FMO DATABASE

FMODB ID: QY48Y

Calculation Name: 4HG4-P-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: P

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:

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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1418476.762948
FMO2-HF: Nuclear repulsion	1357138.255365
FMO2-HF: Total energy	-61338.507584
FMO2-MP2: Total energy	-61519.105545

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(P:1:GLU)

Summations of interaction energy for fragment #1(P:1:GLU)

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.
-5.58	-0.90999999999999	3.456	-3.261	-4.865	0.007

Interaction energy analysis for fragmet #1(P:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.951 / q_NPA : -0.985

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	P	3	GLN	0	-0.002	0.013	3.823	-9.107	-7.262	-0.022	-0.755	-1.068	0.001
4	P	4	LEU	0	0.008	-0.017	6.483	-0.148	-0.148	0.000	0.000	0.000	0.000
5	P	5	VAL	0	-0.037	-0.009	10.211	-1.102	-1.102	0.000	0.000	0.000	0.000
6	P	6	GLU	-1	-0.802	-0.912	13.048	16.811	16.811	0.000	0.000	0.000	0.000
7	P	7	SER	0	-0.059	-0.011	16.395	-0.291	-0.291	0.000	0.000	0.000	0.000
8	P	8	GLY	0	0.041	0.027	19.924	0.023	0.023	0.000	0.000	0.000	0.000
9	P	9	ALA	0	0.004	-0.002	22.311	-0.235	-0.235	0.000	0.000	0.000	0.000
10	P	10	GLU	-1	-0.870	-0.927	24.692	11.016	11.016	0.000	0.000	0.000	0.000
11	P	11	VAL	0	-0.009	-0.015	27.980	-0.124	-0.124	0.000	0.000	0.000	0.000
12	P	12	LYS	1	0.828	0.930	30.049	-10.412	-10.412	0.000	0.000	0.000	0.000
13	P	13	LYS	1	0.884	0.940	33.952	-8.111	-8.111	0.000	0.000	0.000	0.000
14	P	14	PRO	0	0.012	0.026	37.168	0.135	0.135	0.000	0.000	0.000	0.000
15	P	15	GLY	0	0.061	0.051	37.595	-0.229	-0.229	0.000	0.000	0.000	0.000
16	P	16	SER	0	-0.114	-0.087	35.194	0.082	0.082	0.000	0.000	0.000	0.000
17	P	17	SER	0	-0.016	-0.030	31.816	0.066	0.066	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.011	0.003	27.271	-0.090	-0.090	0.000	0.000	0.000	0.000
19	P	19	LYS	1	0.972	0.991	24.360	-12.213	-12.213	0.000	0.000	0.000	0.000
20	P	20	VAL	0	0.012	0.030	21.544	0.091	0.091	0.000	0.000	0.000	0.000
21	P	21	SER	0	-0.029	-0.034	18.185	0.329	0.329	0.000	0.000	0.000	0.000
22	P	22	CYS	0	0.018	0.019	14.225	0.503	0.503	0.000	0.000	0.000	0.000
23	P	23	LYS	1	0.901	0.974	11.620	-24.742	-24.742	0.000	0.000	0.000	0.000
24	P	24	ALA	0	0.043	0.034	8.548	0.862	0.862	0.000	0.000	0.000	0.000
25	P	25	SER	0	-0.047	-0.033	6.884	-1.785	-1.785	0.000	0.000	0.000	0.000
26	P	26	GLY	0	0.060	0.035	3.002	-4.337	-2.154	0.387	-1.510	-1.060	0.012
