FMO DATABASE

FMODB ID: 9RZM2

Calculation Name: 3QW9-A-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: 3QW9

Chain ID: A

ChEMBL ID:

UniProt ID: P26342

Base Structure: X-ray

Registration Date: 2025-10-05

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1751906.443287
FMO2-HF: Nuclear repulsion	1682810.953985
FMO2-HF: Total energy	-69095.489302
FMO2-MP2: Total energy	-69291.688989

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:11:PRO)

Summations of interaction energy for fragment #1(A:11: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.
13.187	18.614	4.879	-4.21	-6.095	-0.034

Interaction energy analysis for fragmet #1(A:11:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.908

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	13	SER	0	0.028	0.013	3.837	4.212	6.118	-0.020	-0.856	-1.030	-0.003
43	A	53	ASP	-1	-0.784	-0.902	2.614	-76.005	-72.958	0.742	-2.002	-1.787	-0.023
129	A	140	SER	0	-0.021	-0.014	2.365	0.671	1.020	1.382	-0.510	-1.221	-0.002
130	A	141	LEU	0	-0.013	0.010	2.316	-7.283	-7.217	2.776	-0.832	-2.009	-0.006
131	A	142	LYS	1	0.946	0.983	4.732	38.427	38.486	-0.001	-0.010	-0.048	0.000
4	A	14	ASN	0	-0.060	-0.024	5.620	7.722	7.722	0.000	0.000	0.000	0.000
5	A	15	ALA	0	0.011	-0.003	8.951	-0.234	-0.234	0.000	0.000	0.000	0.000
6	A	16	THR	0	-0.022	0.000	11.455	0.935	0.935	0.000	0.000	0.000	0.000
7	A	17	PHE	0	0.012	-0.016	13.660	-0.686	-0.686	0.000	0.000	0.000	0.000
8	A	18	ASN	0	0.017	0.017	17.678	0.641	0.641	0.000	0.000	0.000	0.000
9	A	19	MET	0	0.011	0.010	21.332	-0.316	-0.316	0.000	0.000	0.000	0.000
10	A	20	GLU	-1	-0.921	-0.950	24.155	-11.232	-11.232	0.000	0.000	0.000	0.000
11	A	21	LEU	0	0.050	0.030	27.300	-0.098	-0.098	0.000	0.000	0.000	0.000
12	A	22	TYR	0	-0.058	-0.039	27.034	0.145	0.145	0.000	0.000	0.000	0.000
13	A	23	ASN	0	0.027	0.001	32.243	0.085	0.085	0.000	0.000	0.000	0.000
14	A	24	THR	0	0.028	0.018	34.285	0.132	0.132	0.000	0.000	0.000	0.000
15	A	25	ASP	-1	-0.866	-0.929	32.072	-9.223	-9.223	0.000	0.000	0.000	0.000
16	A	26	LEU	0	-0.014	-0.013	31.392	-0.291	-0.291	0.000	0.000	0.000	0.000
17	A	27	PHE	0	-0.103	-0.065	28.308	-0.380	-0.380	0.000	0.000	0.000	0.000
18	A	28	LEU	0	-0.004	-0.006	29.384	-0.296	-0.296	0.000	0.000	0.000	0.000
19	A	29	VAL	0	0.010	0.009	32.051	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	30	PRO	0	-0.016	-0.006	29.911	0.060	0.060	0.000	0.000	0.000	0.000
21	A	31	SER	0	0.001	-0.008	32.214	0.377	0.377	0.000	0.000	0.000	0.000
22	A	32	PRO	0	0.001	-0.001	34.198	-0.166	-0.166	0.000	0.000	0.000	0.000
23	A	33	GLY	0	-0.031	-0.025	34.305	-0.114	-0.114	0.000	0.000	0.000	0.000
