FMO DATABASE

FMODB ID: 72ZJK

Calculation Name: 4HG4-X-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: X

ChEMBL ID:

UniProt ID: P03451

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1450372.191152
FMO2-HF: Nuclear repulsion	1388992.162067
FMO2-HF: Total energy	-61380.029085
FMO2-MP2: Total energy	-61559.73946

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(X:2:VAL)

Summations of interaction energy for fragment #1(X:2:VAL)

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.
-11.828	-2.113	4.993	-5.963	-8.746	-0.02

Interaction energy analysis for fragmet #1(X:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / 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

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	X	4	LEU	0	-0.014	-0.020	3.434	-2.642	1.789	0.007	-2.312	-2.126	0.007
4	X	5	VAL	0	0.000	0.003	5.206	0.076	0.102	-0.001	-0.002	-0.024	0.000
5	X	6	GLU	-1	-0.763	-0.878	8.893	-0.635	-0.635	0.000	0.000	0.000	0.000
6	X	7	SER	0	0.006	0.019	11.431	0.027	0.027	0.000	0.000	0.000	0.000
7	X	8	GLY	0	0.005	0.005	15.004	-0.028	-0.028	0.000	0.000	0.000	0.000
8	X	9	ALA	0	-0.020	-0.006	17.976	0.012	0.012	0.000	0.000	0.000	0.000
9	X	10	GLU	-1	-0.878	-0.952	20.614	-0.149	-0.149	0.000	0.000	0.000	0.000
10	X	11	VAL	0	-0.029	-0.016	23.397	-0.003	-0.003	0.000	0.000	0.000	0.000
11	X	12	LYS	1	0.867	0.925	23.824	0.140	0.140	0.000	0.000	0.000	0.000
12	X	13	LYS	1	0.976	0.994	28.421	0.082	0.082	0.000	0.000	0.000	0.000
13	X	14	PRO	0	0.032	0.023	31.524	0.002	0.002	0.000	0.000	0.000	0.000
14	X	15	GLY	0	0.028	0.027	31.520	0.007	0.007	0.000	0.000	0.000	0.000
15	X	16	SER	0	-0.111	-0.069	29.391	0.002	0.002	0.000	0.000	0.000	0.000
16	X	17	SER	0	0.065	0.011	26.028	0.000	0.000	0.000	0.000	0.000	0.000
17	X	18	VAL	0	-0.066	-0.024	20.965	-0.001	-0.001	0.000	0.000	0.000	0.000
18	X	19	LYS	1	0.872	0.930	18.574	0.066	0.066	0.000	0.000	0.000	0.000
19	X	20	VAL	0	0.013	0.032	14.452	-0.004	-0.004	0.000	0.000	0.000	0.000
20	X	21	SER	0	-0.003	-0.014	13.583	0.021	0.021	0.000	0.000	0.000	0.000
21	X	22	CYS	0	-0.024	-0.010	8.419	-0.005	-0.005	0.000	0.000	0.000	0.000
22	X	23	LYS	1	0.899	0.965	7.994	0.217	0.217	0.000	0.000	0.000	0.000
23	X	24	ALA	0	0.044	0.029	3.263	-0.641	-0.362	0.038	-0.067	-0.249	0.000
24	X	25	SER	0	-0.024	0.007	4.348	0.228	0.522	0.000	-0.052	-0.242	0.000
25	X	26	GLY	0	0.049	0.001	2.064	-3.543	-1.584	3.695	-3.313	-2.342	-0.019
26	X	27	GLY	0	0.013	0.014	2.779	-0.020	0.244	0.555	0.450	-1.269	-0.005
