FMO DATABASE

FMODB ID: RY928

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

Total energy (hartree)

FMO2-HF: Electronic energy	-636998.01493
FMO2-HF: Nuclear repulsion	598955.882444
FMO2-HF: Total energy	-38042.132486
FMO2-MP2: Total energy	-38151.861818

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.
-9.514	-4.982	4.56	-3.641	-5.451	0.005

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 : -0.005 / q_NPA : -0.022

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	-0.013	-0.015	3.739	0.244	1.408	-0.002	-0.442	-0.720	0.002
4	Q	22	CYS	0	-0.026	0.003	6.005	0.371	0.371	0.000	0.000	0.000	0.000
5	Q	23	THR	0	0.014	0.014	9.619	0.145	0.145	0.000	0.000	0.000	0.000
6	Q	24	VAL	0	-0.006	-0.001	11.649	0.016	0.016	0.000	0.000	0.000	0.000
7	Q	25	SER	0	0.012	0.009	15.233	0.023	0.023	0.000	0.000	0.000	0.000
8	Q	26	GLY	0	0.025	0.015	18.513	0.017	0.017	0.000	0.000	0.000	0.000
9	Q	27	PHE	0	-0.003	-0.007	17.082	0.016	0.016	0.000	0.000	0.000	0.000
10	Q	28	SER	0	0.075	0.052	19.634	-0.017	-0.017	0.000	0.000	0.000	0.000
11	Q	29	LEU	0	-0.033	-0.018	13.214	0.016	0.016	0.000	0.000	0.000	0.000
12	Q	30	ILE	0	-0.027	-0.023	17.769	0.038	0.038	0.000	0.000	0.000	0.000
13	Q	31	ASP	-1	-0.863	-0.934	20.589	0.030	0.030	0.000	0.000	0.000	0.000
14	Q	32	TYR	0	-0.046	-0.028	19.351	0.001	0.001	0.000	0.000	0.000	0.000
15	Q	33	GLY	0	0.021	0.008	16.651	0.014	0.014	0.000	0.000	0.000	0.000
16	Q	34	VAL	0	-0.074	-0.045	11.645	-0.048	-0.048	0.000	0.000	0.000	0.000
17	Q	35	HIS	0	0.022	0.016	13.457	0.095	0.095	0.000	0.000	0.000	0.000
18	Q	36	TRP	0	0.024	0.003	6.964	0.001	0.001	0.000	0.000	0.000	0.000
19	Q	50	VAL	0	0.005	0.008	12.920	0.006	0.006	0.000	0.000	0.000	0.000
20	Q	51	ILE	0	-0.090	-0.027	11.632	0.044	0.044	0.000	0.000	0.000	0.000
21	Q	52	TRP	0	0.056	-0.007	14.326	-0.082	-0.082	0.000	0.000	0.000	0.000
22	Q	53	THR	0	0.041	0.028	17.138	0.025	0.025	0.000	0.000	0.000	0.000
23	Q	54	GLY	0	0.036	0.019	19.245	-0.001	-0.001	0.000	0.000	0.000	0.000
24	Q	55	GLY	0	-0.042	-0.021	15.863	0.023	0.023	0.000	0.000	0.000	0.000
25	Q	56	SER	0	-0.005	-0.016	16.797	-0.016	-0.016	0.000	0.000	0.000	0.000
26	Q	57	THR	0	-0.017	-0.022	14.229	0.039	0.039	0.000	0.000	0.000	0.000
27	Q	58	ASP	-1	-0.834	-0.877	16.398	0.241	0.241	0.000	0.000	0.000	0.000
28	Q	59	TYR	0	-0.021	-0.030	11.484	0.055	0.055	0.000	0.000	0.000	0.000
