FMO DATABASE

FMODB ID: 2J5KR

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1450954.84459
FMO2-HF: Nuclear repulsion	1389573.861453
FMO2-HF: Total energy	-61380.983137
FMO2-MP2: Total energy	-61560.64257

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.
-11.673	-1.987	4.256	-5.213	-8.731	-0.027

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 : -0.022 / q_NPA : -0.010

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	-0.016	-0.020	3.061	-1.822	1.734	0.223	-1.856	-1.923	0.002
4	X	5	VAL	0	-0.002	0.002	5.010	0.079	0.101	-0.001	-0.003	-0.017	0.000
5	X	6	GLU	-1	-0.751	-0.861	8.692	-0.619	-0.619	0.000	0.000	0.000	0.000
6	X	7	SER	0	-0.017	0.012	11.538	0.041	0.041	0.000	0.000	0.000	0.000
7	X	8	GLY	0	0.009	0.002	15.174	-0.032	-0.032	0.000	0.000	0.000	0.000
8	X	9	ALA	0	-0.011	-0.002	17.892	0.016	0.016	0.000	0.000	0.000	0.000
9	X	10	GLU	-1	-0.822	-0.915	20.411	-0.145	-0.145	0.000	0.000	0.000	0.000
10	X	11	VAL	0	-0.038	-0.023	23.094	-0.002	-0.002	0.000	0.000	0.000	0.000
11	X	12	LYS	1	0.779	0.896	23.642	0.146	0.146	0.000	0.000	0.000	0.000
12	X	13	LYS	1	0.983	0.998	28.671	0.082	0.082	0.000	0.000	0.000	0.000
13	X	14	PRO	0	0.042	0.022	31.356	0.000	0.000	0.000	0.000	0.000	0.000
14	X	15	GLY	0	-0.005	0.010	32.082	0.005	0.005	0.000	0.000	0.000	0.000
15	X	16	SER	0	-0.078	-0.052	29.783	0.002	0.002	0.000	0.000	0.000	0.000
16	X	17	SER	0	0.047	0.008	25.576	0.000	0.000	0.000	0.000	0.000	0.000
17	X	18	VAL	0	-0.034	-0.012	20.640	-0.004	-0.004	0.000	0.000	0.000	0.000
18	X	19	LYS	1	0.861	0.914	18.528	0.080	0.080	0.000	0.000	0.000	0.000
19	X	20	VAL	0	0.022	0.037	14.326	-0.008	-0.008	0.000	0.000	0.000	0.000
20	X	21	SER	0	-0.011	-0.014	13.940	0.036	0.036	0.000	0.000	0.000	0.000
21	X	22	CYS	0	-0.071	-0.032	8.433	-0.015	-0.015	0.000	0.000	0.000	0.000
22	X	23	LYS	1	0.866	0.941	7.626	0.231	0.231	0.000	0.000	0.000	0.000
23	X	24	ALA	0	0.035	0.026	3.297	-0.675	-0.382	0.040	-0.076	-0.258	0.000
24	X	25	SER	0	-0.030	-0.006	3.305	0.010	0.609	0.036	-0.185	-0.450	-0.001
25	X	26	GLY	0	0.053	0.008	2.224	-3.902	-2.000	2.636	-2.390	-2.149	-0.018
26	X	27	GLY	0	0.012	0.009	3.064	0.456	0.922	0.394	0.208	-1.068	-0.004
27	X	28	THR	0	0.009	0.004	3.821	-0.711	-0.680	0.001	0.041	-0.072	0.000
28	X	29	PHE	0	0.104	0.059	6.527	0.232	0.232	0.000	0.000	0.000	0.000
29	X	30	ILE	0	0.064	0.017	7.916	0.000	0.000	0.000	0.000	0.000	0.000
30	X	31	THR	0	-0.076	-0.051	4.858	-0.045	-0.045	0.000	0.000	0.000	0.000
