FMO DATABASE

FMODB ID: R92M8

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	OptAll
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	-1444834.803957
FMO2-HF: Nuclear repulsion	1376647.215117
FMO2-HF: Total energy	-68187.588841
FMO2-MP2: Total energy	-68382.756283

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.
-11.129	-12.135	12.819	-5.75	-6.063	-0.035

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 : -0.007 / q_NPA : -0.016

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	-0.066	-0.045	2.431	0.167	1.897	0.338	-0.934	-1.134	0.003
4	B	4	GLY	0	0.008	0.023	2.981	-0.243	0.744	0.785	-0.643	-1.129	0.006
5	B	5	ALA	0	-0.014	-0.012	3.699	-3.102	-3.043	0.122	0.098	-0.278	0.004
6	B	6	ILE	0	0.008	-0.009	5.754	-0.647	-0.647	0.000	0.000	0.000	0.000
7	B	7	ALA	0	-0.049	-0.025	5.831	0.516	0.516	0.000	0.000	0.000	0.000
8	B	8	GLY	0	-0.026	0.003	7.627	0.079	0.079	0.000	0.000	0.000	0.000
9	B	9	PHE	0	-0.054	-0.044	8.389	-0.311	-0.311	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.014	0.002	10.358	-0.171	-0.171	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.951	-0.973	11.522	0.435	0.435	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.027	-0.017	13.689	-0.053	-0.053	0.000	0.000	0.000	0.000
13	B	13	GLY	0	0.002	0.012	13.911	0.035	0.035	0.000	0.000	0.000	0.000
14	B	14	TRP	0	-0.006	-0.020	14.825	-0.033	-0.033	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.019	-0.004	18.176	-0.030	-0.030	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.017	0.005	20.465	-0.016	-0.016	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.038	0.008	16.455	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.019	0.000	20.069	0.002	0.002	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.888	-0.942	22.076	0.083	0.083	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.035	-0.047	19.355	-0.013	-0.013	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.030	-0.009	13.707	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	22	TYR	0	0.025	-0.011	10.600	0.027	0.027	0.000	0.000	0.000	0.000
23	B	23	GLY	0	-0.019	-0.011	14.985	-0.038	-0.038	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.012	-0.027	17.288	0.039	0.039	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.009	-0.018	20.066	-0.015	-0.015	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.029	0.027	22.309	0.016	0.016	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.015	-0.023	25.558	-0.006	-0.006	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.030	-0.022	28.562	0.001	0.001	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.846	-0.916	32.056	0.072	0.072	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.051	-0.012	34.146	0.000	0.000	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.013	0.015	32.957	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.046	-0.018	27.561	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	GLY	0	-0.018	-0.009	26.945	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.020	-0.005	20.505	0.004	0.004	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.019	0.006	22.257	-0.015	-0.015	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.002	0.010	19.509	0.016	0.016	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.750	-0.829	17.699	0.090	0.090	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.952	0.959	19.078	-0.055	-0.055	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.878	-0.913	19.623	0.039	0.039	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.024	-0.054	14.738	-0.012	-0.012	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.012	0.003	16.037	-0.018	-0.018	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.067	-0.037	17.572	-0.010	-0.010	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.984	0.990	16.060	0.036	0.036	0.000	0.000	0.000	0.000
44	B	44	ALA	0	0.003	0.007	13.612	-0.030	-0.030	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.000	0.008	15.280	-0.030	-0.030	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.842	-0.915	18.035	-0.056	-0.056	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.019	-0.005	15.961	-0.011	-0.011	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.001	-0.013	13.226	-0.025	-0.025	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.020	-0.004	15.888	-0.009	-0.009	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.017	-0.025	19.480	0.001	0.001	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.875	0.950	11.165	0.441	0.441	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.028	0.020	17.007	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	53	ASN	0	-0.003	-0.005	18.750	0.006	0.006	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.070	-0.042	18.322	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	55	ILE	0	0.005	-0.003	16.304	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	56	ILE	0	0.035	0.015	19.237	0.006	0.006	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.846	-0.912	22.576	-0.131	-0.131	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.838	0.919	19.407	0.184	0.184	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.016	0.000	20.889	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.013	0.002	23.332	0.010	0.010	0.000	0.000	0.000	0.000
