FMO DATABASE

FMODB ID: R9K18

Calculation Name: 4HG4-Q-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: Q

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1406528.403663
FMO2-HF: Nuclear repulsion	1345778.722474
FMO2-HF: Total energy	-60749.681189
FMO2-MP2: Total energy	-60927.862924

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(Q:1:ASP)

Summations of interaction energy for fragment #1(Q:1:ASP)

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.
-6.888	-0.32300000000001	4.633	-4.446	-6.751	0.022

Interaction energy analysis for fragmet #1(Q:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.893 / q_NPA : -0.954

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	Q	3	GLN	0	0.010	0.017	2.604	1.833	4.726	1.347	-1.687	-2.553	-0.003
4	Q	4	LEU	0	0.007	0.003	5.248	-3.065	-3.043	-0.001	-0.002	-0.019	0.000
5	Q	5	THR	0	0.029	0.017	8.680	-0.384	-0.384	0.000	0.000	0.000	0.000
6	Q	6	GLN	0	0.000	-0.029	11.575	0.236	0.236	0.000	0.000	0.000	0.000
7	Q	7	SER	0	-0.006	0.014	14.681	-0.135	-0.135	0.000	0.000	0.000	0.000
8	Q	8	PRO	0	0.025	0.008	18.261	-0.232	-0.232	0.000	0.000	0.000	0.000
9	Q	9	SER	0	0.088	0.029	18.084	0.387	0.387	0.000	0.000	0.000	0.000
10	Q	10	SER	0	-0.024	-0.008	19.424	-0.020	-0.020	0.000	0.000	0.000	0.000
11	Q	11	LEU	0	-0.031	-0.013	23.071	-0.100	-0.100	0.000	0.000	0.000	0.000
12	Q	12	SER	0	0.020	-0.008	26.032	0.077	0.077	0.000	0.000	0.000	0.000
13	Q	13	ALA	0	-0.034	-0.025	29.825	-0.159	-0.159	0.000	0.000	0.000	0.000
14	Q	14	SER	0	-0.005	-0.027	31.653	-0.062	-0.062	0.000	0.000	0.000	0.000
15	Q	15	VAL	0	-0.012	-0.010	34.456	0.170	0.170	0.000	0.000	0.000	0.000
16	Q	16	GLY	0	0.003	0.006	35.445	-0.254	-0.254	0.000	0.000	0.000	0.000
17	Q	17	ASP	-1	-0.769	-0.831	32.538	8.938	8.938	0.000	0.000	0.000	0.000
18	Q	18	ARG	1	0.932	0.971	29.569	-9.607	-9.607	0.000	0.000	0.000	0.000
19	Q	19	VAL	0	0.000	0.003	26.556	-0.004	-0.004	0.000	0.000	0.000	0.000
20	Q	20	THR	0	-0.030	-0.035	24.802	-0.155	-0.155	0.000	0.000	0.000	0.000
21	Q	21	ILE	0	0.001	0.027	18.950	0.022	0.022	0.000	0.000	0.000	0.000
22	Q	22	THR	0	0.004	0.005	18.570	0.019	0.019	0.000	0.000	0.000	0.000
23	Q	23	CYS	0	-0.025	-0.003	12.999	0.384	0.384	0.000	0.000	0.000	0.000
24	Q	24	GLN	0	-0.055	-0.019	12.917	-0.334	-0.334	0.000	0.000	0.000	0.000
25	Q	25	ALA	0	0.003	0.009	8.974	1.375	1.375	0.000	0.000	0.000	0.000
26	Q	26	SER	0	-0.022	-0.022	6.421	-0.060	-0.060	0.000	0.000	0.000	0.000
