FMO DATABASE

FMODB ID: 7M27K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-811365.965926
FMO2-HF: Nuclear repulsion	768050.100592
FMO2-HF: Total energy	-43315.865334
FMO2-MP2: Total energy	-43440.30643

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.
2.116	2.099	20.933	-10.447	-10.467	-0.052

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 : 0.968 / q_NPA : 0.994

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	-0.008	0.004	3.324	-7.363	-3.633	0.034	-2.088	-1.676	0.009
4	W	19	SER	0	0.023	0.012	12.847	1.115	1.115	0.000	0.000	0.000	0.000
5	W	20	ILE	0	-0.020	-0.008	7.207	-2.057	-2.057	0.000	0.000	0.000	0.000
6	W	21	THR	0	-0.001	-0.008	6.573	2.474	2.474	0.000	0.000	0.000	0.000
7	W	22	CYS	0	-0.088	-0.029	4.219	-5.477	-5.338	-0.001	-0.054	-0.084	0.000
8	W	23	THR	0	0.002	0.012	2.412	6.208	7.717	0.458	-0.662	-1.305	0.002
9	W	24	VAL	0	0.024	0.013	1.900	-7.849	-16.028	16.509	-4.844	-3.486	-0.041
10	W	25	SER	0	0.013	0.007	4.584	1.804	1.854	-0.001	-0.024	-0.025	0.000
11	W	26	GLY	0	0.023	0.010	7.546	0.267	0.267	0.000	0.000	0.000	0.000
12	W	27	PHE	0	-0.012	-0.014	8.096	1.633	1.633	0.000	0.000	0.000	0.000
13	W	28	SER	0	0.039	0.030	10.397	-1.723	-1.723	0.000	0.000	0.000	0.000
14	W	29	LEU	0	-0.053	-0.030	10.906	0.577	0.577	0.000	0.000	0.000	0.000
15	W	30	ILE	0	-0.017	-0.009	12.333	0.628	0.628	0.000	0.000	0.000	0.000
16	W	31	ASP	-1	-0.846	-0.926	14.874	-15.234	-15.234	0.000	0.000	0.000	0.000
17	W	32	TYR	0	-0.034	-0.015	12.010	0.446	0.446	0.000	0.000	0.000	0.000
18	W	33	GLY	0	0.046	0.027	12.992	-0.299	-0.299	0.000	0.000	0.000	0.000
19	W	34	VAL	0	-0.069	-0.047	8.148	-1.229	-1.229	0.000	0.000	0.000	0.000
20	W	35	HIS	0	0.063	0.046	10.673	1.215	1.215	0.000	0.000	0.000	0.000
21	W	36	TRP	0	0.014	-0.005	7.772	-1.354	-1.354	0.000	0.000	0.000	0.000
22	W	46	GLU	-1	-0.936	-0.978	17.863	-11.951	-11.951	0.000	0.000	0.000	0.000
23	W	47	TRP	0	-0.004	-0.009	15.996	-0.502	-0.502	0.000	0.000	0.000	0.000
24	W	48	LEU	0	-0.019	0.004	14.015	0.547	0.547	0.000	0.000	0.000	0.000
25	W	49	GLY	0	0.063	0.009	15.236	0.797	0.797	0.000	0.000	0.000	0.000
26	W	50	VAL	0	-0.022	0.002	14.231	-1.101	-1.101	0.000	0.000	0.000	0.000
27	W	51	ILE	0	-0.050	-0.018	12.444	0.621	0.621	0.000	0.000	0.000	0.000
28	W	52	TRP	0	0.037	0.011	14.257	-1.180	-1.180	0.000	0.000	0.000	0.000
29	W	53	THR	0	0.018	-0.004	16.639	-0.402	-0.402	0.000	0.000	0.000	0.000
30	W	54	GLY	0	-0.039	-0.015	17.482	0.524	0.524	0.000	0.000	0.000	0.000
31	W	55	GLY	0	-0.018	-0.008	18.224	0.466	0.466	0.000	0.000	0.000	0.000
32	W	56	SER	0	0.024	0.000	18.954	-0.145	-0.145	0.000	0.000	0.000	0.000