61	B	61	THR	0	0.039	0.004	25.313	0.001	0.001	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.013	-0.017	23.275	0.005	0.005	0.000	0.000	0.000	0.000
63	B	63	PHE	0	0.008	0.024	26.522	0.005	0.005	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.930	-0.977	28.466	-0.078	-0.078	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.054	-0.017	28.546	0.005	0.005	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.061	0.030	27.916	0.005	0.005	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.058	0.034	30.912	0.006	0.006	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.906	0.949	33.744	0.067	0.067	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.964	-0.986	31.687	-0.081	-0.081	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.030	0.018	34.902	0.003	0.003	0.000	0.000	0.000	0.000
71	B	71	ASN	0	-0.016	-0.011	36.732	0.006	0.006	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.036	-0.025	37.465	0.006	0.006	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.017	0.014	37.586	0.001	0.001	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.873	-0.952	40.416	-0.043	-0.043	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.827	0.910	41.250	0.052	0.052	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.841	0.922	39.171	0.056	0.056	0.000	0.000	0.000	0.000
77	B	77	ILE	0	-0.046	-0.022	42.529	0.001	0.001	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.860	-0.921	45.639	-0.032	-0.032	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.066	-0.043	47.960	0.001	0.001	0.000	0.000	0.000	0.000
80	B	80	LEU	0	-0.014	0.010	41.138	0.000	0.000	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.005	-0.002	41.898	0.001	0.001	0.000	0.000	0.000	0.000
82	B	82	LYS	1	1.041	0.990	41.840	0.031	0.031	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.877	0.943	38.228	0.040	0.040	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.038	0.000	36.099	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.909	-0.955	36.096	-0.049	-0.049	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.867	-0.930	34.476	-0.048	-0.048	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.025	0.018	32.570	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	88	PHE	0	0.011	-0.015	31.159	-0.005	-0.005	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.001	0.006	30.271	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.886	-0.925	28.196	-0.072	-0.072	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.042	-0.023	26.542	-0.008	-0.008	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.038	-0.012	25.390	-0.008	-0.008	0.000	0.000	0.000	0.000
93	B	93	THR	0	0.007	-0.013	24.411	-0.009	-0.009	0.000	0.000	0.000	0.000
94	B	94	TYR	0	0.013	0.010	20.147	-0.008	-0.008	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.065	-0.052	20.550	-0.026	-0.026	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.007	0.011	19.803	-0.019	-0.019	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.915	-0.965	19.113	-0.110	-0.110	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.004	0.000	14.942	-0.020	-0.020	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.022	-0.015	14.925	-0.040	-0.040	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.027	0.006	14.871	-0.035	-0.035	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.010	0.000	12.775	-0.022	-0.022	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.028	-0.009	10.517	-0.057	-0.057	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.798	-0.886	9.903	-0.556	-0.556	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.044	-0.019	10.764	-0.017	-0.017	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.899	-0.936	4.087	-0.688	-0.410	0.000	-0.054	-0.223	0.000
106	B	106	ARG	1	0.843	0.898	5.828	0.230	0.230	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.067	-0.049	7.474	-0.034	-0.034	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.016	0.000	5.009	0.125	0.125	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.755	-0.877	1.851	-9.574	-14.181	11.520	-4.083	-2.831	-0.048