27	X	28	THR	0	0.017	0.000	3.711	-0.858	-0.824	0.007	0.039	-0.080	0.000
28	X	29	PHE	0	0.087	0.037	6.858	0.174	0.174	0.000	0.000	0.000	0.000
29	X	30	ILE	0	0.057	0.015	8.346	-0.043	-0.043	0.000	0.000	0.000	0.000
30	X	31	THR	0	-0.082	-0.044	5.214	-0.003	-0.003	0.000	0.000	0.000	0.000
31	X	32	HIS	0	-0.037	0.006	3.119	-0.709	-0.064	0.067	-0.218	-0.494	0.000
32	X	33	VAL	0	0.029	0.016	6.298	-0.084	-0.084	0.000	0.000	0.000	0.000
33	X	34	PHE	0	-0.016	-0.003	7.270	-0.095	-0.095	0.000	0.000	0.000	0.000
34	X	35	THR	0	-0.013	-0.011	9.279	0.053	0.053	0.000	0.000	0.000	0.000
35	X	36	TRP	0	0.008	0.000	11.336	-0.071	-0.071	0.000	0.000	0.000	0.000
36	X	37	VAL	0	-0.009	-0.003	14.005	0.051	0.051	0.000	0.000	0.000	0.000
37	X	38	ARG	1	0.785	0.855	16.007	0.131	0.131	0.000	0.000	0.000	0.000
38	X	39	GLN	0	0.009	0.009	18.767	-0.023	-0.023	0.000	0.000	0.000	0.000
39	X	40	ALA	0	0.047	0.033	20.970	-0.005	-0.005	0.000	0.000	0.000	0.000
40	X	41	PRO	0	0.031	0.001	24.520	-0.007	-0.007	0.000	0.000	0.000	0.000
41	X	42	GLY	0	-0.035	-0.011	26.087	0.017	0.017	0.000	0.000	0.000	0.000
42	X	43	GLN	0	-0.014	0.000	26.067	0.010	0.010	0.000	0.000	0.000	0.000
43	X	44	GLY	0	0.029	0.014	23.251	-0.020	-0.020	0.000	0.000	0.000	0.000
44	X	45	LEU	0	-0.044	-0.024	17.631	0.000	0.000	0.000	0.000	0.000	0.000
45	X	46	GLU	-1	-0.797	-0.861	20.414	-0.139	-0.139	0.000	0.000	0.000	0.000
46	X	47	TRP	0	-0.046	-0.020	15.069	-0.010	-0.010	0.000	0.000	0.000	0.000
47	X	48	VAL	0	-0.013	-0.003	17.370	0.021	0.021	0.000	0.000	0.000	0.000
48	X	49	GLY	0	0.016	-0.013	16.962	0.030	0.030	0.000	0.000	0.000	0.000
49	X	50	GLY	0	0.020	0.009	13.624	-0.036	-0.036	0.000	0.000	0.000	0.000
50	X	51	PHE	0	0.002	0.008	11.304	0.020	0.020	0.000	0.000	0.000	0.000
51	X	52	ILE	0	-0.004	0.013	11.523	0.017	0.017	0.000	0.000	0.000	0.000
52	X	52	ALA	0	0.014	0.011	9.943	-0.010	-0.010	0.000	0.000	0.000	0.000
53	X	53	ILE	0	-0.047	-0.021	11.836	-0.005	-0.005	0.000	0.000	0.000	0.000
54	X	54	PHE	0	-0.027	-0.021	13.768	-0.013	-0.013	0.000	0.000	0.000	0.000
55	X	55	GLY	0	0.023	0.024	15.245	-0.018	-0.018	0.000	0.000	0.000	0.000
56	X	56	THR	0	-0.014	0.001	16.624	-0.023	-0.023	0.000	0.000	0.000	0.000
57	X	57	SER	0	-0.002	-0.009	16.099	0.010	0.010	0.000	0.000	0.000	0.000
58	X	58	ASN	0	-0.039	0.003	17.073	0.014	0.014	0.000	0.000	0.000	0.000
59	X	59	TYR	0	0.090	0.037	18.184	-0.018	-0.018	0.000	0.000	0.000	0.000
60	X	60	ALA	0	0.069	0.034	20.923	0.009	0.009	0.000	0.000	0.000	0.000
61	X	61	GLN	0	-0.045	-0.019	23.020	-0.007	-0.007	0.000	0.000	0.000	0.000
