FMO DATABASE

FMODB ID: 394NL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1487326.62072
FMO2-HF: Nuclear repulsion	1424584.275893
FMO2-HF: Total energy	-62742.344826
FMO2-MP2: Total energy	-62926.232917

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.
-20.522	-14.77	0.534	-2.602	-3.684	0.02

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 : -0.962 / q_NPA : -0.995

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	-0.031	-0.006	2.730	-17.566	-13.478	0.402	-1.790	-2.700	0.016
4	Z	4	LEU	0	-0.002	-0.022	4.630	-1.657	-1.587	-0.001	-0.009	-0.060	0.000
5	Z	5	VAL	0	-0.039	-0.019	8.266	-1.151	-1.151	0.000	0.000	0.000	0.000
6	Z	6	GLU	-1	-0.764	-0.885	10.965	18.655	18.655	0.000	0.000	0.000	0.000
7	Z	7	SER	0	-0.047	-0.012	14.511	-0.319	-0.319	0.000	0.000	0.000	0.000
8	Z	8	GLY	0	0.026	0.037	17.752	0.143	0.143	0.000	0.000	0.000	0.000
9	Z	9	ALA	0	-0.011	-0.003	19.902	-0.356	-0.356	0.000	0.000	0.000	0.000
10	Z	10	GLU	-1	-0.904	-0.953	22.791	12.617	12.617	0.000	0.000	0.000	0.000
11	Z	11	VAL	0	-0.046	-0.017	26.073	-0.210	-0.210	0.000	0.000	0.000	0.000
12	Z	12	LYS	1	0.851	0.904	28.428	-10.761	-10.761	0.000	0.000	0.000	0.000
13	Z	13	LYS	1	0.992	1.014	32.021	-8.892	-8.892	0.000	0.000	0.000	0.000
14	Z	14	PRO	0	0.035	0.071	35.577	0.135	0.135	0.000	0.000	0.000	0.000
15	Z	15	GLY	0	0.010	0.016	36.249	-0.221	-0.221	0.000	0.000	0.000	0.000
16	Z	16	SER	0	-0.123	-0.132	33.172	0.128	0.128	0.000	0.000	0.000	0.000
17	Z	17	SER	0	0.045	-0.001	30.598	-0.032	-0.032	0.000	0.000	0.000	0.000
18	Z	18	VAL	0	-0.009	0.013	24.890	-0.051	-0.051	0.000	0.000	0.000	0.000
19	Z	19	LYS	1	1.011	1.012	23.165	-12.635	-12.635	0.000	0.000	0.000	0.000
20	Z	20	VAL	0	0.031	0.043	18.698	0.135	0.135	0.000	0.000	0.000	0.000
21	Z	21	SER	0	-0.017	-0.019	16.665	0.285	0.285	0.000	0.000	0.000	0.000
22	Z	22	CYS	0	-0.017	-0.008	12.815	0.266	0.266	0.000	0.000	0.000	0.000
23	Z	23	LYS	1	0.894	0.942	10.316	-23.523	-23.523	0.000	0.000	0.000	0.000
24	Z	24	ALA	0	0.065	0.035	7.588	1.248	1.248	0.000	0.000	0.000	0.000
25	Z	25	SER	0	-0.011	0.012	4.229	-3.032	-2.762	-0.001	-0.034	-0.235	0.000
26	Z	26	GLY	0	0.083	0.032	3.150	2.958	4.065	0.127	-0.744	-0.489	0.004
27	Z	27	GLY	0	-0.016	0.000	3.688	-4.423	-4.206	0.007	-0.025	-0.200	0.000
28	Z	28	THR	0	0.007	-0.003	7.096	-0.433	-0.433	0.000	0.000	0.000	0.000
29	Z	29	PHE	0	0.107	0.088	10.640	0.070	0.070	0.000	0.000	0.000	0.000
30	Z	30	ILE	0	0.035	0.006	12.615	-0.181	-0.181	0.000	0.000	0.000	0.000