24	A	34	VAL	0	-0.022	-0.010	35.044	-0.119	-0.119	0.000	0.000	0.000	0.000
25	A	35	PHE	0	-0.004	0.011	34.632	0.112	0.112	0.000	0.000	0.000	0.000
26	A	36	SER	0	-0.001	-0.001	37.086	0.131	0.131	0.000	0.000	0.000	0.000
27	A	37	VAL	0	-0.016	-0.004	37.658	-0.097	-0.097	0.000	0.000	0.000	0.000
28	A	38	ALA	0	0.057	0.021	40.867	0.169	0.169	0.000	0.000	0.000	0.000
29	A	39	GLU	-1	-0.803	-0.902	42.539	-7.302	-7.302	0.000	0.000	0.000	0.000
30	A	40	ASN	0	-0.050	-0.029	42.365	0.084	0.084	0.000	0.000	0.000	0.000
31	A	41	GLU	-1	-0.889	-0.925	41.208	-7.314	-7.314	0.000	0.000	0.000	0.000
32	A	42	HIS	0	-0.026	-0.018	36.041	-0.091	-0.091	0.000	0.000	0.000	0.000
33	A	43	VAL	0	-0.018	0.003	32.471	0.004	0.004	0.000	0.000	0.000	0.000
34	A	44	TYR	0	0.017	0.008	31.562	-0.193	-0.193	0.000	0.000	0.000	0.000
35	A	45	VAL	0	-0.016	-0.013	26.394	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	46	GLU	-1	-0.773	-0.847	23.548	-12.787	-12.787	0.000	0.000	0.000	0.000
37	A	47	VAL	0	0.006	-0.001	19.834	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	48	SER	0	-0.021	-0.015	18.732	-0.282	-0.282	0.000	0.000	0.000	0.000
39	A	49	VAL	0	0.003	0.011	12.754	-0.165	-0.165	0.000	0.000	0.000	0.000
40	A	50	THR	0	-0.003	-0.004	14.420	0.649	0.649	0.000	0.000	0.000	0.000
41	A	51	LYS	1	0.765	0.879	8.975	26.947	26.947	0.000	0.000	0.000	0.000
42	A	52	ALA	0	0.070	0.034	8.353	2.012	2.012	0.000	0.000	0.000	0.000
44	A	54	GLN	0	0.049	0.032	5.973	4.007	4.007	0.000	0.000	0.000	0.000
45	A	55	ASP	-1	-0.812	-0.880	5.185	-34.697	-34.697	0.000	0.000	0.000	0.000
46	A	56	LEU	0	-0.027	-0.007	5.969	2.262	2.262	0.000	0.000	0.000	0.000
47	A	57	GLY	0	-0.033	-0.028	7.626	2.412	2.412	0.000	0.000	0.000	0.000
48	A	58	PHE	0	-0.002	-0.020	11.190	-1.055	-1.055	0.000	0.000	0.000	0.000
49	A	59	ALA	0	0.016	0.001	13.963	0.676	0.676	0.000	0.000	0.000	0.000
50	A	60	ILE	0	0.002	-0.005	17.202	-0.409	-0.409	0.000	0.000	0.000	0.000
51	A	61	GLN	0	0.000	0.009	19.116	-0.052	-0.052	0.000	0.000	0.000	0.000
52	A	62	THR	0	0.060	0.022	20.939	0.485	0.485	0.000	0.000	0.000	0.000
53	A	63	CYS	0	-0.065	-0.034	23.807	-0.262	-0.262	0.000	0.000	0.000	0.000
54	A	64	PHE	0	0.037	0.032	27.147	0.274	0.274	0.000	0.000	0.000	0.000
55	A	65	LEU	0	0.034	0.034	30.679	-0.171	-0.171	0.000	0.000	0.000	0.000
56	A	66	SER	0	0.023	0.023	33.682	0.132	0.132	0.000	0.000	0.000	0.000
57	A	67	PRO	0	0.039	0.017	35.623	-0.093	-0.093	0.000	0.000	0.000	0.000
58	A	68	TYR	0	-0.028	-0.011	34.971	0.211	0.211	0.000	0.000	0.000	0.000
59	A	69	SER	0	0.031	0.012	33.350	-0.218	-0.218	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.037	-0.032	30.658	-0.563	-0.563	0.000	0.000	0.000	0.000
