FMO DATABASE

FMODB ID: J38Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-788884.700742
FMO2-HF: Nuclear repulsion	743493.724458
FMO2-HF: Total energy	-45390.976284
FMO2-MP2: Total energy	-45520.404493

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.
31.257	38.943	3.926	-6.115	-5.496	-0.059

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 : 0.925 / q_NPA : 0.973

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

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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	0.033	0.011	3.659	1.058	3.551	-0.009	-1.438	-1.046	0.006
4	A	8	ARG	1	0.960	0.980	6.842	20.022	20.022	0.000	0.000	0.000	0.000
5	A	9	GLY	0	0.025	0.024	10.238	1.117	1.117	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.966	-0.972	8.725	-27.958	-27.958	0.000	0.000	0.000	0.000
7	A	11	TYR	0	-0.003	-0.011	8.592	-1.741	-1.741	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.030	0.024	4.721	2.062	2.093	-0.001	0.001	-0.029	0.000
9	A	13	VAL	0	0.028	0.016	7.873	1.400	1.400	0.000	0.000	0.000	0.000
10	A	14	CYS	0	-0.030	-0.006	8.794	2.886	2.886	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.783	-0.853	5.075	-46.713	-46.713	0.000	0.000	0.000	0.000
12	A	16	SER	0	-0.009	-0.003	2.409	-10.143	-8.464	1.365	-1.342	-1.702	-0.017
13	A	17	GLU	-1	-0.852	-0.906	2.146	-64.417	-61.223	2.572	-3.250	-2.516	-0.048
14	A	18	SER	0	0.011	-0.018	4.013	-0.824	-0.535	-0.001	-0.086	-0.203	0.000
15	A	19	LEU	0	-0.032	-0.006	5.413	2.176	2.176	0.000	0.000	0.000	0.000
16	A	20	TRP	0	0.022	0.015	9.085	0.353	0.353	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.028	0.016	12.328	0.952	0.952	0.000	0.000	0.000	0.000
18	A	22	THR	0	0.000	-0.026	14.854	0.523	0.523	0.000	0.000	0.000	0.000
19	A	23	ASP	-1	-0.888	-0.948	18.323	-15.326	-15.326	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.835	0.920	15.843	19.121	19.121	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.065	0.033	20.492	0.196	0.196	0.000	0.000	0.000	0.000
22	A	26	SER	0	-0.021	-0.013	23.390	0.668	0.668	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.011	0.007	21.304	-0.650	-0.650	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.018	0.009	22.478	0.636	0.636	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.810	-0.938	23.100	-11.968	-11.968	0.000	0.000	0.000	0.000
26	A	30	ILE	0	-0.003	0.004	23.852	0.035	0.035	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.860	0.946	25.510	10.362	10.362	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.021	0.009	26.853	0.344	0.344	0.000	0.000	0.000	0.000
29	A	33	HIS	1	0.839	0.910	27.883	10.114	10.114	0.000	0.000	0.000	0.000
30	A	34	GLN	0	0.010	0.006	26.757	-0.811	-0.811	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.043	-0.018	25.714	0.428	0.428	0.000	0.000	0.000	0.000
32	A	36	THR	0	0.036	0.010	26.397	-0.427	-0.427	0.000	0.000	0.000	0.000
33	A	37	VAL	0	-0.065	-0.040	21.635	0.053	0.053	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.014	0.006	25.079	0.122	0.122	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.069	0.035	24.228	-0.560	-0.560	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.895	-0.931	24.446	-10.926	-10.926	0.000	0.000	0.000	0.000
37	A	41	ILE	0	0.003	-0.007	23.458	0.209	0.209	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.864	0.906	27.554	9.886	9.886	0.000	0.000	0.000	0.000
39	A	43	THR	0	0.012	0.013	28.792	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.004	0.006	31.287	0.220	0.220	0.000	0.000	0.000	0.000
41	A	45	ASN	0	0.019	-0.002	33.048	0.244	0.244	0.000	0.000	0.000	0.000
42	A	46	SER	0	0.013	0.016	29.311	0.112	0.112	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.024	0.002	29.010	-0.164	-0.164	0.000	0.000	0.000	0.000
44	A	48	VAL	0	0.030	0.012	24.049	-0.188	-0.188	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.909	0.949	21.217	14.063	14.063	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.035	-0.017	21.160	-0.545	-0.545	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.054	-0.025	15.362	0.508	0.508	0.000	0.000	0.000	0.000
48	A	52	PHE	0	0.021	0.007	14.782	0.242	0.242	0.000	0.000	0.000	0.000
49	A	53	TYR	0	0.008	0.021	5.809	-3.156	-3.156	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.778	-0.883	9.982	-21.311	-21.311	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.077	-0.050	5.058	-5.498	-5.498	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.926	0.953	6.691	33.497	33.497	0.000	0.000	0.000	0.000