31	Z	31	THR	0	-0.092	-0.086	10.211	-0.743	-0.743	0.000	0.000	0.000	0.000
32	Z	32	HIS	0	-0.031	-0.005	7.683	-1.132	-1.132	0.000	0.000	0.000	0.000
33	Z	33	VAL	0	0.000	0.005	12.306	-1.464	-1.464	0.000	0.000	0.000	0.000
34	Z	34	PHE	0	0.017	0.012	12.239	0.404	0.404	0.000	0.000	0.000	0.000
35	Z	35	THR	0	-0.009	-0.008	15.134	-1.344	-1.344	0.000	0.000	0.000	0.000
36	Z	36	TRP	0	0.029	0.022	16.846	0.532	0.532	0.000	0.000	0.000	0.000
37	Z	37	VAL	0	0.006	-0.001	19.208	-0.833	-0.833	0.000	0.000	0.000	0.000
38	Z	38	ARG	1	0.806	0.904	20.626	-10.338	-10.338	0.000	0.000	0.000	0.000
39	Z	39	GLN	0	-0.004	-0.019	22.751	0.241	0.241	0.000	0.000	0.000	0.000
40	Z	40	ALA	0	0.036	0.021	24.812	0.084	0.084	0.000	0.000	0.000	0.000
41	Z	41	PRO	0	0.036	0.000	27.881	0.073	0.073	0.000	0.000	0.000	0.000
42	Z	42	GLY	0	-0.034	-0.004	28.436	-0.378	-0.378	0.000	0.000	0.000	0.000
43	Z	43	GLN	0	-0.009	0.005	29.513	-0.242	-0.242	0.000	0.000	0.000	0.000
44	Z	44	GLY	0	0.019	0.007	26.127	0.318	0.318	0.000	0.000	0.000	0.000
45	Z	45	LEU	0	-0.046	-0.022	20.933	0.010	0.010	0.000	0.000	0.000	0.000
46	Z	46	GLU	-1	-0.826	-0.892	24.694	10.101	10.101	0.000	0.000	0.000	0.000
47	Z	47	TRP	0	-0.036	-0.019	20.594	0.058	0.058	0.000	0.000	0.000	0.000
48	Z	48	VAL	0	-0.014	-0.009	22.612	-0.460	-0.460	0.000	0.000	0.000	0.000
49	Z	49	GLY	0	0.007	-0.015	22.477	-0.452	-0.452	0.000	0.000	0.000	0.000
50	Z	50	GLY	0	0.023	-0.003	19.579	0.428	0.428	0.000	0.000	0.000	0.000
51	Z	51	PHE	0	-0.026	-0.012	17.238	-0.497	-0.497	0.000	0.000	0.000	0.000
52	Z	52	ILE	0	0.022	0.033	17.539	1.055	1.055	0.000	0.000	0.000	0.000
53	Z	52	ALA	0	0.018	0.004	15.616	-0.678	-0.678	0.000	0.000	0.000	0.000
54	Z	53	ILE	0	-0.020	-0.003	17.670	-0.305	-0.305	0.000	0.000	0.000	0.000
55	Z	54	PHE	0	-0.052	-0.022	19.230	-0.555	-0.555	0.000	0.000	0.000	0.000
56	Z	55	GLY	0	0.016	0.013	20.962	-0.467	-0.467	0.000	0.000	0.000	0.000
57	Z	56	THR	0	-0.014	-0.005	22.218	-0.374	-0.374	0.000	0.000	0.000	0.000
58	Z	57	SER	0	0.012	-0.006	22.358	0.647	0.647	0.000	0.000	0.000	0.000
59	Z	58	ASN	0	-0.065	-0.022	23.447	-0.223	-0.223	0.000	0.000	0.000	0.000
60	Z	59	TYR	0	0.074	0.026	24.461	0.384	0.384	0.000	0.000	0.000	0.000
61	Z	60	ALA	0	0.076	0.043	26.963	-0.117	-0.117	0.000	0.000	0.000	0.000
62	Z	61	GLN	0	-0.028	-0.012	28.912	-0.307	-0.307	0.000	0.000	0.000	0.000
63	Z	62	LYS	1	1.006	0.993	32.299	-8.808	-8.808	0.000	0.000	0.000	0.000
64	Z	63	PHE	0	-0.043	-0.013	27.968	0.105	0.105	0.000	0.000	0.000	0.000
65	Z	64	GLN	0	0.013	-0.033	32.005	0.225	0.225	0.000	0.000	0.000	0.000
