FMO DATABASE

FMODB ID: Z6G2N

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:

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1401698.651337
FMO2-HF: Nuclear repulsion	1340949.673647
FMO2-HF: Total energy	-60748.977691
FMO2-MP2: Total energy	-60927.147628

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.
0.15599999999999	7.071	4.557	-4.749	-6.72	0.02

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 : -0.914 / q_NPA : -0.962

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	0.015	2.808	1.812	5.231	0.665	-1.654	-2.430	-0.001
4	Q	4	LEU	0	-0.005	-0.009	5.378	-3.552	-3.527	-0.001	-0.001	-0.022	0.000
5	Q	5	THR	0	0.007	0.011	8.650	-0.018	-0.018	0.000	0.000	0.000	0.000
6	Q	6	GLN	0	-0.005	-0.048	11.570	0.210	0.210	0.000	0.000	0.000	0.000
7	Q	7	SER	0	-0.008	0.025	14.731	-0.190	-0.190	0.000	0.000	0.000	0.000
8	Q	8	PRO	0	0.020	0.006	18.149	-0.208	-0.208	0.000	0.000	0.000	0.000
9	Q	9	SER	0	0.091	0.020	18.153	0.377	0.377	0.000	0.000	0.000	0.000
10	Q	10	SER	0	-0.012	-0.010	19.378	0.063	0.063	0.000	0.000	0.000	0.000
11	Q	11	LEU	0	-0.023	-0.016	22.951	-0.120	-0.120	0.000	0.000	0.000	0.000
12	Q	12	SER	0	0.013	0.004	25.821	0.043	0.043	0.000	0.000	0.000	0.000
13	Q	13	ALA	0	-0.033	-0.042	29.562	-0.105	-0.105	0.000	0.000	0.000	0.000
14	Q	14	SER	0	-0.033	-0.020	31.514	0.011	0.011	0.000	0.000	0.000	0.000
15	Q	15	VAL	0	0.020	-0.006	34.324	0.140	0.140	0.000	0.000	0.000	0.000
16	Q	16	GLY	0	-0.006	0.008	35.233	-0.223	-0.223	0.000	0.000	0.000	0.000
17	Q	17	ASP	-1	-0.776	-0.850	32.695	8.888	8.888	0.000	0.000	0.000	0.000
18	Q	18	ARG	1	0.959	0.979	29.737	-9.741	-9.741	0.000	0.000	0.000	0.000
19	Q	19	VAL	0	-0.025	-0.016	26.425	0.008	0.008	0.000	0.000	0.000	0.000
20	Q	20	THR	0	-0.025	-0.025	24.383	-0.034	-0.034	0.000	0.000	0.000	0.000
21	Q	21	ILE	0	-0.021	0.007	18.668	-0.027	-0.027	0.000	0.000	0.000	0.000
22	Q	22	THR	0	-0.011	-0.010	18.135	-0.024	-0.024	0.000	0.000	0.000	0.000
23	Q	23	CYS	0	-0.027	0.036	12.756	0.245	0.245	0.000	0.000	0.000	0.000
24	Q	24	GLN	0	-0.048	-0.019	12.966	-0.454	-0.454	0.000	0.000	0.000	0.000
25	Q	25	ALA	0	0.030	0.019	9.201	1.428	1.428	0.000	0.000	0.000	0.000
26	Q	26	SER	0	-0.006	-0.007	6.495	0.342	0.342	0.000	0.000	0.000	0.000
27	Q	27	GLN	0	-0.020	-0.013	4.445	-3.248	-3.103	-0.001	-0.026	-0.119	0.000
28	Q	28	ASP	-1	-0.891	-0.943	9.329	17.939	17.939	0.000	0.000	0.000	0.000
