FMO DATABASE

FMODB ID: Z68LN

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	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1438198.503782
FMO2-HF: Nuclear repulsion	1370011.533369
FMO2-HF: Total energy	-68186.970412
FMO2-MP2: Total energy	-68382.065305

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.
-7.682	-4.36	5.193	-3.984	-4.531	-0.028

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 : 0.012 / q_NPA : 0.000

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	-0.070	-0.048	3.068	0.678	1.988	0.012	-0.596	-0.726	0.002
4	B	4	GLY	0	0.033	0.030	3.192	0.490	1.304	0.263	-0.433	-0.645	0.004
5	B	5	ALA	0	-0.031	-0.019	3.921	-2.925	-2.708	0.039	-0.047	-0.209	0.002
6	B	6	ILE	0	-0.052	-0.037	5.706	-0.650	-0.650	0.000	0.000	0.000	0.000
7	B	7	ALA	0	-0.040	-0.021	5.346	0.677	0.677	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.007	0.017	7.607	0.271	0.271	0.000	0.000	0.000	0.000
9	B	9	PHE	0	-0.046	-0.032	8.451	-0.306	-0.306	0.000	0.000	0.000	0.000
10	B	10	ILE	0	0.002	0.008	11.158	-0.119	-0.119	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.959	-0.972	11.929	0.470	0.470	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.011	-0.011	13.245	-0.063	-0.063	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.020	0.000	14.350	0.004	0.004	0.000	0.000	0.000	0.000
14	B	14	TRP	0	0.001	-0.016	15.013	-0.023	-0.023	0.000	0.000	0.000	0.000
15	B	15	GLN	0	0.018	-0.006	18.593	-0.025	-0.025	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.017	-0.004	20.975	-0.014	-0.014	0.000	0.000	0.000	0.000
17	B	17	MET	0	-0.042	0.008	16.911	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.014	0.002	20.552	0.002	0.002	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.936	-0.962	22.733	0.052	0.052	0.000	0.000	0.000	0.000
20	B	20	GLY	0	-0.026	-0.040	19.910	-0.014	-0.014	0.000	0.000	0.000	0.000
21	B	21	TRP	0	-0.026	-0.008	14.307	0.001	0.001	0.000	0.000	0.000	0.000
22	B	22	TYR	0	0.019	-0.012	11.203	0.021	0.021	0.000	0.000	0.000	0.000
23	B	23	GLY	0	-0.020	-0.026	15.561	-0.028	-0.028	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.037	-0.042	17.795	0.028	0.028	0.000	0.000	0.000	0.000
25	B	25	HIS	0	-0.003	-0.011	20.504	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	26	HIS	0	0.030	0.028	22.830	0.012	0.012	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.017	-0.027	25.939	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.031	-0.018	28.844	0.002	0.002	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.888	-0.948	32.248	0.055	0.055	0.000	0.000	0.000	0.000
30	B	30	GLN	0	-0.030	-0.002	34.673	0.001	0.001	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.036	0.017	33.402	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.049	-0.010	27.989	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	GLY	0	-0.012	-0.008	27.390	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	34	TYR	0	-0.032	-0.011	21.167	0.002	0.002	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.043	0.023	22.888	-0.012	-0.012	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.034	0.032	20.124	0.012	0.012	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.782	-0.845	18.332	0.024	0.024	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.987	0.970	19.887	-0.022	-0.022	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.888	-0.925	20.256	-0.023	-0.023	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.024	-0.051	15.486	-0.011	-0.011	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.005	-0.004	16.598	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.049	-0.028	18.053	-0.006	-0.006	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.977	0.991	16.312	0.120	0.120	0.000	0.000	0.000	0.000
44	B	44	ALA	0	-0.004	-0.002	14.185	-0.025	-0.025	0.000	0.000	0.000	0.000
45	B	45	ILE	0	-0.003	0.001	15.868	-0.023	-0.023	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.836	-0.914	18.529	-0.074	-0.074	0.000	0.000	0.000	0.000
47	B	47	GLY	0	-0.038	-0.015	16.419	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.010	-0.017	13.453	-0.023	-0.023	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.010	-0.001	16.168	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	50	ASN	0	-0.016	-0.016	19.678	0.010	0.010	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.869	0.942	11.565	0.426	0.426	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.033	0.012	17.489	-0.008	-0.008	0.000	0.000	0.000	0.000
