FMO DATABASE

FMODB ID: MV2MZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1449261.969502
FMO2-HF: Nuclear repulsion	1387883.035461
FMO2-HF: Total energy	-61378.934041
FMO2-MP2: Total energy	-61558.677441

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.
-9.883	-1.428	5.276	-5.254	-8.478	-0.024

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 : -0.040 / q_NPA : -0.037

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	0.003	-0.011	3.236	-1.829	1.264	0.062	-1.464	-1.691	-0.001
4	X	5	VAL	0	-0.014	0.001	5.050	0.205	0.235	-0.001	-0.003	-0.026	0.000
5	X	6	GLU	-1	-0.753	-0.884	8.723	-0.573	-0.573	0.000	0.000	0.000	0.000
6	X	7	SER	0	-0.044	0.000	11.298	0.051	0.051	0.000	0.000	0.000	0.000
7	X	8	GLY	0	0.022	0.020	14.863	-0.021	-0.021	0.000	0.000	0.000	0.000
8	X	9	ALA	0	-0.003	0.005	17.828	-0.003	-0.003	0.000	0.000	0.000	0.000
9	X	10	GLU	-1	-0.902	-0.957	20.484	-0.122	-0.122	0.000	0.000	0.000	0.000
10	X	11	VAL	0	-0.052	-0.022	23.275	-0.005	-0.005	0.000	0.000	0.000	0.000
11	X	12	LYS	1	0.861	0.903	24.408	0.114	0.114	0.000	0.000	0.000	0.000
12	X	13	LYS	1	0.981	1.001	28.322	0.065	0.065	0.000	0.000	0.000	0.000
13	X	14	PRO	0	0.036	0.026	31.443	-0.001	-0.001	0.000	0.000	0.000	0.000
14	X	15	GLY	0	0.034	0.029	31.464	0.007	0.007	0.000	0.000	0.000	0.000
15	X	16	SER	0	-0.115	-0.071	29.255	-0.001	-0.001	0.000	0.000	0.000	0.000
16	X	17	SER	0	0.080	0.015	26.020	-0.003	-0.003	0.000	0.000	0.000	0.000
17	X	18	VAL	0	-0.041	-0.008	20.717	0.007	0.007	0.000	0.000	0.000	0.000
18	X	19	LYS	1	1.006	1.007	18.726	0.081	0.081	0.000	0.000	0.000	0.000
19	X	20	VAL	0	0.034	0.051	14.257	0.009	0.009	0.000	0.000	0.000	0.000
20	X	21	SER	0	-0.002	-0.015	13.564	-0.018	-0.018	0.000	0.000	0.000	0.000
21	X	22	CYS	0	0.007	0.007	8.348	-0.060	-0.060	0.000	0.000	0.000	0.000
22	X	23	LYS	1	0.878	0.954	8.127	0.124	0.124	0.000	0.000	0.000	0.000
23	X	24	ALA	0	0.063	0.033	3.236	-0.577	-0.272	0.053	-0.071	-0.287	0.000
24	X	25	SER	0	0.007	0.016	4.355	0.048	0.311	0.000	-0.051	-0.212	0.000
25	X	26	GLY	0	0.040	0.005	2.049	-2.827	-0.882	3.771	-3.371	-2.345	-0.017
26	X	27	GLY	0	0.000	0.010	3.031	-0.350	-0.210	0.118	0.537	-0.795	-0.003
27	X	28	THR	0	0.013	-0.001	4.072	-0.363	-0.293	0.001	-0.011	-0.060	0.000
28	X	29	PHE	0	0.101	0.055	7.127	-0.009	-0.009	0.000	0.000	0.000	0.000
29	X	30	ILE	0	0.049	0.013	8.422	-0.069	-0.069	0.000	0.000	0.000	0.000
30	X	31	THR	0	-0.080	-0.045	5.338	-0.021	-0.021	0.000	0.000	0.000	0.000
