-0.155	0.000	0.000	0.000	0.000
110	A	186	ARG	1	0.872	0.942	35.293	8.461	8.461	0.000	0.000	0.000	0.000
111	A	187	MET	0	0.038	0.054	31.554	0.042	0.042	0.000	0.000	0.000	0.000
112	A	188	TRP	0	-0.008	-0.023	27.366	0.287	0.287	0.000	0.000	0.000	0.000
113	A	189	ILE	0	0.024	0.026	24.424	-0.209	-0.209	0.000	0.000	0.000	0.000
114	A	191	SER	0	0.011	-0.004	20.656	-0.247	-0.247	0.000	0.000	0.000	0.000
115	A	192	LYS	1	0.921	0.959	16.436	17.617	17.617	0.000	0.000	0.000	0.000
116	A	193	LEU	0	0.021	0.007	14.130	-0.496	-0.496	0.000	0.000	0.000	0.000
117	A	194	ASN	0	-0.085	-0.047	9.187	0.953	0.953	0.000	0.000	0.000	0.000
118	A	195	ALA	0	-0.016	-0.013	10.316	-2.270	-2.270	0.000	0.000	0.000	0.000
119	A	196	SER	-1	-0.953	-0.963	9.739	-22.860	-22.860	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:76:THR)