FMO DATABASE

FMODB ID: 6NR3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1401091.743029
FMO2-HF: Nuclear repulsion	1340344.085456
FMO2-HF: Total energy	-60747.657572
FMO2-MP2: Total energy	-60925.910225

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.
5.585	11.498	6.112	-5.202	-6.819	0.024

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 : -0.910 / q_NPA : -0.967

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	-0.020	0.023	2.978	2.732	6.029	0.311	-1.472	-2.135	0.000
4	Q	4	LEU	0	-0.011	-0.006	5.252	-3.805	-3.787	-0.001	-0.001	-0.015	0.000
5	Q	5	THR	0	0.018	0.012	8.560	0.203	0.203	0.000	0.000	0.000	0.000
6	Q	6	GLN	0	-0.036	-0.055	11.459	0.119	0.119	0.000	0.000	0.000	0.000
7	Q	7	SER	0	-0.048	0.000	14.642	-0.219	-0.219	0.000	0.000	0.000	0.000
8	Q	8	PRO	0	0.042	0.007	18.046	-0.218	-0.218	0.000	0.000	0.000	0.000
9	Q	9	SER	0	0.085	0.012	18.156	0.289	0.289	0.000	0.000	0.000	0.000
10	Q	10	SER	0	-0.016	-0.011	19.301	0.087	0.087	0.000	0.000	0.000	0.000
11	Q	11	LEU	0	-0.008	-0.013	22.884	-0.149	-0.149	0.000	0.000	0.000	0.000
12	Q	12	SER	0	-0.007	0.008	25.751	0.033	0.033	0.000	0.000	0.000	0.000
13	Q	13	ALA	0	-0.044	-0.032	29.496	-0.102	-0.102	0.000	0.000	0.000	0.000
14	Q	14	SER	0	-0.010	-0.001	31.448	0.017	0.017	0.000	0.000	0.000	0.000
15	Q	15	VAL	0	0.006	-0.004	34.267	0.142	0.142	0.000	0.000	0.000	0.000
16	Q	16	GLY	0	-0.007	0.007	35.174	-0.227	-0.227	0.000	0.000	0.000	0.000
17	Q	17	ASP	-1	-0.855	-0.917	32.681	8.900	8.900	0.000	0.000	0.000	0.000
18	Q	18	ARG	1	0.930	0.962	29.615	-9.831	-9.831	0.000	0.000	0.000	0.000
19	Q	19	VAL	0	-0.004	-0.005	26.210	0.012	0.012	0.000	0.000	0.000	0.000
20	Q	20	THR	0	-0.040	-0.048	24.359	0.048	0.048	0.000	0.000	0.000	0.000
21	Q	21	ILE	0	-0.003	0.026	18.888	-0.062	-0.062	0.000	0.000	0.000	0.000
22	Q	22	THR	0	0.004	0.005	17.942	-0.027	-0.027	0.000	0.000	0.000	0.000
23	Q	23	CYS	0	-0.038	0.032	12.634	0.173	0.173	0.000	0.000	0.000	0.000
24	Q	24	GLN	0	-0.039	-0.016	12.876	-0.524	-0.524	0.000	0.000	0.000	0.000
25	Q	25	ALA	0	0.031	0.016	9.144	1.438	1.438	0.000	0.000	0.000	0.000
26	Q	26	SER	0	-0.013	-0.008	6.404	0.162	0.162	0.000	0.000	0.000	0.000
27	Q	27	GLN	0	-0.002	-0.009	4.610	-3.119	-2.990	-0.001	-0.015	-0.113	0.000
28	Q	28	ASP	-1	-0.942	-0.965	9.278	17.673	17.673	0.000	0.000	0.000	0.000
29	Q	29	ILE	0	0.040	0.014	8.782	1.176	1.176	0.000	0.000	0.000	0.000
30	Q	30	ARG	1	0.956	0.976	11.722	-17.664	-17.664	0.000	0.000	0.000	0.000
31	Q	31	LYS	1	0.941	0.961	15.360	-13.864	-13.864	0.000	0.000	0.000	0.000
