FMO DATABASE

FMODB ID: K36J3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-584137.847595
FMO2-HF: Nuclear repulsion	545760.626368
FMO2-HF: Total energy	-38377.221228
FMO2-MP2: Total energy	-38484.60213

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.
-3.03	0.895	0.071	-1.911	-2.087	-0.007

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 : 0.026 / q_NPA : -0.009

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	0.019	0.010	3.062	-3.586	0.287	0.073	-1.900	-2.047	-0.007
4	L	12	CYS	0	-0.071	-0.046	4.540	0.500	0.552	-0.002	-0.011	-0.040	0.000
5	L	13	LYN	0	-0.003	0.018	7.405	-0.051	-0.051	0.000	0.000	0.000	0.000
6	L	14	TYR	0	0.015	0.006	8.881	0.026	0.026	0.000	0.000	0.000	0.000
7	L	15	LYS	1	0.853	0.929	12.246	0.006	0.006	0.000	0.000	0.000	0.000
8	L	16	LYS	1	0.835	0.910	15.790	0.061	0.061	0.000	0.000	0.000	0.000
9	L	17	GLU	-1	-0.892	-0.939	18.466	-0.022	-0.022	0.000	0.000	0.000	0.000
10	L	18	ILE	0	-0.031	-0.023	22.036	-0.010	-0.010	0.000	0.000	0.000	0.000
11	L	19	GLU	-1	-0.844	-0.915	25.457	-0.052	-0.052	0.000	0.000	0.000	0.000
12	L	20	ASP	-1	-0.809	-0.893	27.821	-0.026	-0.026	0.000	0.000	0.000	0.000
13	L	21	LEU	0	0.002	-0.003	29.640	0.000	0.000	0.000	0.000	0.000	0.000
14	L	22	GLY	0	0.023	0.021	33.188	0.000	0.000	0.000	0.000	0.000	0.000
15	L	23	GLU	-1	-0.892	-0.957	36.055	-0.021	-0.021	0.000	0.000	0.000	0.000
16	L	24	ASN	0	-0.049	-0.034	38.383	0.001	0.001	0.000	0.000	0.000	0.000
17	L	25	SER	0	-0.018	-0.013	34.668	-0.002	-0.002	0.000	0.000	0.000	0.000
18	L	26	VAL	0	-0.047	-0.022	35.637	0.001	0.001	0.000	0.000	0.000	0.000
19	L	27	PRO	0	-0.046	-0.015	30.707	0.002	0.002	0.000	0.000	0.000	0.000
20	L	28	ARG	1	0.815	0.897	32.078	0.022	0.022	0.000	0.000	0.000	0.000
21	L	29	PHE	0	0.016	0.003	28.719	-0.001	-0.001	0.000	0.000	0.000	0.000
22	L	30	ILE	0	-0.011	-0.002	25.160	-0.005	-0.005	0.000	0.000	0.000	0.000
23	L	31	GLU	-1	-0.766	-0.845	18.947	-0.104	-0.104	0.000	0.000	0.000	0.000
24	L	32	THR	0	0.004	0.005	20.623	-0.015	-0.015	0.000	0.000	0.000	0.000
25	L	33	ARG	1	0.757	0.846	15.451	0.185	0.185	0.000	0.000	0.000	0.000
26	L	34	ASN	0	0.062	0.051	16.465	-0.049	-0.049	0.000	0.000	0.000	0.000
27	L	35	CYS	0	-0.013	0.002	10.885	0.021	0.021	0.000	0.000	0.000	0.000
28	L	36	GLN	0	-0.077	-0.036	13.189	0.012	0.012	0.000	0.000	0.000	0.000
29	L	37	LYS	1	0.891	0.946	14.785	-0.060	-0.060	0.000	0.000	0.000	0.000
30	L	38	THR	-1	-0.719	-0.870	15.168	0.114	0.114	0.000	0.000	0.000	0.000
31	L	39	GLN	0	-0.011	-0.008	14.779	-0.046	-0.046	0.000	0.000	0.000	0.000
32	L	40	GLN	0	-0.012	-0.003	10.587	-0.016	-0.016	0.000	0.000	0.000	0.000
33	L	41	PRO	0	0.008	0.006	9.482	0.073	0.073	0.000	0.000	0.000	0.000
34	L	42	THR	0	0.008	0.003	5.362	-0.054	-0.054	0.000	0.000	0.000	0.000
35	L	43	CYS	0	-0.028	-0.013	5.908	-0.084	-0.084	0.000	0.000	0.000	0.000
36	L	44	ARG	1	0.957	0.973	7.395	0.163	0.163	0.000	0.000	0.000	0.000
37	L	45	PRO	0	0.059	0.034	10.703	-0.089	-0.089	0.000	0.000	0.000	0.000
38	L	46	PRO	0	-0.003	-0.017	12.604	-0.001	-0.001	0.000	0.000	0.000	0.000
39	L	47	TYR	0	-0.040	-0.007	10.246	0.027	0.027	0.000	0.000	0.000	0.000
40	L	48	ILE	0	0.034	0.009	12.345	0.038	0.038	0.000	0.000	0.000	0.000
41	L	50	LYS	1	0.831	0.911	12.158	0.410	0.410	0.000	0.000	0.000	0.000
42	L	51	GLU	-1	-0.870	-0.959	13.744	-0.188	-0.188	0.000	0.000	0.000	0.000