61	A	71	PRO	0	-0.002	-0.003	26.841	0.236	0.236	0.000	0.000	0.000	0.000
62	A	72	ASP	-1	-0.806	-0.902	28.648	-10.402	-10.402	0.000	0.000	0.000	0.000
63	A	73	ARG	1	0.821	0.925	30.457	8.340	8.340	0.000	0.000	0.000	0.000
64	A	74	MET	0	0.039	0.030	30.176	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	75	SER	0	-0.045	-0.063	32.977	0.383	0.383	0.000	0.000	0.000	0.000
66	A	76	ASP	-1	-0.834	-0.914	34.115	-8.251	-8.251	0.000	0.000	0.000	0.000
67	A	77	TYR	0	-0.042	-0.005	35.433	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	78	THR	0	-0.027	-0.032	29.628	-0.292	-0.292	0.000	0.000	0.000	0.000
69	A	79	ILE	0	-0.007	-0.005	29.496	0.123	0.123	0.000	0.000	0.000	0.000
70	A	80	ILE	0	-0.032	-0.014	24.611	-0.068	-0.068	0.000	0.000	0.000	0.000
71	A	81	GLU	-1	-0.825	-0.910	26.371	-10.072	-10.072	0.000	0.000	0.000	0.000
72	A	82	ASN	0	0.020	0.021	22.884	-0.302	-0.302	0.000	0.000	0.000	0.000
73	A	83	ILE	0	-0.037	-0.027	18.253	-0.254	-0.254	0.000	0.000	0.000	0.000
74	A	84	CYS	0	-0.037	0.014	22.734	0.364	0.364	0.000	0.000	0.000	0.000
75	A	85	PRO	0	-0.053	-0.044	26.314	0.119	0.119	0.000	0.000	0.000	0.000
76	A	86	LYS	1	0.884	0.928	29.045	9.536	9.536	0.000	0.000	0.000	0.000
77	A	87	ASP	-1	-0.824	-0.876	31.851	-8.249	-8.249	0.000	0.000	0.000	0.000
78	A	88	ASP	-1	-0.870	-0.937	33.683	-8.516	-8.516	0.000	0.000	0.000	0.000
79	A	89	SER	0	-0.078	-0.052	35.978	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	90	VAL	0	-0.076	-0.037	29.050	-0.145	-0.145	0.000	0.000	0.000	0.000
81	A	91	LYS	1	0.959	0.994	31.413	9.330	9.330	0.000	0.000	0.000	0.000
82	A	92	PHE	0	0.013	-0.005	23.725	-0.300	-0.300	0.000	0.000	0.000	0.000
83	A	93	TYR	0	0.005	-0.020	27.054	0.365	0.365	0.000	0.000	0.000	0.000
84	A	94	SER	0	-0.038	-0.023	24.535	-0.402	-0.402	0.000	0.000	0.000	0.000
85	A	95	SER	0	0.015	0.005	20.157	-0.203	-0.203	0.000	0.000	0.000	0.000
86	A	96	LYS	1	0.911	0.956	21.053	12.755	12.755	0.000	0.000	0.000	0.000
87	A	97	ARG	1	0.949	0.978	14.309	18.102	18.102	0.000	0.000	0.000	0.000
88	A	98	VAL	0	0.006	0.014	17.421	0.799	0.799	0.000	0.000	0.000	0.000
89	A	99	HIS	0	0.007	0.003	13.421	0.169	0.169	0.000	0.000	0.000	0.000
90	A	100	PHE	0	0.007	-0.001	15.408	1.217	1.217	0.000	0.000	0.000	0.000
91	A	101	PRO	0	0.022	-0.004	15.421	-1.099	-1.099	0.000	0.000	0.000	0.000
92	A	102	ILE	0	0.007	0.014	16.035	-0.350	-0.350	0.000	0.000	0.000	0.000
93	A	103	PRO	0	-0.039	-0.024	14.547	-0.420	-0.420	0.000	0.000	0.000	0.000
94	A	104	HIS	0	-0.019	0.000	10.694	-2.641	-2.641	0.000	0.000	0.000	0.000
95	A	105	ALA	0	0.029	0.022	10.496	-2.585	-2.585	0.000	0.000	0.000	0.000
