FMO DATABASE

FMODB ID: N1RMQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-788842.99872
FMO2-HF: Nuclear repulsion	743452.831997
FMO2-HF: Total energy	-45390.166723
FMO2-MP2: Total energy	-45519.667309

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.
34.825	41.175	2.229	-4.175	-4.402	-0.042

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 : 0.919 / q_NPA : 0.959

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	0.038	0.015	3.489	2.190	3.780	0.000	-0.785	-0.804	0.001
4	A	8	ARG	1	0.956	0.975	6.771	19.570	19.570	0.000	0.000	0.000	0.000
5	A	9	GLY	0	0.027	0.026	10.004	1.222	1.222	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.954	-0.976	8.948	-27.269	-27.269	0.000	0.000	0.000	0.000
7	A	11	TYR	0	-0.012	-0.007	8.274	-1.870	-1.870	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.007	0.016	5.235	-1.294	-1.294	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.027	0.002	7.568	1.316	1.316	0.000	0.000	0.000	0.000
10	A	14	CYS	0	-0.033	-0.006	8.398	3.089	3.089	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.788	-0.864	4.663	-47.922	-47.868	-0.001	-0.002	-0.050	0.000
12	A	16	SER	0	-0.022	-0.014	2.617	-8.463	-6.868	1.163	-1.166	-1.592	-0.014
13	A	17	GLU	-1	-0.932	-0.978	2.422	-60.017	-57.044	1.068	-2.213	-1.828	-0.029
14	A	18	SER	0	0.038	-0.004	4.276	0.116	0.254	-0.001	-0.009	-0.128	0.000
15	A	19	LEU	0	-0.040	-0.013	5.757	1.740	1.740	0.000	0.000	0.000	0.000
16	A	20	TRP	0	0.027	0.019	9.418	0.721	0.721	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.021	0.009	12.715	0.955	0.955	0.000	0.000	0.000	0.000
18	A	22	THR	0	-0.036	-0.052	15.223	0.638	0.638	0.000	0.000	0.000	0.000
19	A	23	ASP	-1	-0.885	-0.934	18.698	-15.250	-15.250	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.868	0.945	16.176	18.768	18.768	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.036	0.015	20.853	0.221	0.221	0.000	0.000	0.000	0.000
22	A	26	SER	0	-0.040	-0.019	23.685	0.622	0.622	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.033	0.024	21.653	-0.660	-0.660	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.025	0.018	22.670	0.630	0.630	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.818	-0.930	23.214	-11.819	-11.819	0.000	0.000	0.000	0.000
26	A	30	ILE	0	0.002	-0.008	23.638	0.088	0.088	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.856	0.941	25.588	10.345	10.345	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.024	0.011	26.973	0.348	0.348	0.000	0.000	0.000	0.000
29	A	33	HIS	1	0.852	0.929	28.001	10.039	10.039	0.000	0.000	0.000	0.000
30	A	34	GLN	0	0.020	0.015	26.918	-0.885	-0.885	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.041	-0.013	26.052	0.424	0.424	0.000	0.000	0.000	0.000
32	A	36	THR	0	0.009	-0.002	26.772	-0.304	-0.304	0.000	0.000	0.000	0.000
33	A	37	VAL	0	-0.061	-0.042	22.144	0.058	0.058	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.023	-0.001	25.492	0.113	0.113	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.081	0.040	24.645	-0.540	-0.540	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.938	-0.967	24.877	-10.945	-10.945	0.000	0.000	0.000	0.000
37	A	41	ILE	0	0.008	-0.005	23.939	0.223	0.223	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.884	0.935	28.024	10.030	10.030	0.000	0.000	0.000	0.000
39	A	43	THR	0	0.022	0.021	28.254	-0.076	-0.076	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.012	-0.005	31.004	0.220	0.220	0.000	0.000	0.000	0.000
41	A	45	ASN	0	0.029	0.006	32.654	0.267	0.267	0.000	0.000	0.000	0.000
42	A	46	SER	0	0.013	0.010	29.105	0.132	0.132	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.018	0.007	29.454	-0.158	-0.158	0.000	0.000	0.000	0.000
44	A	48	VAL	0	0.016	0.012	23.407	-0.173	-0.173	0.000	0.000	0.000	0.000
45	A	49	LYS	1	1.003	0.985	21.177	14.172	14.172	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.042	-0.019	21.482	-0.596	-0.596	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.050	-0.016	15.888	0.469	0.469	0.000	0.000	0.000	0.000
48	A	52	PHE	0	0.010	-0.003	15.137	0.165	0.165	0.000	0.000	0.000	0.000
49	A	53	TYR	0	-0.008	0.008	5.863	-0.489	-0.489	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.816	-0.899	10.393	-21.724	-21.724	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.088	-0.051	5.427	-7.284	-7.284	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.990	1.011	6.888	31.876	31.876	0.000	0.000	0.000	0.000