31	X	32	HIS	0	-0.061	-0.022	3.202	-0.927	-0.307	0.088	-0.202	-0.506	0.000
32	X	33	VAL	0	0.036	0.026	6.373	0.028	0.028	0.000	0.000	0.000	0.000
33	X	34	PHE	0	-0.025	-0.007	7.492	-0.138	-0.138	0.000	0.000	0.000	0.000
34	X	35	THR	0	-0.015	-0.016	9.234	0.094	0.094	0.000	0.000	0.000	0.000
35	X	36	TRP	0	0.010	0.006	11.372	-0.076	-0.076	0.000	0.000	0.000	0.000
36	X	37	VAL	0	-0.001	-0.004	14.027	0.047	0.047	0.000	0.000	0.000	0.000
37	X	38	ARG	1	0.834	0.899	16.036	0.176	0.176	0.000	0.000	0.000	0.000
38	X	39	GLN	0	-0.010	-0.006	18.767	-0.019	-0.019	0.000	0.000	0.000	0.000
39	X	40	ALA	0	0.040	0.028	20.967	0.005	0.005	0.000	0.000	0.000	0.000
40	X	41	PRO	0	0.041	0.007	24.505	-0.006	-0.006	0.000	0.000	0.000	0.000
41	X	42	GLY	0	-0.039	-0.014	26.057	0.013	0.013	0.000	0.000	0.000	0.000
42	X	43	GLN	0	-0.004	0.003	26.151	0.002	0.002	0.000	0.000	0.000	0.000
43	X	44	GLY	0	0.020	0.008	23.282	-0.014	-0.014	0.000	0.000	0.000	0.000
44	X	45	LEU	0	-0.038	-0.025	17.584	0.002	0.002	0.000	0.000	0.000	0.000
45	X	46	GLU	-1	-0.841	-0.905	20.454	-0.176	-0.176	0.000	0.000	0.000	0.000
46	X	47	TRP	0	-0.050	-0.024	14.907	0.000	0.000	0.000	0.000	0.000	0.000
47	X	48	VAL	0	-0.018	-0.005	17.295	0.027	0.027	0.000	0.000	0.000	0.000
48	X	49	GLY	0	0.011	-0.016	16.882	0.029	0.029	0.000	0.000	0.000	0.000
49	X	50	GLY	0	0.025	0.020	13.585	-0.049	-0.049	0.000	0.000	0.000	0.000
50	X	51	PHE	0	0.007	0.003	11.458	0.041	0.041	0.000	0.000	0.000	0.000
51	X	52	ILE	0	0.008	0.017	11.528	-0.036	-0.036	0.000	0.000	0.000	0.000
52	X	52	ALA	0	0.014	0.012	10.026	0.025	0.025	0.000	0.000	0.000	0.000
53	X	53	ILE	0	-0.036	-0.019	11.891	0.025	0.025	0.000	0.000	0.000	0.000
54	X	54	PHE	0	-0.035	-0.017	13.866	0.008	0.008	0.000	0.000	0.000	0.000
55	X	55	GLY	0	0.016	0.022	15.304	0.007	0.007	0.000	0.000	0.000	0.000
56	X	56	THR	0	-0.015	-0.001	16.664	-0.001	-0.001	0.000	0.000	0.000	0.000
57	X	57	SER	0	0.011	-0.005	16.117	-0.016	-0.016	0.000	0.000	0.000	0.000
58	X	58	ASN	0	-0.052	-0.011	17.068	0.009	0.009	0.000	0.000	0.000	0.000
59	X	59	TYR	0	0.081	0.027	18.150	-0.020	-0.020	0.000	0.000	0.000	0.000
60	X	60	ALA	0	0.069	0.038	20.882	0.004	0.004	0.000	0.000	0.000	0.000
61	X	61	GLN	0	-0.018	-0.005	22.975	0.002	0.002	0.000	0.000	0.000	0.000
62	X	62	LYS	1	1.000	0.991	26.593	0.123	0.123	0.000	0.000	0.000	0.000
63	X	63	PHE	0	-0.025	-0.012	22.616	-0.005	-0.005	0.000	0.000	0.000	0.000
64	X	64	GLN	0	0.023	-0.023	26.208	-0.002	-0.002	0.000	0.000	0.000	0.000
