FMO DATABASE

FMODB ID: 4GRZN

Calculation Name: 4BH2-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid | beta-d-mannopyranose | alpha-d-mannopyranose

Ligand 3-letter code: NAG | EPE | BMA | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4BH2

Chain ID: B

ChEMBL ID:

UniProt ID: Q5EP31

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1424738.462741
FMO2-HF: Nuclear repulsion	1356023.25683
FMO2-HF: Total energy	-68715.205912
FMO2-MP2: Total energy	-68911.822348

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(B:1:GLY)

Summations of interaction energy for fragment #1(B:1:GLY)

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.
-284.889	-279.743	9.54	-7.695	-6.991	-0.096

Interaction energy analysis for fragmet #1(B:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.902

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	B	3	PHE	0	-0.038	-0.018	3.456	12.950	14.210	-0.005	-0.561	-0.693	-0.002
4	B	4	GLY	0	-0.003	0.005	2.818	11.584	12.116	0.019	-0.215	-0.336	-0.001
5	B	5	ALA	0	0.021	0.023	4.110	8.679	8.836	-0.001	-0.014	-0.143	0.000
6	B	6	ILE	0	-0.004	-0.016	4.170	4.481	4.616	-0.001	-0.024	-0.110	0.000
7	B	7	ALA	0	-0.053	-0.024	3.014	-21.395	-20.115	0.135	-0.713	-0.702	-0.007
8	B	8	GLY	0	-0.026	-0.006	4.792	-5.297	-5.247	-0.001	-0.009	-0.040	0.000
109	B	109	ASP	-1	-0.781	-0.903	2.619	-74.853	-72.890	0.825	-1.455	-1.333	-0.016
110	B	110	PHE	0	-0.063	-0.010	4.487	1.747	1.707	-0.001	-0.007	0.048	0.000
112	B	112	ASP	-1	-0.740	-0.871	1.882	-113.431	-113.618	8.571	-4.695	-3.689	-0.070
113	B	113	SER	0	-0.037	-0.011	5.166	5.001	4.997	-0.001	-0.002	0.007	0.000
9	B	9	PHE	0	-0.052	-0.021	5.476	5.414	5.414	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.030	-0.017	7.480	4.578	4.578	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.936	-0.968	7.963	-28.224	-28.224	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.013	-0.012	9.215	-0.662	-0.662	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.011	0.005	10.589	0.255	0.255	0.000	0.000	0.000	0.000
14	B	14	TRP	0	-0.001	-0.018	12.165	1.331	1.331	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.027	-0.003	15.953	0.783	0.783	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.003	0.008	18.447	0.695	0.695	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.054	0.001	14.850	0.681	0.681	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.000	-0.006	18.625	-0.588	-0.588	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.914	-0.956	21.172	-14.049	-14.049	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.027	-0.031	18.794	0.378	0.378	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.022	-0.007	13.459	-0.609	-0.609	0.000	0.000	0.000	0.000
22	B	22	TYR	0	0.006	-0.034	10.712	-1.460	-1.460	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.011	-0.001	14.233	1.520	1.520	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.016	-0.023	15.751	-1.121	-1.121	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.027	-0.015	18.387	0.548	0.548	0.000	0.000	0.000	0.000
26	B	26	HIS	0	-0.002	-0.002	19.883	-0.631	-0.631	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.017	-0.012	23.069	0.371	0.371	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.012	0.006	25.721	0.036	0.036	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.850	-0.916	29.165	-9.094	-9.094	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.033	-0.008	31.981	0.068	0.068	0.000	0.000	0.000	0.000
31	B	31	GLY	0	-0.014	0.002	30.551	0.152	0.152	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.026	-0.011	25.089	-0.342	-0.342	0.000	0.000	0.000	0.000
33	B	33	GLY	0	-0.012	-0.003	24.630	0.410	0.410	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.019	-0.010	18.575	-0.324	-0.324	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.036	0.016	20.765	0.707	0.707	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.024	0.034	18.861	-0.795	-0.795	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.792	-0.863	17.064	-16.063	-16.063	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.953	0.963	18.562	12.246	12.246	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.903	-0.946	20.115	-15.061	-15.061	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.021	-0.056	15.017	-0.488	-0.488	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.014	0.008	16.255	-1.055	-1.055	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.061	-0.032	17.275	-0.137	-0.137	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.962	0.978	17.636	14.956	14.956	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.024	0.022	13.648	-0.171	-0.171	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.017	0.013	15.465	-0.151	-0.151	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.858	-0.909	18.056	-13.796	-13.796	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.007	