27	P	27	GLY	0	-0.013	0.005	2.657	10.180	10.682	3.092	-0.990	-2.604	-0.006
28	P	28	THR	0	-0.009	-0.004	5.059	-5.561	-5.421	-0.001	-0.006	-0.133	0.000
29	P	29	PHE	0	0.112	0.037	8.232	-0.346	-0.346	0.000	0.000	0.000	0.000
30	P	30	ILE	0	0.036	0.012	11.215	-0.669	-0.669	0.000	0.000	0.000	0.000
31	P	31	THR	0	-0.072	-0.034	8.372	-0.128	-0.128	0.000	0.000	0.000	0.000
32	P	32	HIS	0	0.003	0.012	6.529	-1.117	-1.117	0.000	0.000	0.000	0.000
33	P	33	VAL	0	0.006	0.001	11.059	-1.539	-1.539	0.000	0.000	0.000	0.000
34	P	34	PHE	0	0.011	0.016	12.578	0.585	0.585	0.000	0.000	0.000	0.000
35	P	35	THR	0	0.042	0.022	15.323	-1.387	-1.387	0.000	0.000	0.000	0.000
36	P	36	TRP	0	-0.001	0.004	17.480	0.556	0.556	0.000	0.000	0.000	0.000
37	P	37	VAL	0	-0.015	0.008	19.601	-0.763	-0.763	0.000	0.000	0.000	0.000
38	P	38	ARG	1	0.819	0.925	21.523	-10.074	-10.074	0.000	0.000	0.000	0.000
39	P	39	GLN	0	-0.016	-0.010	24.113	0.251	0.251	0.000	0.000	0.000	0.000
40	P	40	ALA	0	0.018	0.015	26.143	-0.042	-0.042	0.000	0.000	0.000	0.000
41	P	41	PRO	0	0.040	0.008	28.886	0.069	0.069	0.000	0.000	0.000	0.000
42	P	42	GLY	0	-0.025	-0.001	29.189	-0.334	-0.334	0.000	0.000	0.000	0.000
43	P	43	GLN	0	-0.018	-0.008	30.791	-0.208	-0.208	0.000	0.000	0.000	0.000
44	P	44	GLY	0	0.017	0.000	27.903	0.280	0.280	0.000	0.000	0.000	0.000
45	P	45	LEU	0	-0.012	-0.008	21.836	0.067	0.067	0.000	0.000	0.000	0.000
46	P	46	GLU	-1	-0.778	-0.889	25.489	9.731	9.731	0.000	0.000	0.000	0.000
47	P	47	TRP	0	-0.036	-0.023	20.458	-0.052	-0.052	0.000	0.000	0.000	0.000
48	P	48	VAL	0	-0.038	-0.033	23.479	-0.511	-0.511	0.000	0.000	0.000	0.000
49	P	49	GLY	0	0.016	-0.011	23.048	-0.435	-0.435	0.000	0.000	0.000	0.000
50	P	50	GLY	0	-0.024	-0.012	20.034	0.534	0.534	0.000	0.000	0.000	0.000
51	P	51	PHE	0	0.006	0.000	17.100	-0.572	-0.572	0.000	0.000	0.000	0.000
52	P	52	ILE	0	0.021	0.011	16.969	1.178	1.178	0.000	0.000	0.000	0.000
53	P	52	ALA	0	0.005	0.013	14.220	-0.657	-0.657	0.000	0.000	0.000	0.000
54	P	53	ILE	0	-0.024	-0.011	15.794	-0.543	-0.543	0.000	0.000	0.000	0.000
55	P	54	PHE	0	-0.042	-0.016	17.428	-0.624	-0.624	0.000	0.000	0.000	0.000
56	P	55	GLY	0	0.007	0.011	19.606	-0.598	-0.598	0.000	0.000	0.000	0.000
57	P	56	THR	0	-0.021	-0.012	21.025	-0.464	-0.464	0.000	0.000	0.000	0.000
58	P	57	SER	0	-0.012	-0.009	21.659	0.501	0.501	0.000	0.000	0.000	0.000
59	P	58	ASN	0	0.011	0.067	23.281	-0.090	-0.090	0.000	0.000	0.000	0.000
60	P	59	TYR	0	0.078	0.027	24.706	0.395	0.395	0.000	0.000	0.000	0.000
61	P	60	ALA	0	0.067	0.042	27.376	-0.070	-0.070	0.000	0.000	0.000	0.000