62	X	62	LYS	1	0.982	0.991	26.636	0.064	0.064	0.000	0.000	0.000	0.000
63	X	63	PHE	0	0.007	-0.006	22.563	-0.008	-0.008	0.000	0.000	0.000	0.000
64	X	64	GLN	0	0.037	-0.004	26.281	-0.001	-0.001	0.000	0.000	0.000	0.000
65	X	65	GLY	0	0.004	0.009	27.057	0.000	0.000	0.000	0.000	0.000	0.000
66	X	66	ARG	1	0.761	0.862	26.157	0.100	0.100	0.000	0.000	0.000	0.000
67	X	67	VAL	0	0.008	-0.007	20.238	-0.004	-0.004	0.000	0.000	0.000	0.000
68	X	68	THR	0	-0.014	-0.007	21.797	0.013	0.013	0.000	0.000	0.000	0.000
69	X	69	ILE	0	-0.038	-0.017	15.396	-0.008	-0.008	0.000	0.000	0.000	0.000
70	X	70	THR	0	-0.018	-0.012	16.699	0.018	0.018	0.000	0.000	0.000	0.000
71	X	71	ALA	0	-0.005	-0.002	12.754	-0.019	-0.019	0.000	0.000	0.000	0.000
72	X	72	ASP	-1	-0.743	-0.819	13.683	0.152	0.152	0.000	0.000	0.000	0.000
73	X	73	GLU	-1	-0.948	-0.977	11.830	0.385	0.385	0.000	0.000	0.000	0.000
74	X	74	SER	0	-0.087	-0.049	12.112	0.060	0.060	0.000	0.000	0.000	0.000
75	X	75	THR	0	-0.085	-0.064	12.340	-0.003	-0.003	0.000	0.000	0.000	0.000
76	X	76	SER	0	-0.018	0.004	6.501	0.046	0.046	0.000	0.000	0.000	0.000
77	X	77	THR	0	-0.011	-0.032	8.286	-0.099	-0.099	0.000	0.000	0.000	0.000
78	X	78	ALA	0	-0.007	0.004	10.748	0.051	0.051	0.000	0.000	0.000	0.000
79	X	79	TYR	0	-0.034	-0.034	12.259	-0.080	-0.080	0.000	0.000	0.000	0.000
80	X	80	MET	0	0.016	0.022	15.330	0.034	0.034	0.000	0.000	0.000	0.000
81	X	81	GLU	-1	-0.860	-0.912	17.202	-0.080	-0.080	0.000	0.000	0.000	0.000
82	X	82	LEU	0	0.030	0.018	20.846	0.008	0.008	0.000	0.000	0.000	0.000
83	X	82	THR	0	0.007	-0.012	23.329	-0.005	-0.005	0.000	0.000	0.000	0.000
84	X	82	SER	0	0.015	0.013	27.016	-0.001	-0.001	0.000	0.000	0.000	0.000
85	X	82	LEU	0	-0.077	-0.007	24.915	-0.002	-0.002	0.000	0.000	0.000	0.000
86	X	83	THR	0	0.062	0.018	29.012	0.006	0.006	0.000	0.000	0.000	0.000
87	X	84	SER	0	0.057	0.005	29.631	-0.004	-0.004	0.000	0.000	0.000	0.000
88	X	85	GLU	-1	-0.954	-0.974	29.155	-0.115	-0.115	0.000	0.000	0.000	0.000
89	X	86	ASP	-1	-0.744	-0.811	25.072	-0.127	-0.127	0.000	0.000	0.000	0.000
90	X	87	THR	0	-0.036	-0.008	24.237	-0.016	-0.016	0.000	0.000	0.000	0.000
91	X	88	ALA	0	0.002	0.000	21.503	0.004	0.004	0.000	0.000	0.000	0.000
92	X	89	VAL	0	-0.038	-0.007	16.855	0.002	0.002	0.000	0.000	0.000	0.000
93	X	90	TYR	0	-0.038	-0.064	16.502	0.019	0.019	0.000	0.000	0.000	0.000
94	X	91	TYR	0	-0.016	-0.008	12.653	-0.030	-0.030	0.000	0.000	0.000	0.000
95	X	93	ALA	0	0.036	0.002	7.783	-0.198	-0.198	0.000	0.000	0.000	0.000