31	X	32	HIS	0	-0.020	0.014	3.216	-0.792	0.039	0.075	-0.320	-0.587	-0.001
32	X	33	VAL	0	0.001	0.002	6.167	-0.102	-0.102	0.000	0.000	0.000	0.000
33	X	34	PHE	0	0.020	0.011	7.166	-0.097	-0.097	0.000	0.000	0.000	0.000
34	X	35	THR	0	-0.021	-0.026	8.941	0.061	0.061	0.000	0.000	0.000	0.000
35	X	36	TRP	0	0.018	0.000	11.289	-0.075	-0.075	0.000	0.000	0.000	0.000
36	X	37	VAL	0	-0.011	-0.004	14.020	0.055	0.055	0.000	0.000	0.000	0.000
37	X	38	ARG	1	0.760	0.835	16.188	0.125	0.125	0.000	0.000	0.000	0.000
38	X	39	GLN	0	0.027	0.015	18.950	-0.027	-0.027	0.000	0.000	0.000	0.000
39	X	40	ALA	0	0.052	0.039	21.335	-0.006	-0.006	0.000	0.000	0.000	0.000
40	X	41	PRO	0	0.003	-0.021	24.819	-0.009	-0.009	0.000	0.000	0.000	0.000
41	X	42	GLY	0	-0.002	0.005	26.216	0.016	0.016	0.000	0.000	0.000	0.000
42	X	43	GLN	0	-0.042	-0.003	25.782	0.016	0.016	0.000	0.000	0.000	0.000
43	X	44	GLY	0	0.024	0.009	23.775	-0.020	-0.020	0.000	0.000	0.000	0.000
44	X	45	LEU	0	-0.023	-0.012	17.331	-0.003	-0.003	0.000	0.000	0.000	0.000
45	X	46	GLU	-1	-0.798	-0.865	20.302	-0.136	-0.136	0.000	0.000	0.000	0.000
46	X	47	TRP	0	-0.026	-0.011	15.125	-0.004	-0.004	0.000	0.000	0.000	0.000
47	X	48	VAL	0	0.001	0.001	17.592	0.021	0.021	0.000	0.000	0.000	0.000
48	X	49	GLY	0	0.034	-0.005	17.169	0.030	0.030	0.000	0.000	0.000	0.000
49	X	50	GLY	0	-0.020	0.005	13.592	-0.048	-0.048	0.000	0.000	0.000	0.000
50	X	51	PHE	0	0.000	0.009	11.053	0.018	0.018	0.000	0.000	0.000	0.000
51	X	52	ILE	0	-0.005	0.021	11.079	0.030	0.030	0.000	0.000	0.000	0.000
52	X	52	ALA	0	0.007	0.010	9.494	-0.012	-0.012	0.000	0.000	0.000	0.000
53	X	53	ILE	0	-0.039	-0.016	11.406	-0.010	-0.010	0.000	0.000	0.000	0.000
54	X	54	PHE	0	-0.040	-0.030	13.301	-0.022	-0.022	0.000	0.000	0.000	0.000
55	X	55	GLY	0	0.021	0.024	14.897	-0.027	-0.027	0.000	0.000	0.000	0.000
56	X	56	THR	0	-0.023	-0.009	16.284	-0.025	-0.025	0.000	0.000	0.000	0.000
57	X	57	SER	0	0.006	-0.013	15.958	0.011	0.011	0.000	0.000	0.000	0.000
58	X	58	ASN	0	-0.034	-0.002	17.101	0.018	0.018	0.000	0.000	0.000	0.000
59	X	59	TYR	0	0.089	0.033	18.200	-0.019	-0.019	0.000	0.000	0.000	0.000
60	X	60	ALA	0	0.034	0.031	20.828	0.013	0.013	0.000	0.000	0.000	0.000
61	X	61	GLN	0	-0.019	-0.003	22.579	-0.005	-0.005	0.000	0.000	0.000	0.000
62	X	62	LYS	1	0.890	0.941	26.095	0.059	0.059	0.000	0.000	0.000	0.000
63	X	63	PHE	0	0.057	0.017	23.031	-0.005	-0.005	0.000	0.000	0.000	0.000
64	X	64	GLN	0	0.030	0.011	26.331	0.000	0.000	0.000	0.000	0.000	0.000