32	Q	32	TYR	0	-0.025	0.007	12.531	-0.819	-0.819	0.000	0.000	0.000	0.000
33	Q	33	LEU	0	0.009	0.005	12.163	1.653	1.653	0.000	0.000	0.000	0.000
34	Q	34	ASN	0	-0.054	-0.022	14.479	-2.466	-2.466	0.000	0.000	0.000	0.000
35	Q	35	TRP	0	0.023	-0.003	15.453	1.068	1.068	0.000	0.000	0.000	0.000
36	Q	36	TYR	0	-0.041	-0.033	15.412	-1.248	-1.248	0.000	0.000	0.000	0.000
37	Q	37	GLN	0	-0.018	-0.032	19.208	-0.171	-0.171	0.000	0.000	0.000	0.000
38	Q	38	GLN	0	-0.007	-0.015	19.435	0.433	0.433	0.000	0.000	0.000	0.000
39	Q	39	LYS	1	0.921	0.963	22.465	-10.712	-10.712	0.000	0.000	0.000	0.000
40	Q	40	PRO	0	0.108	0.058	25.138	0.248	0.248	0.000	0.000	0.000	0.000
41	Q	41	GLY	0	-0.005	-0.002	25.452	-0.402	-0.402	0.000	0.000	0.000	0.000
42	Q	42	LYS	1	0.887	0.951	25.869	-10.829	-10.829	0.000	0.000	0.000	0.000
43	Q	43	ALA	0	0.022	0.005	22.453	0.511	0.511	0.000	0.000	0.000	0.000
44	Q	44	PRO	0	-0.008	-0.008	18.217	-0.456	-0.456	0.000	0.000	0.000	0.000
45	Q	45	ASN	0	0.018	0.012	21.095	-0.308	-0.308	0.000	0.000	0.000	0.000
46	Q	46	LEU	0	-0.004	0.021	19.431	0.163	0.163	0.000	0.000	0.000	0.000
47	Q	47	LEU	0	-0.054	-0.022	21.704	-0.751	-0.751	0.000	0.000	0.000	0.000
48	Q	48	ILE	0	-0.024	-0.009	20.474	-0.512	-0.512	0.000	0.000	0.000	0.000
49	Q	49	TYR	0	0.049	0.008	19.170	0.711	0.711	0.000	0.000	0.000	0.000
50	Q	50	ASP	-1	-0.763	-0.869	17.444	15.888	15.888	0.000	0.000	0.000	0.000
51	Q	51	ALA	0	-0.041	-0.016	18.128	-0.822	-0.822	0.000	0.000	0.000	0.000
52	Q	52	SER	0	-0.108	-0.077	19.300	-0.547	-0.547	0.000	0.000	0.000	0.000
53	Q	53	ASN	0	-0.042	-0.004	22.543	-0.820	-0.820	0.000	0.000	0.000	0.000
54	Q	54	VAL	0	0.045	0.022	23.664	0.456	0.456	0.000	0.000	0.000	0.000
55	Q	55	LYS	1	0.953	0.994	25.215	-12.304	-12.304	0.000	0.000	0.000	0.000
56	Q	56	THR	0	0.021	-0.047	26.906	-0.338	-0.338	0.000	0.000	0.000	0.000
57	Q	57	GLY	0	-0.005	0.038	30.505	0.020	0.020	0.000	0.000	0.000	0.000
58	Q	58	VAL	0	-0.051	-0.010	26.616	-0.010	-0.010	0.000	0.000	0.000	0.000
59	Q	59	PRO	0	-0.001	0.001	29.953	-0.176	-0.176	0.000	0.000	0.000	0.000
60	Q	60	SER	0	0.085	0.029	30.428	0.244	0.244	0.000	0.000	0.000	0.000
61	Q	61	ARG	1	0.800	0.866	30.938	-9.709	-9.709	0.000	0.000	0.000	0.000
62	Q	62	PHE	0	-0.009	0.007	26.019	0.143	0.143	0.000	0.000	0.000	0.000
63	Q	63	ARG	1	0.914	0.957	26.554	-10.112	-10.112	0.000	0.000	0.000	0.000
64	Q	64	GLY	0	0.020	0.018	22.516	0.295	0.295	0.000	0.000	0.000	0.000
65	Q	65	SER	0	-0.026	-0.018	22.025	-0.352	-0.352	0.000	0.000	0.000	0.000
