FMO DATABASE

FMODB ID: LZ6L9

Calculation Name: 4HG4-Z-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: Z

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1487642.477928
FMO2-HF: Nuclear repulsion	1424899.089363
FMO2-HF: Total energy	-62743.388565
FMO2-MP2: Total energy	-62927.246116

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(Z:1:GLU)

Summations of interaction energy for fragment #1(Z: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.
-43.209	-42.441	15.443	-8.218	-7.994	0.084

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.909 / q_NPA : -0.957

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	Z	3	GLN	0	-0.081	-0.041	1.748	-35.968	-37.203	15.405	-7.223	-6.948	0.078
4	Z	4	LEU	0	-0.015	-0.029	4.193	-2.087	-2.010	0.001	-0.013	-0.065	0.000
5	Z	5	VAL	0	-0.017	-0.007	7.895	-1.321	-1.321	0.000	0.000	0.000	0.000
6	Z	6	GLU	-1	-0.802	-0.897	10.531	19.863	19.863	0.000	0.000	0.000	0.000
7	Z	7	SER	0	-0.006	-0.005	14.225	-0.061	-0.061	0.000	0.000	0.000	0.000
8	Z	8	GLY	0	0.028	0.025	17.206	0.132	0.132	0.000	0.000	0.000	0.000
9	Z	9	ALA	0	-0.021	-0.011	19.478	-0.407	-0.407	0.000	0.000	0.000	0.000
10	Z	10	GLU	-1	-0.832	-0.911	22.629	12.461	12.461	0.000	0.000	0.000	0.000
11	Z	11	VAL	0	-0.029	-0.015	25.776	-0.202	-0.202	0.000	0.000	0.000	0.000
12	Z	12	LYS	1	0.819	0.895	27.284	-11.412	-11.412	0.000	0.000	0.000	0.000
13	Z	13	LYS	1	0.967	0.993	31.730	-8.905	-8.905	0.000	0.000	0.000	0.000
14	Z	14	PRO	0	0.026	0.015	35.260	0.126	0.126	0.000	0.000	0.000	0.000
15	Z	15	GLY	0	0.004	0.013	35.922	-0.227	-0.227	0.000	0.000	0.000	0.000
16	Z	16	SER	0	-0.090	-0.064	33.054	0.181	0.181	0.000	0.000	0.000	0.000
17	Z	17	SER	0	0.058	0.005	30.270	-0.067	-0.067	0.000	0.000	0.000	0.000
18	Z	18	VAL	0	-0.037	0.002	24.620	-0.015	-0.015	0.000	0.000	0.000	0.000
19	Z	19	LYS	1	0.872	0.927	22.752	-12.259	-12.259	0.000	0.000	0.000	0.000
20	Z	20	VAL	0	0.006	0.026	18.362	0.159	0.159	0.000	0.000	0.000	0.000
21	Z	21	SER	0	-0.003	-0.008	16.537	0.241	0.241	0.000	0.000	0.000	0.000
22	Z	22	CYS	0	-0.014	0.004	12.649	0.221	0.221	0.000	0.000	0.000	0.000
23	Z	23	LYS	1	0.884	0.955	9.369	-25.620	-25.620	0.000	0.000	0.000	0.000
24	Z	24	ALA	0	0.058	0.040	7.585	1.693	1.693	0.000	0.000	0.000	0.000
25	Z	25	SER	0	0.000	0.013	3.170	-10.243	-9.071	0.020	-0.615	-0.577	0.005
26	Z	26	GLY	0	0.063	0.024	3.765	5.510	6.050	0.016	-0.304	-0.252	0.001
27	Z	27	GLY	0	0.002	0.005	4.373	-5.019	-4.805	0.001	-0.063	-0.152	0.000
28	Z	28	THR	0	-0.005	-0.010	7.561	-0.256	-0.256	0.000	0.000	0.000	0.000