65	X	65	GLY	0	-0.003	-0.002	27.426	-0.001	-0.001	0.000	0.000	0.000	0.000
66	X	66	ARG	1	0.775	0.859	26.421	0.094	0.094	0.000	0.000	0.000	0.000
67	X	67	VAL	0	-0.001	-0.002	20.529	-0.007	-0.007	0.000	0.000	0.000	0.000
68	X	68	THR	0	-0.028	-0.007	21.613	0.015	0.015	0.000	0.000	0.000	0.000
69	X	69	ILE	0	-0.010	-0.003	15.089	-0.014	-0.014	0.000	0.000	0.000	0.000
70	X	70	THR	0	-0.020	0.003	16.497	0.022	0.022	0.000	0.000	0.000	0.000
71	X	71	ALA	0	-0.004	-0.011	12.390	-0.025	-0.025	0.000	0.000	0.000	0.000
72	X	72	ASP	-1	-0.761	-0.828	13.134	0.147	0.147	0.000	0.000	0.000	0.000
73	X	73	GLU	-1	-0.918	-0.954	11.539	0.393	0.393	0.000	0.000	0.000	0.000
74	X	74	SER	0	-0.083	-0.059	11.741	0.048	0.048	0.000	0.000	0.000	0.000
75	X	75	THR	0	-0.061	-0.051	12.173	-0.018	-0.018	0.000	0.000	0.000	0.000
76	X	76	SER	0	-0.015	-0.025	6.104	0.020	0.020	0.000	0.000	0.000	0.000
77	X	77	THR	0	-0.013	-0.013	7.985	-0.123	-0.123	0.000	0.000	0.000	0.000
78	X	78	ALA	0	0.018	0.019	10.424	0.066	0.066	0.000	0.000	0.000	0.000
79	X	79	TYR	0	-0.004	-0.024	11.843	-0.091	-0.091	0.000	0.000	0.000	0.000
80	X	80	MET	0	-0.020	0.003	14.983	0.040	0.040	0.000	0.000	0.000	0.000
81	X	81	GLU	-1	-0.850	-0.907	17.089	-0.085	-0.085	0.000	0.000	0.000	0.000
82	X	82	LEU	0	0.012	0.003	20.732	0.008	0.008	0.000	0.000	0.000	0.000
83	X	82	THR	0	0.008	-0.012	23.296	-0.005	-0.005	0.000	0.000	0.000	0.000
84	X	82	SER	0	0.012	0.007	27.036	0.000	0.000	0.000	0.000	0.000	0.000
85	X	82	LEU	0	-0.043	0.005	24.816	-0.002	-0.002	0.000	0.000	0.000	0.000
86	X	83	THR	0	0.034	-0.003	28.941	0.007	0.007	0.000	0.000	0.000	0.000
87	X	84	SER	0	0.059	0.011	29.290	-0.006	-0.006	0.000	0.000	0.000	0.000
88	X	85	GLU	-1	-0.949	-0.958	29.524	-0.110	-0.110	0.000	0.000	0.000	0.000
89	X	86	ASP	-1	-0.752	-0.807	25.208	-0.123	-0.123	0.000	0.000	0.000	0.000
90	X	87	THR	0	-0.054	-0.029	24.500	-0.017	-0.017	0.000	0.000	0.000	0.000
91	X	88	ALA	0	0.014	0.005	21.625	0.001	0.001	0.000	0.000	0.000	0.000
92	X	89	VAL	0	-0.003	0.015	17.139	0.002	0.002	0.000	0.000	0.000	0.000
93	X	90	TYR	0	-0.024	-0.043	16.645	0.017	0.017	0.000	0.000	0.000	0.000
94	X	91	TYR	0	0.000	-0.004	12.761	-0.034	-0.034	0.000	0.000	0.000	0.000
95	X	93	ALA	0	0.036	0.007	7.849	-0.179	-0.179	0.000	0.000	0.000	0.000
96	X	94	ARG	1	0.894	0.947	2.812	-2.962	-1.592	0.774	-0.486	-1.659	-0.004
97	X	95	GLY	0	0.050	0.034	6.602	-0.146	-0.146	0.000	0.000	0.000	0.000