53	A	57	CYS	0	-0.092	-0.025	6.043	-4.113	-4.113	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.897	0.927	5.600	43.750	43.750	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.926	-0.958	7.703	-24.280	-24.280	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.000	-0.009	10.807	-0.930	-0.930	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.941	0.955	13.537	18.666	18.666	0.000	0.000	0.000	0.000
58	A	62	PRO	0	0.031	0.029	9.949	0.747	0.747	0.000	0.000	0.000	0.000
59	A	63	VAL	0	0.005	0.014	12.364	0.586	0.586	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.963	0.965	15.791	13.935	13.935	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.037	-0.041	19.224	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	66	GLY	0	0.011	0.020	16.378	0.515	0.515	0.000	0.000	0.000	0.000
63	A	67	CYS	0	-0.042	-0.018	10.967	0.034	0.034	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.836	0.887	7.727	33.594	33.594	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.014	-0.006	13.705	-0.523	-0.523	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.020	0.001	16.211	0.777	0.777	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.774	-0.871	18.637	-12.337	-12.337	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.851	-0.918	21.145	-13.428	-13.428	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.909	0.959	22.869	10.989	10.989	0.000	0.000	0.000	0.000
70	A	74	HIS	0	-0.015	-0.028	25.578	0.984	0.984	0.000	0.000	0.000	0.000
71	A	75	TRP	0	-0.022	-0.012	22.256	0.317	0.317	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.012	0.014	22.162	-0.280	-0.280	0.000	0.000	0.000	0.000
73	A	77	SER	0	0.008	-0.010	17.280	-0.531	-0.531	0.000	0.000	0.000	0.000
74	A	78	GLN	0	0.043	0.014	15.861	0.373	0.373	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.927	0.955	12.532	18.160	18.160	0.000	0.000	0.000	0.000
76	A	81	THR	0	0.041	0.013	10.336	-2.484	-2.484	0.000	0.000	0.000	0.000
77	A	82	SER	0	0.002	0.013	10.958	1.826	1.826	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.015	-0.034	11.962	-0.412	-0.412	0.000	0.000	0.000	0.000
79	A	84	THR	0	-0.003	-0.001	13.738	0.891	0.891	0.000	0.000	0.000	0.000
80	A	85	TYR	0	0.011	0.008	15.806	0.184	0.184	0.000	0.000	0.000	0.000
81	A	86	VAL	0	0.024	0.020	15.361	-0.281	-0.281	0.000	0.000	0.000	0.000
82	A	87	ARG	1	0.922	0.974	18.694	12.753	12.753	0.000	0.000	0.000	0.000
83	A	88	ALA	0	0.024	0.011	20.986	-0.461	-0.461	0.000	0.000	0.000	0.000
84	A	89	LEU	0	-0.019	0.005	23.063	0.553	0.553	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.016	-0.013	25.229	-0.138	-0.138	0.000	0.000	0.000	0.000
86	A	91	SER	0	0.014	0.000	27.776	0.374	0.374	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.773	-0.860	30.242	-10.104	-10.104	0.000	0.000	0.000	0.000
88	A	93	ASN	0	0.045	0.011	32.672	0.229	0.229	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.038	-0.026	33.549	0.100	0.100	0.000	0.000	0.000	0.000
90	A	95	LYS	1	0.994	0.991	34.921	7.866	7.866	0.000	0.000	0.000	0.000
91	A	96	LEU	0	-0.016	0.007	34.777	0.128	0.128	0.000	0.000	0.000	0.000
92	A	97	VAL	0	0.003	-0.001	32.156	-0.291	-0.291	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.044	0.022	30.676	0.267	0.267	0.000	0.000	0.000	0.000
94	A	99	TRP	0	-0.001	0.008	23.184	-0.390	-0.390	0.000	0.000	0.000	0.000
95	A	100	ARG	1	0.809	0.897	25.996	10.709	10.709	0.000	0.000	0.000	0.000
96	A	101	TRP	0	0.005	0.000	20.088	-0.479	-0.479	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.003	-0.002	19.702	0.430	0.430	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.921	0.964	18.531	14.980	14.980	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.041	-0.016	13.879	0.389	0.389	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.828	-0.907	11.101	-22.878	-22.878	0.000	0.000	0.000	0.000
101	A	106	THR	0	0.011	-0.009	9.754	-0.209	-0.209	0.000	0.000	0.000	0.000
102	A	107	SER	0	0.010	0.017	6.844	-2.743	-2.743	0.000	0.000	0.000	0.000
103	A	109	VAL	0	0.036	0.026	8.185	-1.473	-1.473	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.045	-0.013	13.631	0.907	0.907	0.000	0.000	0.000	0.000
105	A	112	LEU	0	0.037	0.002	17.190	0.014	0.014	0.000	0.000	0.000	0.000
106	A	113	SER	0	-0.005	-0.009	20.256	0.563	0.563	0.000	0.000	0.000	0.000
107	A	114	ARG	1	0.970	0.987	23.734	10.852	10.852	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.825	0.932	25.294	12.404	12.404	0.000	0.000	0.000	0.000

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