27	Q	27	GLN	0	-0.007	-0.013	3.473	-4.079	-3.275	0.030	-0.398	-0.436	0.003
28	Q	28	ASP	-1	-0.875	-0.930	8.677	18.856	18.856	0.000	0.000	0.000	0.000
29	Q	29	ILE	0	0.024	0.011	8.474	1.611	1.611	0.000	0.000	0.000	0.000
30	Q	30	ARG	1	0.852	0.920	11.378	-20.248	-20.248	0.000	0.000	0.000	0.000
31	Q	31	LYS	1	0.869	0.902	15.249	-15.004	-15.004	0.000	0.000	0.000	0.000
32	Q	32	TYR	0	-0.034	0.010	12.414	-0.878	-0.878	0.000	0.000	0.000	0.000
33	Q	33	LEU	0	0.002	-0.004	11.709	1.957	1.957	0.000	0.000	0.000	0.000
34	Q	34	ASN	0	-0.043	-0.020	13.909	-2.430	-2.430	0.000	0.000	0.000	0.000
35	Q	35	TRP	0	0.036	0.002	15.579	0.908	0.908	0.000	0.000	0.000	0.000
36	Q	36	TYR	0	-0.033	-0.024	15.683	-1.423	-1.423	0.000	0.000	0.000	0.000
37	Q	37	GLN	0	-0.023	-0.026	19.665	-0.130	-0.130	0.000	0.000	0.000	0.000
38	Q	38	GLN	0	0.007	0.003	20.165	0.459	0.459	0.000	0.000	0.000	0.000
39	Q	39	LYS	1	0.865	0.928	22.950	-10.727	-10.727	0.000	0.000	0.000	0.000
40	Q	40	PRO	0	0.063	0.016	26.087	0.259	0.259	0.000	0.000	0.000	0.000
41	Q	41	GLY	0	0.023	0.018	26.366	-0.353	-0.353	0.000	0.000	0.000	0.000
42	Q	42	LYS	1	0.903	0.965	26.075	-10.735	-10.735	0.000	0.000	0.000	0.000
43	Q	43	ALA	0	0.057	0.027	22.502	0.482	0.482	0.000	0.000	0.000	0.000
44	Q	44	PRO	0	-0.007	-0.011	18.330	-0.525	-0.525	0.000	0.000	0.000	0.000
45	Q	45	ASN	0	-0.016	-0.002	21.322	-0.248	-0.248	0.000	0.000	0.000	0.000
46	Q	46	LEU	0	0.006	0.017	19.151	0.176	0.176	0.000	0.000	0.000	0.000
47	Q	47	LEU	0	-0.065	-0.037	21.717	-0.770	-0.770	0.000	0.000	0.000	0.000
48	Q	48	ILE	0	-0.036	-0.018	20.809	-0.627	-0.627	0.000	0.000	0.000	0.000
49	Q	49	TYR	0	0.023	0.009	18.903	0.742	0.742	0.000	0.000	0.000	0.000
50	Q	50	ASP	-1	-0.762	-0.875	17.163	16.086	16.086	0.000	0.000	0.000	0.000
51	Q	51	ALA	0	0.009	0.009	17.312	-0.767	-0.767	0.000	0.000	0.000	0.000
52	Q	52	SER	0	-0.050	-0.019	18.825	-0.320	-0.320	0.000	0.000	0.000	0.000
53	Q	53	ASN	0	-0.054	-0.002	22.195	-0.945	-0.945	0.000	0.000	0.000	0.000
54	Q	54	VAL	0	0.040	0.015	23.599	0.405	0.405	0.000	0.000	0.000	0.000
55	Q	55	LYS	1	0.920	0.971	24.906	-11.632	-11.632	0.000	0.000	0.000	0.000
56	Q	56	THR	0	0.033	0.005	26.470	-0.304	-0.304	0.000	0.000	0.000	0.000
57	Q	57	GLY	0	-0.011	-0.007	29.945	0.095	0.095	0.000	0.000	0.000	0.000
58	Q	58	VAL	0	-0.007	0.007	26.755	0.055	0.055	0.000	0.000	0.000	0.000
59	Q	59	PRO	0	0.018	0.008	30.139	-0.167	-0.167	0.000	0.000	0.000	0.000