65	X	65	GLY	0	-0.005	0.013	27.016	0.004	0.004	0.000	0.000	0.000	0.000
66	X	66	ARG	1	0.844	0.944	26.294	0.128	0.128	0.000	0.000	0.000	0.000
67	X	67	VAL	0	0.018	0.001	20.145	-0.001	-0.001	0.000	0.000	0.000	0.000
68	X	68	THR	0	-0.008	-0.006	21.727	0.005	0.005	0.000	0.000	0.000	0.000
69	X	69	ILE	0	-0.052	-0.007	15.406	-0.002	-0.002	0.000	0.000	0.000	0.000
70	X	70	THR	0	-0.048	-0.023	16.662	0.019	0.019	0.000	0.000	0.000	0.000
71	X	71	ALA	0	-0.009	-0.012	12.689	-0.029	-0.029	0.000	0.000	0.000	0.000
72	X	72	ASP	-1	-0.768	-0.836	13.747	0.058	0.058	0.000	0.000	0.000	0.000
73	X	73	GLU	-1	-0.941	-0.979	11.890	0.134	0.134	0.000	0.000	0.000	0.000
74	X	74	SER	0	-0.034	0.000	12.157	0.046	0.046	0.000	0.000	0.000	0.000
75	X	75	THR	0	-0.123	-0.086	12.376	0.022	0.022	0.000	0.000	0.000	0.000
76	X	76	SER	0	-0.025	-0.002	6.457	0.000	0.000	0.000	0.000	0.000	0.000
77	X	77	THR	0	0.008	-0.030	8.337	-0.085	-0.085	0.000	0.000	0.000	0.000
78	X	78	ALA	0	0.001	0.009	10.682	0.043	0.043	0.000	0.000	0.000	0.000
79	X	79	TYR	0	-0.062	-0.046	12.177	-0.034	-0.034	0.000	0.000	0.000	0.000
80	X	80	MET	0	0.023	0.028	15.276	0.021	0.021	0.000	0.000	0.000	0.000
81	X	81	GLU	-1	-0.953	-0.985	17.168	-0.097	-0.097	0.000	0.000	0.000	0.000
82	X	82	LEU	0	0.027	0.021	20.799	0.001	0.001	0.000	0.000	0.000	0.000
83	X	82	THR	0	-0.002	-0.016	23.291	0.005	0.005	0.000	0.000	0.000	0.000
84	X	82	SER	0	-0.011	-0.006	26.972	-0.002	-0.002	0.000	0.000	0.000	0.000
85	X	82	LEU	0	-0.075	-0.014	24.881	-0.002	-0.002	0.000	0.000	0.000	0.000
86	X	83	THR	0	0.062	0.035	28.964	0.007	0.007	0.000	0.000	0.000	0.000
87	X	84	SER	0	0.012	-0.011	29.581	-0.005	-0.005	0.000	0.000	0.000	0.000
88	X	85	GLU	-1	-0.910	-0.947	29.111	-0.119	-0.119	0.000	0.000	0.000	0.000
89	X	86	ASP	-1	-0.818	-0.894	24.970	-0.147	-0.147	0.000	0.000	0.000	0.000
90	X	87	THR	0	-0.057	-0.058	24.194	-0.011	-0.011	0.000	0.000	0.000	0.000
91	X	88	ALA	0	-0.014	-0.008	21.433	0.001	0.001	0.000	0.000	0.000	0.000
92	X	89	VAL	0	-0.043	-0.006	17.014	0.010	0.010	0.000	0.000	0.000	0.000
93	X	90	TYR	0	-0.026	-0.022	16.456	0.000	0.000	0.000	0.000	0.000	0.000
94	X	91	TYR	0	-0.003	0.009	12.585	-0.010	-0.010	0.000	0.000	0.000	0.000
95	X	93	ALA	0	0.042	0.005	7.830	-0.162	-0.162	0.000	0.000	0.000	0.000
96	X	94	ARG	1	0.939	0.972	2.489	-0.878	0.546	1.091	-0.484	-2.031	-0.002
97	X	95	GLY	0	0.026	0.017	6.413	-0.089	-0.089	0.000	0.000	0.000	0.000
98	X	96	ILE	0	-0.011	0.015	7.848	0.033	0.033	0.000	0.000	0.000	0.000
