FMO DATABASE

FMODB ID: 6GN2Z

Calculation Name: 5KOV-Q-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5KOV

Chain ID: Q

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-633429.630118
FMO2-HF: Nuclear repulsion	595388.855899
FMO2-HF: Total energy	-38040.774218
FMO2-MP2: Total energy	-38150.529354

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(Q:19:SER)

Summations of interaction energy for fragment #1(Q:19:SER)

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.
-8.078	-3.524	3.126	-3.525	-4.156	-0.016

Interaction energy analysis for fragmet #1(Q:19:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.027

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	Q	21	THR	0	-0.005	-0.007	3.804	-0.584	0.738	-0.009	-0.531	-0.782	0.002
4	Q	22	CYS	0	-0.047	0.000	6.271	0.403	0.403	0.000	0.000	0.000	0.000
5	Q	23	THR	0	0.010	-0.007	9.471	0.047	0.047	0.000	0.000	0.000	0.000
6	Q	24	VAL	0	-0.001	0.012	12.270	0.044	0.044	0.000	0.000	0.000	0.000
7	Q	25	SER	0	0.013	0.001	15.519	0.004	0.004	0.000	0.000	0.000	0.000
8	Q	26	GLY	0	0.008	0.007	18.868	0.014	0.014	0.000	0.000	0.000	0.000
9	Q	27	PHE	0	0.001	0.002	16.849	0.015	0.015	0.000	0.000	0.000	0.000
10	Q	28	SER	0	0.090	0.043	19.799	-0.024	-0.024	0.000	0.000	0.000	0.000
11	Q	29	LEU	0	-0.022	-0.025	13.790	0.007	0.007	0.000	0.000	0.000	0.000
12	Q	30	ILE	0	-0.040	-0.017	17.951	0.014	0.014	0.000	0.000	0.000	0.000
13	Q	31	ASP	-1	-0.874	-0.930	20.712	-0.059	-0.059	0.000	0.000	0.000	0.000
14	Q	32	TYR	0	-0.056	-0.031	19.395	0.010	0.010	0.000	0.000	0.000	0.000
15	Q	33	GLY	0	0.028	0.006	16.516	-0.002	-0.002	0.000	0.000	0.000	0.000
16	Q	34	VAL	0	-0.052	-0.035	11.177	-0.028	-0.028	0.000	0.000	0.000	0.000
17	Q	35	HIS	0	0.008	0.018	13.874	0.038	0.038	0.000	0.000	0.000	0.000
18	Q	36	TRP	0	0.030	0.007	7.478	-0.049	-0.049	0.000	0.000	0.000	0.000
19	Q	50	VAL	0	0.006	0.012	12.857	-0.001	-0.001	0.000	0.000	0.000	0.000
20	Q	51	ILE	0	-0.066	-0.022	11.842	0.028	0.028	0.000	0.000	0.000	0.000
21	Q	52	TRP	0	0.079	0.023	14.374	-0.042	-0.042	0.000	0.000	0.000	0.000
22	Q	53	THR	0	0.045	0.017	16.988	0.004	0.004	0.000	0.000	0.000	0.000
23	Q	54	GLY	0	0.023	0.015	19.173	-0.005	-0.005	0.000	0.000	0.000	0.000
24	Q	55	GLY	0	-0.055	-0.021	15.946	0.013	0.013	0.000	0.000	0.000	0.000
25	Q	56	SER	0	-0.031	-0.027	16.514	0.001	0.001	0.000	0.000	0.000	0.000
26	Q	57	THR	0	-0.111	-0.117	14.522	0.006	0.006	0.000	0.000	0.000	0.000