66	Z	65	GLY	0	0.006	0.015	32.767	-0.182	-0.182	0.000	0.000	0.000	0.000
67	Z	66	ARG	1	0.863	0.954	31.539	-9.551	-9.551	0.000	0.000	0.000	0.000
68	Z	67	VAL	0	0.015	0.015	25.926	0.220	0.220	0.000	0.000	0.000	0.000
69	Z	68	THR	0	-0.014	0.003	27.208	-0.220	-0.220	0.000	0.000	0.000	0.000
70	Z	69	ILE	0	-0.048	-0.005	21.005	0.287	0.287	0.000	0.000	0.000	0.000
71	Z	70	THR	0	-0.031	-0.015	21.824	-0.246	-0.246	0.000	0.000	0.000	0.000
72	Z	71	ALA	0	0.009	-0.001	17.598	0.667	0.667	0.000	0.000	0.000	0.000
73	Z	72	ASP	-1	-0.817	-0.860	17.722	16.032	16.032	0.000	0.000	0.000	0.000
74	Z	73	GLU	-1	-0.932	-0.975	15.693	18.138	18.138	0.000	0.000	0.000	0.000
75	Z	74	SER	0	-0.037	-0.002	14.976	0.794	0.794	0.000	0.000	0.000	0.000
76	Z	75	THR	0	-0.106	-0.100	13.725	1.239	1.239	0.000	0.000	0.000	0.000
77	Z	76	SER	0	-0.011	-0.003	10.596	1.986	1.986	0.000	0.000	0.000	0.000
78	Z	77	THR	0	-0.030	-0.003	11.839	2.195	2.195	0.000	0.000	0.000	0.000
79	Z	78	ALA	0	0.003	0.015	14.414	-1.199	-1.199	0.000	0.000	0.000	0.000
80	Z	79	TYR	0	-0.030	-0.045	16.824	0.315	0.315	0.000	0.000	0.000	0.000
81	Z	80	MET	0	0.008	0.024	19.943	-0.707	-0.707	0.000	0.000	0.000	0.000
82	Z	81	GLU	-1	-0.933	-0.977	22.233	11.056	11.056	0.000	0.000	0.000	0.000
83	Z	82	LEU	0	0.022	0.020	25.722	-0.269	-0.269	0.000	0.000	0.000	0.000
84	Z	82	THR	0	-0.021	-0.040	28.201	-0.219	-0.219	0.000	0.000	0.000	0.000
85	Z	82	SER	0	-0.010	-0.008	31.800	-0.151	-0.151	0.000	0.000	0.000	0.000
86	Z	82	LEU	0	-0.049	-0.010	29.496	-0.072	-0.072	0.000	0.000	0.000	0.000
87	Z	83	THR	0	0.032	0.010	33.636	-0.341	-0.341	0.000	0.000	0.000	0.000
88	Z	84	SER	0	0.026	-0.003	33.768	0.252	0.252	0.000	0.000	0.000	0.000
89	Z	85	GLU	-1	-0.919	-0.949	33.426	8.683	8.683	0.000	0.000	0.000	0.000
90	Z	86	ASP	-1	-0.793	-0.878	29.760	10.030	10.030	0.000	0.000	0.000	0.000
91	Z	87	THR	0	-0.061	-0.032	28.463	0.447	0.447	0.000	0.000	0.000	0.000
92	Z	88	ALA	0	-0.019	-0.004	25.627	-0.161	-0.161	0.000	0.000	0.000	0.000
93	Z	89	VAL	0	-0.008	0.015	20.263	0.160	0.160	0.000	0.000	0.000	0.000
94	Z	90	TYR	0	-0.052	-0.054	20.973	-0.167	-0.167	0.000	0.000	0.000	0.000
95	Z	91	TYR	0	0.007	0.014	16.385	0.579	0.579	0.000	0.000	0.000	0.000
96	Z	93	ALA	0	0.030	0.008	12.587	0.960	0.960	0.000	0.000	0.000	0.000
97	Z	94	ARG	1	0.922	0.962	8.518	-26.927	-26.927	0.000	0.000	0.000	0.000
98	Z	95	GLY	0	0.011	0.012	11.916	-0.161	-0.161	0.000	0.000	0.000	0.000
99	Z	96	ILE	0	-0.006	0.018	13.829	0.744	0.744	0.000	0.000	0.000	0.000
100	Z	97	SER	0	0.041	0.011	15.275	-1.178	-1.178	0.000	0.000	0.000	0.000
