FMO DATABASE

FMODB ID: 4345N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-585226.330857
FMO2-HF: Nuclear repulsion	546848.733443
FMO2-HF: Total energy	-38377.597415
FMO2-MP2: Total energy	-38484.992978

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.
-6.403	-2.512	1.809	-2.487	-3.212	-0.019

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 : 0.013 / q_NPA : -0.011

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	0.028	0.012	2.317	-6.368	-2.712	1.812	-2.456	-3.012	-0.019
4	L	12	CYS	0	-0.069	-0.039	4.187	1.303	1.429	-0.002	-0.020	-0.104	0.000
5	L	13	LYN	0	0.026	0.027	7.097	-0.162	-0.162	0.000	0.000	0.000	0.000
6	L	14	TYR	0	-0.004	-0.013	8.801	-0.100	-0.100	0.000	0.000	0.000	0.000
7	L	15	LYS	1	0.830	0.917	12.172	-0.176	-0.176	0.000	0.000	0.000	0.000
8	L	16	LYS	1	0.844	0.910	15.773	-0.042	-0.042	0.000	0.000	0.000	0.000
9	L	17	GLU	-1	-0.891	-0.941	18.205	0.083	0.083	0.000	0.000	0.000	0.000
10	L	18	ILE	0	-0.036	-0.028	21.658	-0.012	-0.012	0.000	0.000	0.000	0.000
11	L	19	GLU	-1	-0.771	-0.878	24.974	0.000	0.000	0.000	0.000	0.000	0.000
12	L	20	ASP	-1	-0.808	-0.906	27.276	0.008	0.008	0.000	0.000	0.000	0.000
13	L	21	LEU	0	-0.024	-0.012	29.374	-0.003	-0.003	0.000	0.000	0.000	0.000
14	L	22	GLY	0	0.034	0.041	32.793	-0.002	-0.002	0.000	0.000	0.000	0.000
15	L	23	GLU	-1	-0.888	-0.946	36.085	0.002	0.002	0.000	0.000	0.000	0.000
16	L	24	ASN	0	-0.044	-0.032	38.166	-0.001	-0.001	0.000	0.000	0.000	0.000
17	L	25	SER	0	-0.040	-0.030	34.308	-0.004	-0.004	0.000	0.000	0.000	0.000
18	L	26	VAL	0	-0.021	-0.014	35.708	0.001	0.001	0.000	0.000	0.000	0.000
19	L	27	PRO	0	-0.047	-0.016	30.590	0.001	0.001	0.000	0.000	0.000	0.000
20	L	28	ARG	1	0.799	0.877	31.565	-0.007	-0.007	0.000	0.000	0.000	0.000
21	L	29	PHE	0	-0.004	-0.001	28.468	0.000	0.000	0.000	0.000	0.000	0.000
22	L	30	ILE	0	-0.015	0.004	24.463	-0.006	-0.006	0.000	0.000	0.000	0.000
23	L	31	GLU	-1	-0.768	-0.845	18.607	-0.020	-0.020	0.000	0.000	0.000	0.000
24	L	32	THR	0	-0.008	0.006	20.257	-0.016	-0.016	0.000	0.000	0.000	0.000
25	L	33	ARG	1	0.747	0.834	15.070	0.103	0.103	0.000	0.000	0.000	0.000
26	L	34	ASN	0	0.087	0.062	15.617	-0.046	-0.046	0.000	0.000	0.000	0.000
27	L	35	CYS	0	-0.042	0.006	10.373	0.040	0.040	0.000	0.000	0.000	0.000
28	L	36	GLN	0	-0.089	-0.055	12.624	0.057	0.057	0.000	0.000	0.000	0.000
29	L	37	LYS	1	0.897	0.956	14.455	-0.187	-0.187	0.000	0.000	0.000	0.000
30	L	38	THR	-1	-0.712	-0.862	14.901	0.296	0.296	0.000	0.000	0.000	0.000
31	L	39	GLN	0	-0.018	-0.010	14.913	-0.054	-0.054	0.000	0.000	0.000	0.000
32	L	40	GLN	0	-0.003	-0.001	10.649	-0.031	-0.031	0.000	0.000	0.000	0.000
33	L	41	PRO	0	0.014	0.024	9.821	0.214	0.214	0.000	0.000	0.000	0.000
34	L	42	THR	0	0.039	0.016	4.738	-0.941	-0.832	-0.001	-0.011	-0.096	0.000
35	L	43	CYS	0	-0.047	-0.033	5.610	-0.285	-0.285	0.000	0.000	0.000	0.000
36	L	44	ARG	1	0.949	0.972	7.064	-0.118	-0.118	0.000	0.000	0.000	0.000
37	L	45	PRO	0	0.057	0.023	10.277	-0.110	-0.110	0.000	0.000	0.000	0.000
38	L	46	PRO	0	-0.002	-0.010	12.835	0.001	0.001	0.000	0.000	0.000	0.000
39	L	47	TYR	0	-0.045	-0.010	9.869	-0.013	-0.013	0.000	0.000	0.000	0.000
40	L	48	ILE	0	0.035	0.012	11.861	0.083	0.083	0.000	0.000	0.000	0.000
41	L	50	LYS	1	0.824	0.899	11.715	0.272	0.272	0.000	0.000	0.000	0.000
42	L	51	GLU	-1	-0.844	-0.944	13.416	-0.058	-0.058	0.000	0.000	0.000	0.000