33	W	57	THR	0	-0.055	-0.018	16.994	-0.199	-0.199	0.000	0.000	0.000	0.000
34	W	58	ASP	-1	-0.826	-0.899	18.617	-11.378	-11.378	0.000	0.000	0.000	0.000
35	W	59	TYR	0	-0.042	-0.058	17.412	-1.006	-1.006	0.000	0.000	0.000	0.000
36	W	60	ASN	0	-0.011	-0.013	19.943	0.939	0.939	0.000	0.000	0.000	0.000
37	W	61	ALA	0	0.024	0.007	21.747	0.096	0.096	0.000	0.000	0.000	0.000
38	W	62	ALA	0	-0.006	0.000	24.230	0.275	0.275	0.000	0.000	0.000	0.000
39	W	63	PHE	0	-0.042	-0.038	20.002	0.040	0.040	0.000	0.000	0.000	0.000
40	W	64	ILE	0	0.006	0.010	22.576	-0.285	-0.285	0.000	0.000	0.000	0.000
41	W	65	SER	0	-0.020	0.005	24.351	-0.172	-0.172	0.000	0.000	0.000	0.000
42	W	66	ARG	1	0.958	0.967	22.796	11.896	11.896	0.000	0.000	0.000	0.000
43	W	67	LEU	0	-0.002	0.024	16.333	-0.607	-0.607	0.000	0.000	0.000	0.000
44	W	68	THR	0	0.006	-0.005	18.432	0.499	0.499	0.000	0.000	0.000	0.000
45	W	69	ILE	0	-0.005	0.003	13.107	-0.919	-0.919	0.000	0.000	0.000	0.000
46	W	70	SER	0	-0.004	0.006	14.548	0.669	0.669	0.000	0.000	0.000	0.000
47	W	71	LYS	1	0.922	0.959	12.768	14.594	14.594	0.000	0.000	0.000	0.000
48	W	72	ASP	-1	-0.803	-0.895	12.512	-17.221	-17.221	0.000	0.000	0.000	0.000
49	W	73	ASN	0	0.006	-0.012	12.461	-1.324	-1.324	0.000	0.000	0.000	0.000
50	W	74	SER	0	-0.029	-0.013	13.384	-0.755	-0.755	0.000	0.000	0.000	0.000
51	W	75	LYS	1	0.931	0.973	10.216	24.606	24.606	0.000	0.000	0.000	0.000
52	W	76	SER	0	-0.018	0.001	8.834	-2.448	-2.448	0.000	0.000	0.000	0.000
53	W	77	GLN	0	-0.038	-0.040	5.931	0.400	0.400	0.000	0.000	0.000	0.000
54	W	78	VAL	0	0.003	0.002	7.420	2.711	2.711	0.000	0.000	0.000	0.000
55	W	79	PHE	0	-0.040	-0.023	8.609	-1.916	-1.916	0.000	0.000	0.000	0.000
56	W	80	PHE	0	0.019	0.009	10.695	1.617	1.617	0.000	0.000	0.000	0.000
57	W	81	LYS	1	0.929	0.965	12.356	17.123	17.123	0.000	0.000	0.000	0.000
58	W	93	TYR	0	0.018	0.000	10.152	0.269	0.269	0.000	0.000	0.000	0.000
59	W	94	TYR	0	-0.009	-0.003	7.198	-1.928	-1.928	0.000	0.000	0.000	0.000
60	W	96	GLY	0	0.066	0.022	6.264	-2.183	-2.183	0.000	0.000	0.000	0.000
61	W	97	ARG	1	0.781	0.900	8.295	18.945	18.945	0.000	0.000	0.000	0.000
62	W	98	PRO	0	-0.022	0.001	10.429	0.491	0.491	0.000	0.000	0.000	0.000
63	W	99	TYR	0	0.017	-0.001	14.180	0.158	0.158	0.000	0.000	0.000	0.000
64	W	100	TYR	0	-0.032	-0.028	16.550	0.547	0.547	0.000	0.000	0.000	0.000
65	W	101	GLY	0	0.022	0.009	18.573	0.665	0.665	0.000	0.000	0.000	0.000
66	W	102	ASN	0	-0.040	-0.035	17.162	-0.682	-0.682	0.000	0.000	0.000	0.000
67	W	103	VAL	0	0.018	0.023	16.578	-0.477	-0.477	0.000	0.000	0.000	0.000
68	W	104	MET	0	-0.009	0.015	10.773	-0.077	-0.077	0.000	0.000	0.000	0.000