101	Z	98	GLY	0	0.070	0.019	18.372	0.276	0.276	0.000	0.000	0.000	0.000
102	Z	99	SER	0	-0.063	-0.042	21.314	-0.583	-0.583	0.000	0.000	0.000	0.000
103	Z	100	TYR	0	-0.045	-0.018	18.548	-0.045	-0.045	0.000	0.000	0.000	0.000
104	Z	100	GLY	0	-0.060	-0.034	17.823	-0.350	-0.350	0.000	0.000	0.000	0.000
105	Z	100	TRP	0	0.031	0.016	12.848	-1.178	-1.178	0.000	0.000	0.000	0.000
106	Z	100	PHE	0	-0.017	-0.033	13.816	0.610	0.610	0.000	0.000	0.000	0.000
107	Z	101	ASP	-1	-0.918	-0.963	8.578	25.264	25.264	0.000	0.000	0.000	0.000
108	Z	102	PRO	0	0.009	0.030	6.912	0.242	0.242	0.000	0.000	0.000	0.000
109	Z	103	TRP	0	-0.017	-0.030	9.035	-1.467	-1.467	0.000	0.000	0.000	0.000
110	Z	104	GLY	0	-0.020	-0.003	10.995	1.543	1.543	0.000	0.000	0.000	0.000
111	Z	105	GLN	0	-0.010	-0.025	12.281	-0.342	-0.342	0.000	0.000	0.000	0.000
112	Z	106	GLY	0	-0.012	-0.010	14.702	-1.187	-1.187	0.000	0.000	0.000	0.000
113	Z	107	THR	0	-0.040	-0.018	17.623	0.400	0.400	0.000	0.000	0.000	0.000
114	Z	108	LEU	0	-0.028	-0.015	19.857	-0.530	-0.530	0.000	0.000	0.000	0.000
115	Z	109	VAL	0	0.019	0.016	23.316	-0.093	-0.093	0.000	0.000	0.000	0.000
116	Z	110	THR	0	-0.001	-0.021	25.938	-0.321	-0.321	0.000	0.000	0.000	0.000
117	Z	111	VAL	0	-0.035	-0.017	29.344	-0.045	-0.045	0.000	0.000	0.000	0.000
118	Z	112	SER	0	0.018	0.002	32.295	-0.293	-0.293	0.000	0.000	0.000	0.000
119	Z	113	SER	0	0.050	0.008	35.772	0.117	0.117	0.000	0.000	0.000	0.000
120	Z	114	ALA	0	-0.039	0.004	37.175	-0.117	-0.117	0.000	0.000	0.000	0.000
121	Z	115	SER	0	0.046	-0.006	35.373	0.209	0.209	0.000	0.000	0.000	0.000
122	Z	116	THR	0	-0.059	-0.012	31.353	-0.211	-0.211	0.000	0.000	0.000	0.000
123	Z	117	LYS	1	0.875	0.921	34.309	-8.598	-8.598	0.000	0.000	0.000	0.000
124	Z	118	GLY	0	0.085	0.052	35.411	0.209	0.209	0.000	0.000	0.000	0.000
125	Z	119	PRO	0	0.012	0.024	34.791	-0.186	-0.186	0.000	0.000	0.000	0.000
126	Z	120	SER	0	-0.019	-0.014	37.649	-0.225	-0.225	0.000	0.000	0.000	0.000
127	Z	121	VAL	0	0.007	-0.006	38.835	0.134	0.134	0.000	0.000	0.000	0.000
128	Z	122	PHE	0	-0.014	0.022	41.779	-0.139	-0.139	0.000	0.000	0.000	0.000
129	Z	123	PRO	0	0.001	-0.001	42.771	-0.041	-0.041	0.000	0.000	0.000	0.000
130	Z	141	LEU	0	-0.033	-0.025	40.040	0.069	0.069	0.000	0.000	0.000	0.000
131	Z	142	VAL	0	-0.016	-0.019	35.506	-0.065	-0.065	0.000	0.000	0.000	0.000
132	Z	143	LYS	1	0.883	0.932	37.951	-7.335	-7.335	0.000	0.000	0.000	0.000
133	Z	144	ASP	-1	-0.864	-0.948	39.122	7.691	7.691	0.000	0.000	0.000	0.000