96	A	106	GLU	-1	-0.806	-0.915	9.728	-26.985	-26.985	0.000	0.000	0.000	0.000
97	A	107	VAL	0	-0.015	0.004	13.531	-0.577	-0.577	0.000	0.000	0.000	0.000
98	A	108	ASP	-1	-0.831	-0.914	13.103	-20.523	-20.523	0.000	0.000	0.000	0.000
99	A	109	LYS	1	0.853	0.898	16.314	13.149	13.149	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.858	0.941	16.635	16.982	16.982	0.000	0.000	0.000	0.000
101	A	111	ARG	1	0.814	0.908	21.629	11.667	11.667	0.000	0.000	0.000	0.000
102	A	112	PHE	0	0.026	0.000	25.296	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	113	SER	0	0.054	0.036	28.043	0.109	0.109	0.000	0.000	0.000	0.000
104	A	114	PHE	0	-0.032	-0.003	31.421	-0.178	-0.178	0.000	0.000	0.000	0.000
105	A	115	LEU	0	0.055	0.025	34.036	0.048	0.048	0.000	0.000	0.000	0.000
106	A	116	PHE	0	-0.020	-0.020	37.589	-0.126	-0.126	0.000	0.000	0.000	0.000
107	A	117	LYS	1	0.928	0.964	37.803	8.322	8.322	0.000	0.000	0.000	0.000
108	A	118	SER	0	-0.013	-0.017	40.698	-0.178	-0.178	0.000	0.000	0.000	0.000
109	A	119	VAL	0	-0.063	-0.034	39.862	0.160	0.160	0.000	0.000	0.000	0.000
110	A	120	PHE	0	-0.030	-0.026	37.622	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	121	ASN	0	0.010	0.005	43.311	0.068	0.068	0.000	0.000	0.000	0.000
112	A	122	THR	0	-0.020	-0.028	41.441	0.075	0.075	0.000	0.000	0.000	0.000
113	A	123	SER	0	0.052	0.032	43.486	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	124	LEU	0	-0.017	0.002	39.679	-0.114	-0.114	0.000	0.000	0.000	0.000
115	A	125	LEU	0	-0.001	0.014	37.204	0.038	0.038	0.000	0.000	0.000	0.000
116	A	126	PHE	0	0.002	-0.008	32.760	-0.147	-0.147	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.036	0.033	29.459	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	128	HIS	1	0.802	0.896	27.783	9.746	9.746	0.000	0.000	0.000	0.000
119	A	130	GLU	-1	-0.862	-0.933	20.167	-13.797	-13.797	0.000	0.000	0.000	0.000
120	A	131	LEU	0	-0.046	-0.017	17.526	-0.198	-0.198	0.000	0.000	0.000	0.000
121	A	132	THR	0	0.024	-0.008	14.929	-0.532	-0.532	0.000	0.000	0.000	0.000
122	A	133	LEU	0	-0.005	-0.014	8.835	-0.188	-0.188	0.000	0.000	0.000	0.000
123	A	134	CYS	0	-0.078	-0.028	10.955	0.854	0.854	0.000	0.000	0.000	0.000
124	A	135	SER	0	0.010	-0.016	7.628	-3.305	-3.305	0.000	0.000	0.000	0.000
125	A	136	ARG	1	0.826	0.890	9.291	26.928	26.928	0.000	0.000	0.000	0.000
126	A	137	LYS	1	0.869	0.939	7.307	36.295	36.295	0.000	0.000	0.000	0.000
127	A	138	LYS	1	0.983	1.002	8.829	21.606	21.606	0.000	0.000	0.000	0.000
128	A	139	GLY	0	0.049	0.007	6.612	0.476	0.476	0.000	0.000	0.000	0.000
132	A	143	LEU	0	-0.027	-0.013	7.012	0.841	0.841	0.000	0.000	0.000	0.000