29	Z	29	PHE	0	0.108	0.054	11.208	0.166	0.166	0.000	0.000	0.000	0.000
30	Z	30	ILE	0	0.039	0.008	13.127	-0.076	-0.076	0.000	0.000	0.000	0.000
31	Z	31	THR	0	-0.058	-0.037	10.122	-1.022	-1.022	0.000	0.000	0.000	0.000
32	Z	32	HIS	0	-0.020	0.007	7.675	-1.109	-1.109	0.000	0.000	0.000	0.000
33	Z	33	VAL	0	0.006	0.002	12.541	-1.478	-1.478	0.000	0.000	0.000	0.000
34	Z	34	PHE	0	0.019	0.015	12.039	0.380	0.380	0.000	0.000	0.000	0.000
35	Z	35	THR	0	-0.006	-0.013	15.076	-1.402	-1.402	0.000	0.000	0.000	0.000
36	Z	36	TRP	0	0.015	0.015	16.566	0.573	0.573	0.000	0.000	0.000	0.000
37	Z	37	VAL	0	-0.007	-0.006	18.599	-0.883	-0.883	0.000	0.000	0.000	0.000
38	Z	38	ARG	1	0.793	0.866	20.591	-10.520	-10.520	0.000	0.000	0.000	0.000
39	Z	39	GLN	0	0.012	0.006	22.652	0.285	0.285	0.000	0.000	0.000	0.000
40	Z	40	ALA	0	0.031	0.021	24.816	0.090	0.090	0.000	0.000	0.000	0.000
41	Z	41	PRO	0	0.043	0.003	27.882	0.064	0.064	0.000	0.000	0.000	0.000
42	Z	42	GLY	0	-0.036	-0.008	28.442	-0.399	-0.399	0.000	0.000	0.000	0.000
43	Z	43	GLN	0	-0.027	-0.004	29.498	-0.327	-0.327	0.000	0.000	0.000	0.000
44	Z	44	GLY	0	0.025	0.001	26.121	0.319	0.319	0.000	0.000	0.000	0.000
45	Z	45	LEU	0	-0.042	-0.024	20.990	0.012	0.012	0.000	0.000	0.000	0.000
46	Z	46	GLU	-1	-0.810	-0.862	24.688	10.353	10.353	0.000	0.000	0.000	0.000
47	Z	47	TRP	0	-0.041	-0.022	20.451	0.073	0.073	0.000	0.000	0.000	0.000
48	Z	48	VAL	0	-0.024	-0.012	22.435	-0.452	-0.452	0.000	0.000	0.000	0.000
49	Z	49	GLY	0	0.021	-0.005	22.220	-0.480	-0.480	0.000	0.000	0.000	0.000
50	Z	50	GLY	0	0.024	0.004	19.471	0.436	0.436	0.000	0.000	0.000	0.000
51	Z	51	PHE	0	-0.028	-0.011	17.158	-0.507	-0.507	0.000	0.000	0.000	0.000
52	Z	52	ILE	0	0.012	0.022	17.626	1.055	1.055	0.000	0.000	0.000	0.000
53	Z	52	ALA	0	0.013	0.010	15.972	-0.718	-0.718	0.000	0.000	0.000	0.000
54	Z	53	ILE	0	-0.025	-0.011	17.974	-0.355	-0.355	0.000	0.000	0.000	0.000
55	Z	54	PHE	0	-0.052	-0.027	19.627	-0.564	-0.564	0.000	0.000	0.000	0.000
56	Z	55	GLY	0	0.024	0.022	21.257	-0.481	-0.481	0.000	0.000	0.000	0.000
57	Z	56	THR	0	-0.015	-0.004	22.514	-0.394	-0.394	0.000	0.000	0.000	0.000
58	Z	57	SER	0	0.014	-0.006	22.501	0.759	0.759	0.000	0.000	0.000	0.000
59	Z	58	ASN	0	-0.044	-0.004	23.436	-0.187	-0.187	0.000	0.000	0.000	0.000
60	Z	59	TYR	0	0.071	0.033	24.364	0.409	0.409	0.000	0.000	0.000	0.000
61	Z	60	ALA	0	0.076	0.038	26.841	-0.128	-0.128	0.000	0.000	0.000	0.000
62	Z	61	GLN	0	-0.047	-0.024	28.760	-0.439	-0.439	0.000	0.000	0.000	0.000
63	Z	62	LYS	1	0.991	0.993	32.483	-8.800	-8.800	0.000	0.000	0.000	0.000