-0.009	16.511	0.388	0.388	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.016	-0.016	13.423	-0.104	-0.104	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.018	-0.019	16.150	0.529	0.529	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.051	-0.024	19.547	0.238	0.238	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.848	0.927	11.823	23.223	23.223	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.004	-0.005	17.562	0.400	0.400	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.012	0.005	19.768	0.322	0.322	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.040	-0.024	20.800	0.668	0.668	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.055	-0.029	17.381	0.267	0.267	0.000	0.000	0.000	0.000
56	B	56	ILE	0	-0.033	-0.002	22.010	0.369	0.369	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.891	-0.961	25.360	-10.942	-10.942	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.862	0.929	24.907	11.753	11.753	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.014	0.013	27.053	0.240	0.240	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.038	-0.021	29.018	0.314	0.314	0.000	0.000	0.000	0.000
61	B	61	THR	0	-0.015	-0.001	32.346	0.050	0.050	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.057	-0.038	34.553	0.029	0.029	0.000	0.000	0.000	0.000
63	B	63	PHE	0	-0.045	-0.023	38.296	-0.047	-0.047	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.836	-0.916	39.093	-7.598	-7.598	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.040	-0.020	41.845	-0.020	-0.020	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.011	0.015	39.846	0.077	0.077	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.050	0.022	43.320	0.054	0.054	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.696	0.790	42.181	7.155	7.155	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.892	-0.941	48.780	-6.155	-6.155	0.000	0.000	0.000	0.000
70	B	70	PHE	0	-0.024	0.002	48.261	0.103	0.103	0.000	0.000	0.000	0.000
71	B	71	ASN	0	0.048	0.016	52.970	0.023	0.023	0.000	0.000	0.000	0.000
72	B	72	ASN	0	0.010	-0.008	55.006	-0.158	-0.158	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.031	-0.013	56.650	0.001	0.001	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.861	-0.928	53.929	-5.703	-5.703	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.870	0.910	51.396	5.944	5.944	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.928	0.959	50.007	5.623	5.623	0.000	0.000	0.000	0.000
77	B	77	ILE	0	0.014	0.013	49.195	-0.117	-0.117	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.818	-0.883	47.506	-6.556	-6.556	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.001	-0.012	44.960	-0.292	-0.292	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.066	-0.032	44.305	-0.163	-0.163	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.017	-0.006	43.416	-0.150	-0.150	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.853	0.907	39.760	7.680	7.680	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.923	0.959	39.734	6.998	6.998	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.011	0.016	38.494	-0.173	-0.173	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.748	-0.830	37.461	-7.834	-7.834	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.822	-0.892	35.852	-8.382	-8.382	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.028	0.019	34.064	-0.282	-0.282	0.000	0.000	0.000	0.000
88	B	88	PHE	0	-0.009	-0.020	32.817	-0.282	-0.282	0.000	0.000	0.000	0.000
89	B	89	LEU	0	-0.015	0.009	30.891	-0.327	-0.327	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.879	-0.933	29.757	-10.186	-10.186	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.055	-0.029	28.063	-0.488	-0.488	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.006	-0.014	26.570	-0.590	-0.590	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.015	-0.015	25.649	-0.472	-0.472	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.025	-0.011	22.503	-0.695	-0.695	0.000	0.000	0.000	0.000
95	B	95	ASN	0	0.000	-0.017	22.175	-0.859	-0.859	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.003	0.012	21.297	-0.639	-0.639	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.911	-0.958	20.015	-15.131	-15.131	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.028	-0.012	17.524	-1.150	-1.150	0.000	0.000	0.000	0.000
99	B	99	LEU	0	0.008	0.007	16.420	-1.161	-1.161	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.002	-0.001	15.879	-1.130	-1.130	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.023	-0.013	13.690	-1.507	-1.507	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.020	-0.014	11.920	-1.705	-1.705	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.827	-0.924	11.196	-23.065	-23.065	0.000	0.000	0.000	0.000