98	X	96	ILE	0	-0.030	-0.009	7.767	0.190	0.190	0.000	0.000	0.000	0.000
99	X	97	SER	0	-0.013	-0.014	9.963	-0.080	-0.080	0.000	0.000	0.000	0.000
100	X	98	GLY	0	0.065	0.010	12.668	-0.033	-0.033	0.000	0.000	0.000	0.000
101	X	99	SER	0	-0.035	-0.017	15.292	-0.021	-0.021	0.000	0.000	0.000	0.000
102	X	100	TYR	0	-0.072	-0.045	12.791	-0.030	-0.030	0.000	0.000	0.000	0.000
103	X	100	GLY	0	0.037	0.024	13.613	-0.038	-0.038	0.000	0.000	0.000	0.000
104	X	100	TRP	0	0.014	-0.015	9.843	0.037	0.037	0.000	0.000	0.000	0.000
105	X	100	PHE	0	-0.016	-0.014	9.632	0.035	0.035	0.000	0.000	0.000	0.000
106	X	101	ASP	-1	-0.909	-0.940	6.148	-1.449	-1.449	0.000	0.000	0.000	0.000
107	X	102	PRO	0	-0.006	-0.002	3.118	-0.802	-0.186	0.078	-0.146	-0.548	-0.001
108	X	103	TRP	0	-0.029	-0.032	5.944	0.615	0.615	0.000	0.000	0.000	0.000
109	X	104	GLY	0	-0.004	0.004	8.497	-0.281	-0.281	0.000	0.000	0.000	0.000
110	X	105	GLN	0	-0.059	-0.045	9.659	0.049	0.049	0.000	0.000	0.000	0.000
111	X	106	GLY	0	0.005	-0.008	13.062	0.086	0.086	0.000	0.000	0.000	0.000
112	X	107	THR	0	-0.044	-0.022	14.843	0.027	0.027	0.000	0.000	0.000	0.000
113	X	108	LEU	0	-0.013	-0.001	16.705	0.029	0.029	0.000	0.000	0.000	0.000
114	X	109	VAL	0	-0.004	0.001	19.977	0.015	0.015	0.000	0.000	0.000	0.000
115	X	110	THR	0	-0.001	-0.004	22.498	0.008	0.008	0.000	0.000	0.000	0.000
116	X	111	VAL	0	-0.018	-0.020	26.216	0.007	0.007	0.000	0.000	0.000	0.000
117	X	112	SER	0	0.020	0.008	28.926	0.005	0.005	0.000	0.000	0.000	0.000
118	X	113	SER	0	0.024	-0.002	32.686	0.001	0.001	0.000	0.000	0.000	0.000
119	X	114	ALA	0	-0.020	0.015	34.191	0.004	0.004	0.000	0.000	0.000	0.000
120	X	115	SER	0	0.038	0.014	33.149	-0.002	-0.002	0.000	0.000	0.000	0.000
121	X	116	THR	0	0.033	0.007	29.824	0.002	0.002	0.000	0.000	0.000	0.000
122	X	117	LYS	1	0.837	0.913	32.629	0.115	0.115	0.000	0.000	0.000	0.000
123	X	118	GLY	0	0.019	0.020	34.041	-0.009	-0.009	0.000	0.000	0.000	0.000
124	X	119	PRO	0	-0.013	0.002	34.630	0.003	0.003	0.000	0.000	0.000	0.000
125	X	120	SER	0	0.007	0.018	37.238	0.004	0.004	0.000	0.000	0.000	0.000
126	X	141	LEU	0	-0.031	-0.023	39.973	-0.002	-0.002	0.000	0.000	0.000	0.000
127	X	142	VAL	0	-0.043	-0.011	35.156	0.003	0.003	0.000	0.000	0.000	0.000
128	X	143	LYS	1	0.882	0.914	37.126	0.098	0.098	0.000	0.000	0.000	0.000
129	X	144	ASP	-1	-0.729	-0.865	37.659	-0.105	-0.105	0.000	0.000	0.000	0.000
130	X	145	TYR	0	0.012	0.025	30.939	0.005	0.005	0.000	0.000	0.000	0.000