96	X	94	ARG	1	0.934	0.966	2.750	-2.459	-1.129	0.602	-0.386	-1.546	-0.002
97	X	95	GLY	0	0.033	0.021	6.455	-0.101	-0.101	0.000	0.000	0.000	0.000
98	X	96	ILE	0	-0.005	0.007	7.785	0.148	0.148	0.000	0.000	0.000	0.000
99	X	97	SER	0	0.046	0.004	9.804	-0.068	-0.068	0.000	0.000	0.000	0.000
100	X	98	GLY	0	0.061	0.017	12.637	-0.018	-0.018	0.000	0.000	0.000	0.000
101	X	99	SER	0	-0.048	-0.031	15.136	-0.015	-0.015	0.000	0.000	0.000	0.000
102	X	100	TYR	0	-0.069	-0.047	12.337	-0.031	-0.031	0.000	0.000	0.000	0.000
103	X	100	GLY	0	-0.056	-0.022	12.099	-0.019	-0.019	0.000	0.000	0.000	0.000
104	X	100	TRP	0	0.035	0.027	9.781	0.031	0.031	0.000	0.000	0.000	0.000
105	X	100	PHE	0	-0.018	-0.038	9.609	0.040	0.040	0.000	0.000	0.000	0.000
106	X	101	ASP	-1	-0.928	-0.959	5.877	-1.454	-1.454	0.000	0.000	0.000	0.000
107	X	102	PRO	0	-0.005	0.022	3.401	-0.651	-0.198	0.023	-0.102	-0.374	-0.001
108	X	103	TRP	0	-0.026	-0.033	6.208	0.470	0.470	0.000	0.000	0.000	0.000
109	X	104	GLY	0	-0.009	-0.003	8.779	-0.223	-0.223	0.000	0.000	0.000	0.000
110	X	105	GLN	0	-0.027	-0.028	9.285	0.099	0.099	0.000	0.000	0.000	0.000
111	X	106	GLY	0	0.010	-0.003	12.847	0.094	0.094	0.000	0.000	0.000	0.000
112	X	107	THR	0	-0.042	-0.009	14.772	-0.002	-0.002	0.000	0.000	0.000	0.000
113	X	108	LEU	0	-0.020	-0.006	16.896	0.022	0.022	0.000	0.000	0.000	0.000
114	X	109	VAL	0	0.006	0.003	20.181	0.017	0.017	0.000	0.000	0.000	0.000
115	X	110	THR	0	-0.010	-0.002	22.672	0.009	0.009	0.000	0.000	0.000	0.000
116	X	111	VAL	0	-0.008	-0.006	26.294	0.006	0.006	0.000	0.000	0.000	0.000
117	X	112	SER	0	-0.009	-0.020	28.646	0.005	0.005	0.000	0.000	0.000	0.000
118	X	113	SER	0	0.021	0.003	32.331	0.001	0.001	0.000	0.000	0.000	0.000
119	X	114	ALA	0	-0.020	0.014	34.623	0.004	0.004	0.000	0.000	0.000	0.000
120	X	115	SER	0	0.049	0.015	32.919	-0.002	-0.002	0.000	0.000	0.000	0.000
121	X	116	THR	0	0.014	0.001	29.890	0.001	0.001	0.000	0.000	0.000	0.000
122	X	117	LYS	1	0.873	0.930	32.689	0.112	0.112	0.000	0.000	0.000	0.000
123	X	118	GLY	0	-0.013	0.006	34.490	-0.008	-0.008	0.000	0.000	0.000	0.000
124	X	119	PRO	0	0.000	0.016	34.684	0.002	0.002	0.000	0.000	0.000	0.000
125	X	120	SER	0	-0.002	0.006	37.218	0.004	0.004	0.000	0.000	0.000	0.000
126	X	141	LEU	0	-0.030	-0.032	39.970	-0.002	-0.002	0.000	0.000	0.000	0.000
127	X	142	VAL	0	-0.019	0.001	35.106	0.003	0.003	0.000	0.000	0.000	0.000
128	X	143	LYS	1	0.913	0.954	37.517	0.099	0.099	0.000	0.000	0.000	0.000
129	X	144	ASP	-1	-0.774	-0.913	37.661	-0.102	-0.102	0.000	0.000	0.000	0.000
