FMO DATABASE

FMODB ID: 2LJQR

Calculation Name: 5KOV-W-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5KOV

Chain ID: W

ChEMBL ID:

UniProt ID: Q82446

Base Structure: X-ray

Registration Date: 2023-09-26

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-813836.563952
FMO2-HF: Nuclear repulsion	770520.239107
FMO2-HF: Total energy	-43316.324845
FMO2-MP2: Total energy	-43440.762788

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(W:5:LYS)

Summations of interaction energy for fragment #1(W: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.
-1.107	3.563	12.474	-8.288	-8.858	-0.063

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.971 / q_NPA : 0.989

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	W	7	SER	0	-0.034	-0.004	3.408	-4.771	-1.714	0.017	-1.606	-1.468	0.004
4	W	19	SER	0	0.026	0.013	13.351	1.030	1.030	0.000	0.000	0.000	0.000
5	W	20	ILE	0	-0.018	-0.004	7.693	-1.791	-1.791	0.000	0.000	0.000	0.000
6	W	21	THR	0	-0.001	-0.004	7.535	1.667	1.667	0.000	0.000	0.000	0.000
7	W	22	CYS	0	-0.050	-0.001	4.832	-4.855	-4.855	0.000	0.000	0.000	0.000
8	W	23	THR	0	0.007	0.011	3.133	6.154	7.158	0.024	-0.323	-0.705	0.000
9	W	24	VAL	0	0.008	0.011	1.927	-12.338	-15.003	8.413	-3.276	-2.473	-0.036
10	W	25	SER	0	0.008	0.001	4.296	1.546	1.615	-0.001	-0.030	-0.038	0.000
11	W	26	GLY	0	0.029	0.011	7.402	0.320	0.320	0.000	0.000	0.000	0.000
12	W	27	PHE	0	-0.017	-0.011	7.886	1.600	1.600	0.000	0.000	0.000	0.000
13	W	28	SER	0	0.004	-0.007	10.411	-1.685	-1.685	0.000	0.000	0.000	0.000
14	W	29	LEU	0	-0.061	-0.031	10.710	0.457	0.457	0.000	0.000	0.000	0.000
15	W	30	ILE	0	-0.014	-0.012	12.400	0.691	0.691	0.000	0.000	0.000	0.000
16	W	31	ASP	-1	-0.805	-0.882	14.705	-15.733	-15.733	0.000	0.000	0.000	0.000
17	W	32	TYR	0	-0.035	-0.019	12.219	0.432	0.432	0.000	0.000	0.000	0.000
18	W	33	GLY	0	0.027	0.020	13.218	-0.386	-0.386	0.000	0.000	0.000	0.000
19	W	34	VAL	0	-0.082	-0.051	8.104	-1.238	-1.238	0.000	0.000	0.000	0.000
20	W	35	HIS	0	0.062	0.038	10.801	0.965	0.965	0.000	0.000	0.000	0.000
21	W	36	TRP	0	-0.002	-0.024	8.385	-1.220	-1.220	0.000	0.000	0.000	0.000
22	W	46	GLU	-1	-0.926	-0.970	18.161	-11.756	-11.756	0.000	0.000	0.000	0.000
23	W	47	TRP	0	-0.002	-0.001	15.918	-0.433	-0.433	0.000	0.000	0.000	0.000
24	W	48	LEU	0	0.005	0.001	14.009	0.618	0.618	0.000	0.000	0.000	0.000
25	W	49	GLY	0	0.042	0.006	15.881	0.740	0.740	0.000	0.000	0.000	0.000
26	W	50	VAL	0	-0.056	-0.009	14.305	-0.996	-0.996	0.000	0.000	0.000	0.000
27	W	51	ILE	0	-0.042	-0.009	12.689	0.616	0.616	0.000	0.000	0.000	0.000
28	W	52	TRP	0	0.004	-0.007	14.453	-1.134	-1.134	0.000	0.000	0.000	0.000
29	W	53	THR	0	0.038	0.001	16.895	-0.452	-0.452	0.000	0.000	0.000	0.000
