FMO DATABASE

FMODB ID: Q13ZY

Calculation Name: 5AOQ-L-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5AOQ

Chain ID: L

ChEMBL ID:

UniProt ID: P17219

Base Structure: X-ray

Registration Date: 2023-06-20

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-584229.325644
FMO2-HF: Nuclear repulsion	545852.648155
FMO2-HF: Total energy	-38376.677489
FMO2-MP2: Total energy	-38484.081137

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(L:9:PRO)

Summations of interaction energy for fragment #1(L:9:PRO)

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.
-2.772	1.462	0.082	-1.981	-2.336	-0.004

Interaction energy analysis for fragmet #1(L:9:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.008

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	L	11	THR	0	0.009	0.002	3.022	-3.241	0.882	0.085	-1.962	-2.247	-0.004
4	L	12	CYS	0	-0.057	-0.040	4.604	0.084	0.139	-0.002	-0.013	-0.040	0.000
5	L	13	LYN	0	0.006	0.015	7.335	0.008	0.008	0.000	0.000	0.000	0.000
6	L	14	TYR	0	0.009	0.003	8.796	0.081	0.081	0.000	0.000	0.000	0.000
7	L	15	LYS	1	0.923	0.968	12.222	0.139	0.139	0.000	0.000	0.000	0.000
8	L	16	LYS	1	0.890	0.947	15.451	0.131	0.131	0.000	0.000	0.000	0.000
9	L	17	GLU	-1	-0.913	-0.969	18.163	-0.095	-0.095	0.000	0.000	0.000	0.000
10	L	18	ILE	0	-0.020	-0.014	21.834	-0.007	-0.007	0.000	0.000	0.000	0.000
11	L	19	GLU	-1	-0.917	-0.950	25.138	-0.091	-0.091	0.000	0.000	0.000	0.000
12	L	20	ASP	-1	-0.844	-0.913	27.580	-0.050	-0.050	0.000	0.000	0.000	0.000
13	L	21	LEU	0	0.007	-0.008	29.349	0.002	0.002	0.000	0.000	0.000	0.000
14	L	22	GLY	0	0.011	0.012	32.928	0.002	0.002	0.000	0.000	0.000	0.000
15	L	23	GLU	-1	-0.944	-0.990	35.628	-0.038	-0.038	0.000	0.000	0.000	0.000
16	L	24	ASN	0	-0.048	-0.029	37.904	0.002	0.002	0.000	0.000	0.000	0.000
17	L	25	SER	0	-0.007	-0.008	34.220	-0.001	-0.001	0.000	0.000	0.000	0.000
18	L	26	VAL	0	-0.044	-0.017	34.774	0.001	0.001	0.000	0.000	0.000	0.000
19	L	27	PRO	0	-0.045	-0.016	30.197	0.002	0.002	0.000	0.000	0.000	0.000
20	L	28	ARG	1	0.888	0.954	31.528	0.043	0.043	0.000	0.000	0.000	0.000
21	L	29	PHE	0	0.031	0.003	28.231	-0.002	-0.002	0.000	0.000	0.000	0.000
22	L	30	ILE	0	-0.017	-0.003	24.581	-0.004	-0.004	0.000	0.000	0.000	0.000
23	L	31	GLU	-1	-0.839	-0.911	18.640	-0.157	-0.157	0.000	0.000	0.000	0.000
24	L	32	THR	0	0.016	0.008	20.470	-0.014	-0.014	0.000	0.000	0.000	0.000
25	L	33	ARG	1	0.760	0.872	14.740	0.255	0.255	0.000	0.000	0.000	0.000
26	L	34	ASN	0	0.082	0.081	16.446	-0.049	-0.049	0.000	0.000	0.000	0.000
27	L	35	CYS	0	-0.017	0.003	10.852	0.016	0.016	0.000	0.000	0.000	0.000
28	L	36	GLN	0	-0.107	-0.050	13.063	-0.026	-0.026	0.000	0.000	0.000	0.000
29	L	37	LYS	1	0.854	0.927	14.609	0.042	0.042	0.000	0.000	0.000	0.000
30	L	38	THR	-1	-0.728	-0.867	14.666	-0.006	-0.006	0.000	0.000	0.000	0.000
31	L	39	GLN	0	0.015	-0.004	14.581	-0.045	-0.045	0.000	0.000	0.000	0.000
32	L	40	GLN	0	-0.040	-0.013	10.615	-0.012	-0.012	0.000	0.000	0.000	0.000
33	L	41	PRO	0	-0.007	-0.012	9.224	0.043	0.043	0.000	0.000	0.000	0.000
34	L	42	THR	0	0.018	0.023	5.136	-0.184	-0.128	-0.001	-0.006	-0.049	0.000
35	L	43	CYS	0	-0.029	-0.011	5.922	-0.017	-0.017	0.000	0.000	0.000	0.000
36	L	44	ARG	1	0.963	0.976	7.313	0.403	0.403	0.000	0.000	0.000	0.000
37	L	45	PRO	0	0.044	0.024	10.742	-0.077	-0.077	0.000	0.000	0.000	0.000
38	L	46	PRO	0	-0.008	-0.016	12.505	0.001	0.001	0.000	0.000	0.000	0.000
39	L	47	TYR	0	-0.028	-0.002	9.996	0.041	0.041	0.000	0.000	0.000	0.000
