FMO DATABASE

FMODB ID: 3Q25L

Calculation Name: 3BUK-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3BUK

Chain ID: A

ChEMBL ID:

UniProt ID: P20783

Base Structure: X-ray

Registration Date: 2023-06-21

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-790342.807633
FMO2-HF: Nuclear repulsion	744951.39879
FMO2-HF: Total energy	-45391.408843
FMO2-MP2: Total energy	-45520.862276

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(A:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
20.845	23.561	14.045	-9.304	-7.456	-0.09

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.904 / q_NPA : 0.953

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	7	HIS	0	0.023	0.018	3.892	0.514	2.866	-0.012	-1.370	-0.971	0.004
4	A	8	ARG	1	0.939	0.966	6.671	20.052	20.052	0.000	0.000	0.000	0.000
5	A	9	GLY	0	0.015	0.016	10.084	1.416	1.416	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.885	-0.935	7.685	-30.870	-30.870	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.010	-0.016	8.740	-1.224	-1.224	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.003	0.013	4.440	3.240	3.280	-0.001	0.000	-0.038	0.000
9	A	13	VAL	0	0.068	0.033	7.678	1.178	1.178	0.000	0.000	0.000	0.000
10	A	14	CYS	0	-0.052	-0.017	8.489	3.248	3.248	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.785	-0.849	5.260	-45.695	-45.695	0.000	0.000	0.000	0.000
12	A	16	SER	0	0.024	0.000	2.348	-12.303	-10.506	2.345	-1.861	-2.282	-0.022
13	A	17	GLU	-1	-0.838	-0.878	1.768	-74.486	-76.403	11.714	-5.933	-3.863	-0.071
14	A	18	SER	0	0.020	-0.010	3.790	-1.508	-1.123	0.000	-0.140	-0.244	-0.001
15	A	19	LEU	0	-0.034	-0.004	5.489	2.122	2.122	0.000	0.000	0.000	0.000
16	A	20	TRP	0	0.039	0.011	9.199	-0.066	-0.066	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.027	0.021	12.419	1.264	1.264	0.000	0.000	0.000	0.000
18	A	22	THR	0	0.009	-0.013	14.863	0.580	0.580	0.000	0.000	0.000	0.000
19	A	23	ASP	-1	-0.908	-0.959	18.074	-15.728	-15.728	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.857	0.926	15.692	19.516	19.516	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.061	0.036	20.242	0.109	0.109	0.000	0.000	0.000	0.000
22	A	26	SER	0	-0.038	-0.019	22.968	0.598	0.598	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.011	0.011	21.027	-0.751	-0.751	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.020	0.021	22.105	0.676	0.676	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.776	-0.912	22.535	-12.244	-12.244	0.000	0.000	0.000	0.000
26	A	30	ILE	0	-0.031	-0.016	23.533	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.871	0.940	25.069	10.567	10.567	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.018	0.016	26.535	0.369	0.369	0.000	0.000	0.000	0.000
29	A	33	HIS	1	0.834	0.903	27.566	10.194	10.194	0.000	0.000	0.000	0.000
30	A	34	GLN	0	0.030	0.016	26.416	-0.734	-0.734	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.057	-0.029	25.539	0.465	0.465	0.000	0.000	0.000	0.000
32	A	36	THR	0	0.023	0.010	26.072	-0.487	-0.487	0.000	0.000	0.000	0.000
33	A	37	VAL	0	-0.036	-0.019	21.414	0.137	0.137	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.011	0.008	24.842	0.167	0.167	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.068	0.038	24.073	-0.542	-0.542	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.873	-0.924	23.883	-11.085	-11.085	0.000	0.000	0.000	0.000
37	A	41	ILE	0	0.005	-0.001	22.889	0.247	0.247	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.902	0.929	26.950	9.868	9.868	0.000	0.000	0.000	0.000
39	A	43	THR	0	-0.009	-0.012	29.105	-0.245	-0.245	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.003	0.006	31.371	0.171	0.171	0.000	0.000	0.000	0.000
41	A	45	ASN	0	-0.001	0.000	33.165	0.211	0.211	0.000	0.000	0.000	0.000
42	A	46	SER	0	0.007	0.006	29.030	0.118	0.118	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.013	0.004	28.571	-0.089	-0.089	0.000	0.000	0.000	0.000
44	A	48	VAL	0	0.027	0.016	23.771	-0.131	-0.131	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.870	0.923	21.125	14.093	14.093	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.032	-0.021	20.814	-0.561	-0.561	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.048	-0.032	15.239	0.495	0.495	0.000	0.000	0.000	0.000
48	A	52	PHE	0	0.007	0.007	14.413	0.199	0.199	0.000	0.000	0.000	0.000
49	A	53	TYR	0	0.010	0.022	5.633	-3.511	-3.511	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.770	-0.881	9.844	-20.912	-20.912	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.088	-0.068	4.781	-5.390	-5.331	-0.001	0.000	-0.058	0.000