43	L	52	SER	0	-0.045	-0.019	14.506	-0.020	-0.020	0.000	0.000	0.000	0.000
44	L	53	LEU	0	-0.015	-0.012	16.343	0.011	0.011	0.000	0.000	0.000	0.000
45	L	54	TYR	0	-0.027	-0.014	19.801	-0.021	-0.021	0.000	0.000	0.000	0.000
46	L	55	SER	0	0.001	0.001	21.711	0.013	0.013	0.000	0.000	0.000	0.000
47	L	56	ILE	0	-0.008	0.008	24.379	-0.006	-0.006	0.000	0.000	0.000	0.000
48	L	57	THR	0	0.012	0.003	27.078	0.004	0.004	0.000	0.000	0.000	0.000
49	L	58	ILE	0	0.001	0.005	28.875	0.001	0.001	0.000	0.000	0.000	0.000
50	L	59	LEU	0	-0.033	-0.017	32.729	0.000	0.000	0.000	0.000	0.000	0.000
51	L	60	LYS	1	0.926	0.963	35.063	0.022	0.022	0.000	0.000	0.000	0.000
52	L	61	ARG	1	0.893	0.947	38.468	0.009	0.009	0.000	0.000	0.000	0.000
53	L	62	ARG	1	0.871	0.931	42.320	0.013	0.013	0.000	0.000	0.000	0.000
54	L	63	GLU	-1	-0.728	-0.846	43.288	-0.009	-0.009	0.000	0.000	0.000	0.000
55	L	64	THR	0	-0.102	-0.055	45.911	-0.001	-0.001	0.000	0.000	0.000	0.000
56	L	65	LYS	1	0.765	0.854	45.343	0.024	0.024	0.000	0.000	0.000	0.000
57	L	66	SER	0	-0.002	0.004	42.538	0.000	0.000	0.000	0.000	0.000	0.000
58	L	67	GLN	0	0.017	0.004	37.645	-0.003	-0.003	0.000	0.000	0.000	0.000
59	L	68	GLU	-1	-0.819	-0.878	41.094	-0.026	-0.026	0.000	0.000	0.000	0.000
60	L	69	SER	0	-0.030	-0.010	39.580	-0.001	-0.001	0.000	0.000	0.000	0.000
61	L	70	LEU	0	-0.007	-0.019	33.399	-0.001	-0.001	0.000	0.000	0.000	0.000
62	L	71	GLU	-1	-0.927	-0.948	37.743	-0.047	-0.047	0.000	0.000	0.000	0.000
63	L	72	ILE	0	-0.034	-0.020	39.464	-0.001	-0.001	0.000	0.000	0.000	0.000
64	L	73	PRO	0	0.055	0.025	40.915	0.002	0.002	0.000	0.000	0.000	0.000
65	L	74	ASN	0	-0.052	-0.029	44.188	0.002	0.002	0.000	0.000	0.000	0.000
66	L	75	GLU	-1	-0.940	-0.965	46.713	-0.028	-0.028	0.000	0.000	0.000	0.000
67	L	76	LEU	0	-0.007	-0.018	46.106	0.002	0.002	0.000	0.000	0.000	0.000
68	L	77	LYS	1	0.800	0.898	40.198	0.028	0.028	0.000	0.000	0.000	0.000
69	L	78	TYR	0	0.136	0.091	44.164	0.000	0.000	0.000	0.000	0.000	0.000
70	L	79	ARG	1	0.897	0.945	46.050	0.013	0.013	0.000	0.000	0.000	0.000
71	L	80	TRP	0	-0.005	-0.026	40.565	0.002	0.002	0.000	0.000	0.000	0.000
72	L	81	VAL	0	0.044	0.025	39.730	-0.001	-0.001	0.000	0.000	0.000	0.000
73	L	82	ALA	0	-0.007	0.005	36.603	0.000	0.000	0.000	0.000	0.000	0.000
74	L	83	GLU	-1	-0.778	-0.882	34.229	-0.023	-0.023	0.000	0.000	0.000	0.000
75	L	84	SER	0	-0.015	-0.018	30.141	-0.004	-0.004	0.000	0.000	0.000	0.000
76	L	85	HIS	0	-0.001	-0.009	28.063	-0.001	-0.001	0.000	0.000	0.000	0.000
77	L	86	PRO	0	-0.020	0.005	24.644	-0.006	-0.006	0.000	0.000	0.000	0.000
78	L	87	VAL	0	0.049	0.023	22.004	0.009	0.009	0.000	0.000	0.000	0.000
79	L	88	SER	0	0.017	-0.002	16.396	-0.029	-0.029	0.000	0.000	0.000	0.000
80	L	89	VAL	0	0.021	0.008	16.812	0.015	0.015	0.000	0.000	0.000	0.000
81	L	90	ALA	0	-0.006	-0.013	11.994	-0.019	-0.019	0.000	0.000	0.000	0.000
82	L	92	LEU	0	0.024	0.022	9.289	-0.119	-0.119	0.000	0.000	0.000	0.000
83	L	94	THR	0	0.022	-0.002	9.762	-0.041	-0.041	0.000	0.000	0.000	0.000
84	L	95	ARG	1	0.904	0.937	12.055	0.393	0.393	0.000	0.000	0.000	0.000
85	L	96	ASP	-1	-0.849	-0.894	14.380	-0.277	-0.277	0.000	0.000	0.000	0.000
86	L	97	TYR	0	0.017	-0.002	17.201	0.005	0.005	0.000	0.000	0.000	0.000
87	L	98	GLN	0	0.048	0.054	16.225	0.011	0.011	0.000	0.000	0.000	0.000

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