40	L	48	ILE	0	0.033	0.006	12.247	0.021	0.021	0.000	0.000	0.000	0.000
41	L	50	LYS	1	0.869	0.951	12.105	0.500	0.500	0.000	0.000	0.000	0.000
42	L	51	GLU	-1	-0.864	-0.954	13.787	-0.288	-0.288	0.000	0.000	0.000	0.000
43	L	52	SER	0	-0.055	-0.032	14.806	0.018	0.018	0.000	0.000	0.000	0.000
44	L	53	LEU	0	0.007	0.001	16.726	0.014	0.014	0.000	0.000	0.000	0.000
45	L	54	TYR	0	-0.020	-0.013	19.828	-0.007	-0.007	0.000	0.000	0.000	0.000
46	L	55	SER	0	-0.004	0.003	21.698	0.014	0.014	0.000	0.000	0.000	0.000
47	L	56	ILE	0	-0.018	0.001	24.394	0.001	0.001	0.000	0.000	0.000	0.000
48	L	57	THR	0	0.011	-0.002	27.070	0.006	0.006	0.000	0.000	0.000	0.000
49	L	58	ILE	0	0.005	0.005	29.016	0.001	0.001	0.000	0.000	0.000	0.000
50	L	59	LEU	0	-0.031	-0.021	32.660	0.003	0.003	0.000	0.000	0.000	0.000
51	L	60	LYS	1	0.971	1.004	34.547	0.075	0.075	0.000	0.000	0.000	0.000
52	L	61	ARG	1	0.932	0.960	38.353	0.042	0.042	0.000	0.000	0.000	0.000
53	L	62	ARG	1	0.840	0.929	42.165	0.038	0.038	0.000	0.000	0.000	0.000
54	L	63	GLU	-1	-0.805	-0.886	42.979	-0.044	-0.044	0.000	0.000	0.000	0.000
55	L	64	THR	0	-0.040	-0.034	46.201	0.002	0.002	0.000	0.000	0.000	0.000
56	L	65	LYS	1	0.918	0.961	46.686	0.047	0.047	0.000	0.000	0.000	0.000
57	L	66	SER	0	0.041	0.026	42.895	0.000	0.000	0.000	0.000	0.000	0.000
58	L	67	GLN	0	-0.024	-0.014	38.174	-0.003	-0.003	0.000	0.000	0.000	0.000
59	L	68	GLU	-1	-0.946	-0.974	41.096	-0.055	-0.055	0.000	0.000	0.000	0.000
60	L	69	SER	0	-0.061	-0.026	39.797	-0.002	-0.002	0.000	0.000	0.000	0.000
61	L	70	LEU	0	0.005	-0.001	33.614	0.001	0.001	0.000	0.000	0.000	0.000
62	L	71	GLU	-1	-0.955	-0.972	37.469	-0.070	-0.070	0.000	0.000	0.000	0.000
63	L	72	ILE	0	0.031	0.007	38.575	-0.002	-0.002	0.000	0.000	0.000	0.000
64	L	73	PRO	0	-0.012	0.008	40.824	0.002	0.002	0.000	0.000	0.000	0.000
65	L	74	ASN	0	-0.063	-0.050	44.189	0.003	0.003	0.000	0.000	0.000	0.000
66	L	75	GLU	-1	-0.887	-0.924	46.269	-0.042	-0.042	0.000	0.000	0.000	0.000
67	L	76	LEU	0	-0.024	-0.022	45.167	0.001	0.001	0.000	0.000	0.000	0.000
68	L	77	LYS	1	0.859	0.923	40.155	0.052	0.052	0.000	0.000	0.000	0.000
69	L	78	TYR	0	0.132	0.079	44.559	0.000	0.000	0.000	0.000	0.000	0.000
70	L	79	ARG	1	0.888	0.939	45.874	0.034	0.034	0.000	0.000	0.000	0.000
71	L	80	TRP	0	-0.023	-0.029	39.800	0.001	0.001	0.000	0.000	0.000	0.000
72	L	81	VAL	0	0.038	0.011	39.346	0.001	0.001	0.000	0.000	0.000	0.000
73	L	82	ALA	0	-0.007	0.010	36.104	-0.001	-0.001	0.000	0.000	0.000	0.000
74	L	83	GLU	-1	-0.835	-0.927	34.809	-0.069	-0.069	0.000	0.000	0.000	0.000
75	L	84	SER	0	0.015	0.002	30.141	-0.005	-0.005	0.000	0.000	0.000	0.000
76	L	85	HIS	0	0.040	0.013	27.303	0.006	0.006	0.000	0.000	0.000	0.000
77	L	86	PRO	0	-0.007	0.009	25.138	-0.008	-0.008	0.000	0.000	0.000	0.000
78	L	87	VAL	0	0.028	0.012	22.250	0.005	0.005	0.000	0.000	0.000	0.000
79	L	88	SER	0	0.043	0.006	17.397	-0.028	-0.028	0.000	0.000	0.000	0.000
80	L	89	VAL	0	0.009	0.003	16.669	0.015	0.015	0.000	0.000	0.000	0.000
81	L	90	ALA	0	-0.010	-0.028	12.404	-0.027	-0.027	0.000	0.000	0.000	0.000
82	L	92	LEU	0	0.017	0.022	9.915	-0.185	-0.185	0.000	0.000	0.000	0.000
83	L	94	THR	0	0.036	0.026	9.955	-0.060	-0.060	0.000	0.000	0.000	0.000
84	L	95	ARG	1	0.977	0.973	12.004	0.395	0.395	0.000	0.000	0.000	0.000
85	L	96	ASP	-1	-0.946	-0.966	14.685	-0.311	-0.311	0.000	0.000	0.000	0.000
86	L	97	TYR	0	0.003	0.001	17.272	0.000	0.000	0.000	0.000	0.000	0.000
87	L	98	GLN	0	0.032	0.022	17.070	-0.043	-0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:9:PRO)