60	Q	60	SER	0	0.068	0.024	30.892	0.213	0.213	0.000	0.000	0.000	0.000
61	Q	61	ARG	1	0.739	0.847	30.891	-9.586	-9.586	0.000	0.000	0.000	0.000
62	Q	62	PHE	0	0.008	0.012	26.300	0.131	0.131	0.000	0.000	0.000	0.000
63	Q	63	ARG	1	0.874	0.923	26.455	-10.141	-10.141	0.000	0.000	0.000	0.000
64	Q	64	GLY	0	0.018	0.017	22.246	0.286	0.286	0.000	0.000	0.000	0.000
65	Q	65	SER	0	-0.016	-0.012	21.603	-0.459	-0.459	0.000	0.000	0.000	0.000
66	Q	66	GLY	0	0.063	0.026	18.681	0.597	0.597	0.000	0.000	0.000	0.000
67	Q	67	SER	0	-0.081	-0.044	18.331	-0.585	-0.585	0.000	0.000	0.000	0.000
68	Q	68	GLY	0	0.079	0.045	15.364	-0.384	-0.384	0.000	0.000	0.000	0.000
69	Q	69	THR	0	0.040	0.034	12.312	1.927	1.927	0.000	0.000	0.000	0.000
70	Q	70	ASP	-1	-0.873	-0.911	13.654	17.555	17.555	0.000	0.000	0.000	0.000
71	Q	71	PHE	0	0.005	-0.013	13.230	-0.849	-0.849	0.000	0.000	0.000	0.000
72	Q	72	THR	0	-0.070	-0.042	17.759	-0.298	-0.298	0.000	0.000	0.000	0.000
73	Q	73	PHE	0	0.005	0.014	20.406	-0.148	-0.148	0.000	0.000	0.000	0.000
74	Q	74	THR	0	-0.036	-0.031	22.042	-0.307	-0.307	0.000	0.000	0.000	0.000
75	Q	75	ILE	0	0.016	0.024	25.764	-0.054	-0.054	0.000	0.000	0.000	0.000
76	Q	76	SER	0	-0.052	-0.051	28.540	-0.119	-0.119	0.000	0.000	0.000	0.000
77	Q	77	SER	0	-0.013	-0.016	31.724	-0.239	-0.239	0.000	0.000	0.000	0.000
78	Q	78	LEU	0	-0.012	0.016	29.422	-0.018	-0.018	0.000	0.000	0.000	0.000
79	Q	79	GLN	0	-0.014	-0.015	32.492	-0.537	-0.537	0.000	0.000	0.000	0.000
80	Q	80	PRO	0	0.064	0.026	32.912	0.296	0.296	0.000	0.000	0.000	0.000
81	Q	81	GLU	-1	-0.801	-0.884	32.361	9.241	9.241	0.000	0.000	0.000	0.000
82	Q	82	ASP	-1	-0.771	-0.859	28.842	10.505	10.505	0.000	0.000	0.000	0.000
83	Q	83	ILE	0	0.013	0.033	27.746	0.483	0.483	0.000	0.000	0.000	0.000
84	Q	84	ALA	0	-0.012	-0.017	24.652	-0.057	-0.057	0.000	0.000	0.000	0.000
85	Q	85	THR	0	0.008	0.014	19.178	-0.116	-0.116	0.000	0.000	0.000	0.000
86	Q	86	TYR	0	-0.027	-0.030	19.948	-0.074	-0.074	0.000	0.000	0.000	0.000
87	Q	87	TYR	0	0.011	0.004	14.673	0.249	0.249	0.000	0.000	0.000	0.000
88	Q	89	GLN	0	0.067	0.030	11.166	-1.031	-1.031	0.000	0.000	0.000	0.000
89	Q	90	GLN	0	0.016	0.021	6.294	0.875	0.875	0.000	0.000	0.000	0.000
90	Q	91	TYR	0	-0.042	-0.043	8.868	0.827	0.827	0.000	0.000	0.000	0.000
91	Q	92	ASP	-1	-0.879	-0.921	8.667	25.920	25.920	0.000	0.000	0.000	0.000
92	Q	93	ASN	0	0.042	0.022	4.481	1.333	1.558	-0.001	-0.029	-0.195	0.000
