FMO DATABASE

FMODB ID: 6N27Z

Calculation Name: 5A3I-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 5A3I

Chain ID: B

ChEMBL ID:

UniProt ID: A8UDR1

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1436438.067951
FMO2-HF: Nuclear repulsion	1368251.966163
FMO2-HF: Total energy	-68186.101789
FMO2-MP2: Total energy	-68381.160612

3D Structure

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.
-10.038	-2.986	1.674	-4.087	-4.637	-0.024

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 : 0 / q_Mulliken : 0.027 / q_NPA : 0.013

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	-0.071	-0.047	3.164	0.061	1.478	0.008	-0.673	-0.752	0.003
4	B	4	GLY	0	0.053	0.038	3.192	0.304	1.129	0.268	-0.445	-0.648	0.004
5	B	5	ALA	0	0.003	0.009	3.921	-2.646	-2.402	0.040	-0.066	-0.218	0.002
6	B	6	ILE	0	-0.013	-0.010	5.558	-0.381	-0.381	0.000	0.000	0.000	0.000
7	B	7	ALA	0	-0.030	-0.016	5.193	0.304	0.384	-0.001	-0.001	-0.077	0.000
8	B	8	GLY	0	-0.003	0.011	7.465	0.268	0.268	0.000	0.000	0.000	0.000
9	B	9	PHE	0	-0.032	-0.025	8.410	-0.222	-0.222	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.001	0.007	11.364	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.959	-0.973	11.776	0.328	0.328	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.013	-0.012	13.111	-0.047	-0.047	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.015	0.001	14.224	0.007	0.007	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.009	-0.012	14.916	-0.010	-0.010	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.018	-0.008	18.503	-0.019	-0.019	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.016	-0.002	20.901	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.034	0.007	16.965	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.012	0.001	20.505	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.930	-0.959	22.699	0.016	0.016	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.031	-0.042	19.840	-0.009	-0.009	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.024	-0.006	14.195	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	22	TYR	0	-0.005	-0.039	10.999	0.018	0.018	0.000	0.000	0.000	0.000
23	B	23	GLY	0	-0.015	-0.024	15.500	-0.016	-0.016	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.034	-0.023	17.752	0.022	0.022	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.001	-0.006	20.461	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.010	0.019	22.735	0.010	0.010	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.021	-0.023	25.903	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.030	-0.022	28.734	0.003	0.003	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.891	-0.952	32.208	0.037	0.037	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.024	0.002	34.673	0.001	0.001	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.033	0.017	33.301	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.048	-0.010	27.877	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	33	GLY	0	-0.011	-0.008	27.304	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.037	-0.015	21.289	0.002	0.002	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.039	0.019	22.832	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.029	0.029	20.111	0.009	0.009	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.836	-0.913	18.307	0.011	0.011	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.973	0.966	19.837	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.930	-0.945	20.487	-0.027	-0.027	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.009	-0.020	15.460	-0.012	-0.012	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.002	-0.010	16.552	-0.020	-0.020	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.016	0.000	17.996	-0.008	-0.008	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.955	0.982	15.770	0.102	0.102	0.000	0.000	0.000	0.000
44	B	44	ALA	0	-0.009	-0.004	14.178	-0.019	-0.019	0.000	0.000	0.000	0.000
45	B	45	ILE	0	-0.001	0.002	15.815	-0.021	-0.021	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.843	-0.937	18.464	-0.072	-0.072	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.052	-0.025	16.379	-0.004	-0.004	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.016	-0.019	13.380	-0.016	-0.016	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.012	0.004	16.108	0.000	0.000	0.000	0.000	0.000	0.000
50	B	50	ASN	0	0.006	-0.002	19.640	0.011	0.011	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.922	0.973	11.211	0.349	0.349	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.024	0.011	17.441	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.021	0.010	19.073	0.012	0.012	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.033	-0.012	19.038	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.028	-0.003	16.221	0.005	0.005	0.000	0.000	0.000	0.000