27	Q	58	ASP	-1	-0.798	-0.831	17.113	0.079	0.079	0.000	0.000	0.000	0.000
28	Q	59	TYR	0	-0.037	-0.021	11.432	0.040	0.040	0.000	0.000	0.000	0.000
29	Q	60	ASN	0	0.020	0.002	14.686	-0.029	-0.029	0.000	0.000	0.000	0.000
30	Q	61	ALA	0	0.057	0.024	16.135	0.019	0.019	0.000	0.000	0.000	0.000
31	Q	62	ALA	0	-0.034	-0.009	16.137	0.007	0.007	0.000	0.000	0.000	0.000
32	Q	63	PHE	0	-0.054	-0.035	11.697	0.019	0.019	0.000	0.000	0.000	0.000
33	Q	64	ILE	0	0.055	0.030	13.816	-0.010	-0.010	0.000	0.000	0.000	0.000
34	Q	65	SER	0	-0.004	0.001	13.955	0.048	0.048	0.000	0.000	0.000	0.000
35	Q	66	ARG	1	0.927	0.962	5.944	-1.667	-1.667	0.000	0.000	0.000	0.000
36	Q	67	LEU	0	0.001	-0.006	7.282	0.008	0.008	0.000	0.000	0.000	0.000
37	Q	68	THR	0	-0.018	-0.005	6.818	0.105	0.105	0.000	0.000	0.000	0.000
38	Q	69	ILE	0	0.018	0.026	6.630	0.040	0.040	0.000	0.000	0.000	0.000
39	Q	70	SER	0	0.011	0.013	8.088	0.101	0.101	0.000	0.000	0.000	0.000
40	Q	71	LYS	1	0.823	0.909	9.349	-0.060	-0.060	0.000	0.000	0.000	0.000
41	Q	72	ASP	-1	-0.830	-0.916	11.303	-0.145	-0.145	0.000	0.000	0.000	0.000
42	Q	73	ASN	0	0.009	-0.018	13.318	-0.048	-0.048	0.000	0.000	0.000	0.000
43	Q	74	SER	0	-0.037	-0.001	16.336	-0.010	-0.010	0.000	0.000	0.000	0.000
44	Q	75	LYS	1	0.966	0.977	11.593	0.450	0.450	0.000	0.000	0.000	0.000
45	Q	76	SER	0	-0.018	0.014	14.697	-0.028	-0.028	0.000	0.000	0.000	0.000
46	Q	77	GLN	0	-0.016	-0.017	9.557	-0.076	-0.076	0.000	0.000	0.000	0.000
47	Q	78	VAL	0	0.019	0.010	8.819	0.109	0.109	0.000	0.000	0.000	0.000
48	Q	79	PHE	0	-0.061	-0.028	4.829	-0.218	-0.218	0.000	0.000	0.000	0.000
49	Q	80	PHE	0	0.056	0.029	3.583	0.364	0.719	0.001	-0.076	-0.281	0.000
50	Q	81	LYS	1	0.980	0.976	2.469	-7.093	-4.216	3.134	-2.918	-3.093	-0.018
51	Q	93	TYR	0	-0.020	-0.027	6.034	0.079	0.079	0.000	0.000	0.000	0.000
52	Q	94	TYR	0	0.000	0.002	10.052	-0.032	-0.032	0.000	0.000	0.000	0.000
53	Q	96	GLY	0	0.053	0.007	12.293	0.001	0.001	0.000	0.000	0.000	0.000
54	Q	97	ARG	1	0.814	0.911	15.854	0.088	0.088	0.000	0.000	0.000	0.000
55	Q	98	PRO	0	-0.045	-0.013	17.642	0.014	0.014	0.000	0.000	0.000	0.000
56	Q	99	TYR	0	0.019	0.002	20.439	-0.006	-0.006	0.000	0.000	0.000	0.000
57	Q	100	TYR	0	-0.031	-0.025	24.131	0.008	0.008	0.000	0.000	0.000	0.000
58	Q	101	GLY	0	0.037	0.015	24.228	0.007	0.007	0.000	0.000	0.000	0.000
59	Q	102	ASN	0	0.026	-0.008	20.688	-0.013	-0.013	0.000	0.000	0.000	0.000
60	Q	103	VAL	0	-0.034	0.007	20.738	-0.001	-0.001	0.000	0.000	0.000	0.000