93	Q	94	LEU	0	-0.024	-0.026	5.907	-1.931	-1.931	0.000	0.000	0.000	0.000
94	Q	95	PRO	0	-0.005	0.021	2.245	-3.890	-1.740	3.253	-2.208	-3.195	0.022
95	Q	96	ILE	0	-0.069	-0.034	4.515	-5.765	-5.685	-0.001	-0.034	-0.044	0.000
96	Q	97	THR	0	0.015	-0.009	3.627	-2.649	-2.258	0.006	-0.088	-0.309	0.000
97	Q	98	PHE	0	-0.013	-0.038	6.814	-4.870	-4.870	0.000	0.000	0.000	0.000
98	Q	99	GLY	0	0.021	0.016	8.936	1.653	1.653	0.000	0.000	0.000	0.000
99	Q	100	GLN	0	-0.045	-0.043	11.363	0.770	0.770	0.000	0.000	0.000	0.000
100	Q	101	GLY	0	0.006	0.008	13.013	-0.957	-0.957	0.000	0.000	0.000	0.000
101	Q	102	THR	0	-0.042	-0.037	16.276	0.021	0.021	0.000	0.000	0.000	0.000
102	Q	103	ARG	1	0.836	0.921	19.690	-11.675	-11.675	0.000	0.000	0.000	0.000
103	Q	104	LEU	0	-0.037	-0.019	22.876	-0.190	-0.190	0.000	0.000	0.000	0.000
104	Q	105	GLU	-1	-0.783	-0.808	26.194	9.978	9.978	0.000	0.000	0.000	0.000
105	Q	106	ILE	0	-0.005	-0.020	29.683	-0.014	-0.014	0.000	0.000	0.000	0.000
106	Q	107	LYS	1	0.827	0.913	33.187	-9.012	-9.012	0.000	0.000	0.000	0.000
107	Q	108	ARG	1	0.815	0.904	34.560	-7.970	-7.970	0.000	0.000	0.000	0.000
108	Q	109	THR	0	0.014	0.005	37.936	0.109	0.109	0.000	0.000	0.000	0.000
109	Q	110	VAL	0	0.048	0.034	39.459	0.099	0.099	0.000	0.000	0.000	0.000
110	Q	111	ALA	0	-0.023	-0.009	40.765	-0.133	-0.133	0.000	0.000	0.000	0.000
111	Q	112	ALA	0	0.040	0.022	41.845	0.096	0.096	0.000	0.000	0.000	0.000
112	Q	113	PRO	0	0.000	0.000	40.653	-0.022	-0.022	0.000	0.000	0.000	0.000
113	Q	114	SER	0	-0.033	-0.009	42.596	-0.193	-0.193	0.000	0.000	0.000	0.000
114	Q	115	VAL	0	0.003	-0.001	44.157	0.101	0.101	0.000	0.000	0.000	0.000
115	Q	116	PHE	0	-0.002	0.006	45.314	-0.120	-0.120	0.000	0.000	0.000	0.000
116	Q	132	VAL	0	-0.037	-0.037	42.341	-0.038	-0.038	0.000	0.000	0.000	0.000
117	Q	133	VAL	0	-0.001	0.005	42.023	0.118	0.118	0.000	0.000	0.000	0.000
118	Q	134	CYS	0	-0.042	-0.011	41.925	-0.221	-0.221	0.000	0.000	0.000	0.000
119	Q	135	LEU	0	0.003	0.006	40.869	0.216	0.216	0.000	0.000	0.000	0.000
120	Q	136	LEU	0	0.020	0.011	38.878	-0.206	-0.206	0.000	0.000	0.000	0.000
121	Q	137	ASN	0	0.012	-0.016	39.931	0.356	0.356	0.000	0.000	0.000	0.000
122	Q	138	ASN	0	-0.046	-0.014	40.734	-0.049	-0.049	0.000	0.000	0.000	0.000
123	Q	139	PHE	0	0.007	0.014	35.891	-0.164	-0.164	0.000	0.000	0.000	0.000
124	Q	140	TYR	0	0.035	-0.007	32.700	0.150	0.150	0.000	0.000	0.000	0.000