29	Q	29	ILE	0	0.014	0.004	8.662	1.426	1.426	0.000	0.000	0.000	0.000
30	Q	30	ARG	1	0.953	0.974	11.729	-18.413	-18.413	0.000	0.000	0.000	0.000
31	Q	31	LYS	1	0.867	0.918	15.364	-14.114	-14.114	0.000	0.000	0.000	0.000
32	Q	32	TYR	0	-0.032	0.000	12.575	-0.939	-0.939	0.000	0.000	0.000	0.000
33	Q	33	LEU	0	0.008	0.002	12.291	1.575	1.575	0.000	0.000	0.000	0.000
34	Q	34	ASN	0	-0.045	-0.018	14.469	-2.414	-2.414	0.000	0.000	0.000	0.000
35	Q	35	TRP	0	0.029	-0.007	15.448	0.965	0.965	0.000	0.000	0.000	0.000
36	Q	36	TYR	0	-0.048	-0.038	15.443	-1.356	-1.356	0.000	0.000	0.000	0.000
37	Q	37	GLN	0	-0.030	-0.040	19.184	-0.120	-0.120	0.000	0.000	0.000	0.000
38	Q	38	GLN	0	-0.013	-0.019	19.755	0.409	0.409	0.000	0.000	0.000	0.000
39	Q	39	LYS	1	0.862	0.923	22.477	-10.817	-10.817	0.000	0.000	0.000	0.000
40	Q	40	PRO	0	0.116	0.052	25.284	0.207	0.207	0.000	0.000	0.000	0.000
41	Q	41	GLY	0	-0.004	0.002	25.589	-0.397	-0.397	0.000	0.000	0.000	0.000
42	Q	42	LYS	1	0.894	0.955	25.958	-10.720	-10.720	0.000	0.000	0.000	0.000
43	Q	43	ALA	0	0.025	0.010	22.452	0.500	0.500	0.000	0.000	0.000	0.000
44	Q	44	PRO	0	0.008	-0.003	18.159	-0.453	-0.453	0.000	0.000	0.000	0.000
45	Q	45	ASN	0	0.014	0.008	21.056	-0.370	-0.370	0.000	0.000	0.000	0.000
46	Q	46	LEU	0	-0.001	0.026	19.404	0.146	0.146	0.000	0.000	0.000	0.000
47	Q	47	LEU	0	-0.053	-0.022	21.679	-0.737	-0.737	0.000	0.000	0.000	0.000
48	Q	48	ILE	0	-0.028	-0.019	20.592	-0.505	-0.505	0.000	0.000	0.000	0.000
49	Q	49	TYR	0	0.039	0.015	19.146	0.733	0.733	0.000	0.000	0.000	0.000
50	Q	50	ASP	-1	-0.746	-0.854	17.414	15.897	15.897	0.000	0.000	0.000	0.000
51	Q	51	ALA	0	-0.030	-0.009	17.925	-0.827	-0.827	0.000	0.000	0.000	0.000
52	Q	52	SER	0	-0.058	-0.041	19.296	-0.269	-0.269	0.000	0.000	0.000	0.000
53	Q	53	ASN	0	-0.042	-0.006	22.561	-0.891	-0.891	0.000	0.000	0.000	0.000
54	Q	54	VAL	0	0.044	0.022	23.656	0.434	0.434	0.000	0.000	0.000	0.000
55	Q	55	LYS	1	0.964	0.997	25.213	-12.051	-12.051	0.000	0.000	0.000	0.000
56	Q	56	THR	0	0.022	-0.005	26.895	-0.266	-0.266	0.000	0.000	0.000	0.000
57	Q	57	GLY	0	-0.005	-0.003	30.494	0.015	0.015	0.000	0.000	0.000	0.000
58	Q	58	VAL	0	-0.054	-0.011	26.615	-0.009	-0.009	0.000	0.000	0.000	0.000
59	Q	59	PRO	0	0.016	0.007	29.934	-0.152	-0.152	0.000	0.000	0.000	0.000
60	Q	60	SER	0	0.074	0.027	30.432	0.222	0.222	0.000	0.000	0.000	0.000
61	Q	61	ARG	1	0.742	0.848	30.460	-9.567	-9.567	0.000	0.000	0.000	0.000
