FMO DATABASE

FMODB ID: M9VYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-811199.780216
FMO2-HF: Nuclear repulsion	767884.388911
FMO2-HF: Total energy	-43315.391305
FMO2-MP2: Total energy	-43439.829407

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.
4.171	0.052000000000004	26.14	-11.218	-10.801	-0.051

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 : 0.957 / q_NPA : 0.985

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	-0.019	-0.002	3.318	-7.855	-4.089	0.034	-2.079	-1.721	0.009
4	W	19	SER	0	0.019	0.009	12.768	1.145	1.145	0.000	0.000	0.000	0.000
5	W	20	ILE	0	-0.016	-0.003	7.279	-2.029	-2.029	0.000	0.000	0.000	0.000
6	W	21	THR	0	-0.015	-0.015	6.573	2.659	2.659	0.000	0.000	0.000	0.000
7	W	22	CYS	0	-0.053	-0.013	4.293	-6.073	-5.905	0.000	-0.061	-0.107	0.000
8	W	23	THR	0	-0.013	-0.004	2.601	6.407	7.749	0.231	-0.493	-1.080	0.001
9	W	24	VAL	0	0.028	0.017	1.874	-8.258	-16.589	17.063	-5.165	-3.567	-0.043
10	W	25	SER	0	0.004	0.004	4.575	1.932	1.979	-0.001	-0.024	-0.022	0.000
11	W	26	GLY	0	0.024	0.008	7.570	0.259	0.259	0.000	0.000	0.000	0.000
12	W	27	PHE	0	-0.002	-0.011	8.068	1.605	1.605	0.000	0.000	0.000	0.000
13	W	28	SER	0	0.065	0.031	10.387	-1.722	-1.722	0.000	0.000	0.000	0.000
14	W	29	LEU	0	-0.019	-0.014	10.949	0.543	0.543	0.000	0.000	0.000	0.000
15	W	30	ILE	0	-0.043	-0.016	12.333	0.532	0.532	0.000	0.000	0.000	0.000
16	W	31	ASP	-1	-0.870	-0.930	14.995	-14.346	-14.346	0.000	0.000	0.000	0.000
17	W	32	TYR	0	-0.050	-0.020	12.030	0.512	0.512	0.000	0.000	0.000	0.000
18	W	33	GLY	0	0.046	0.024	13.021	-0.298	-0.298	0.000	0.000	0.000	0.000
19	W	34	VAL	0	-0.065	-0.044	8.250	-1.212	-1.212	0.000	0.000	0.000	0.000
20	W	35	HIS	0	0.067	0.041	10.673	1.155	1.155	0.000	0.000	0.000	0.000
21	W	36	TRP	0	0.030	0.005	7.891	-2.089	-2.089	0.000	0.000	0.000	0.000
22	W	46	GLU	-1	-0.969	-0.992	17.873	-11.875	-11.875	0.000	0.000	0.000	0.000
23	W	47	TRP	0	-0.009	-0.004	15.557	-0.501	-0.501	0.000	0.000	0.000	0.000
24	W	48	LEU	0	-0.029	-0.005	13.815	0.548	0.548	0.000	0.000	0.000	0.000
25	W	49	GLY	0	0.071	0.013	15.265	0.809	0.809	0.000	0.000	0.000	0.000
26	W	50	VAL	0	-0.014	0.006	14.263	-1.069	-1.069	0.000	0.000	0.000	0.000
27	W	51	ILE	0	-0.059	-0.017	12.403	0.639	0.639	0.000	0.000	0.000	0.000
28	W	52	TRP	0	0.052	0.014	14.298	-1.101	-1.101	0.000	0.000	0.000	0.000
29	W	53	THR	0	0.016	-0.008	16.681	-0.406	-0.406	0.000	0.000	0.000	0.000
30	W	54	GLY	0	-0.034	-0.010	17.524	0.521	0.521	0.000	0.000	0.000	0.000
31	W	55	GLY	0	-0.014	-0.002	18.280	0.467	0.467	0.000	0.000	0.000	0.000
32	W	56	SER	0	0.016	-0.007	19.005	-0.147	-0.147	0.000	0.000	0.000	0.000