99	X	97	SER	0	0.080	0.030	9.590	0.029	0.029	0.000	0.000	0.000	0.000
100	X	98	GLY	0	0.072	0.025	12.585	-0.020	-0.020	0.000	0.000	0.000	0.000
101	X	99	SER	0	-0.075	-0.055	15.215	0.015	0.015	0.000	0.000	0.000	0.000
102	X	100	TYR	0	-0.047	-0.027	12.381	-0.012	-0.012	0.000	0.000	0.000	0.000
103	X	100	GLY	0	-0.054	-0.033	12.146	0.000	0.000	0.000	0.000	0.000	0.000
104	X	100	TRP	0	0.027	0.023	9.382	0.099	0.099	0.000	0.000	0.000	0.000
105	X	100	PHE	0	-0.028	-0.038	9.531	-0.026	-0.026	0.000	0.000	0.000	0.000
106	X	101	ASP	-1	-0.925	-0.968	6.474	-1.797	-1.797	0.000	0.000	0.000	0.000
107	X	102	PRO	0	-0.007	0.017	2.936	-0.728	-0.163	0.093	-0.134	-0.525	-0.001
108	X	103	TRP	0	-0.005	-0.020	5.952	0.369	0.369	0.000	0.000	0.000	0.000
109	X	104	GLY	0	-0.033	-0.011	8.730	-0.120	-0.120	0.000	0.000	0.000	0.000
110	X	105	GLN	0	-0.007	-0.022	9.215	0.091	0.091	0.000	0.000	0.000	0.000
111	X	106	GLY	0	-0.009	-0.014	12.772	0.065	0.065	0.000	0.000	0.000	0.000
112	X	107	THR	0	-0.038	-0.014	14.692	0.012	0.012	0.000	0.000	0.000	0.000
113	X	108	LEU	0	-0.014	-0.005	16.798	0.007	0.007	0.000	0.000	0.000	0.000
114	X	109	VAL	0	0.001	0.004	20.131	0.021	0.021	0.000	0.000	0.000	0.000
115	X	110	THR	0	-0.009	-0.015	22.587	0.006	0.006	0.000	0.000	0.000	0.000
116	X	111	VAL	0	-0.010	0.002	26.207	0.008	0.008	0.000	0.000	0.000	0.000
117	X	112	SER	0	-0.009	-0.025	28.567	0.004	0.004	0.000	0.000	0.000	0.000
118	X	113	SER	0	0.022	0.007	32.247	0.001	0.001	0.000	0.000	0.000	0.000
119	X	114	ALA	0	-0.019	0.010	34.488	0.005	0.005	0.000	0.000	0.000	0.000
120	X	115	SER	0	0.026	-0.005	32.794	-0.002	-0.002	0.000	0.000	0.000	0.000
121	X	116	THR	0	-0.008	0.006	29.550	0.001	0.001	0.000	0.000	0.000	0.000
122	X	117	LYS	1	0.929	0.954	32.555	0.066	0.066	0.000	0.000	0.000	0.000
123	X	118	GLY	0	-0.005	0.004	34.355	-0.005	-0.005	0.000	0.000	0.000	0.000
124	X	119	PRO	0	0.013	0.022	34.484	0.000	0.000	0.000	0.000	0.000	0.000
125	X	120	SER	0	-0.010	0.002	37.087	0.004	0.004	0.000	0.000	0.000	0.000
126	X	141	LEU	0	-0.026	-0.029	39.836	-0.001	-0.001	0.000	0.000	0.000	0.000
127	X	142	VAL	0	-0.028	-0.002	35.359	0.003	0.003	0.000	0.000	0.000	0.000
128	X	143	LYS	1	0.903	0.939	37.409	0.061	0.061	0.000	0.000	0.000	0.000
129	X	144	ASP	-1	-0.823	-0.928	37.629	-0.064	-0.064	0.000	0.000	0.000	0.000
130	X	145	TYR	0	-0.009	0.000	30.359	0.005	0.005	0.000	0.000	0.000	0.000
131	X	146	PHE	0	0.023	0.020	30.979	-0.006	-0.006	0.000	0.000	0.000	0.000