53	A	57	CYS	0	-0.096	-0.031	6.238	-3.843	-3.843	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.934	0.960	5.291	46.284	46.284	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.928	-0.955	7.821	-24.983	-24.983	0.000	0.000	0.000	0.000
56	A	60	ALA	0	-0.022	-0.024	10.693	-0.804	-0.804	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.936	0.957	13.417	19.004	19.004	0.000	0.000	0.000	0.000
58	A	62	PRO	0	0.041	0.040	9.855	0.743	0.743	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.007	0.006	12.099	0.602	0.602	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.960	0.961	15.476	14.065	14.065	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.035	-0.028	18.963	0.047	0.047	0.000	0.000	0.000	0.000
62	A	66	GLY	0	0.017	0.019	16.077	0.524	0.524	0.000	0.000	0.000	0.000
63	A	67	CYS	0	-0.037	-0.022	11.068	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.883	0.931	7.919	34.007	34.007	0.000	0.000	0.000	0.000
65	A	69	GLY	0	-0.001	-0.014	13.525	-0.509	-0.509	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.020	0.000	15.961	0.757	0.757	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.791	-0.887	18.407	-12.488	-12.488	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.885	-0.951	20.820	-13.506	-13.506	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.908	0.975	22.497	11.013	11.013	0.000	0.000	0.000	0.000
70	A	74	HIS	0	-0.062	-0.067	25.287	0.952	0.952	0.000	0.000	0.000	0.000
71	A	75	TRP	0	-0.043	-0.019	21.800	0.341	0.341	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.009	0.014	21.797	-0.253	-0.253	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.012	-0.013	16.833	-0.525	-0.525	0.000	0.000	0.000	0.000
74	A	78	GLN	0	0.047	0.006	15.596	0.826	0.826	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.945	0.963	12.272	17.784	17.784	0.000	0.000	0.000	0.000
76	A	81	THR	0	0.049	0.019	10.662	-2.547	-2.547	0.000	0.000	0.000	0.000
77	A	82	SER	0	0.003	0.009	11.106	1.871	1.871	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.021	-0.032	12.088	-0.380	-0.380	0.000	0.000	0.000	0.000
79	A	84	THR	0	-0.024	-0.012	13.968	0.809	0.809	0.000	0.000	0.000	0.000
80	A	85	TYR	0	-0.004	-0.008	15.866	0.218	0.218	0.000	0.000	0.000	0.000
81	A	86	VAL	0	0.035	0.022	15.664	-0.281	-0.281	0.000	0.000	0.000	0.000
82	A	87	ARG	1	0.935	0.974	18.728	12.537	12.537	0.000	0.000	0.000	0.000
83	A	88	ALA	0	0.022	0.017	21.332	-0.450	-0.450	0.000	0.000	0.000	0.000
84	A	89	LEU	0	-0.036	0.004	23.477	0.554	0.554	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.030	0.005	25.707	-0.124	-0.124	0.000	0.000	0.000	0.000
86	A	91	SER	0	0.004	0.000	28.214	0.350	0.350	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.817	-0.911	30.648	-9.981	-9.981	0.000	0.000	0.000	0.000
88	A	93	ASN	0	0.021	0.004	33.071	0.338	0.338	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.013	-0.010	33.948	0.062	0.062	0.000	0.000	0.000	0.000
90	A	95	LYS	1	0.986	0.984	35.327	7.724	7.724	0.000	0.000	0.000	0.000
91	A	96	LEU	0	-0.018	0.006	35.226	0.123	0.123	0.000	0.000	0.000	0.000
92	A	97	VAL	0	0.009	0.004	32.617	-0.289	-0.289	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.045	0.023	31.122	0.264	0.264	0.000	0.000	0.000	0.000
94	A	99	TRP	0	-0.004	0.006	23.733	-0.416	-0.416	0.000	0.000	0.000	0.000
95	A	100	ARG	1	0.813	0.892	26.256	10.641	10.641	0.000	0.000	0.000	0.000
96	A	101	TRP	0	0.002	0.002	20.013	-0.459	-0.459	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.025	0.007	19.782	0.406	0.406	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.938	0.978	18.626	14.698	14.698	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.019	-0.009	14.154	0.378	0.378	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.828	-0.910	11.189	-22.690	-22.690	0.000	0.000	0.000	0.000
101	A	106	THR	0	-0.012	-0.020	9.850	-1.517	-1.517	0.000	0.000	0.000	0.000
102	A	107	SER	0	0.016	0.014	6.939	-2.481	-2.481	0.000	0.000	0.000	0.000
103	A	109	VAL	0	0.027	0.027	8.281	-1.645	-1.645	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.044	-0.009	13.577	0.933	0.933	0.000	0.000	0.000	0.000
105	A	112	LEU	0	0.033	0.004	17.157	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	113	SER	0	-0.002	-0.010	20.119	0.464	0.464	0.000	0.000	0.000	0.000
107	A	114	ARG	1	0.973	0.988	23.524	10.813	10.813	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.944	1.004	25.678	11.874	11.874	0.000	0.000	0.000	0.000

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