30	W	54	GLY	0	-0.008	0.008	17.912	0.604	0.604	0.000	0.000	0.000	0.000
31	W	55	GLY	0	-0.014	-0.038	18.446	-0.262	-0.262	0.000	0.000	0.000	0.000
32	W	56	SER	0	-0.011	0.004	18.846	-0.333	-0.333	0.000	0.000	0.000	0.000
33	W	57	THR	0	-0.022	-0.004	17.102	-0.150	-0.150	0.000	0.000	0.000	0.000
34	W	58	ASP	-1	-0.815	-0.878	18.879	-11.512	-11.512	0.000	0.000	0.000	0.000
35	W	59	TYR	0	-0.008	-0.038	17.657	-1.001	-1.001	0.000	0.000	0.000	0.000
36	W	60	ASN	0	-0.017	-0.020	20.152	0.949	0.949	0.000	0.000	0.000	0.000
37	W	61	ALA	0	0.031	0.006	21.957	0.034	0.034	0.000	0.000	0.000	0.000
38	W	62	ALA	0	-0.011	0.007	24.063	0.252	0.252	0.000	0.000	0.000	0.000
39	W	63	PHE	0	-0.030	-0.031	19.997	-0.030	-0.030	0.000	0.000	0.000	0.000
40	W	64	ILE	0	0.016	0.007	23.094	-0.258	-0.258	0.000	0.000	0.000	0.000
41	W	65	SER	0	-0.010	0.005	24.550	-0.135	-0.135	0.000	0.000	0.000	0.000
42	W	66	ARG	1	0.923	0.952	23.225	11.945	11.945	0.000	0.000	0.000	0.000
43	W	67	LEU	0	-0.017	0.026	16.501	-0.551	-0.551	0.000	0.000	0.000	0.000
44	W	68	THR	0	-0.007	-0.008	18.581	0.541	0.541	0.000	0.000	0.000	0.000
45	W	69	ILE	0	0.012	0.013	13.247	-0.972	-0.972	0.000	0.000	0.000	0.000
46	W	70	SER	0	-0.007	0.010	14.458	0.834	0.834	0.000	0.000	0.000	0.000
47	W	71	LYS	1	0.876	0.931	12.766	14.412	14.412	0.000	0.000	0.000	0.000
48	W	72	ASP	-1	-0.802	-0.873	12.596	-17.066	-17.066	0.000	0.000	0.000	0.000
49	W	73	ASN	0	0.025	-0.016	12.675	-1.443	-1.443	0.000	0.000	0.000	0.000
50	W	74	SER	0	-0.045	-0.025	13.961	-0.412	-0.412	0.000	0.000	0.000	0.000
51	W	75	LYS	1	0.936	0.969	10.985	24.280	24.280	0.000	0.000	0.000	0.000
52	W	76	SER	0	-0.031	-0.001	8.660	-2.686	-2.686	0.000	0.000	0.000	0.000
53	W	77	GLN	0	-0.042	-0.038	6.761	0.054	0.054	0.000	0.000	0.000	0.000
54	W	78	VAL	0	0.031	0.008	7.977	2.686	2.686	0.000	0.000	0.000	0.000
55	W	79	PHE	0	-0.023	-0.022	9.038	-1.973	-1.973	0.000	0.000	0.000	0.000
56	W	80	PHE	0	0.010	0.016	11.286	1.780	1.780	0.000	0.000	0.000	0.000
57	W	81	LYS	1	0.919	0.944	13.120	16.801	16.801	0.000	0.000	0.000	0.000
58	W	93	TYR	0	0.027	0.005	10.219	0.318	0.318	0.000	0.000	0.000	0.000
59	W	94	TYR	0	-0.008	-0.001	7.526	-1.864	-1.864	0.000	0.000	0.000	0.000
60	W	96	GLY	0	0.071	0.015	6.576	-1.920	-1.920	0.000	0.000	0.000	0.000
61	W	97	ARG	1	0.799	0.909	8.167	19.389	19.389	0.000	0.000	0.000	0.000
62	W	98	PRO	0	-0.017	0.005	10.219	0.585	0.585	0.000	0.000	0.000	0.000
63	W	99	TYR	0	0.031	0.006	14.039	0.236	0.236	0.000	0.000	0.000	0.000
64	W	100	TYR	0	-0.025	-0.030	16.360	0.569	0.569	0.000	0.000	0.000	0.000
65	W	101	GLY	0	0.020	0.016	18.435	0.586	0.586	0.000	0.000	0.000	0.000
66	W	102	ASN	0	-0.003	-0.014	17.154	-0.667	-0.667	0.000	0.000	0.000	0.000
67	W	103	VAL	0	0.019	0.030	16.870	-0.267	-0.267	0.000	0.000	0.000	0.000