53	B	53	ASN	0	0.030	0.015	19.135	0.011	0.011	0.000	0.000	0.000	0.000
54	B	54	SER	0	-0.024	-0.010	18.710	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	55	ILE	0	-0.028	-0.010	16.243	0.000	0.000	0.000	0.000	0.000	0.000
56	B	56	ILE	0	0.035	0.016	19.335	0.007	0.007	0.000	0.000	0.000	0.000
57	B	57	ASP	-1	-0.945	-0.968	22.563	-0.107	-0.107	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.903	0.948	18.413	0.201	0.201	0.000	0.000	0.000	0.000
59	B	59	MET	0	-0.032	-0.007	20.790	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	ASN	0	0.007	0.005	23.229	0.010	0.010	0.000	0.000	0.000	0.000
61	B	61	THR	0	0.032	0.007	25.238	0.003	0.003	0.000	0.000	0.000	0.000
62	B	62	GLN	0	-0.017	-0.023	23.550	0.006	0.006	0.000	0.000	0.000	0.000
63	B	63	PHE	0	0.021	0.032	26.840	0.004	0.004	0.000	0.000	0.000	0.000
64	B	64	GLU	-1	-0.920	-0.957	28.618	-0.066	-0.066	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.060	-0.016	28.513	0.004	0.004	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.041	0.015	27.649	0.004	0.004	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.059	0.037	30.680	0.005	0.005	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.900	0.942	33.639	0.058	0.058	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.977	-0.996	31.533	-0.065	-0.065	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.037	0.028	34.963	0.003	0.003	0.000	0.000	0.000	0.000
71	B	71	ASN	0	-0.021	-0.017	36.666	0.005	0.005	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.050	-0.043	37.479	0.005	0.005	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.032	-0.004	37.215	0.002	0.002	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.929	-0.975	40.349	-0.033	-0.033	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.864	0.938	41.334	0.043	0.043	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.872	0.952	38.946	0.046	0.046	0.000	0.000	0.000	0.000
77	B	77	ILE	0	-0.030	-0.015	42.698	0.001	0.001	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.842	-0.904	45.779	-0.024	-0.024	0.000	0.000	0.000	0.000
79	B	79	ASN	0	-0.090	-0.053	48.202	0.001	0.001	0.000	0.000	0.000	0.000
80	B	80	LEU	0	0.009	0.017	41.387	0.000	0.000	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.024	-0.022	41.562	0.000	0.000	0.000	0.000	0.000	0.000
82	B	82	LYS	1	1.048	0.993	41.887	0.020	0.020	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.947	0.976	38.810	0.023	0.023	0.000	0.000	0.000	0.000
84	B	84	MET	0	-0.018	0.012	35.958	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	85	GLU	-1	-0.900	-0.953	36.117	-0.038	-0.038	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.891	-0.950	34.293	-0.034	-0.034	0.000	0.000	0.000	0.000
87	B	87	GLY	0	-0.002	0.011	32.489	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	88	PHE	0	-0.007	-0.027	31.221	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	89	LEU	0	0.011	0.008	30.177	-0.005	-0.005	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.885	-0.922	28.340	-0.046	-0.046	0.000	0.000	0.000	0.000
91	B	91	VAL	0	-0.034	-0.014	26.505	-0.006	-0.006	0.000	0.000	0.000	0.000
92	B	92	TRP	0	-0.013	-0.006	25.318	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	93	THR	0	0.026	0.002	24.498	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.020	-0.006	20.077	-0.003	-0.003	0.000	0.000	0.000	0.000
95	B	95	ASN	0	-0.072	-0.064	20.678	-0.019	-0.019	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.032	0.002	20.056	-0.015	-0.015	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.916	-0.971	19.387	-0.070	-0.070	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.019	-0.007	15.112	-0.012	-0.012	0.000	0.000	0.000	0.000
99	B	99	LEU	0	-0.014	-0.015	15.111	-0.031	-0.031	0.000	0.000	0.000	0.000
100	B	100	VAL	0	0.011	0.003	15.232	-0.030	-0.030	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.007	-0.008	12.887	-0.023	-0.023	0.000	0.000	0.000	0.000
102	B	102	MET	0	-0.024	-0.003	10.657	-0.041	-0.041	0.000	0.000	0.000	0.000
103	B	103	GLU	-1	-0.808	-0.894	9.981	-0.496	-0.496	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.010	-0.012	10.786	-0.060	-0.060	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.915	-0.937	4.458	-0.175	0.030	-0.001	-0.018	-0.186	0.000
106	B	106	ARG	1	0.858	0.911	5.788	0.160	0.160	0.000	0.000	0.000	0.000
107	B	107	THR	0	-0.043	-0.033	7.138	-0.130	-0.130	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.002	-0.002	5.540	0.104	0.104	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.800	-0.890	2.096	-10.039	-9.742	4.851	-2.730	-2.418	-0.036