62	Q	62	PHE	0	-0.006	0.004	26.095	0.140	0.140	0.000	0.000	0.000	0.000
63	Q	63	ARG	1	0.893	0.939	26.588	-10.002	-10.002	0.000	0.000	0.000	0.000
64	Q	64	GLY	0	0.032	0.023	22.549	0.278	0.278	0.000	0.000	0.000	0.000
65	Q	65	SER	0	-0.033	-0.023	22.088	-0.394	-0.394	0.000	0.000	0.000	0.000
66	Q	66	GLY	0	0.066	0.027	19.470	0.513	0.513	0.000	0.000	0.000	0.000
67	Q	67	SER	0	-0.092	-0.031	19.329	0.033	0.033	0.000	0.000	0.000	0.000
68	Q	68	GLY	0	0.097	0.042	15.846	-0.011	-0.011	0.000	0.000	0.000	0.000
69	Q	69	THR	0	0.057	0.026	13.224	1.660	1.660	0.000	0.000	0.000	0.000
70	Q	70	ASP	-1	-0.882	-0.913	14.222	17.136	17.136	0.000	0.000	0.000	0.000
71	Q	71	PHE	0	-0.018	-0.022	13.520	-0.919	-0.919	0.000	0.000	0.000	0.000
72	Q	72	THR	0	-0.037	-0.032	17.719	-0.216	-0.216	0.000	0.000	0.000	0.000
73	Q	73	PHE	0	0.009	0.017	20.227	-0.292	-0.292	0.000	0.000	0.000	0.000
74	Q	74	THR	0	-0.023	-0.022	21.929	-0.359	-0.359	0.000	0.000	0.000	0.000
75	Q	75	ILE	0	0.015	0.024	25.670	-0.077	-0.077	0.000	0.000	0.000	0.000
76	Q	76	SER	0	-0.057	-0.051	28.216	-0.112	-0.112	0.000	0.000	0.000	0.000
77	Q	77	SER	0	0.002	-0.005	31.647	-0.248	-0.248	0.000	0.000	0.000	0.000
78	Q	78	LEU	0	-0.016	0.012	29.609	0.033	0.033	0.000	0.000	0.000	0.000
79	Q	79	GLN	0	0.001	-0.014	32.135	-0.510	-0.510	0.000	0.000	0.000	0.000
80	Q	80	PRO	0	0.045	0.029	32.374	0.327	0.327	0.000	0.000	0.000	0.000
81	Q	81	GLU	-1	-0.800	-0.893	32.296	9.153	9.153	0.000	0.000	0.000	0.000
82	Q	82	ASP	-1	-0.821	-0.878	28.558	10.489	10.489	0.000	0.000	0.000	0.000
83	Q	83	ILE	0	0.027	0.034	27.590	0.438	0.438	0.000	0.000	0.000	0.000
84	Q	84	ALA	0	-0.013	-0.018	24.558	-0.054	-0.054	0.000	0.000	0.000	0.000
85	Q	85	THR	0	-0.004	0.010	19.059	-0.074	-0.074	0.000	0.000	0.000	0.000
86	Q	86	TYR	0	-0.038	-0.040	19.577	-0.035	-0.035	0.000	0.000	0.000	0.000
87	Q	87	TYR	0	0.021	0.034	14.252	0.390	0.390	0.000	0.000	0.000	0.000
88	Q	89	GLN	0	0.084	0.036	10.855	-0.867	-0.867	0.000	0.000	0.000	0.000
89	Q	90	GLN	0	0.066	0.053	6.236	-0.163	-0.163	0.000	0.000	0.000	0.000
90	Q	91	TYR	0	-0.058	-0.056	9.311	0.900	0.900	0.000	0.000	0.000	0.000
91	Q	92	ASP	-1	-0.932	-0.954	8.504	27.672	27.672	0.000	0.000	0.000	0.000
92	Q	93	ASN	0	-0.006	-0.006	4.447	4.626	4.814	-0.001	-0.013	-0.173	0.000
93	Q	94	LEU	0	-0.027	-0.039	5.783	-2.520	-2.520	0.000	0.000	0.000	0.000