68	W	104	MET	0	-0.021	-0.001	10.682	0.019	0.019	0.000	0.000	0.000	0.000
69	W	105	ASP	-1	-0.773	-0.859	12.208	-18.128	-18.128	0.000	0.000	0.000	0.000
70	W	106	TYR	0	-0.074	-0.036	8.183	-0.648	-0.648	0.000	0.000	0.000	0.000
71	W	107	TRP	0	-0.002	-0.022	7.186	0.001	0.001	0.000	0.000	0.000	0.000
72	W	108	GLY	0	0.008	0.018	3.795	-2.171	-1.934	0.002	-0.054	-0.186	0.000
73	W	109	GLN	0	-0.009	-0.018	2.229	-1.731	1.237	4.019	-2.999	-3.988	-0.031
74	W	1023	CYS	0	-0.023	-0.015	21.788	0.108	0.108	0.000	0.000	0.000	0.000
75	W	1024	ARG	1	0.968	0.985	28.519	8.234	8.234	0.000	0.000	0.000	0.000
76	W	1025	ALA	0	0.053	0.036	30.235	-0.184	-0.184	0.000	0.000	0.000	0.000
77	W	1026	SER	0	-0.042	-0.039	31.135	0.218	0.218	0.000	0.000	0.000	0.000
78	W	1027	GLN	0	0.004	0.006	31.741	0.275	0.275	0.000	0.000	0.000	0.000
79	W	1028	ASP	-1	-0.811	-0.901	32.710	-8.334	-8.334	0.000	0.000	0.000	0.000
80	W	1029	ILE	0	-0.048	-0.032	27.481	-0.280	-0.280	0.000	0.000	0.000	0.000
81	W	1030	SER	0	0.026	0.010	30.575	-0.080	-0.080	0.000	0.000	0.000	0.000
82	W	1031	ASN	0	-0.026	-0.008	29.255	-0.086	-0.086	0.000	0.000	0.000	0.000
83	W	1032	TYR	0	-0.018	0.002	25.329	-0.289	-0.289	0.000	0.000	0.000	0.000
84	W	1033	LEU	0	0.028	0.007	24.499	-0.195	-0.195	0.000	0.000	0.000	0.000
85	W	1034	ASN	0	0.028	0.013	19.679	0.165	0.165	0.000	0.000	0.000	0.000
86	W	1047	LEU	0	-0.013	-0.016	15.606	0.079	0.079	0.000	0.000	0.000	0.000
87	W	1048	ILE	0	-0.002	-0.001	17.485	0.235	0.235	0.000	0.000	0.000	0.000
88	W	1049	TYR	0	0.010	0.000	19.620	-0.046	-0.046	0.000	0.000	0.000	0.000
89	W	1050	TYR	0	0.014	0.003	21.566	0.435	0.435	0.000	0.000	0.000	0.000
90	W	1051	THR	0	-0.011	0.001	24.917	0.273	0.273	0.000	0.000	0.000	0.000
91	W	1052	SER	0	-0.003	-0.011	26.197	-0.063	-0.063	0.000	0.000	0.000	0.000
92	W	1053	ARG	1	0.859	0.964	23.680	10.716	10.716	0.000	0.000	0.000	0.000
93	W	1054	LEU	0	0.049	0.013	22.806	-0.423	-0.423	0.000	0.000	0.000	0.000
94	W	1055	HIS	0	0.026	0.027	14.028	-0.110	-0.110	0.000	0.000	0.000	0.000
95	W	1089	GLN	0	-0.003	-0.006	17.689	0.321	0.321	0.000	0.000	0.000	0.000
96	W	1090	GLN	0	0.027	0.020	21.259	-0.084	-0.084	0.000	0.000	0.000	0.000
97	W	1091	GLY	0	0.009	0.005	22.135	-0.319	-0.319	0.000	0.000	0.000	0.000
98	W	1092	ASN	0	-0.008	-0.004	23.110	-0.047	-0.047	0.000	0.000	0.000	0.000
99	W	1093	THR	0	-0.069	-0.034	26.005	-0.080	-0.080	0.000	0.000	0.000	0.000
100	W	1094	PHE	0	0.017	0.021	21.696	-0.355	-0.355	0.000	0.000	0.000	0.000
101	W	1095	PRO	0	0.024	0.020	21.360	0.350	0.350	0.000	0.000	0.000	0.000
102	W	1096	PRO	0	-0.029	-0.011	18.755	0.279	0.279	0.000	0.000	0.000	0.000
103	W	1097	THR	0	-0.024	-0.032	20.512	-0.563	-0.563	0.000	0.000	0.000	0.000

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