FMO DATABASE

FMODB ID: ZN68N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-634332.616182
FMO2-HF: Nuclear repulsion	596291.388585
FMO2-HF: Total energy	-38041.227597
FMO2-MP2: Total energy	-38151.009658

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.
-9.32	-4.479	4.098	-4.051	-4.889	-0.008

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 : -0.025 / q_NPA : -0.026

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	Q	21	THR	0	-0.003	-0.008	3.804	0.103	1.434	-0.008	-0.525	-0.798	0.002
4	Q	22	CYS	0	-0.055	-0.003	6.271	0.344	0.344	0.000	0.000	0.000	0.000
5	Q	23	THR	0	0.018	-0.002	9.460	0.143	0.143	0.000	0.000	0.000	0.000
6	Q	24	VAL	0	0.002	0.013	12.257	0.018	0.018	0.000	0.000	0.000	0.000
7	Q	25	SER	0	0.015	-0.001	15.515	0.022	0.022	0.000	0.000	0.000	0.000
8	Q	26	GLY	0	0.005	0.008	18.854	0.021	0.021	0.000	0.000	0.000	0.000
9	Q	27	PHE	0	-0.006	-0.004	16.746	0.017	0.017	0.000	0.000	0.000	0.000
10	Q	28	SER	0	0.090	0.048	19.797	-0.018	-0.018	0.000	0.000	0.000	0.000
11	Q	29	LEU	0	-0.033	-0.029	13.683	0.001	0.001	0.000	0.000	0.000	0.000
12	Q	30	ILE	0	-0.042	-0.020	17.953	0.014	0.014	0.000	0.000	0.000	0.000
13	Q	31	ASP	-1	-0.868	-0.933	20.716	-0.057	-0.057	0.000	0.000	0.000	0.000
14	Q	32	TYR	0	-0.043	-0.025	19.388	0.002	0.002	0.000	0.000	0.000	0.000
15	Q	33	GLY	0	0.034	0.011	16.502	0.009	0.009	0.000	0.000	0.000	0.000
16	Q	34	VAL	0	-0.064	-0.043	11.243	-0.032	-0.032	0.000	0.000	0.000	0.000
17	Q	35	HIS	0	0.011	0.018	13.845	0.025	0.025	0.000	0.000	0.000	0.000
18	Q	36	TRP	0	0.025	0.004	7.183	-0.127	-0.127	0.000	0.000	0.000	0.000
19	Q	50	VAL	0	-0.007	0.001	12.845	-0.023	-0.023	0.000	0.000	0.000	0.000
20	Q	51	ILE	0	-0.080	-0.025	11.713	0.048	0.048	0.000	0.000	0.000	0.000
21	Q	52	TRP	0	0.061	0.001	14.356	-0.050	-0.050	0.000	0.000	0.000	0.000
22	Q	53	THR	0	0.022	0.015	16.982	0.017	0.017	0.000	0.000	0.000	0.000
23	Q	54	GLY	0	0.034	0.012	19.175	0.010	0.010	0.000	0.000	0.000	0.000
24	Q	55	GLY	0	-0.059	-0.023	15.940	0.023	0.023	0.000	0.000	0.000	0.000
25	Q	56	SER	0	-0.105	-0.078	16.526	-0.013	-0.013	0.000	0.000	0.000	0.000
26	Q	57	THR	0	-0.165	-0.204	14.523	-0.002	-0.002	0.000	0.000	0.000	0.000
27	Q	58	ASP	-1	-0.651	-0.672	16.551	-0.020	-0.020	0.000	0.000	0.000	0.000
28	Q	59	TYR	0	0.008	-0.015	11.723	0.035	0.035	0.000	0.000	0.000	0.000
29	Q	60	ASN	0	0.010	0.001	14.692	-0.005	-0.005	0.000	0.000	0.000	0.000