130	X	145	TYR	0	0.010	0.017	30.720	0.004	0.004	0.000	0.000	0.000	0.000
131	X	146	PHE	0	0.029	0.020	30.494	-0.003	-0.003	0.000	0.000	0.000	0.000
132	X	147	PRO	0	-0.040	-0.035	26.668	0.006	0.006	0.000	0.000	0.000	0.000
133	X	148	GLU	-1	-0.839	-0.974	27.632	-0.209	-0.209	0.000	0.000	0.000	0.000
134	X	149	PRO	0	-0.026	0.037	23.689	-0.013	-0.013	0.000	0.000	0.000	0.000
135	X	150	VAL	0	-0.026	-0.022	25.812	0.021	0.021	0.000	0.000	0.000	0.000
136	X	165	THR	0	-0.033	-0.021	31.640	-0.003	-0.003	0.000	0.000	0.000	0.000
137	X	166	PHE	0	-0.005	-0.023	32.572	0.005	0.005	0.000	0.000	0.000	0.000
138	X	167	PRO	0	0.023	0.035	29.705	-0.010	-0.010	0.000	0.000	0.000	0.000
139	X	168	ALA	0	0.000	0.003	30.474	0.012	0.012	0.000	0.000	0.000	0.000
140	X	169	VAL	0	-0.006	-0.012	32.154	-0.002	-0.002	0.000	0.000	0.000	0.000
141	X	170	LEU	0	-0.001	-0.001	31.719	0.004	0.004	0.000	0.000	0.000	0.000
142	X	171	GLN	0	-0.047	-0.029	34.854	0.007	0.007	0.000	0.000	0.000	0.000
143	X	172	SER	0	0.045	0.013	38.159	-0.002	-0.002	0.000	0.000	0.000	0.000
144	X	173	SER	0	-0.029	-0.024	40.224	0.000	0.000	0.000	0.000	0.000	0.000
145	X	174	GLY	0	0.020	0.013	36.322	0.001	0.001	0.000	0.000	0.000	0.000
146	X	175	LEU	0	-0.087	-0.034	35.041	-0.007	-0.007	0.000	0.000	0.000	0.000
147	X	176	TYR	0	0.017	0.017	28.812	0.006	0.006	0.000	0.000	0.000	0.000
148	X	177	SER	0	0.005	0.002	34.343	0.008	0.008	0.000	0.000	0.000	0.000
149	X	178	LEU	0	0.009	0.029	31.586	-0.003	-0.003	0.000	0.000	0.000	0.000
150	X	179	SER	0	0.005	-0.023	35.144	0.009	0.009	0.000	0.000	0.000	0.000
151	X	180	SER	0	0.031	0.040	35.823	-0.003	-0.003	0.000	0.000	0.000	0.000
152	X	196	CYS	0	-0.006	-0.014	33.312	-0.003	-0.003	0.000	0.000	0.000	0.000
153	X	197	ASN	0	-0.026	0.003	34.021	0.000	0.000	0.000	0.000	0.000	0.000
154	X	198	VAL	0	0.053	0.021	33.898	-0.010	-0.010	0.000	0.000	0.000	0.000
155	X	199	ASN	0	0.052	0.021	29.239	0.011	0.011	0.000	0.000	0.000	0.000
156	X	200	HIS	1	0.913	0.976	29.911	0.145	0.145	0.000	0.000	0.000	0.000
157	X	201	LYS	1	0.995	0.983	23.315	0.277	0.277	0.000	0.000	0.000	0.000
158	X	202	PRO	0	0.031	0.034	26.364	0.002	0.002	0.000	0.000	0.000	0.000
159	X	203	SER	0	-0.018	-0.012	28.068	0.004	0.004	0.000	0.000	0.000	0.000
160	X	204	ASN	0	-0.060	-0.033	29.254	0.006	0.006	0.000	0.000	0.000	0.000
161	X	205	THR	0	0.027	0.023	31.599	0.007	0.007	0.000	0.000	0.000	0.000
162	X	206	LYS	1	0.901	0.939	29.912	0.158	0.158	0.000	0.000	0.000	0.000
163	X	207	VAL	0	0.051	0.032	34.977	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:2:VAL)