56	B	56	ILE	0	0.029	0.011	19.337	0.007	0.007	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.944	-0.972	22.564	-0.078	-0.078	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.928	0.955	17.364	0.166	0.166	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.027	-0.004	20.774	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	ASN	0	0.008	0.010	23.230	0.009	0.009	0.000	0.000	0.000	0.000
61	B	61	THR	0	0.019	0.008	24.983	0.003	0.003	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.018	-0.028	23.514	0.003	0.003	0.000	0.000	0.000	0.000
63	B	63	PHE	0	0.020	0.028	26.840	0.003	0.003	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.918	-0.960	28.618	-0.052	-0.052	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.060	-0.015	28.521	0.003	0.003	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.035	0.016	27.664	0.003	0.003	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.051	0.031	30.679	0.004	0.004	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.899	0.939	33.641	0.042	0.042	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.981	-0.995	31.500	-0.046	-0.046	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.041	0.028	34.963	0.002	0.002	0.000	0.000	0.000	0.000
71	B	71	ASN	0	-0.023	-0.016	36.665	0.003	0.003	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.075	-0.056	37.557	0.003	0.003	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.030	-0.011	37.542	0.002	0.002	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.948	-0.973	40.348	-0.026	-0.026	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.897	0.957	41.590	0.031	0.031	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.878	0.953	39.178	0.032	0.032	0.000	0.000	0.000	0.000
77	B	77	ILE	0	-0.022	-0.008	42.269	0.001	0.001	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.899	-0.937	45.777	-0.018	-0.018	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.043	-0.024	48.199	0.000	0.000	0.000	0.000	0.000	0.000
80	B	80	LEU	0	0.020	0.017	41.301	0.000	0.000	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.027	-0.025	41.675	0.000	0.000	0.000	0.000	0.000	0.000
82	B	82	LYS	1	1.040	0.991	41.885	0.017	0.017	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.944	0.967	38.920	0.018	0.018	0.000	0.000	0.000	0.000
84	B	84	MET	0	0.001	0.020	36.002	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.899	-0.952	36.114	-0.031	-0.031	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.896	-0.946	34.266	-0.028	-0.028	0.000	0.000	0.000	0.000
87	B	87	GLY	0	-0.006	0.013	32.486	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	88	PHE	0	0.000	-0.026	31.218	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.014	0.010	30.175	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.889	-0.927	28.350	-0.037	-0.037	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.036	-0.016	26.502	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.024	-0.016	25.315	-0.003	-0.003	0.000	0.000	0.000	0.000
93	B	93	THR	0	0.028	0.006	24.496	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.023	-0.006	20.114	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.047	-0.044	20.675	-0.010	-0.010	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.028	0.003	20.054	-0.011	-0.011	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.921	-0.973	19.359	-0.062	-0.062	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.023	-0.006	15.033	-0.010	-0.010	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.010	-0.018	15.110	-0.019	-0.019	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.014	0.009	15.231	-0.023	-0.023	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.011	-0.010	12.790	-0.024	-0.024	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.033	-0.011	10.654	-0.027	-0.027	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.897	-0.959	9.981	-0.320	-0.320	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.012	-0.010	10.909	-0.066	-0.066	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.936	-0.949	4.609	-0.003	0.179	-0.001	-0.013	-0.168	0.000
106	B	106	ARG	1	0.954	0.968	5.789	0.107	0.107	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.070	-0.045	7.089	-0.133	-0.133	0.000	0.000	0.000	0.000
108	B	108	LEU	0	0.006	-0.005	5.621	0.086	0.086	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.820	-0.904	2.500	-7.806	-5.286	0.967	-1.886	-1.601	-0.024