30	Q	61	ALA	0	0.062	0.030	16.242	0.019	0.019	0.000	0.000	0.000	0.000
31	Q	62	ALA	0	-0.012	0.000	16.216	0.013	0.013	0.000	0.000	0.000	0.000
32	Q	63	PHE	0	-0.054	-0.031	11.835	0.003	0.003	0.000	0.000	0.000	0.000
33	Q	64	ILE	0	0.048	0.023	13.977	0.002	0.002	0.000	0.000	0.000	0.000
34	Q	65	SER	0	0.008	0.007	14.203	0.041	0.041	0.000	0.000	0.000	0.000
35	Q	66	ARG	1	0.918	0.953	6.241	-1.096	-1.096	0.000	0.000	0.000	0.000
36	Q	67	LEU	0	0.013	0.006	7.732	-0.089	-0.089	0.000	0.000	0.000	0.000
37	Q	68	THR	0	-0.046	-0.021	6.828	0.194	0.194	0.000	0.000	0.000	0.000
38	Q	69	ILE	0	0.019	0.027	6.612	0.032	0.032	0.000	0.000	0.000	0.000
39	Q	70	SER	0	-0.003	0.006	8.082	0.041	0.041	0.000	0.000	0.000	0.000
40	Q	71	LYS	1	0.875	0.930	9.354	-0.132	-0.132	0.000	0.000	0.000	0.000
41	Q	72	ASP	-1	-0.770	-0.857	11.317	0.100	0.100	0.000	0.000	0.000	0.000
42	Q	73	ASN	0	0.035	-0.002	13.274	-0.077	-0.077	0.000	0.000	0.000	0.000
43	Q	74	SER	0	-0.050	-0.019	16.052	-0.018	-0.018	0.000	0.000	0.000	0.000
44	Q	75	LYS	1	0.853	0.904	10.913	0.073	0.073	0.000	0.000	0.000	0.000
45	Q	76	SER	0	-0.013	0.018	14.674	-0.038	-0.038	0.000	0.000	0.000	0.000
46	Q	77	GLN	0	-0.001	-0.004	9.546	0.012	0.012	0.000	0.000	0.000	0.000
47	Q	78	VAL	0	0.023	0.010	8.935	0.148	0.148	0.000	0.000	0.000	0.000
48	Q	79	PHE	0	-0.059	-0.026	4.884	-0.183	-0.183	0.000	0.000	0.000	0.000
49	Q	80	PHE	0	0.065	0.032	3.442	0.365	0.778	0.003	-0.097	-0.320	0.000
50	Q	81	LYS	1	0.950	0.970	2.427	-9.409	-6.312	4.103	-3.429	-3.771	-0.010
51	Q	93	TYR	0	-0.007	-0.005	6.311	0.042	0.042	0.000	0.000	0.000	0.000
52	Q	94	TYR	0	-0.012	-0.017	9.832	-0.003	-0.003	0.000	0.000	0.000	0.000
53	Q	96	GLY	0	0.058	0.011	12.129	0.022	0.022	0.000	0.000	0.000	0.000
54	Q	97	ARG	1	0.809	0.911	15.771	0.134	0.134	0.000	0.000	0.000	0.000
55	Q	98	PRO	0	-0.025	-0.005	17.666	0.009	0.009	0.000	0.000	0.000	0.000
56	Q	99	TYR	0	0.004	-0.012	20.409	0.007	0.007	0.000	0.000	0.000	0.000
57	Q	100	TYR	0	-0.028	-0.024	24.101	0.005	0.005	0.000	0.000	0.000	0.000
58	Q	101	GLY	0	0.031	0.015	24.195	0.011	0.011	0.000	0.000	0.000	0.000
59	Q	102	ASN	0	0.012	-0.011	20.486	-0.007	-0.007	0.000	0.000	0.000	0.000
60	Q	103	VAL	0	-0.034	0.007	20.669	-0.014	-0.014	0.000	0.000	0.000	0.000
61	Q	104	MET	0	0.011	0.026	15.427	0.003	0.003	0.000	0.000	0.000	0.000
62	Q	105	ASP	-1	-0.765	-0.871	20.916	-0.138	-0.138	0.000	0.000	0.000	0.000