131	X	146	PHE	0	0.007	0.003	30.716	-0.003	-0.003	0.000	0.000	0.000	0.000
132	X	147	PRO	0	0.020	0.007	26.931	0.007	0.007	0.000	0.000	0.000	0.000
133	X	148	GLU	-1	-0.823	-0.917	26.755	-0.207	-0.207	0.000	0.000	0.000	0.000
134	X	149	PRO	0	0.004	0.005	23.643	-0.006	-0.006	0.000	0.000	0.000	0.000
135	X	150	VAL	0	-0.013	-0.014	26.304	0.018	0.018	0.000	0.000	0.000	0.000
136	X	165	THR	0	-0.019	-0.015	31.885	-0.004	-0.004	0.000	0.000	0.000	0.000
137	X	166	PHE	0	-0.016	-0.014	33.023	0.002	0.002	0.000	0.000	0.000	0.000
138	X	167	PRO	0	0.029	0.022	29.323	-0.008	-0.008	0.000	0.000	0.000	0.000
139	X	168	ALA	0	-0.035	-0.022	30.321	0.013	0.013	0.000	0.000	0.000	0.000
140	X	169	VAL	0	-0.003	0.004	32.297	-0.001	-0.001	0.000	0.000	0.000	0.000
141	X	170	LEU	0	-0.017	-0.013	31.694	0.002	0.002	0.000	0.000	0.000	0.000
142	X	171	GLN	0	-0.037	-0.021	35.069	0.008	0.008	0.000	0.000	0.000	0.000
143	X	172	SER	0	0.035	0.008	38.175	-0.002	-0.002	0.000	0.000	0.000	0.000
144	X	173	SER	0	-0.034	-0.036	39.885	0.002	0.002	0.000	0.000	0.000	0.000
145	X	174	GLY	0	0.016	0.013	36.490	0.001	0.001	0.000	0.000	0.000	0.000
146	X	175	LEU	0	-0.078	-0.030	35.062	-0.007	-0.007	0.000	0.000	0.000	0.000
147	X	176	TYR	0	0.044	0.016	28.447	0.005	0.005	0.000	0.000	0.000	0.000
148	X	177	SER	0	-0.016	-0.003	34.347	0.008	0.008	0.000	0.000	0.000	0.000
149	X	178	LEU	0	0.007	0.019	31.526	-0.004	-0.004	0.000	0.000	0.000	0.000
150	X	179	SER	0	0.014	-0.008	35.360	0.009	0.009	0.000	0.000	0.000	0.000
151	X	180	SER	0	0.035	0.031	36.008	-0.002	-0.002	0.000	0.000	0.000	0.000
152	X	196	CYS	0	0.003	-0.010	33.212	-0.003	-0.003	0.000	0.000	0.000	0.000
153	X	197	ASN	0	-0.035	-0.006	34.201	0.001	0.001	0.000	0.000	0.000	0.000
154	X	198	VAL	0	0.047	0.028	33.578	-0.011	-0.011	0.000	0.000	0.000	0.000
155	X	199	ASN	0	0.063	0.018	29.199	0.012	0.012	0.000	0.000	0.000	0.000
156	X	200	HIS	1	0.855	0.936	29.604	0.149	0.149	0.000	0.000	0.000	0.000
157	X	201	LYS	1	0.998	0.976	22.890	0.290	0.290	0.000	0.000	0.000	0.000
158	X	202	PRO	0	0.005	0.013	26.232	0.005	0.005	0.000	0.000	0.000	0.000
159	X	203	SER	0	0.032	0.025	28.059	0.006	0.006	0.000	0.000	0.000	0.000
160	X	204	ASN	0	0.012	-0.002	29.530	0.004	0.004	0.000	0.000	0.000	0.000
161	X	205	THR	0	-0.006	0.008	31.423	0.000	0.000	0.000	0.000	0.000	0.000
162	X	206	LYS	1	0.831	0.907	30.399	0.156	0.156	0.000	0.000	0.000	0.000
163	X	207	VAL	0	0.053	0.042	35.210	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)