69	W	105	ASP	-1	-0.767	-0.863	12.833	-17.650	-17.650	0.000	0.000	0.000	0.000
70	W	106	TYR	0	-0.052	-0.015	8.757	-0.701	-0.701	0.000	0.000	0.000	0.000
71	W	107	TRP	0	-0.010	-0.021	8.097	-0.146	-0.146	0.000	0.000	0.000	0.000
72	W	108	GLY	0	0.030	0.020	4.419	-2.176	-2.048	-0.001	-0.016	-0.110	0.000
73	W	109	GLN	0	-0.016	-0.007	1.978	-1.862	0.744	3.935	-2.759	-3.781	-0.022
74	W	1023	CYS	0	-0.038	-0.018	21.441	0.075	0.075	0.000	0.000	0.000	0.000
75	W	1024	ARG	1	0.990	0.995	28.889	8.186	8.186	0.000	0.000	0.000	0.000
76	W	1025	ALA	0	0.038	0.024	30.141	-0.254	-0.254	0.000	0.000	0.000	0.000
77	W	1026	SER	0	-0.037	-0.020	31.094	0.225	0.225	0.000	0.000	0.000	0.000
78	W	1027	GLN	0	0.004	-0.006	31.845	0.336	0.336	0.000	0.000	0.000	0.000
79	W	1028	ASP	-1	-0.887	-0.936	32.656	-8.176	-8.176	0.000	0.000	0.000	0.000
80	W	1029	ILE	0	-0.052	-0.033	28.123	-0.289	-0.289	0.000	0.000	0.000	0.000
81	W	1030	SER	0	0.042	0.022	30.886	0.156	0.156	0.000	0.000	0.000	0.000
82	W	1031	ASN	0	-0.053	-0.029	29.645	-0.129	-0.129	0.000	0.000	0.000	0.000
83	W	1032	TYR	0	0.062	0.021	25.421	-0.190	-0.190	0.000	0.000	0.000	0.000
84	W	1033	LEU	0	-0.017	-0.001	24.362	-0.364	-0.364	0.000	0.000	0.000	0.000
85	W	1034	ASN	0	0.048	0.036	20.073	0.169	0.169	0.000	0.000	0.000	0.000
86	W	1047	LEU	0	-0.015	-0.023	16.349	0.050	0.050	0.000	0.000	0.000	0.000
87	W	1048	ILE	0	-0.033	-0.007	18.362	0.204	0.204	0.000	0.000	0.000	0.000
88	W	1049	TYR	0	0.020	0.005	19.857	-0.029	-0.029	0.000	0.000	0.000	0.000
89	W	1050	TYR	0	0.016	-0.004	21.813	0.440	0.440	0.000	0.000	0.000	0.000
90	W	1051	THR	0	0.000	0.000	25.099	0.260	0.260	0.000	0.000	0.000	0.000
91	W	1052	SER	0	-0.012	-0.002	25.740	-0.244	-0.244	0.000	0.000	0.000	0.000
92	W	1053	ARG	1	0.924	0.971	24.379	10.651	10.651	0.000	0.000	0.000	0.000
93	W	1054	LEU	0	-0.001	0.004	23.605	-0.391	-0.391	0.000	0.000	0.000	0.000
94	W	1055	HIS	0	0.024	0.020	15.010	-0.142	-0.142	0.000	0.000	0.000	0.000
95	W	1089	GLN	0	-0.009	-0.024	17.745	0.306	0.306	0.000	0.000	0.000	0.000
96	W	1090	GLN	0	0.030	0.020	21.555	0.032	0.032	0.000	0.000	0.000	0.000
97	W	1091	GLY	0	0.007	0.002	22.288	-0.237	-0.237	0.000	0.000	0.000	0.000
98	W	1092	ASN	0	0.017	0.019	23.342	-0.140	-0.140	0.000	0.000	0.000	0.000
99	W	1093	THR	0	-0.063	-0.038	25.822	-0.099	-0.099	0.000	0.000	0.000	0.000
100	W	1094	PHE	0	0.008	0.044	21.721	-0.359	-0.359	0.000	0.000	0.000	0.000
101	W	1095	PRO	0	0.023	0.005	21.561	0.356	0.356	0.000	0.000	0.000	0.000
102	W	1096	PRO	0	-0.032	-0.022	19.269	0.263	0.263	0.000	0.000	0.000	0.000
103	W	1097	THR	0	0.010	-0.004	20.912	-0.434	-0.434	0.000	0.000	0.000	0.000

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