63	Q	106	TYR	0	-0.054	-0.030	20.560	0.002	0.002	0.000	0.000	0.000	0.000
64	Q	107	TRP	0	-0.012	-0.014	16.005	-0.025	-0.025	0.000	0.000	0.000	0.000
65	Q	108	GLY	0	0.020	0.017	13.164	0.017	0.017	0.000	0.000	0.000	0.000
66	Q	1022	SER	0	-0.011	-0.044	34.197	-0.002	-0.002	0.000	0.000	0.000	0.000
67	Q	1023	CYS	0	-0.042	-0.008	33.145	0.000	0.000	0.000	0.000	0.000	0.000
68	Q	1024	ARG	1	0.969	0.976	28.183	0.046	0.046	0.000	0.000	0.000	0.000
69	Q	1025	ALA	0	-0.019	-0.010	29.619	0.001	0.001	0.000	0.000	0.000	0.000
70	Q	1026	SER	0	0.024	0.009	30.475	0.002	0.002	0.000	0.000	0.000	0.000
71	Q	1027	GLN	0	-0.054	-0.016	31.754	0.002	0.002	0.000	0.000	0.000	0.000
72	Q	1028	ASP	-1	-0.752	-0.866	32.673	-0.022	-0.022	0.000	0.000	0.000	0.000
73	Q	1029	ILE	0	-0.122	-0.051	30.714	-0.002	-0.002	0.000	0.000	0.000	0.000
74	Q	1030	SER	0	0.044	0.022	32.167	0.001	0.001	0.000	0.000	0.000	0.000
75	Q	1031	ASN	0	0.010	0.001	33.808	0.000	0.000	0.000	0.000	0.000	0.000
76	Q	1032	TYR	0	-0.016	-0.003	28.937	-0.003	-0.003	0.000	0.000	0.000	0.000
77	Q	1033	LEU	0	0.029	0.005	28.105	-0.001	-0.001	0.000	0.000	0.000	0.000
78	Q	1034	ASN	0	0.034	0.014	23.619	0.004	0.004	0.000	0.000	0.000	0.000
79	Q	1046	LEU	0	-0.043	-0.007	22.965	-0.001	-0.001	0.000	0.000	0.000	0.000
80	Q	1047	LEU	0	-0.012	-0.010	24.627	0.004	0.004	0.000	0.000	0.000	0.000
81	Q	1048	ILE	0	0.015	0.006	28.179	0.005	0.005	0.000	0.000	0.000	0.000
82	Q	1049	TYR	0	0.014	0.000	27.610	-0.003	-0.003	0.000	0.000	0.000	0.000
83	Q	1050	TYR	0	-0.005	-0.004	29.397	0.004	0.004	0.000	0.000	0.000	0.000
84	Q	1051	THR	0	-0.054	-0.018	31.406	0.005	0.005	0.000	0.000	0.000	0.000
85	Q	1052	SER	0	0.009	-0.013	33.169	0.001	0.001	0.000	0.000	0.000	0.000
86	Q	1053	ARG	1	0.916	0.972	32.144	0.052	0.052	0.000	0.000	0.000	0.000
87	Q	1054	LEU	0	0.033	0.031	31.982	-0.004	-0.004	0.000	0.000	0.000	0.000
88	Q	1055	HIS	0	0.026	0.013	24.791	0.009	0.009	0.000	0.000	0.000	0.000
89	Q	1056	SER	0	-0.009	-0.012	28.758	0.003	0.003	0.000	0.000	0.000	0.000
90	Q	1057	GLY	0	0.028	0.009	30.126	0.005	0.005	0.000	0.000	0.000	0.000
91	Q	1058	VAL	0	-0.063	-0.005	28.921	0.000	0.000	0.000	0.000	0.000	0.000
92	Q	1059	PRO	0	0.025	0.018	32.065	0.004	0.004	0.000	0.000	0.000	0.000
93	Q	1060	SER	0	-0.007	-0.010	34.557	-0.001	-0.001	0.000	0.000	0.000	0.000

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