61	Q	104	MET	0	-0.001	0.022	15.605	-0.001	-0.001	0.000	0.000	0.000	0.000
62	Q	105	ASP	-1	-0.746	-0.861	21.039	-0.070	-0.070	0.000	0.000	0.000	0.000
63	Q	106	TYR	0	-0.031	-0.032	20.645	0.004	0.004	0.000	0.000	0.000	0.000
64	Q	107	TRP	0	-0.009	-0.013	16.282	-0.008	-0.008	0.000	0.000	0.000	0.000
65	Q	108	GLY	0	0.010	0.010	13.464	-0.002	-0.002	0.000	0.000	0.000	0.000
66	Q	1022	SER	0	0.022	0.002	34.261	-0.001	-0.001	0.000	0.000	0.000	0.000
67	Q	1023	CYS	0	0.000	-0.008	32.748	-0.001	-0.001	0.000	0.000	0.000	0.000
68	Q	1024	ARG	1	0.913	0.964	28.132	-0.049	-0.049	0.000	0.000	0.000	0.000
69	Q	1025	ALA	0	-0.001	-0.007	29.658	0.004	0.004	0.000	0.000	0.000	0.000
70	Q	1026	SER	0	0.003	0.005	30.493	-0.001	-0.001	0.000	0.000	0.000	0.000
71	Q	1027	GLN	0	-0.035	-0.012	31.753	-0.004	-0.004	0.000	0.000	0.000	0.000
72	Q	1028	ASP	-1	-0.753	-0.881	32.679	0.028	0.028	0.000	0.000	0.000	0.000
73	Q	1029	ILE	0	-0.152	-0.068	30.636	0.003	0.003	0.000	0.000	0.000	0.000
74	Q	1030	SER	0	0.046	0.016	32.203	-0.001	-0.001	0.000	0.000	0.000	0.000
75	Q	1031	ASN	0	0.024	0.009	33.853	-0.002	-0.002	0.000	0.000	0.000	0.000
76	Q	1032	TYR	0	-0.034	-0.010	29.032	-0.002	-0.002	0.000	0.000	0.000	0.000
77	Q	1033	LEU	0	0.012	0.000	28.460	0.004	0.004	0.000	0.000	0.000	0.000
78	Q	1034	ASN	0	0.045	0.016	23.716	-0.005	-0.005	0.000	0.000	0.000	0.000
79	Q	1046	LEU	0	-0.036	-0.010	23.317	0.002	0.002	0.000	0.000	0.000	0.000
80	Q	1047	LEU	0	-0.033	-0.011	24.819	-0.002	-0.002	0.000	0.000	0.000	0.000
81	Q	1048	ILE	0	0.006	0.007	28.373	-0.001	-0.001	0.000	0.000	0.000	0.000
82	Q	1049	TYR	0	0.022	0.002	27.795	0.002	0.002	0.000	0.000	0.000	0.000
83	Q	1050	TYR	0	-0.002	-0.002	29.525	-0.001	-0.001	0.000	0.000	0.000	0.000
84	Q	1051	THR	0	-0.067	-0.027	31.523	0.001	0.001	0.000	0.000	0.000	0.000
85	Q	1052	SER	0	0.019	-0.006	33.290	0.000	0.000	0.000	0.000	0.000	0.000
86	Q	1053	ARG	1	0.915	0.961	32.351	0.008	0.008	0.000	0.000	0.000	0.000
87	Q	1054	LEU	0	0.041	0.035	32.143	0.000	0.000	0.000	0.000	0.000	0.000
88	Q	1055	HIS	0	0.045	0.036	25.167	0.004	0.004	0.000	0.000	0.000	0.000
89	Q	1056	SER	0	-0.031	-0.024	29.284	0.001	0.001	0.000	0.000	0.000	0.000
90	Q	1057	GLY	0	0.021	0.003	30.339	0.002	0.002	0.000	0.000	0.000	0.000
91	Q	1058	VAL	0	-0.061	-0.002	29.127	0.001	0.001	0.000	0.000	0.000	0.000
92	Q	1059	PRO	0	0.024	0.016	32.289	0.002	0.002	0.000	0.000	0.000	0.000
93	Q	1060	SER	0	-0.011	-0.009	34.778	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(Q:19:SER)