110	B	110	PHE	0	-0.064	-0.032	3.781	0.543	0.544	0.000	0.004	-0.005	0.000
111	B	111	HIS	0	0.008	0.022	7.059	0.207	0.207	0.000	0.000	0.000	0.000
112	B	112	ASP	-1	-0.746	-0.860	3.412	3.109	3.586	0.030	-0.163	-0.344	0.000
113	B	113	SER	0	0.012	0.005	5.368	0.328	0.329	-0.001	-0.001	0.002	0.000
114	B	114	ASN	0	-0.035	-0.035	6.697	0.101	0.101	0.000	0.000	0.000	0.000
115	B	115	VAL	0	-0.015	0.002	8.789	0.003	0.003	0.000	0.000	0.000	0.000
116	B	116	LYS	1	0.883	0.946	7.987	-0.174	-0.174	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.056	-0.047	9.885	-0.033	-0.033	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.031	0.000	12.273	-0.021	-0.021	0.000	0.000	0.000	0.000
119	B	119	TYR	0	-0.041	-0.053	13.160	0.001	0.001	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.780	-0.879	13.717	0.115	0.115	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.848	0.929	15.896	-0.052	-0.052	0.000	0.000	0.000	0.000
122	B	122	VAL	0	-0.010	0.000	18.107	-0.012	-0.012	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.916	0.944	15.905	-0.142	-0.142	0.000	0.000	0.000	0.000
124	B	124	LEU	0	-0.049	-0.017	19.046	-0.012	-0.012	0.000	0.000	0.000	0.000
125	B	125	GLN	0	-0.056	-0.021	22.116	-0.016	-0.016	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.006	0.005	23.113	-0.005	-0.005	0.000	0.000	0.000	0.000
127	B	127	ARG	1	0.812	0.895	24.327	-0.041	-0.041	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.827	-0.877	25.512	0.053	0.053	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.036	0.015	28.208	0.000	0.000	0.000	0.000	0.000	0.000
130	B	130	ALA	0	-0.056	-0.028	25.458	0.000	0.000	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.853	0.946	26.240	-0.091	-0.091	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.845	-0.915	18.490	0.198	0.198	0.000	0.000	0.000	0.000
133	B	133	LEU	0	-0.029	-0.017	22.005	0.001	0.001	0.000	0.000	0.000	0.000
134	B	134	GLY	0	-0.014	0.008	17.947	0.002	0.002	0.000	0.000	0.000	0.000
135	B	135	ASN	0	0.018	-0.008	16.302	0.021	0.021	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.005	0.008	15.863	0.009	0.009	0.000	0.000	0.000	0.000
137	B	137	CYS	0	-0.054	-0.019	16.426	-0.034	-0.034	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.005	-0.004	18.017	0.002	0.002	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.915	-0.953	22.885	0.105	0.105	0.000	0.000	0.000	0.000
140	B	140	PHE	0	0.011	0.002	26.576	-0.002	-0.002	0.000	0.000	0.000	0.000
141	B	141	TYR	0	-0.045	-0.020	29.040	0.004	0.004	0.000	0.000	0.000	0.000
142	B	142	HIS	0	0.096	0.063	31.107	0.000	0.000	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.898	0.937	32.918	-0.048	-0.048	0.000	0.000	0.000	0.000
144	B	144	CYS	0	-0.040	-0.005	30.245	-0.003	-0.003	0.000	0.000	0.000	0.000
145	B	145	ASP	-1	-0.803	-0.890	32.431	0.048	0.048	0.000	0.000	0.000	0.000
146	B	146	ASN	0	0.024	-0.019	31.892	0.007	0.007	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.919	-0.959	31.857	0.039	0.039	0.000	0.000	0.000	0.000
148	B	149	MET	0	-0.032	-0.007	27.647	0.005	0.005	0.000	0.000	0.000	0.000
149	B	150	GLU	-1	-0.921	-0.956	27.268	0.035	0.035	0.000	0.000	0.000	0.000
150	B	151	SER	0	-0.055	-0.031	28.212	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	152	VAL	0	0.005	0.006	23.450	-0.002	-0.002	0.000	0.000	0.000	0.000
152	B	153	ARG	1	0.874	0.949	23.122	-0.068	-0.068	0.000	0.000	0.000	0.000
153	B	154	ASN	0	-0.126	-0.057	23.443	-0.009	-0.009	0.000	0.000	0.000	0.000
154	B	155	GLY	0	0.040	0.015	24.599	-0.007	-0.007	0.000	0.000	0.000	0.000
155	B	156	THR	0	-0.086	-0.028	25.499	-0.004	-0.004	0.000	0.000	0.000	0.000
156	B	157	TYR	0	0.027	0.016	27.176	0.001	0.001	0.000	0.000	0.000	0.000
157	B	158	ASP	-1	-0.881	-0.942	28.948	0.017	0.017	0.000	0.000	0.000	0.000
158	B	159	TYR	0	-0.046	-0.069	29.713	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	160	PRO	0	-0.047	-0.037	31.662	0.001	0.001	0.000	0.000	0.000	0.000
160	B	161	GLN	0	-0.076	-0.026	35.076	0.000	0.000	0.000	0.000	0.000	0.000
161	B	162	TYR	0	-0.012	-0.011	32.371	0.001	0.001	0.000	0.000	0.000	0.000
162	B	163	SER	0	0.010	0.014	34.147	0.000	0.000	0.000	0.000	0.000	0.000
163	B	164	GLU	-1	-0.963	-0.972	34.102	0.051	0.051	0.000	0.000	0.000	0.000
164	B	165	GLU	-1	-0.892	-0.970	35.170	0.051	0.051	0.000	0.000	0.000	0.000
165	B	166	ALA	0	-0.100	-0.032	36.950	-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)