29	Q	60	ASN	0	0.025	0.000	15.171	-0.056	-0.056	0.000	0.000	0.000	0.000
30	Q	61	ALA	0	0.046	0.022	16.920	0.034	0.034	0.000	0.000	0.000	0.000
31	Q	62	ALA	0	0.000	0.012	17.429	-0.007	-0.007	0.000	0.000	0.000	0.000
32	Q	63	PHE	0	-0.072	-0.041	12.665	0.038	0.038	0.000	0.000	0.000	0.000
33	Q	64	ILE	0	0.066	0.029	14.074	0.049	0.049	0.000	0.000	0.000	0.000
34	Q	65	SER	0	0.005	-0.006	14.169	0.089	0.089	0.000	0.000	0.000	0.000
35	Q	66	ARG	1	0.918	0.954	7.219	-1.650	-1.650	0.000	0.000	0.000	0.000
36	Q	67	LEU	0	-0.006	0.029	8.342	0.260	0.260	0.000	0.000	0.000	0.000
37	Q	68	THR	0	-0.045	-0.037	6.852	-0.020	-0.020	0.000	0.000	0.000	0.000
38	Q	69	ILE	0	0.003	0.015	6.646	0.384	0.384	0.000	0.000	0.000	0.000
39	Q	70	SER	0	-0.007	-0.001	8.206	-0.046	-0.046	0.000	0.000	0.000	0.000
40	Q	71	LYS	1	0.829	0.907	9.160	-0.271	-0.271	0.000	0.000	0.000	0.000
41	Q	72	ASP	-1	-0.758	-0.837	10.955	0.099	0.099	0.000	0.000	0.000	0.000
42	Q	73	ASN	0	0.037	-0.001	12.618	-0.078	-0.078	0.000	0.000	0.000	0.000
43	Q	74	SER	0	-0.057	-0.033	15.053	-0.025	-0.025	0.000	0.000	0.000	0.000
44	Q	75	LYS	1	0.852	0.901	10.535	0.117	0.117	0.000	0.000	0.000	0.000
45	Q	76	SER	0	-0.018	0.001	14.027	-0.044	-0.044	0.000	0.000	0.000	0.000
46	Q	77	GLN	0	-0.002	-0.011	9.036	0.020	0.020	0.000	0.000	0.000	0.000
47	Q	78	VAL	0	0.026	0.011	8.816	0.176	0.176	0.000	0.000	0.000	0.000
48	Q	79	PHE	0	-0.041	-0.025	4.224	-0.238	-0.122	-0.001	-0.013	-0.102	0.000
49	Q	80	PHE	0	0.045	0.022	4.228	0.353	0.563	-0.001	-0.032	-0.177	0.000
50	Q	81	LYS	1	0.938	0.973	2.362	-9.958	-6.916	4.564	-3.154	-4.452	0.003
51	Q	93	TYR	0	0.010	0.002	8.402	0.174	0.174	0.000	0.000	0.000	0.000
52	Q	94	TYR	0	-0.023	-0.017	11.007	-0.129	-0.129	0.000	0.000	0.000	0.000
53	Q	96	GLY	0	0.064	0.016	12.410	-0.057	-0.057	0.000	0.000	0.000	0.000
54	Q	97	ARG	1	0.779	0.889	15.862	0.048	0.048	0.000	0.000	0.000	0.000
55	Q	98	PRO	0	-0.021	0.007	17.762	0.002	0.002	0.000	0.000	0.000	0.000
56	Q	99	TYR	0	0.016	-0.005	20.568	-0.013	-0.013	0.000	0.000	0.000	0.000
57	Q	100	TYR	0	-0.020	-0.024	24.290	0.005	0.005	0.000	0.000	0.000	0.000
58	Q	101	GLY	0	0.029	0.021	24.456	0.004	0.004	0.000	0.000	0.000	0.000
59	Q	102	ASN	0	-0.015	-0.017	20.244	-0.016	-0.016	0.000	0.000	0.000	0.000
60	Q	103	VAL	0	-0.017	0.013	21.186	0.004	0.004	0.000	0.000	0.000	0.000
61	Q	104	MET	0	0.001	0.012	15.751	0.010	0.010	0.000	0.000	0.000	0.000