94	Q	95	PRO	0	0.001	0.040	2.090	-4.373	-1.923	3.866	-2.874	-3.441	0.021
95	Q	96	ILE	0	-0.055	-0.036	4.747	-5.425	-5.354	-0.001	-0.016	-0.053	0.000
96	Q	97	THR	0	0.004	-0.018	3.211	-1.088	-0.471	0.030	-0.165	-0.482	0.000
97	Q	98	PHE	0	-0.020	-0.038	6.521	-5.166	-5.166	0.000	0.000	0.000	0.000
98	Q	99	GLY	0	0.021	0.019	8.668	1.428	1.428	0.000	0.000	0.000	0.000
99	Q	100	GLN	0	-0.029	-0.033	11.266	1.460	1.460	0.000	0.000	0.000	0.000
100	Q	101	GLY	0	-0.007	-0.005	13.006	-1.039	-1.039	0.000	0.000	0.000	0.000
101	Q	102	THR	0	-0.030	-0.026	16.261	0.157	0.157	0.000	0.000	0.000	0.000
102	Q	103	ARG	1	0.862	0.928	19.487	-11.974	-11.974	0.000	0.000	0.000	0.000
103	Q	104	LEU	0	-0.026	-0.005	22.664	-0.240	-0.240	0.000	0.000	0.000	0.000
104	Q	105	GLU	-1	-0.790	-0.817	26.028	10.014	10.014	0.000	0.000	0.000	0.000
105	Q	106	ILE	0	0.002	-0.021	29.462	0.011	0.011	0.000	0.000	0.000	0.000
106	Q	107	LYS	1	0.816	0.917	32.759	-8.972	-8.972	0.000	0.000	0.000	0.000
107	Q	108	ARG	1	0.851	0.940	34.767	-7.985	-7.985	0.000	0.000	0.000	0.000
108	Q	109	THR	0	0.002	-0.001	37.980	0.109	0.109	0.000	0.000	0.000	0.000
109	Q	110	VAL	0	0.051	0.030	39.255	0.119	0.119	0.000	0.000	0.000	0.000
110	Q	111	ALA	0	-0.025	-0.022	40.327	-0.126	-0.126	0.000	0.000	0.000	0.000
111	Q	112	ALA	0	0.035	0.012	41.909	0.026	0.026	0.000	0.000	0.000	0.000
112	Q	113	PRO	0	0.026	0.014	40.772	-0.023	-0.023	0.000	0.000	0.000	0.000
113	Q	114	SER	0	-0.023	-0.001	42.687	-0.192	-0.192	0.000	0.000	0.000	0.000
114	Q	115	VAL	0	-0.019	-0.016	43.700	0.084	0.084	0.000	0.000	0.000	0.000
115	Q	116	PHE	0	-0.041	-0.008	45.217	-0.178	-0.178	0.000	0.000	0.000	0.000
116	Q	132	VAL	0	-0.030	-0.036	41.972	-0.034	-0.034	0.000	0.000	0.000	0.000
117	Q	133	VAL	0	0.006	0.000	41.677	0.142	0.142	0.000	0.000	0.000	0.000
118	Q	134	CYS	0	-0.014	0.015	41.859	-0.188	-0.188	0.000	0.000	0.000	0.000
119	Q	135	LEU	0	0.020	0.017	40.801	0.209	0.209	0.000	0.000	0.000	0.000
120	Q	136	LEU	0	0.003	0.000	38.673	-0.194	-0.194	0.000	0.000	0.000	0.000
121	Q	137	ASN	0	0.002	-0.019	40.165	0.310	0.310	0.000	0.000	0.000	0.000
122	Q	138	ASN	0	-0.038	-0.017	40.464	-0.123	-0.123	0.000	0.000	0.000	0.000
123	Q	139	PHE	0	0.002	0.005	35.110	-0.167	-0.167	0.000	0.000	0.000	0.000
124	Q	140	TYR	0	0.015	0.006	32.789	0.128	0.128	0.000	0.000	0.000	0.000
125	Q	141	PRO	0	-0.029	-0.018	32.688	-0.284	-0.284	0.000	0.000	0.000	0.000