43	L	52	SER	0	-0.063	-0.035	15.139	0.003	0.003	0.000	0.000	0.000	0.000
44	L	53	LEU	0	0.003	0.000	16.972	0.013	0.013	0.000	0.000	0.000	0.000
45	L	54	TYR	0	-0.024	-0.017	20.106	-0.013	-0.013	0.000	0.000	0.000	0.000
46	L	55	SER	0	0.005	0.004	22.042	0.010	0.010	0.000	0.000	0.000	0.000
47	L	56	ILE	0	-0.012	0.006	24.703	-0.002	-0.002	0.000	0.000	0.000	0.000
48	L	57	THR	0	0.015	0.000	27.387	0.003	0.003	0.000	0.000	0.000	0.000
49	L	58	ILE	0	0.003	0.005	29.290	0.001	0.001	0.000	0.000	0.000	0.000
50	L	59	LEU	0	-0.037	-0.022	33.192	0.002	0.002	0.000	0.000	0.000	0.000
51	L	60	LYS	1	0.951	0.978	35.158	0.052	0.052	0.000	0.000	0.000	0.000
52	L	61	ARG	1	0.899	0.946	38.816	0.028	0.028	0.000	0.000	0.000	0.000
53	L	62	ARG	1	0.858	0.938	42.636	0.027	0.027	0.000	0.000	0.000	0.000
54	L	63	GLU	-1	-0.763	-0.873	43.533	-0.028	-0.028	0.000	0.000	0.000	0.000
55	L	64	THR	0	-0.076	-0.044	46.452	0.001	0.001	0.000	0.000	0.000	0.000
56	L	65	LYS	1	0.797	0.889	46.066	0.038	0.038	0.000	0.000	0.000	0.000
57	L	66	SER	0	0.023	0.022	43.259	0.000	0.000	0.000	0.000	0.000	0.000
58	L	67	GLN	0	-0.012	-0.010	38.362	-0.004	-0.004	0.000	0.000	0.000	0.000
59	L	68	GLU	-1	-0.844	-0.912	41.462	-0.040	-0.040	0.000	0.000	0.000	0.000
60	L	69	SER	0	-0.044	-0.014	40.132	-0.002	-0.002	0.000	0.000	0.000	0.000
61	L	70	LEU	0	0.006	-0.006	33.713	0.000	0.000	0.000	0.000	0.000	0.000
62	L	71	GLU	-1	-0.956	-0.974	37.827	-0.060	-0.060	0.000	0.000	0.000	0.000
63	L	72	ILE	0	0.014	0.001	38.846	-0.002	-0.002	0.000	0.000	0.000	0.000
64	L	73	PRO	0	0.006	0.006	41.087	0.002	0.002	0.000	0.000	0.000	0.000
65	L	74	ASN	0	-0.064	-0.040	44.447	0.002	0.002	0.000	0.000	0.000	0.000
66	L	75	GLU	-1	-0.882	-0.924	46.518	-0.036	-0.036	0.000	0.000	0.000	0.000
67	L	76	LEU	0	-0.024	-0.020	45.852	0.002	0.002	0.000	0.000	0.000	0.000
68	L	77	LYS	1	0.856	0.920	40.561	0.042	0.042	0.000	0.000	0.000	0.000
69	L	78	TYR	0	0.131	0.078	44.796	0.000	0.000	0.000	0.000	0.000	0.000
70	L	79	ARG	1	0.886	0.942	46.369	0.025	0.025	0.000	0.000	0.000	0.000
71	L	80	TRP	0	-0.015	-0.028	40.524	0.001	0.001	0.000	0.000	0.000	0.000
72	L	81	VAL	0	0.044	0.017	39.697	0.000	0.000	0.000	0.000	0.000	0.000
73	L	82	ALA	0	-0.008	0.010	36.462	-0.001	-0.001	0.000	0.000	0.000	0.000
74	L	83	GLU	-1	-0.812	-0.902	34.765	-0.050	-0.050	0.000	0.000	0.000	0.000
75	L	84	SER	0	-0.004	-0.005	30.543	-0.004	-0.004	0.000	0.000	0.000	0.000
76	L	85	HIS	0	0.004	-0.005	28.043	0.003	0.003	0.000	0.000	0.000	0.000
77	L	86	PRO	0	-0.018	0.009	25.218	-0.007	-0.007	0.000	0.000	0.000	0.000
78	L	87	VAL	0	0.042	0.017	22.396	0.007	0.007	0.000	0.000	0.000	0.000
79	L	88	SER	0	0.029	0.003	17.238	-0.027	-0.027	0.000	0.000	0.000	0.000
80	L	89	VAL	0	0.002	0.001	17.137	0.015	0.015	0.000	0.000	0.000	0.000
81	L	90	ALA	0	-0.006	-0.018	12.678	-0.025	-0.025	0.000	0.000	0.000	0.000
82	L	92	LEU	0	0.022	0.025	9.858	-0.153	-0.153	0.000	0.000	0.000	0.000
83	L	94	THR	0	0.034	0.007	10.107	-0.092	-0.092	0.000	0.000	0.000	0.000
84	L	95	ARG	1	0.908	0.943	12.398	0.396	0.396	0.000	0.000	0.000	0.000
85	L	96	ASP	-1	-0.883	-0.916	14.752	-0.308	-0.308	0.000	0.000	0.000	0.000
86	L	97	TYR	0	0.018	0.009	17.452	0.002	0.002	0.000	0.000	0.000	0.000
87	L	98	GLN	0	0.073	0.059	16.894	-0.031	-0.031	0.000	0.000	0.000	0.000

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