62	P	61	GLN	0	0.005	-0.018	29.355	0.099	0.099	0.000	0.000	0.000	0.000
63	P	62	LYS	1	0.867	0.944	31.709	-9.550	-9.550	0.000	0.000	0.000	0.000
64	P	63	PHE	0	-0.021	-0.010	28.410	-0.216	-0.216	0.000	0.000	0.000	0.000
65	P	64	GLN	0	0.040	0.023	32.190	0.329	0.329	0.000	0.000	0.000	0.000
66	P	65	GLY	0	-0.031	-0.012	33.673	-0.256	-0.256	0.000	0.000	0.000	0.000
67	P	66	ARG	1	0.830	0.895	32.386	-9.193	-9.193	0.000	0.000	0.000	0.000
68	P	67	VAL	0	0.010	0.000	26.584	0.089	0.089	0.000	0.000	0.000	0.000
69	P	68	THR	0	-0.014	-0.003	27.808	-0.219	-0.219	0.000	0.000	0.000	0.000
70	P	69	ILE	0	-0.046	-0.013	21.380	0.251	0.251	0.000	0.000	0.000	0.000
71	P	70	THR	0	-0.025	0.002	22.512	-0.109	-0.109	0.000	0.000	0.000	0.000
72	P	71	ALA	0	0.008	-0.007	17.454	0.526	0.526	0.000	0.000	0.000	0.000
73	P	72	ASP	-1	-0.836	-0.900	17.717	15.321	15.321	0.000	0.000	0.000	0.000
74	P	73	GLU	-1	-0.922	-0.959	15.330	19.762	19.762	0.000	0.000	0.000	0.000
75	P	74	SER	0	-0.052	-0.022	14.742	1.335	1.335	0.000	0.000	0.000	0.000
76	P	75	THR	0	-0.047	-0.043	14.419	1.231	1.231	0.000	0.000	0.000	0.000
77	P	76	SER	0	-0.031	-0.027	10.210	1.673	1.673	0.000	0.000	0.000	0.000
78	P	77	THR	0	-0.049	-0.037	12.458	0.968	0.968	0.000	0.000	0.000	0.000
79	P	78	ALA	0	-0.004	0.011	15.221	-0.916	-0.916	0.000	0.000	0.000	0.000
80	P	79	TYR	0	0.004	-0.032	17.415	0.100	0.100	0.000	0.000	0.000	0.000
81	P	80	MET	0	-0.017	0.017	20.818	-0.589	-0.589	0.000	0.000	0.000	0.000
82	P	81	GLU	-1	-0.866	-0.947	23.128	10.693	10.693	0.000	0.000	0.000	0.000
83	P	82	LEU	0	-0.021	-0.007	26.772	-0.216	-0.216	0.000	0.000	0.000	0.000
84	P	82	THR	0	0.004	-0.005	29.548	-0.236	-0.236	0.000	0.000	0.000	0.000
85	P	82	SER	0	-0.006	-0.025	33.173	-0.083	-0.083	0.000	0.000	0.000	0.000
86	P	82	LEU	0	-0.040	0.005	31.192	-0.108	-0.108	0.000	0.000	0.000	0.000
87	P	83	THR	0	0.039	0.017	35.119	-0.278	-0.278	0.000	0.000	0.000	0.000
88	P	84	SER	0	-0.020	-0.014	34.972	0.241	0.241	0.000	0.000	0.000	0.000
89	P	85	GLU	-1	-0.920	-0.963	35.156	8.206	8.206	0.000	0.000	0.000	0.000
90	P	86	ASP	-1	-0.823	-0.904	31.227	9.589	9.589	0.000	0.000	0.000	0.000
91	P	87	THR	0	-0.038	0.016	30.154	0.386	0.386	0.000	0.000	0.000	0.000
92	P	88	ALA	0	-0.030	-0.013	27.207	-0.114	-0.114	0.000	0.000	0.000	0.000
93	P	89	VAL	0	0.003	0.021	21.925	0.079	0.079	0.000	0.000	0.000	0.000
94	P	90	TYR	0	-0.034	-0.049	22.462	-0.079	-0.079	0.000	0.000	0.000	0.000
95	P	91	TYR	0	0.013	0.035	17.657	0.408	0.408	0.000	0.000	0.000	0.000
96	P	93	ALA	0	0.034	0.002	13.094	0.560	0.560	0.000	0.000	0.000	0.000