110	B	110	PHE	0	-0.044	-0.011	3.506	0.945	0.898	0.001	0.088	-0.042	0.000
111	B	111	HIS	0	0.022	0.036	6.895	0.277	0.277	0.000	0.000	0.000	0.000
112	B	112	ASP	-1	-0.756	-0.869	3.342	1.511	2.105	0.053	-0.222	-0.426	0.000
113	B	113	SER	0	0.013	0.008	4.975	0.389	0.389	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.041	-0.036	6.378	0.047	0.047	0.000	0.000	0.000	0.000
115	B	115	VAL	0	-0.010	0.003	8.495	-0.020	-0.020	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.874	0.936	7.360	-0.621	-0.621	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.049	-0.034	9.368	-0.078	-0.078	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.025	-0.003	11.937	-0.047	-0.047	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.028	-0.049	12.889	-0.019	-0.019	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.797	-0.889	13.731	0.265	0.265	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.830	0.905	15.895	-0.134	-0.134	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.007	0.019	17.893	-0.025	-0.025	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.845	0.916	15.860	-0.292	-0.292	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.038	-0.021	18.316	-0.020	-0.020	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.062	-0.029	21.577	-0.028	-0.028	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.003	-0.004	22.923	-0.009	-0.009	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.816	0.896	24.060	-0.087	-0.087	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.788	-0.861	25.419	0.091	0.091	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.031	0.019	28.132	-0.003	-0.003	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.051	-0.024	25.216	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.796	0.912	25.696	-0.125	-0.125	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.803	-0.893	17.829	0.298	0.298	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.028	-0.021	21.271	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.025	0.000	17.614	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.022	0.001	16.221	0.040	0.040	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.029	0.013	15.205	0.006	0.006	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.080	-0.021	15.804	-0.039	-0.039	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.013	-0.010	17.542	0.002	0.002	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.885	-0.933	22.451	0.127	0.127	0.000	0.000	0.000	0.000
140	B	140	PHE	0	0.028	0.007	26.242	0.000	0.000	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.058	-0.011	28.846	0.003	0.003	0.000	0.000	0.000	0.000
142	B	142	HIS	0	0.073	0.049	31.076	0.001	0.001	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.849	0.910	32.604	-0.066	-0.066	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.003	0.017	30.061	0.001	0.001	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.794	-0.885	31.836	0.073	0.073	0.000	0.000	0.000	0.000
146	B	146	ASN	0	0.022	-0.004	31.209	0.010	0.010	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.886	-0.949	31.149	0.063	0.063	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.031	-0.003	27.457	0.008	0.008	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.861	-0.925	26.891	0.078	0.078	0.000	0.000	0.000	0.000
150	B	151	SER	0	-0.075	-0.042	27.560	0.000	0.000	0.000	0.000	0.000	0.000
151	B	152	VAL	0	0.031	0.015	23.003	-0.001	-0.001	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.821	0.927	22.838	-0.093	-0.093	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.113	-0.070	23.129	-0.006	-0.006	0.000	0.000	0.000	0.000
154	B	155	GLY	0	0.004	0.014	24.101	-0.005	-0.005	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.093	-0.046	24.836	-0.009	-0.009	0.000	0.000	0.000	0.000
156	B	157	TYR	0	-0.003	-0.011	26.822	-0.003	-0.003	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.855	-0.924	28.660	0.046	0.046	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.064	-0.072	29.189	-0.004	-0.004	0.000	0.000	0.000	0.000
159	B	160	PRO	0	-0.045	-0.039	31.169	0.000	0.000	0.000	0.000	0.000	0.000
160	B	161	GLN	0	-0.093	-0.037	34.577	-0.003	-0.003	0.000	0.000	0.000	0.000
161	B	162	TYR	0	-0.014	-0.012	32.031	0.000	0.000	0.000	0.000	0.000	0.000
162	B	163	SER	0	-0.037	-0.002	34.264	0.000	0.000	0.000	0.000	0.000	0.000
163	B	164	GLU	-1	-0.948	-0.963	33.557	0.073	0.073	0.000	0.000	0.000	0.000
164	B	165	GLU	-1	-0.838	-0.945	34.474	0.072	0.072	0.000	0.000	0.000	0.000
165	B	166	ALA	0	-0.084	-0.039	36.889	-0.003	-0.003	0.000	0.000	0.000	0.000

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