104	B	104	ASN	0	0.002	0.025	10.974	-0.926	-0.926	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.917	-0.943	5.640	-41.185	-41.185	0.000	0.000	0.000	0.000
106	B	106	ARG	1	0.920	0.951	6.443	20.705	20.705	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.054	-0.039	8.663	1.025	1.025	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.017	-0.006	5.112	-0.074	-0.074	0.000	0.000	0.000	0.000
111	B	111	HIS	0	0.043	0.046	7.204	1.696	1.696	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.022	-0.022	7.923	3.517	3.517	0.000	0.000	0.000	0.000
115	B	115	VAL	0	0.004	0.006	7.693	2.597	2.597	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.847	0.924	7.015	32.718	32.718	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.008	-0.018	8.988	2.518	2.518	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.052	-0.013	12.206	1.979	1.979	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.025	-0.042	11.464	1.251	1.251	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.771	-0.871	12.530	-22.472	-22.472	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.894	0.950	14.898	17.858	17.858	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.001	0.010	16.932	1.162	1.162	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.853	0.922	15.119	20.302	20.302	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.046	-0.031	18.469	0.886	0.886	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.063	-0.027	20.808	1.351	1.351	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.001	0.008	20.999	0.590	0.590	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.858	0.928	22.582	12.725	12.725	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.844	-0.882	23.355	-11.766	-11.766	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.046	0.011	26.152	0.413	0.413	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.034	-0.026	23.342	0.206	0.206	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.840	0.945	22.183	12.956	12.956	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.811	-0.900	15.356	-20.045	-20.045	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.062	-0.040	18.041	0.269	0.269	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.024	0.001	14.228	-0.038	-0.038	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.032	0.009	12.847	-1.675	-1.675	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.022	0.005	12.516	-0.318	-0.318	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.080	-0.028	13.035	0.998	0.998	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.031	-0.002	16.216	-0.239	-0.239	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.862	-0.919	19.979	-12.602	-12.602	0.000	0.000	0.000	0.000
140	B	140	PHE	0	0.002	-0.016	23.238	-0.014	-0.014	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.024	-0.002	26.283	0.061	0.061	0.000	0.000	0.000	0.000
142	B	142	HIS	0	0.017	0.047	28.912	0.006	0.006	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.827	0.875	30.089	8.872	8.872	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.014	0.021	27.752	-0.415	-0.415	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.802	-0.888	29.498	-9.960	-9.960	0.000	0.000	0.000	0.000
146	B	146	ASN	0	-0.013	-0.030	29.237	-0.721	-0.721	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.886	-0.944	29.292	-9.707	-9.707	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.012	0.003	24.975	-0.631	-0.631	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.849	-0.916	25.152	-12.491	-12.491	0.000	0.000	0.000	0.000
150	B	151	SER	0	-0.073	-0.041	26.761	-0.188	-0.188	0.000	0.000	0.000	0.000
151	B	152	VAL	0	0.015	0.009	21.573	-0.230	-0.230	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.837	0.923	21.988	12.313	12.313	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.101	-0.055	22.894	-0.215	-0.215	0.000	0.000	0.000	0.000
154	B	155	GLY	0	-0.045	-0.007	23.681	0.166	0.166	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.080	-0.050	24.458	0.417	0.417	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.016	-0.021	25.924	0.367	0.367	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.879	-0.940	27.791	-9.628	-9.628	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.056	-0.073	27.730	0.164	0.164	0.000	0.000	0.000	0.000
159	B	160	PRO	0	-0.015	-0.015	30.237	0.075	0.075	0.000	0.000	0.000	0.000
160	B	161	GLN	0	-0.053	-0.012	33.593	0.259	0.259	0.000	0.000	0.000	0.000
161	B	162	TYR	0	0.004	-0.013	30.801	0.255	0.255	0.000	0.000	0.000	0.000
162	B	163	SER	0	0.008	0.010	31.941	-0.019	-0.019	0.000	0.000	0.000	0.000
163	B	164	GLU	-1	-0.953	-0.990	33.593	-8.447	-8.447	0.000	0.000	0.000	0.000
164	B	165	GLU	-1	-0.931	-0.957	34.334	-9.200	-9.200	0.000	0.000	0.000	0.000
165	B	166	ALA	0	-0.043	-0.023	30.597	-0.075	-0.075	0.000	0.000	0.000	0.000
166	B	167	ARG	0	-0.019	0.013	32.262	-0.444	-0.444	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:1:GLY)