33	W	57	THR	0	-0.064	-0.031	17.048	-0.170	-0.170	0.000	0.000	0.000	0.000
34	W	58	ASP	-1	-0.831	-0.899	18.654	-11.176	-11.176	0.000	0.000	0.000	0.000
35	W	59	TYR	0	-0.038	-0.049	17.474	-1.054	-1.054	0.000	0.000	0.000	0.000
36	W	60	ASN	0	0.013	0.000	19.969	0.964	0.964	0.000	0.000	0.000	0.000
37	W	61	ALA	0	0.032	0.007	21.780	0.092	0.092	0.000	0.000	0.000	0.000
38	W	62	ALA	0	-0.014	-0.002	24.260	0.243	0.243	0.000	0.000	0.000	0.000
39	W	63	PHE	0	-0.041	-0.036	20.433	0.062	0.062	0.000	0.000	0.000	0.000
40	W	64	ILE	0	0.004	0.011	22.626	-0.287	-0.287	0.000	0.000	0.000	0.000
41	W	65	SER	0	-0.019	0.009	24.400	-0.178	-0.178	0.000	0.000	0.000	0.000
42	W	66	ARG	1	0.969	0.969	22.971	11.914	11.914	0.000	0.000	0.000	0.000
43	W	67	LEU	0	-0.013	0.019	16.427	-0.635	-0.635	0.000	0.000	0.000	0.000
44	W	68	THR	0	0.005	-0.004	18.513	0.507	0.507	0.000	0.000	0.000	0.000
45	W	69	ILE	0	-0.002	0.007	13.383	-0.925	-0.925	0.000	0.000	0.000	0.000
46	W	70	SER	0	-0.047	-0.013	14.510	0.751	0.751	0.000	0.000	0.000	0.000
47	W	71	LYS	1	0.924	0.952	12.696	14.445	14.445	0.000	0.000	0.000	0.000
48	W	72	ASP	-1	-0.824	-0.925	12.462	-16.907	-16.907	0.000	0.000	0.000	0.000
49	W	73	ASN	0	0.005	-0.006	12.423	-1.265	-1.265	0.000	0.000	0.000	0.000
50	W	74	SER	0	-0.012	0.005	13.362	-0.847	-0.847	0.000	0.000	0.000	0.000
51	W	75	LYS	1	0.957	0.985	10.197	23.905	23.905	0.000	0.000	0.000	0.000
52	W	76	SER	0	-0.028	-0.003	8.628	-2.752	-2.752	0.000	0.000	0.000	0.000
53	W	77	GLN	0	-0.018	-0.025	6.251	-0.842	-0.842	0.000	0.000	0.000	0.000
54	W	78	VAL	0	0.000	0.006	7.356	2.723	2.723	0.000	0.000	0.000	0.000
55	W	79	PHE	0	-0.058	-0.026	8.539	-1.859	-1.859	0.000	0.000	0.000	0.000
56	W	80	PHE	0	0.028	0.012	10.742	1.617	1.617	0.000	0.000	0.000	0.000
57	W	81	LYS	1	0.976	0.987	12.423	17.197	17.197	0.000	0.000	0.000	0.000
58	W	93	TYR	0	0.015	-0.002	10.095	0.256	0.256	0.000	0.000	0.000	0.000
59	W	94	TYR	0	-0.036	-0.015	7.178	-2.017	-2.017	0.000	0.000	0.000	0.000
60	W	96	GLY	0	0.056	0.016	6.253	-2.136	-2.136	0.000	0.000	0.000	0.000
61	W	97	ARG	1	0.794	0.902	8.285	18.888	18.888	0.000	0.000	0.000	0.000
62	W	98	PRO	0	-0.048	-0.008	10.421	0.530	0.530	0.000	0.000	0.000	0.000
63	W	99	TYR	0	0.030	0.009	14.175	0.080	0.080	0.000	0.000	0.000	0.000
64	W	100	TYR	0	-0.039	-0.030	16.532	0.524	0.524	0.000	0.000	0.000	0.000
65	W	101	GLY	0	0.024	0.007	18.566	0.654	0.654	0.000	0.000	0.000	0.000
66	W	102	ASN	0	-0.037	-0.038	17.178	-0.656	-0.656	0.000	0.000	0.000	0.000
67	W	103	VAL	0	0.003	0.016	16.568	-0.463	-0.463	0.000	0.000	0.000	0.000
68	W	104	MET	0	-0.009	0.011	10.837	-0.090	-0.090	0.000	0.000	0.000	0.000