97	P	94	ARG	1	0.884	0.958	7.418	-32.389	-32.389	0.000	0.000	0.000	0.000
98	P	95	GLY	0	0.021	0.013	11.676	-0.031	-0.031	0.000	0.000	0.000	0.000
99	P	96	ILE	0	-0.001	0.004	12.104	1.363	1.363	0.000	0.000	0.000	0.000
100	P	97	SER	0	0.060	0.019	13.983	-1.612	-1.612	0.000	0.000	0.000	0.000
101	P	98	GLY	0	0.064	0.027	16.965	0.338	0.338	0.000	0.000	0.000	0.000
102	P	99	SER	0	-0.074	-0.051	19.737	-0.626	-0.626	0.000	0.000	0.000	0.000
103	P	100	TYR	0	-0.077	-0.092	17.694	-0.311	-0.311	0.000	0.000	0.000	0.000
104	P	100	GLY	0	-0.063	-0.028	16.630	-0.382	-0.382	0.000	0.000	0.000	0.000
105	P	100	TRP	0	0.023	0.015	11.986	-1.494	-1.494	0.000	0.000	0.000	0.000
106	P	100	PHE	0	-0.043	-0.046	13.693	0.914	0.914	0.000	0.000	0.000	0.000
107	P	101	ASP	-1	-0.914	-0.955	8.426	25.686	25.686	0.000	0.000	0.000	0.000
108	P	102	PRO	0	0.011	0.032	7.188	0.090	0.090	0.000	0.000	0.000	0.000
109	P	103	TRP	0	-0.016	-0.036	9.696	-1.841	-1.841	0.000	0.000	0.000	0.000
110	P	104	GLY	0	-0.006	0.004	12.276	0.935	0.935	0.000	0.000	0.000	0.000
111	P	105	GLN	0	-0.007	-0.020	13.921	-0.718	-0.718	0.000	0.000	0.000	0.000
112	P	106	GLY	0	0.026	0.019	15.969	-0.940	-0.940	0.000	0.000	0.000	0.000
113	P	107	THR	0	-0.011	-0.018	18.933	0.181	0.181	0.000	0.000	0.000	0.000
114	P	108	LEU	0	-0.030	-0.005	21.593	-0.309	-0.309	0.000	0.000	0.000	0.000
115	P	109	VAL	0	0.025	0.018	25.202	-0.137	-0.137	0.000	0.000	0.000	0.000
116	P	110	THR	0	0.022	-0.020	27.805	-0.165	-0.165	0.000	0.000	0.000	0.000
117	P	111	VAL	0	0.002	-0.011	31.265	-0.111	-0.111	0.000	0.000	0.000	0.000
118	P	112	SER	0	0.051	0.029	34.440	-0.297	-0.297	0.000	0.000	0.000	0.000
119	P	113	SER	0	0.024	-0.002	37.641	0.086	0.086	0.000	0.000	0.000	0.000
120	P	114	ALA	0	0.013	0.010	38.656	-0.090	-0.090	0.000	0.000	0.000	0.000
121	P	115	SER	0	-0.032	-0.022	39.017	0.194	0.194	0.000	0.000	0.000	0.000
122	P	116	THR	0	0.010	-0.024	35.214	-0.005	-0.005	0.000	0.000	0.000	0.000
123	P	117	LYS	1	0.940	1.010	37.318	-7.056	-7.056	0.000	0.000	0.000	0.000
124	P	118	GLY	0	0.053	0.026	37.903	0.140	0.140	0.000	0.000	0.000	0.000
125	P	119	PRO	0	-0.003	0.001	37.905	-0.206	-0.206	0.000	0.000	0.000	0.000
126	P	142	VAL	0	0.020	-0.006	37.604	0.026	0.026	0.000	0.000	0.000	0.000
127	P	143	LYS	1	0.868	0.928	39.758	-6.543	-6.543	0.000	0.000	0.000	0.000
128	P	144	ASP	-1	-0.826	-0.923	41.761	6.875	6.875	0.000	0.000	0.000	0.000
129	P	145	TYR	0	-0.012	0.009	33.651	-0.151	-0.151	0.000	0.000	0.000	0.000
130	P	146	PHE	0	-0.002	0.008	35.728	-0.022	-0.022	0.000	0.000	0.000	0.000
131	P	147	PRO	0	-0.047	-0.014	31.234	-0.005	-0.005	0.000	0.000	0.000	0.000