62	Q	105	ASP	-1	-0.738	-0.859	20.829	-0.015	-0.015	0.000	0.000	0.000	0.000
63	Q	106	TYR	0	-0.039	-0.004	20.500	-0.015	-0.015	0.000	0.000	0.000	0.000
64	Q	107	TRP	0	-0.014	-0.017	16.795	0.023	0.023	0.000	0.000	0.000	0.000
65	Q	108	GLY	0	-0.008	0.002	13.498	-0.013	-0.013	0.000	0.000	0.000	0.000
66	Q	1022	SER	0	0.000	-0.032	35.341	0.000	0.000	0.000	0.000	0.000	0.000
67	Q	1023	CYS	0	-0.036	-0.003	34.684	-0.003	-0.003	0.000	0.000	0.000	0.000
68	Q	1024	ARG	1	0.959	0.962	29.845	-0.065	-0.065	0.000	0.000	0.000	0.000
69	Q	1025	ALA	0	0.030	0.020	30.540	0.006	0.006	0.000	0.000	0.000	0.000
70	Q	1026	SER	0	-0.020	-0.017	31.532	-0.006	-0.006	0.000	0.000	0.000	0.000
71	Q	1027	GLN	0	-0.035	-0.016	33.257	-0.003	-0.003	0.000	0.000	0.000	0.000
72	Q	1028	ASP	-1	-0.782	-0.882	33.907	0.063	0.063	0.000	0.000	0.000	0.000
73	Q	1029	ILE	0	-0.094	-0.043	31.449	0.007	0.007	0.000	0.000	0.000	0.000
74	Q	1030	SER	0	0.059	0.049	33.365	-0.003	-0.003	0.000	0.000	0.000	0.000
75	Q	1031	ASN	0	-0.017	-0.026	34.754	-0.002	-0.002	0.000	0.000	0.000	0.000
76	Q	1032	TYR	0	0.000	-0.002	29.306	-0.004	-0.004	0.000	0.000	0.000	0.000
77	Q	1033	LEU	0	0.020	0.013	28.973	0.008	0.008	0.000	0.000	0.000	0.000
78	Q	1034	ASN	0	0.018	0.013	24.995	-0.010	-0.010	0.000	0.000	0.000	0.000
79	Q	1046	LEU	0	-0.034	-0.007	23.238	0.000	0.000	0.000	0.000	0.000	0.000
80	Q	1047	LEU	0	0.002	-0.002	25.164	-0.008	-0.008	0.000	0.000	0.000	0.000
81	Q	1048	ILE	0	0.027	0.003	28.777	-0.001	-0.001	0.000	0.000	0.000	0.000
82	Q	1049	TYR	0	0.005	-0.001	28.012	0.009	0.009	0.000	0.000	0.000	0.000
83	Q	1050	TYR	0	-0.002	-0.002	29.871	-0.005	-0.005	0.000	0.000	0.000	0.000
84	Q	1051	THR	0	-0.046	-0.021	32.093	-0.004	-0.004	0.000	0.000	0.000	0.000
85	Q	1052	SER	0	-0.010	-0.015	33.955	-0.003	-0.003	0.000	0.000	0.000	0.000
86	Q	1053	ARG	1	0.905	0.975	32.566	-0.033	-0.033	0.000	0.000	0.000	0.000
87	Q	1054	LEU	0	0.047	0.029	32.280	0.002	0.002	0.000	0.000	0.000	0.000
88	Q	1055	HIS	0	-0.002	-0.001	24.886	0.007	0.007	0.000	0.000	0.000	0.000
89	Q	1056	SER	0	-0.020	-0.030	28.780	-0.002	-0.002	0.000	0.000	0.000	0.000
90	Q	1057	GLY	0	0.025	0.018	30.985	-0.001	-0.001	0.000	0.000	0.000	0.000
91	Q	1058	VAL	0	-0.072	-0.013	29.694	-0.005	-0.005	0.000	0.000	0.000	0.000
92	Q	1059	PRO	0	0.026	0.017	32.848	0.005	0.005	0.000	0.000	0.000	0.000
93	Q	1060	SER	0	-0.009	-0.006	35.446	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)