64	Z	63	PHE	0	-0.004	-0.003	27.591	0.148	0.148	0.000	0.000	0.000	0.000
65	Z	64	GLN	0	0.030	-0.015	31.816	0.331	0.331	0.000	0.000	0.000	0.000
66	Z	65	GLY	0	0.008	0.011	32.636	-0.187	-0.187	0.000	0.000	0.000	0.000
67	Z	66	ARG	1	0.777	0.878	31.314	-9.745	-9.745	0.000	0.000	0.000	0.000
68	Z	67	VAL	0	0.014	0.004	25.729	0.237	0.237	0.000	0.000	0.000	0.000
69	Z	68	THR	0	-0.016	0.002	27.116	-0.297	-0.297	0.000	0.000	0.000	0.000
70	Z	69	ILE	0	-0.050	-0.012	20.952	0.295	0.295	0.000	0.000	0.000	0.000
71	Z	70	THR	0	-0.025	-0.013	22.041	-0.284	-0.284	0.000	0.000	0.000	0.000
72	Z	71	ALA	0	0.023	0.010	17.880	0.711	0.711	0.000	0.000	0.000	0.000
73	Z	72	ASP	-1	-0.782	-0.839	17.661	16.575	16.575	0.000	0.000	0.000	0.000
74	Z	73	GLU	-1	-0.935	-0.970	15.687	17.910	17.910	0.000	0.000	0.000	0.000
75	Z	74	SER	0	-0.090	-0.052	15.089	1.064	1.064	0.000	0.000	0.000	0.000
76	Z	75	THR	0	-0.074	-0.062	13.678	1.485	1.485	0.000	0.000	0.000	0.000
77	Z	76	SER	0	-0.018	0.003	10.166	1.232	1.232	0.000	0.000	0.000	0.000
78	Z	77	THR	0	-0.003	-0.018	11.717	2.576	2.576	0.000	0.000	0.000	0.000
79	Z	78	ALA	0	-0.014	0.001	14.228	-1.347	-1.347	0.000	0.000	0.000	0.000
80	Z	79	TYR	0	-0.018	-0.039	16.882	0.427	0.427	0.000	0.000	0.000	0.000
81	Z	80	MET	0	0.002	0.022	19.906	-0.768	-0.768	0.000	0.000	0.000	0.000
82	Z	81	GLU	-1	-0.835	-0.916	22.097	11.532	11.532	0.000	0.000	0.000	0.000
83	Z	82	LEU	0	0.021	0.015	25.587	-0.261	-0.261	0.000	0.000	0.000	0.000
84	Z	82	THR	0	-0.017	-0.031	27.985	-0.210	-0.210	0.000	0.000	0.000	0.000
85	Z	82	SER	0	0.012	0.009	31.600	-0.155	-0.155	0.000	0.000	0.000	0.000
86	Z	82	LEU	0	-0.056	0.001	29.198	-0.071	-0.071	0.000	0.000	0.000	0.000
87	Z	83	THR	0	0.045	0.010	33.309	-0.361	-0.361	0.000	0.000	0.000	0.000
88	Z	84	SER	0	0.066	0.007	33.454	0.179	0.179	0.000	0.000	0.000	0.000
89	Z	85	GLU	-1	-0.974	-0.977	33.201	8.833	8.833	0.000	0.000	0.000	0.000
90	Z	86	ASP	-1	-0.743	-0.821	29.382	10.194	10.194	0.000	0.000	0.000	0.000
91	Z	87	THR	0	-0.055	-0.015	28.167	0.507	0.507	0.000	0.000	0.000	0.000
92	Z	88	ALA	0	-0.001	0.006	25.426	-0.164	-0.164	0.000	0.000	0.000	0.000
93	Z	89	VAL	0	-0.002	0.016	20.030	0.182	0.182	0.000	0.000	0.000	0.000
94	Z	90	TYR	0	-0.035	-0.053	20.543	-0.196	-0.196	0.000	0.000	0.000	0.000
95	Z	91	TYR	0	-0.008	-0.003	16.416	0.706	0.706	0.000	0.000	0.000	0.000
96	Z	93	ALA	0	0.023	0.003	12.577	1.032	1.032	0.000	0.000	0.000	0.000
97	Z	94	ARG	1	0.882	0.934	8.183	-27.021	-27.021	0.000	0.000	0.000	0.000
98	Z	95	GLY	0	0.021	0.017	11.913	-0.191	-0.191	0.000	0.000	0.000	0.000