66	Q	66	GLY	0	0.071	0.037	19.396	0.528	0.528	0.000	0.000	0.000	0.000
67	Q	67	SER	0	-0.040	-0.027	18.771	-0.202	-0.202	0.000	0.000	0.000	0.000
68	Q	68	GLY	0	0.042	0.024	15.837	-0.024	-0.024	0.000	0.000	0.000	0.000
69	Q	69	THR	0	0.064	0.015	13.288	1.172	1.172	0.000	0.000	0.000	0.000
70	Q	70	ASP	-1	-0.890	-0.894	14.107	17.290	17.290	0.000	0.000	0.000	0.000
71	Q	71	PHE	0	-0.023	-0.027	13.908	-0.916	-0.916	0.000	0.000	0.000	0.000
72	Q	72	THR	0	-0.014	-0.019	17.636	-0.132	-0.132	0.000	0.000	0.000	0.000
73	Q	73	PHE	0	-0.001	0.011	20.170	-0.269	-0.269	0.000	0.000	0.000	0.000
74	Q	74	THR	0	-0.028	-0.035	21.874	-0.370	-0.370	0.000	0.000	0.000	0.000
75	Q	75	ILE	0	0.019	0.032	25.613	-0.097	-0.097	0.000	0.000	0.000	0.000
76	Q	76	SER	0	-0.086	-0.063	28.171	-0.102	-0.102	0.000	0.000	0.000	0.000
77	Q	77	SER	0	0.010	-0.018	31.595	-0.295	-0.295	0.000	0.000	0.000	0.000
78	Q	78	LEU	0	-0.018	0.034	29.903	0.033	0.033	0.000	0.000	0.000	0.000
79	Q	79	GLN	0	0.009	-0.008	32.110	-0.480	-0.480	0.000	0.000	0.000	0.000
80	Q	80	PRO	0	0.048	0.025	32.355	0.352	0.352	0.000	0.000	0.000	0.000
81	Q	81	GLU	-1	-0.907	-0.955	32.543	8.964	8.964	0.000	0.000	0.000	0.000
82	Q	82	ASP	-1	-0.830	-0.891	28.581	10.610	10.610	0.000	0.000	0.000	0.000
83	Q	83	ILE	0	0.007	0.021	27.574	0.443	0.443	0.000	0.000	0.000	0.000
84	Q	84	ALA	0	-0.002	-0.012	24.488	-0.048	-0.048	0.000	0.000	0.000	0.000
85	Q	85	THR	0	-0.015	0.004	19.384	-0.111	-0.111	0.000	0.000	0.000	0.000
86	Q	86	TYR	0	-0.038	-0.031	19.563	-0.013	-0.013	0.000	0.000	0.000	0.000
87	Q	87	TYR	0	0.024	0.042	13.976	0.419	0.419	0.000	0.000	0.000	0.000
88	Q	89	GLN	0	0.132	0.062	10.866	-0.457	-0.457	0.000	0.000	0.000	0.000
89	Q	90	GLN	0	0.051	0.046	6.316	1.342	1.342	0.000	0.000	0.000	0.000
90	Q	91	TYR	0	-0.059	-0.064	9.315	0.728	0.728	0.000	0.000	0.000	0.000
91	Q	92	ASP	-1	-0.940	-0.968	8.507	28.470	28.470	0.000	0.000	0.000	0.000
92	Q	93	ASN	0	-0.020	0.003	3.747	6.835	7.180	0.005	-0.073	-0.277	0.000
93	Q	94	LEU	0	-0.024	-0.042	5.845	-2.320	-2.320	0.000	0.000	0.000	0.000
94	Q	95	PRO	0	-0.002	0.043	1.895	-4.461	-3.037	5.776	-3.464	-3.736	0.023
95	Q	96	ILE	0	-0.059	-0.033	4.818	-5.868	-5.791	-0.001	-0.018	-0.057	0.000
96	Q	97	THR	0	-0.008	-0.040	3.282	-0.983	-0.360	0.023	-0.159	-0.486	0.001
97	Q	98	PHE	0	-0.033	-0.041	6.584	-5.076	-5.076	0.000	0.000	0.000	0.000
98	Q	99	GLY	0	0.015	0.010	8.650	1.504	1.504	0.000	0.000	0.000	0.000
99	Q	100	GLN	0	0.023	0.013	11.232	1.894	1.894	0.000	0.000	0.000	0.000