69	W	105	ASP	-1	-0.787	-0.872	12.809	-17.368	-17.368	0.000	0.000	0.000	0.000
70	W	106	TYR	0	-0.049	-0.017	8.718	-0.557	-0.557	0.000	0.000	0.000	0.000
71	W	107	TRP	0	0.015	-0.006	8.072	-0.246	-0.246	0.000	0.000	0.000	0.000
72	W	108	GLY	0	0.037	0.019	4.418	-2.051	-1.924	-0.001	-0.016	-0.109	0.000
73	W	109	GLN	0	-0.014	-0.011	1.922	3.088	1.850	8.814	-3.380	-4.195	-0.018
74	W	1023	CYS	0	-0.054	-0.051	21.991	-0.095	-0.095	0.000	0.000	0.000	0.000
75	W	1024	ARG	1	0.970	0.988	28.884	8.203	8.203	0.000	0.000	0.000	0.000
76	W	1025	ALA	0	0.043	0.026	30.133	-0.257	-0.257	0.000	0.000	0.000	0.000
77	W	1026	SER	0	-0.052	-0.026	31.080	0.301	0.301	0.000	0.000	0.000	0.000
78	W	1027	GLN	0	0.035	0.008	31.917	0.328	0.328	0.000	0.000	0.000	0.000
79	W	1028	ASP	-1	-0.891	-0.941	32.641	-8.174	-8.174	0.000	0.000	0.000	0.000
80	W	1029	ILE	0	-0.068	-0.036	27.829	-0.303	-0.303	0.000	0.000	0.000	0.000
81	W	1030	SER	0	0.036	0.018	30.872	0.163	0.163	0.000	0.000	0.000	0.000
82	W	1031	ASN	0	-0.040	-0.024	29.616	-0.117	-0.117	0.000	0.000	0.000	0.000
83	W	1032	TYR	0	0.062	0.023	25.180	-0.191	-0.191	0.000	0.000	0.000	0.000
84	W	1033	LEU	0	-0.015	-0.004	24.337	-0.372	-0.372	0.000	0.000	0.000	0.000
85	W	1034	ASN	0	0.086	0.062	20.093	0.098	0.098	0.000	0.000	0.000	0.000
86	W	1047	LEU	0	-0.007	-0.018	16.283	0.060	0.060	0.000	0.000	0.000	0.000
87	W	1048	ILE	0	-0.038	-0.009	18.304	0.216	0.216	0.000	0.000	0.000	0.000
88	W	1049	TYR	0	0.029	0.004	19.799	-0.002	-0.002	0.000	0.000	0.000	0.000
89	W	1050	TYR	0	-0.035	-0.026	21.771	0.421	0.421	0.000	0.000	0.000	0.000
90	W	1051	THR	0	-0.011	0.003	25.063	0.272	0.272	0.000	0.000	0.000	0.000
91	W	1052	SER	0	-0.016	-0.009	25.694	-0.242	-0.242	0.000	0.000	0.000	0.000
92	W	1053	ARG	1	0.954	0.975	24.544	10.518	10.518	0.000	0.000	0.000	0.000
93	W	1054	LEU	0	0.010	0.010	23.552	-0.386	-0.386	0.000	0.000	0.000	0.000
94	W	1055	HIS	0	0.017	0.020	15.303	-0.336	-0.336	0.000	0.000	0.000	0.000
95	W	1089	GLN	0	0.003	-0.001	17.409	0.015	0.015	0.000	0.000	0.000	0.000
96	W	1090	GLN	0	0.033	0.032	21.530	-0.004	-0.004	0.000	0.000	0.000	0.000
97	W	1091	GLY	0	-0.018	-0.015	22.275	-0.252	-0.252	0.000	0.000	0.000	0.000
98	W	1092	ASN	0	0.040	0.027	23.329	-0.164	-0.164	0.000	0.000	0.000	0.000
99	W	1093	THR	0	-0.052	-0.031	25.819	-0.099	-0.099	0.000	0.000	0.000	0.000
100	W	1094	PHE	0	-0.009	0.023	22.222	-0.365	-0.365	0.000	0.000	0.000	0.000
101	W	1095	PRO	0	0.011	0.002	21.562	0.346	0.346	0.000	0.000	0.000	0.000
102	W	1096	PRO	0	-0.020	-0.015	19.336	0.228	0.228	0.000	0.000	0.000	0.000
103	W	1097	THR	0	0.023	0.010	20.913	-0.350	-0.350	0.000	0.000	0.000	0.000

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