99	Z	96	ILE	0	-0.003	0.015	13.817	0.725	0.725	0.000	0.000	0.000	0.000
100	Z	97	SER	0	0.009	-0.008	15.368	-1.241	-1.241	0.000	0.000	0.000	0.000
101	Z	98	GLY	0	0.067	0.018	18.473	0.301	0.301	0.000	0.000	0.000	0.000
102	Z	99	SER	0	-0.047	-0.027	21.435	-0.414	-0.414	0.000	0.000	0.000	0.000
103	Z	100	TYR	0	-0.065	-0.043	18.402	-0.045	-0.045	0.000	0.000	0.000	0.000
104	Z	100	GLY	0	-0.047	-0.022	17.802	-0.361	-0.361	0.000	0.000	0.000	0.000
105	Z	100	TRP	0	0.032	0.014	12.675	-1.199	-1.199	0.000	0.000	0.000	0.000
106	Z	100	PHE	0	-0.011	-0.032	13.781	0.608	0.608	0.000	0.000	0.000	0.000
107	Z	101	ASP	-1	-0.921	-0.962	8.397	26.051	26.051	0.000	0.000	0.000	0.000
108	Z	102	PRO	0	-0.006	0.027	6.901	0.288	0.288	0.000	0.000	0.000	0.000
109	Z	103	TRP	0	-0.029	-0.037	9.025	-1.561	-1.561	0.000	0.000	0.000	0.000
110	Z	104	GLY	0	0.003	0.007	11.001	1.683	1.683	0.000	0.000	0.000	0.000
111	Z	105	GLN	0	-0.032	-0.030	12.147	-0.433	-0.433	0.000	0.000	0.000	0.000
112	Z	106	GLY	0	-0.006	-0.014	14.675	-1.336	-1.336	0.000	0.000	0.000	0.000
113	Z	107	THR	0	-0.034	-0.004	17.583	0.371	0.371	0.000	0.000	0.000	0.000
114	Z	108	LEU	0	-0.031	-0.014	19.745	-0.549	-0.549	0.000	0.000	0.000	0.000
115	Z	109	VAL	0	0.022	0.017	23.271	-0.091	-0.091	0.000	0.000	0.000	0.000
116	Z	110	THR	0	0.010	-0.006	25.776	-0.337	-0.337	0.000	0.000	0.000	0.000
117	Z	111	VAL	0	-0.041	-0.021	29.247	-0.053	-0.053	0.000	0.000	0.000	0.000
118	Z	112	SER	0	0.023	0.000	32.109	-0.317	-0.317	0.000	0.000	0.000	0.000
119	Z	113	SER	0	0.025	0.000	35.636	0.118	0.118	0.000	0.000	0.000	0.000
120	Z	114	ALA	0	-0.035	0.008	37.185	-0.120	-0.120	0.000	0.000	0.000	0.000
121	Z	115	SER	0	0.009	-0.013	35.173	0.267	0.267	0.000	0.000	0.000	0.000
122	Z	116	THR	0	0.013	0.009	31.057	-0.188	-0.188	0.000	0.000	0.000	0.000
123	Z	117	LYS	1	0.859	0.925	34.091	-8.760	-8.760	0.000	0.000	0.000	0.000
124	Z	118	GLY	0	0.061	0.040	35.388	0.211	0.211	0.000	0.000	0.000	0.000
125	Z	119	PRO	0	0.005	0.022	34.695	-0.186	-0.186	0.000	0.000	0.000	0.000
126	Z	120	SER	0	-0.013	-0.015	37.574	-0.234	-0.234	0.000	0.000	0.000	0.000
127	Z	121	VAL	0	0.004	-0.010	38.714	0.145	0.145	0.000	0.000	0.000	0.000
128	Z	122	PHE	0	-0.012	0.022	41.611	-0.143	-0.143	0.000	0.000	0.000	0.000
129	Z	123	PRO	0	0.008	0.003	42.593	-0.039	-0.039	0.000	0.000	0.000	0.000
130	Z	141	LEU	0	-0.038	-0.026	39.853	0.072	0.072	0.000	0.000	0.000	0.000
131	Z	142	VAL	0	-0.014	-0.017	35.242	-0.064	-0.064	0.000	0.000	0.000	0.000
132	Z	143	LYS	1	0.872	0.937	37.814	-7.495	-7.495	0.000	0.000	0.000	0.000
133	Z	144	ASP	-1	-0.784	-0.921	38.952	7.854	7.854	0.000	0.000	0.000	0.000