132	P	148	GLU	-1	-0.881	-1.038	29.644	9.353	9.353	0.000	0.000	0.000	0.000
133	P	149	PRO	0	0.091	0.111	25.722	0.036	0.036	0.000	0.000	0.000	0.000
134	P	150	VAL	0	-0.020	-0.002	27.131	0.269	0.269	0.000	0.000	0.000	0.000
135	P	151	THR	0	0.020	0.004	27.459	-0.318	-0.318	0.000	0.000	0.000	0.000
136	P	152	VAL	0	-0.014	-0.007	29.849	0.110	0.110	0.000	0.000	0.000	0.000
137	P	153	SER	0	-0.034	-0.033	30.784	-0.090	-0.090	0.000	0.000	0.000	0.000
138	P	154	TRP	0	0.053	0.051	33.317	0.070	0.070	0.000	0.000	0.000	0.000
139	P	155	ASN	0	-0.017	-0.042	36.169	0.038	0.038	0.000	0.000	0.000	0.000
140	P	156	SER	0	-0.037	-0.024	34.489	-0.029	-0.029	0.000	0.000	0.000	0.000
141	P	157	GLY	0	0.043	0.034	32.628	0.203	0.203	0.000	0.000	0.000	0.000
142	P	158	ALA	0	-0.057	-0.003	33.563	0.039	0.039	0.000	0.000	0.000	0.000
143	P	159	LEU	0	-0.018	0.004	35.869	0.042	0.042	0.000	0.000	0.000	0.000
144	P	160	THR	0	0.086	0.036	31.962	0.100	0.100	0.000	0.000	0.000	0.000
145	P	161	SER	0	0.011	-0.024	34.067	-0.107	-0.107	0.000	0.000	0.000	0.000
146	P	162	GLY	0	0.027	0.024	35.317	-0.186	-0.186	0.000	0.000	0.000	0.000
147	P	163	VAL	0	-0.067	-0.025	34.308	-0.170	-0.170	0.000	0.000	0.000	0.000
148	P	164	HIS	0	-0.045	-0.056	35.503	-0.002	-0.002	0.000	0.000	0.000	0.000
149	P	165	THR	0	0.007	0.009	32.032	-0.229	-0.229	0.000	0.000	0.000	0.000
150	P	166	PHE	0	-0.008	-0.007	34.539	0.040	0.040	0.000	0.000	0.000	0.000
151	P	167	PRO	0	-0.006	0.004	33.024	0.153	0.153	0.000	0.000	0.000	0.000
152	P	168	ALA	0	0.031	0.032	33.605	-0.269	-0.269	0.000	0.000	0.000	0.000
153	P	169	VAL	0	0.026	0.007	35.562	0.046	0.046	0.000	0.000	0.000	0.000
154	P	170	LEU	0	-0.002	-0.010	37.752	0.025	0.025	0.000	0.000	0.000	0.000
155	P	171	GLN	0	0.007	0.004	39.731	-0.131	-0.131	0.000	0.000	0.000	0.000
156	P	172	SER	0	-0.029	-0.028	42.976	0.037	0.037	0.000	0.000	0.000	0.000
157	P	173	SER	0	-0.018	0.013	44.575	-0.045	-0.045	0.000	0.000	0.000	0.000
158	P	174	GLY	0	0.029	-0.002	40.917	0.046	0.046	0.000	0.000	0.000	0.000
159	P	175	LEU	0	-0.107	-0.026	39.434	0.157	0.157	0.000	0.000	0.000	0.000
160	P	176	TYR	0	0.000	0.010	33.152	-0.024	-0.024	0.000	0.000	0.000	0.000
161	P	177	SER	0	-0.050	-0.082	38.226	-0.173	-0.173	0.000	0.000	0.000	0.000
162	P	178	LEU	0	0.022	0.068	34.006	-0.052	-0.052	0.000	0.000	0.000	0.000
163	P	179	SER	0	0.016	-0.007	37.859	-0.321	-0.321	0.000	0.000	0.000	0.000
164	P	180	SER	0	-0.023	-0.026	37.314	0.241	0.241	0.000	0.000	0.000	0.000
165	P	181	VAL	0	0.020	0.054	38.561	-0.045	-0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:1:GLU)