110	B	110	PHE	0	-0.095	-0.044	3.717	0.555	0.555	-0.001	0.008	-0.007	0.000
111	B	111	HIS	0	0.023	0.040	6.978	0.212	0.212	0.000	0.000	0.000	0.000
112	B	112	ASP	-1	-0.837	-0.920	2.848	-1.076	0.705	0.395	-1.010	-1.165	-0.009
113	B	113	SER	0	-0.017	-0.010	5.317	0.432	0.435	-0.001	-0.001	-0.001	0.000
114	B	114	ASN	0	-0.013	-0.017	6.697	0.096	0.096	0.000	0.000	0.000	0.000
115	B	115	VAL	0	-0.009	0.003	8.780	0.020	0.020	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.942	0.983	7.954	-0.337	-0.337	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.030	-0.029	9.892	-0.019	-0.019	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.051	-0.009	12.285	-0.017	-0.017	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.056	-0.046	13.149	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.891	-0.966	13.353	0.166	0.166	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.926	0.960	15.922	-0.043	-0.043	0.000	0.000	0.000	0.000
122	B	122	VAL	0	-0.007	-0.001	18.115	-0.011	-0.011	0.000	0.000	0.000	0.000
123	B	123	ARG	1	1.022	1.018	16.706	-0.135	-0.135	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.058	-0.021	19.293	-0.010	-0.010	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.063	-0.024	22.148	-0.015	-0.015	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.004	0.006	23.547	-0.005	-0.005	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.880	0.927	24.349	-0.040	-0.040	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.895	-0.918	25.544	0.051	0.051	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.053	0.023	28.242	-0.001	-0.001	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.045	-0.025	25.457	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.915	0.969	26.240	-0.069	-0.069	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.850	-0.929	18.876	0.163	0.163	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.046	-0.025	21.974	0.003	0.003	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.018	0.007	17.947	0.002	0.002	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.022	-0.004	16.299	0.021	0.021	0.000	0.000	0.000	0.000
136	B	136	GLY	0	-0.005	0.004	15.834	0.001	0.001	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.057	-0.024	16.426	-0.031	-0.031	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.009	0.002	18.239	0.004	0.004	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.911	-0.955	22.884	0.081	0.081	0.000	0.000	0.000	0.000
140	B	140	PHE	0	-0.023	-0.011	26.317	0.000	0.000	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.066	-0.016	29.048	0.003	0.003	0.000	0.000	0.000	0.000
142	B	142	HIS	0	0.098	0.061	31.080	0.000	0.000	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.873	0.923	32.916	-0.035	-0.035	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.019	0.009	30.230	-0.002	-0.002	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.790	-0.886	32.411	0.033	0.033	0.000	0.000	0.000	0.000
146	B	146	ASN	0	0.023	-0.025	31.869	0.005	0.005	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.932	-0.963	31.826	0.024	0.024	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.037	-0.011	27.612	0.004	0.004	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.941	-0.973	27.244	0.020	0.020	0.000	0.000	0.000	0.000
150	B	151	SER	0	-0.045	-0.029	28.190	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	152	VAL	0	-0.013	0.000	23.427	-0.001	-0.001	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.893	0.956	23.096	-0.044	-0.044	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.094	-0.029	23.421	-0.006	-0.006	0.000	0.000	0.000	0.000
154	B	155	GLY	0	0.022	0.004	24.597	-0.005	-0.005	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.063	-0.014	25.494	-0.002	-0.002	0.000	0.000	0.000	0.000
156	B	157	TYR	0	0.019	0.008	27.118	0.001	0.001	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.916	-0.968	28.952	0.016	0.016	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.072	-0.065	29.673	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	160	PRO	0	-0.040	-0.035	31.682	0.001	0.001	0.000	0.000	0.000	0.000
160	B	161	GLN	0	-0.026	0.008	35.137	-0.001	-0.001	0.000	0.000	0.000	0.000
161	B	162	TYR	0	-0.019	-0.013	32.732	0.000	0.000	0.000	0.000	0.000	0.000
162	B	163	SER	0	0.011	0.011	34.168	0.001	0.001	0.000	0.000	0.000	0.000
163	B	164	GLU	-1	-0.949	-0.967	34.178	0.041	0.041	0.000	0.000	0.000	0.000
164	B	165	GLU	-1	-0.927	-0.973	35.186	0.041	0.041	0.000	0.000	0.000	0.000
165	B	166	ALA	0	-0.083	-0.035	36.962	-0.002	-0.002	0.000	0.000	0.000	0.000

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