125	Q	141	PRO	0	-0.034	-0.017	33.035	-0.286	-0.286	0.000	0.000	0.000	0.000
126	Q	142	ARG	1	0.861	0.887	28.173	-10.854	-10.854	0.000	0.000	0.000	0.000
127	Q	143	GLU	-1	-0.894	-0.951	30.781	9.643	9.643	0.000	0.000	0.000	0.000
128	Q	144	ALA	0	-0.050	-0.037	33.279	-0.146	-0.146	0.000	0.000	0.000	0.000
129	Q	160	GLN	0	0.016	0.009	31.519	-0.161	-0.161	0.000	0.000	0.000	0.000
130	Q	161	GLU	-1	-0.873	-0.923	33.065	8.594	8.594	0.000	0.000	0.000	0.000
131	Q	162	SER	0	-0.036	-0.012	31.902	0.424	0.424	0.000	0.000	0.000	0.000
132	Q	163	VAL	0	0.022	-0.002	31.132	-0.327	-0.327	0.000	0.000	0.000	0.000
133	Q	164	THR	0	-0.040	0.005	31.513	0.286	0.286	0.000	0.000	0.000	0.000
134	Q	165	GLU	-1	-0.820	-0.912	27.913	11.206	11.206	0.000	0.000	0.000	0.000
135	Q	166	GLN	0	-0.031	-0.004	31.008	-0.092	-0.092	0.000	0.000	0.000	0.000
136	Q	167	ASP	-1	-0.807	-0.878	33.004	8.161	8.161	0.000	0.000	0.000	0.000
137	Q	168	SER	0	-0.016	-0.027	35.417	-0.022	-0.022	0.000	0.000	0.000	0.000
138	Q	169	LYS	1	0.803	0.901	36.772	-7.817	-7.817	0.000	0.000	0.000	0.000
139	Q	170	ASP	-1	-0.821	-0.925	39.964	7.524	7.524	0.000	0.000	0.000	0.000
140	Q	171	SER	0	-0.049	-0.020	36.152	-0.066	-0.066	0.000	0.000	0.000	0.000
141	Q	172	THR	0	-0.020	-0.007	36.504	0.176	0.176	0.000	0.000	0.000	0.000
142	Q	173	TYR	0	0.013	-0.018	30.562	0.385	0.385	0.000	0.000	0.000	0.000
143	Q	174	SER	0	-0.002	-0.014	35.823	-0.382	-0.382	0.000	0.000	0.000	0.000
144	Q	175	LEU	0	-0.019	0.010	34.309	0.252	0.252	0.000	0.000	0.000	0.000
145	Q	176	SER	0	0.003	-0.003	36.280	-0.359	-0.359	0.000	0.000	0.000	0.000
146	Q	177	SER	0	-0.003	-0.026	36.878	0.208	0.208	0.000	0.000	0.000	0.000
147	Q	178	THR	0	-0.019	-0.004	37.592	-0.218	-0.218	0.000	0.000	0.000	0.000
148	Q	196	VAL	0	0.010	-0.003	40.965	0.044	0.044	0.000	0.000	0.000	0.000
149	Q	197	THR	0	0.018	0.008	39.954	-0.131	-0.131	0.000	0.000	0.000	0.000
150	Q	198	HIS	0	0.033	0.025	37.433	0.023	0.023	0.000	0.000	0.000	0.000
151	Q	199	GLN	0	0.035	0.010	36.130	-0.271	-0.271	0.000	0.000	0.000	0.000
152	Q	200	GLY	0	-0.013	0.006	40.900	-0.122	-0.122	0.000	0.000	0.000	0.000
153	Q	201	LEU	0	-0.063	-0.024	43.458	-0.160	-0.160	0.000	0.000	0.000	0.000
154	Q	202	SER	0	-0.008	-0.012	45.427	0.003	0.003	0.000	0.000	0.000	0.000
155	Q	203	SER	0	-0.003	0.004	46.993	-0.008	-0.008	0.000	0.000	0.000	0.000
156	Q	204	PRO	0	-0.023	0.004	44.749	-0.078	-0.078	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(Q:1:ASP)