52	A	56	ARG	1	0.895	0.939	6.239	34.968	34.968	0.000	0.000	0.000	0.000
53	A	57	CYS	0	-0.089	-0.030	5.769	-3.791	-3.791	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.881	0.930	5.832	40.315	40.315	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.828	-0.906	7.578	-20.197	-20.197	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.027	0.004	10.662	-1.281	-1.281	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.848	0.907	13.444	20.017	20.017	0.000	0.000	0.000	0.000
58	A	62	PRO	0	0.009	0.020	9.982	0.722	0.722	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.011	0.005	12.482	0.484	0.484	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.937	0.959	16.012	13.896	13.896	0.000	0.000	0.000	0.000
61	A	65	ASN	0	0.001	-0.012	19.506	0.162	0.162	0.000	0.000	0.000	0.000
62	A	66	GLY	0	0.001	0.001	16.990	0.507	0.507	0.000	0.000	0.000	0.000
63	A	67	CYS	0	-0.024	-0.020	10.644	-0.120	-0.120	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.801	0.871	7.596	33.550	33.550	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.027	0.004	13.609	-0.854	-0.854	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.014	0.000	16.101	0.690	0.690	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.782	-0.868	18.376	-12.383	-12.383	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.843	-0.922	20.827	-13.535	-13.535	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.900	0.968	22.530	11.104	11.104	0.000	0.000	0.000	0.000
70	A	74	HIS	0	-0.005	-0.024	25.612	0.992	0.992	0.000	0.000	0.000	0.000
71	A	75	TRP	0	-0.010	-0.011	22.433	0.394	0.394	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.021	0.021	22.394	-0.279	-0.279	0.000	0.000	0.000	0.000
73	A	77	SER	0	0.002	-0.014	17.321	-0.550	-0.550	0.000	0.000	0.000	0.000
74	A	78	GLN	0	0.027	0.011	15.875	0.216	0.216	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.907	0.938	12.105	19.112	19.112	0.000	0.000	0.000	0.000
76	A	81	THR	0	0.038	0.014	10.345	-2.597	-2.597	0.000	0.000	0.000	0.000
77	A	82	SER	0	-0.019	0.006	10.639	1.923	1.923	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.004	-0.017	11.489	-0.525	-0.525	0.000	0.000	0.000	0.000
79	A	84	THR	0	0.003	0.003	13.784	1.164	1.164	0.000	0.000	0.000	0.000
80	A	85	TYR	0	0.021	0.019	15.639	0.072	0.072	0.000	0.000	0.000	0.000
81	A	86	VAL	0	0.021	0.008	14.947	-0.183	-0.183	0.000	0.000	0.000	0.000
82	A	87	ARG	1	0.851	0.935	18.355	13.072	13.072	0.000	0.000	0.000	0.000
83	A	88	ALA	0	0.056	0.028	20.249	-0.568	-0.568	0.000	0.000	0.000	0.000
84	A	89	LEU	0	-0.024	0.008	22.480	0.585	0.585	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.006	-0.001	24.884	-0.185	-0.185	0.000	0.000	0.000	0.000
86	A	91	SER	0	0.001	-0.011	27.339	0.494	0.494	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.760	-0.856	29.882	-10.242	-10.242	0.000	0.000	0.000	0.000
88	A	93	ASN	0	0.033	-0.005	32.366	0.139	0.139	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.019	-0.004	33.552	0.094	0.094	0.000	0.000	0.000	0.000
90	A	95	LYS	1	0.972	0.992	34.766	7.968	7.968	0.000	0.000	0.000	0.000
91	A	96	LEU	0	0.019	0.026	34.387	0.066	0.066	0.000	0.000	0.000	0.000
92	A	97	VAL	0	0.022	0.003	31.956	-0.391	-0.391	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.038	0.018	30.480	0.266	0.266	0.000	0.000	0.000	0.000
94	A	99	TRP	0	0.019	0.018	22.677	-0.421	-0.421	0.000	0.000	0.000	0.000
95	A	100	ARG	1	0.788	0.886	25.993	10.800	10.800	0.000	0.000	0.000	0.000
96	A	101	TRP	0	0.021	-0.005	19.951	-0.394	-0.394	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.004	0.001	19.399	0.541	0.541	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.899	0.946	18.113	15.418	15.418	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.047	-0.013	13.498	0.375	0.375	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.828	-0.915	10.764	-23.742	-23.742	0.000	0.000	0.000	0.000
101	A	106	THR	0	0.004	-0.005	9.491	-0.143	-0.143	0.000	0.000	0.000	0.000
102	A	107	SER	0	0.018	0.025	6.434	-3.250	-3.250	0.000	0.000	0.000	0.000
103	A	109	VAL	0	0.033	0.026	7.883	-1.549	-1.549	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.017	-0.001	13.363	0.825	0.825	0.000	0.000	0.000	0.000
105	A	112	LEU	0	0.041	-0.001	16.930	-0.071	-0.071	0.000	0.000	0.000	0.000
106	A	113	SER	0	0.003	0.003	20.221	0.543	0.543	0.000	0.000	0.000	0.000
107	A	114	ARG	1	0.950	0.984	23.881	10.861	10.861	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.822	0.919	25.342	12.537	12.537	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)