134	Z	145	TYR	0	0.022	0.028	31.627	-0.088	-0.088	0.000	0.000	0.000	0.000
135	Z	146	PHE	0	-0.004	-0.002	33.233	0.050	0.050	0.000	0.000	0.000	0.000
136	Z	147	PRO	0	-0.008	-0.009	28.495	-0.010	-0.010	0.000	0.000	0.000	0.000
137	Z	148	GLU	-1	-0.838	-0.977	29.350	10.674	10.674	0.000	0.000	0.000	0.000
138	Z	149	PRO	0	-0.027	0.037	24.558	0.246	0.246	0.000	0.000	0.000	0.000
139	Z	150	VAL	0	-0.015	-0.019	26.610	-0.412	-0.412	0.000	0.000	0.000	0.000
140	Z	164	HIS	0	-0.009	-0.013	33.336	0.189	0.189	0.000	0.000	0.000	0.000
141	Z	165	THR	0	-0.031	-0.008	29.946	-0.219	-0.219	0.000	0.000	0.000	0.000
142	Z	166	PHE	0	0.020	-0.015	32.164	-0.170	-0.170	0.000	0.000	0.000	0.000
143	Z	167	PRO	0	0.004	0.026	30.610	0.271	0.271	0.000	0.000	0.000	0.000
144	Z	168	ALA	0	-0.008	0.007	31.465	-0.333	-0.333	0.000	0.000	0.000	0.000
145	Z	169	VAL	0	0.002	0.004	33.414	-0.005	-0.005	0.000	0.000	0.000	0.000
146	Z	170	LEU	0	-0.001	0.001	34.760	-0.048	-0.048	0.000	0.000	0.000	0.000
147	Z	171	GLN	0	-0.040	-0.020	37.145	-0.352	-0.352	0.000	0.000	0.000	0.000
148	Z	172	SER	0	0.041	0.010	40.741	0.108	0.108	0.000	0.000	0.000	0.000
149	Z	173	SER	0	-0.038	-0.031	42.232	-0.003	-0.003	0.000	0.000	0.000	0.000
150	Z	174	GLY	0	0.005	0.002	39.120	0.051	0.051	0.000	0.000	0.000	0.000
151	Z	175	LEU	0	-0.074	-0.028	37.306	0.288	0.288	0.000	0.000	0.000	0.000
152	Z	176	TYR	0	0.019	0.020	31.407	-0.182	-0.182	0.000	0.000	0.000	0.000
153	Z	177	SER	0	-0.007	-0.008	35.919	-0.216	-0.216	0.000	0.000	0.000	0.000
154	Z	178	LEU	0	0.022	0.029	31.648	0.029	0.029	0.000	0.000	0.000	0.000
155	Z	179	SER	0	0.025	0.014	35.600	-0.253	-0.253	0.000	0.000	0.000	0.000
156	Z	195	ILE	0	-0.003	-0.019	36.955	-0.050	-0.050	0.000	0.000	0.000	0.000
157	Z	196	CYS	0	0.008	0.004	36.267	0.291	0.291	0.000	0.000	0.000	0.000
158	Z	197	ASN	0	-0.040	-0.006	31.888	0.130	0.130	0.000	0.000	0.000	0.000
159	Z	198	VAL	0	0.048	0.015	32.294	0.299	0.299	0.000	0.000	0.000	0.000
160	Z	199	ASN	0	0.006	0.001	27.423	0.353	0.353	0.000	0.000	0.000	0.000
161	Z	200	HIS	0	0.066	0.044	29.033	0.249	0.249	0.000	0.000	0.000	0.000
162	Z	201	LYS	1	0.938	0.963	23.471	-13.251	-13.251	0.000	0.000	0.000	0.000
163	Z	202	PRO	0	0.019	0.026	27.179	0.182	0.182	0.000	0.000	0.000	0.000
164	Z	203	SER	0	-0.036	-0.018	28.425	-0.068	-0.068	0.000	0.000	0.000	0.000
165	Z	204	ASN	0	-0.070	-0.035	29.047	0.026	0.026	0.000	0.000	0.000	0.000
166	Z	205	THR	0	0.035	0.014	30.933	-0.182	-0.182	0.000	0.000	0.000	0.000

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