132	X	147	PRO	0	-0.035	-0.033	26.522	0.009	0.009	0.000	0.000	0.000	0.000
133	X	148	GLU	-1	-0.875	-0.985	27.565	-0.143	-0.143	0.000	0.000	0.000	0.000
134	X	149	PRO	0	-0.010	0.051	23.605	-0.009	-0.009	0.000	0.000	0.000	0.000
135	X	150	VAL	0	-0.034	-0.029	25.694	0.015	0.015	0.000	0.000	0.000	0.000
136	X	165	THR	0	-0.054	-0.044	31.472	-0.004	-0.004	0.000	0.000	0.000	0.000
137	X	166	PHE	0	0.011	-0.007	32.438	0.002	0.002	0.000	0.000	0.000	0.000
138	X	167	PRO	0	0.028	0.039	29.714	-0.004	-0.004	0.000	0.000	0.000	0.000
139	X	168	ALA	0	0.017	0.002	30.405	0.010	0.010	0.000	0.000	0.000	0.000
140	X	169	VAL	0	-0.003	-0.005	32.086	-0.005	-0.005	0.000	0.000	0.000	0.000
141	X	170	LEU	0	0.002	-0.004	31.585	0.005	0.005	0.000	0.000	0.000	0.000
142	X	171	GLN	0	-0.007	0.011	34.782	0.006	0.006	0.000	0.000	0.000	0.000
143	X	172	SER	0	0.051	0.015	38.091	-0.003	-0.003	0.000	0.000	0.000	0.000
144	X	173	SER	0	-0.019	-0.018	40.421	-0.001	-0.001	0.000	0.000	0.000	0.000
145	X	174	GLY	0	0.013	0.016	36.239	0.001	0.001	0.000	0.000	0.000	0.000
146	X	175	LEU	0	-0.078	-0.018	34.949	-0.004	-0.004	0.000	0.000	0.000	0.000
147	X	176	TYR	0	0.020	0.004	28.956	0.001	0.001	0.000	0.000	0.000	0.000
148	X	177	SER	0	0.009	-0.001	34.248	0.007	0.007	0.000	0.000	0.000	0.000
149	X	178	LEU	0	0.025	0.034	31.435	-0.004	-0.004	0.000	0.000	0.000	0.000
150	X	179	SER	0	0.009	-0.016	35.048	0.005	0.005	0.000	0.000	0.000	0.000
151	X	180	SER	0	0.022	0.033	35.674	-0.003	-0.003	0.000	0.000	0.000	0.000
152	X	196	CYS	0	-0.009	-0.008	33.237	-0.001	-0.001	0.000	0.000	0.000	0.000
153	X	197	ASN	0	0.004	0.011	33.962	-0.003	-0.003	0.000	0.000	0.000	0.000
154	X	198	VAL	0	0.048	0.017	33.759	-0.004	-0.004	0.000	0.000	0.000	0.000
155	X	199	ASN	0	0.015	-0.002	29.249	0.006	0.006	0.000	0.000	0.000	0.000
156	X	200	HIS	1	0.893	0.961	29.769	0.073	0.073	0.000	0.000	0.000	0.000
157	X	201	LYS	1	0.998	0.982	24.200	0.103	0.103	0.000	0.000	0.000	0.000
158	X	202	PRO	0	0.025	0.024	26.269	0.004	0.004	0.000	0.000	0.000	0.000
159	X	203	SER	0	-0.018	-0.011	27.916	0.004	0.004	0.000	0.000	0.000	0.000
160	X	204	ASN	0	-0.064	-0.026	28.816	0.010	0.010	0.000	0.000	0.000	0.000
161	X	205	THR	0	0.040	0.023	31.432	0.004	0.004	0.000	0.000	0.000	0.000
162	X	206	LYS	1	0.941	0.973	30.391	0.041	0.041	0.000	0.000	0.000	0.000
163	X	207	VAL	0	0.031	0.021	34.816	0.003	0.003	0.000	0.000	0.000	0.000

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