126	Q	142	ARG	1	0.890	0.911	27.905	-10.931	-10.931	0.000	0.000	0.000	0.000
127	Q	143	GLU	-1	-0.911	-0.939	30.431	9.765	9.765	0.000	0.000	0.000	0.000
128	Q	144	ALA	0	0.003	0.004	32.839	-0.229	-0.229	0.000	0.000	0.000	0.000
129	Q	160	GLN	0	-0.037	-0.031	31.193	-0.176	-0.176	0.000	0.000	0.000	0.000
130	Q	161	GLU	-1	-0.836	-0.903	32.492	8.803	8.803	0.000	0.000	0.000	0.000
131	Q	162	SER	0	-0.040	-0.011	31.285	0.447	0.447	0.000	0.000	0.000	0.000
132	Q	163	VAL	0	0.004	-0.009	30.517	-0.318	-0.318	0.000	0.000	0.000	0.000
133	Q	164	THR	0	-0.001	0.023	31.036	0.297	0.297	0.000	0.000	0.000	0.000
134	Q	165	GLU	-1	-0.871	-0.952	27.162	11.441	11.441	0.000	0.000	0.000	0.000
135	Q	166	GLN	0	-0.003	0.017	30.984	-0.127	-0.127	0.000	0.000	0.000	0.000
136	Q	167	ASP	-1	-0.803	-0.871	32.912	8.310	8.310	0.000	0.000	0.000	0.000
137	Q	168	SER	0	-0.002	-0.021	35.381	0.044	0.044	0.000	0.000	0.000	0.000
138	Q	169	LYS	1	0.787	0.879	36.555	-7.956	-7.956	0.000	0.000	0.000	0.000
139	Q	170	ASP	-1	-0.820	-0.919	39.968	7.623	7.623	0.000	0.000	0.000	0.000
140	Q	171	SER	0	-0.072	-0.030	35.926	-0.043	-0.043	0.000	0.000	0.000	0.000
141	Q	172	THR	0	-0.042	-0.014	36.931	0.034	0.034	0.000	0.000	0.000	0.000
142	Q	173	TYR	0	0.010	-0.030	30.222	0.322	0.322	0.000	0.000	0.000	0.000
143	Q	174	SER	0	0.029	0.004	35.715	-0.366	-0.366	0.000	0.000	0.000	0.000
144	Q	175	LEU	0	-0.032	-0.001	34.164	0.185	0.185	0.000	0.000	0.000	0.000
145	Q	176	SER	0	0.028	0.002	35.836	-0.344	-0.344	0.000	0.000	0.000	0.000
146	Q	177	SER	0	-0.018	-0.016	36.082	0.235	0.235	0.000	0.000	0.000	0.000
147	Q	178	THR	0	-0.031	-0.008	37.023	-0.217	-0.217	0.000	0.000	0.000	0.000
148	Q	196	VAL	0	-0.009	-0.013	40.679	0.058	0.058	0.000	0.000	0.000	0.000
149	Q	197	THR	0	0.014	-0.005	39.755	-0.132	-0.132	0.000	0.000	0.000	0.000
150	Q	198	HIS	0	0.037	0.016	37.590	-0.003	-0.003	0.000	0.000	0.000	0.000
151	Q	199	GLN	0	0.031	-0.001	36.110	-0.238	-0.238	0.000	0.000	0.000	0.000
152	Q	200	GLY	0	-0.029	0.009	41.129	-0.137	-0.137	0.000	0.000	0.000	0.000
153	Q	201	LEU	0	-0.053	-0.020	43.033	-0.178	-0.178	0.000	0.000	0.000	0.000
154	Q	202	SER	0	-0.012	-0.007	45.611	-0.024	-0.024	0.000	0.000	0.000	0.000
155	Q	203	SER	0	0.001	-0.005	46.794	0.044	0.044	0.000	0.000	0.000	0.000
156	Q	204	PRO	0	-0.021	0.008	44.354	-0.098	-0.098	0.000	0.000	0.000	0.000

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