133	A	144	PRO	0	0.072	0.059	9.534	-0.156	-0.156	0.000	0.000	0.000	0.000
134	A	145	ARG	1	0.878	0.915	11.341	19.106	19.106	0.000	0.000	0.000	0.000
135	A	147	VAL	0	0.048	0.025	14.681	0.065	0.065	0.000	0.000	0.000	0.000
136	A	148	THR	0	-0.064	-0.055	18.470	-0.070	-0.070	0.000	0.000	0.000	0.000
137	A	149	PRO	0	0.010	-0.005	21.476	0.042	0.042	0.000	0.000	0.000	0.000
138	A	150	ASP	-1	-0.846	-0.919	24.306	-10.704	-10.704	0.000	0.000	0.000	0.000
139	A	151	ASP	-1	-0.853	-0.899	22.466	-12.710	-12.710	0.000	0.000	0.000	0.000
140	A	152	ALA	0	-0.068	-0.042	22.542	0.114	0.114	0.000	0.000	0.000	0.000
141	A	154	THR	0	-0.027	-0.022	27.169	0.326	0.326	0.000	0.000	0.000	0.000
142	A	155	SER	0	-0.041	-0.019	23.357	0.278	0.278	0.000	0.000	0.000	0.000
143	A	156	LEU	0	0.020	0.001	26.320	0.215	0.215	0.000	0.000	0.000	0.000
144	A	157	ASP	-1	-0.853	-0.915	21.204	-13.490	-13.490	0.000	0.000	0.000	0.000
145	A	158	ALA	0	-0.001	-0.009	23.594	-0.350	-0.350	0.000	0.000	0.000	0.000
146	A	159	THR	0	-0.097	-0.060	20.788	-0.102	-0.102	0.000	0.000	0.000	0.000
147	A	160	MET	0	-0.024	0.025	19.063	-0.900	-0.900	0.000	0.000	0.000	0.000
148	A	161	ILE	0	-0.044	-0.020	17.488	-1.212	-1.212	0.000	0.000	0.000	0.000
149	A	162	TRP	0	0.021	0.016	11.136	-0.117	-0.117	0.000	0.000	0.000	0.000
150	A	163	THR	0	-0.039	-0.042	14.687	-0.772	-0.772	0.000	0.000	0.000	0.000
151	A	164	MET	0	-0.003	-0.008	12.364	-0.243	-0.243	0.000	0.000	0.000	0.000
152	A	165	MET	0	-0.037	-0.013	11.085	-0.288	-0.288	0.000	0.000	0.000	0.000
153	A	166	GLN	0	0.031	0.033	15.375	-0.079	-0.079	0.000	0.000	0.000	0.000
154	A	167	ASN	0	0.010	0.004	18.267	0.754	0.754	0.000	0.000	0.000	0.000
155	A	168	LYS	0	-0.001	0.008	13.018	-1.632	-1.632	0.000	0.000	0.000	0.000
156	A	169	LYS	1	0.935	0.971	13.794	20.144	20.144	0.000	0.000	0.000	0.000
157	A	170	THR	0	0.058	0.041	18.527	0.161	0.161	0.000	0.000	0.000	0.000
158	A	171	PHE	0	-0.011	-0.005	19.161	-0.135	-0.135	0.000	0.000	0.000	0.000
159	A	172	THR	0	-0.013	-0.015	24.315	0.366	0.366	0.000	0.000	0.000	0.000
160	A	173	LYS	1	0.905	0.965	27.264	11.081	11.081	0.000	0.000	0.000	0.000
161	A	174	PRO	0	0.000	0.015	30.933	0.082	0.082	0.000	0.000	0.000	0.000
162	A	175	LEU	0	0.004	-0.008	33.887	-0.085	-0.085	0.000	0.000	0.000	0.000
163	A	176	ALA	0	0.012	0.000	37.130	0.105	0.105	0.000	0.000	0.000	0.000
164	A	177	VAL	0	-0.025	-0.013	40.907	-0.024	-0.024	0.000	0.000	0.000	0.000
165	A	178	VAL	0	-0.013	-0.025	42.984	0.100	0.100	0.000	0.000	0.000	0.000
166	A	179	LEU	0	-0.074	-0.035	45.839	0.129	0.129	0.000	0.000	0.000	0.000
167	A	180	GLN	-1	-0.938	-0.944	48.149	-6.042	-6.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:PRO)