134	Z	145	TYR	0	0.012	0.012	31.476	-0.085	-0.085	0.000	0.000	0.000	0.000
135	Z	146	PHE	0	-0.007	0.002	33.362	0.045	0.045	0.000	0.000	0.000	0.000
136	Z	147	PRO	0	-0.004	-0.012	28.484	-0.013	-0.013	0.000	0.000	0.000	0.000
137	Z	148	GLU	-1	-0.865	-0.974	29.382	10.645	10.645	0.000	0.000	0.000	0.000
138	Z	149	PRO	0	-0.026	0.040	24.617	0.236	0.236	0.000	0.000	0.000	0.000
139	Z	150	VAL	0	-0.013	-0.020	26.681	-0.364	-0.364	0.000	0.000	0.000	0.000
140	Z	164	HIS	0	-0.009	-0.012	33.748	0.208	0.208	0.000	0.000	0.000	0.000
141	Z	165	THR	0	-0.031	-0.009	30.241	-0.203	-0.203	0.000	0.000	0.000	0.000
142	Z	166	PHE	0	0.020	-0.017	32.401	-0.148	-0.148	0.000	0.000	0.000	0.000
143	Z	167	PRO	0	0.001	0.026	30.834	0.254	0.254	0.000	0.000	0.000	0.000
144	Z	168	ALA	0	0.008	0.011	31.610	-0.322	-0.322	0.000	0.000	0.000	0.000
145	Z	169	VAL	0	-0.002	0.003	33.554	-0.003	-0.003	0.000	0.000	0.000	0.000
146	Z	170	LEU	0	0.007	0.009	34.486	-0.040	-0.040	0.000	0.000	0.000	0.000
147	Z	171	GLN	0	0.004	0.007	37.183	-0.317	-0.317	0.000	0.000	0.000	0.000
148	Z	172	SER	0	0.026	0.002	40.735	0.098	0.098	0.000	0.000	0.000	0.000
149	Z	173	SER	0	0.013	-0.005	42.555	0.005	0.005	0.000	0.000	0.000	0.000
150	Z	174	GLY	0	-0.002	-0.002	39.100	0.050	0.050	0.000	0.000	0.000	0.000
151	Z	175	LEU	0	-0.069	-0.023	37.281	0.263	0.263	0.000	0.000	0.000	0.000
152	Z	176	TYR	0	0.016	0.010	31.972	-0.153	-0.153	0.000	0.000	0.000	0.000
153	Z	177	SER	0	-0.013	-0.007	35.966	-0.195	-0.195	0.000	0.000	0.000	0.000
154	Z	178	LEU	0	0.030	0.030	31.812	0.029	0.029	0.000	0.000	0.000	0.000
155	Z	179	SER	0	0.028	0.016	35.770	-0.237	-0.237	0.000	0.000	0.000	0.000
156	Z	195	ILE	0	0.015	-0.012	37.686	-0.067	-0.067	0.000	0.000	0.000	0.000
157	Z	196	CYS	0	-0.017	-0.007	36.568	0.321	0.321	0.000	0.000	0.000	0.000
158	Z	197	ASN	0	-0.025	-0.009	31.845	0.020	0.020	0.000	0.000	0.000	0.000
159	Z	198	VAL	0	0.043	0.024	32.493	0.289	0.289	0.000	0.000	0.000	0.000
160	Z	199	ASN	0	-0.025	-0.018	28.297	-0.077	-0.077	0.000	0.000	0.000	0.000
161	Z	200	HIS	0	0.058	0.041	29.163	0.218	0.218	0.000	0.000	0.000	0.000
162	Z	201	LYS	1	1.003	0.996	22.824	-13.495	-13.495	0.000	0.000	0.000	0.000
163	Z	202	PRO	0	-0.017	0.000	26.858	0.149	0.149	0.000	0.000	0.000	0.000
164	Z	203	SER	0	-0.068	-0.036	28.693	-0.115	-0.115	0.000	0.000	0.000	0.000
165	Z	204	ASN	0	-0.027	-0.005	29.415	0.063	0.063	0.000	0.000	0.000	0.000
166	Z	205	THR	0	0.021	0.005	31.317	-0.172	-0.172	0.000	0.000	0.000	0.000

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