100	Q	101	GLY	0	-0.019	-0.021	12.969	-1.086	-1.086	0.000	0.000	0.000	0.000
101	Q	102	THR	0	-0.027	-0.025	16.232	0.086	0.086	0.000	0.000	0.000	0.000
102	Q	103	ARG	1	0.927	0.967	19.440	-12.289	-12.289	0.000	0.000	0.000	0.000
103	Q	104	LEU	0	-0.012	0.000	22.628	-0.232	-0.232	0.000	0.000	0.000	0.000
104	Q	105	GLU	-1	-0.794	-0.811	25.990	9.993	9.993	0.000	0.000	0.000	0.000
105	Q	106	ILE	0	0.034	0.004	29.423	0.020	0.020	0.000	0.000	0.000	0.000
106	Q	107	LYS	1	0.901	0.956	32.713	-8.890	-8.890	0.000	0.000	0.000	0.000
107	Q	108	ARG	1	0.945	0.994	34.705	-8.018	-8.018	0.000	0.000	0.000	0.000
108	Q	109	THR	0	-0.014	-0.017	37.914	0.039	0.039	0.000	0.000	0.000	0.000
109	Q	110	VAL	0	-0.006	0.005	39.141	0.107	0.107	0.000	0.000	0.000	0.000
110	Q	111	ALA	0	-0.017	-0.010	40.305	-0.124	-0.124	0.000	0.000	0.000	0.000
111	Q	112	ALA	0	0.042	0.009	41.858	0.028	0.028	0.000	0.000	0.000	0.000
112	Q	113	PRO	0	0.024	0.009	40.887	-0.024	-0.024	0.000	0.000	0.000	0.000
113	Q	114	SER	0	-0.017	0.003	42.650	-0.192	-0.192	0.000	0.000	0.000	0.000
114	Q	115	VAL	0	-0.012	-0.010	43.415	0.084	0.084	0.000	0.000	0.000	0.000
115	Q	116	PHE	0	-0.056	-0.014	44.929	-0.175	-0.175	0.000	0.000	0.000	0.000
116	Q	132	VAL	0	-0.028	-0.031	41.470	-0.041	-0.041	0.000	0.000	0.000	0.000
117	Q	133	VAL	0	0.015	0.004	41.569	0.150	0.150	0.000	0.000	0.000	0.000
118	Q	134	CYS	0	-0.010	0.015	41.415	-0.190	-0.190	0.000	0.000	0.000	0.000
119	Q	135	LEU	0	0.021	0.013	40.439	0.213	0.213	0.000	0.000	0.000	0.000
120	Q	136	LEU	0	-0.002	0.000	38.292	-0.198	-0.198	0.000	0.000	0.000	0.000
121	Q	137	ASN	0	0.023	-0.019	40.074	0.247	0.247	0.000	0.000	0.000	0.000
122	Q	138	ASN	0	-0.021	-0.005	40.451	-0.070	-0.070	0.000	0.000	0.000	0.000
123	Q	139	PHE	0	-0.009	0.010	35.301	-0.164	-0.164	0.000	0.000	0.000	0.000
124	Q	140	TYR	0	0.055	0.034	33.686	0.155	0.155	0.000	0.000	0.000	0.000
125	Q	141	PRO	0	-0.025	-0.017	32.945	-0.279	-0.279	0.000	0.000	0.000	0.000
126	Q	142	ARG	1	0.982	0.975	27.487	-11.123	-11.123	0.000	0.000	0.000	0.000
127	Q	143	GLU	-1	-0.910	-0.935	30.284	9.969	9.969	0.000	0.000	0.000	0.000
128	Q	144	ALA	0	-0.008	-0.003	32.784	-0.253	-0.253	0.000	0.000	0.000	0.000
129	Q	160	GLN	0	-0.027	-0.030	31.035	-0.171	-0.171	0.000	0.000	0.000	0.000
130	Q	161	GLU	-1	-0.894	-0.949	32.068	9.145	9.145	0.000	0.000	0.000	0.000
131	Q	162	SER	0	-0.039	-0.008	30.880	0.433	0.433	0.000	0.000	0.000	0.000
132	Q	163	VAL	0	-0.006	-0.015	30.242	-0.318	-0.318	0.000	0.000	0.000	0.000
133	Q	164	THR	0	-0.014	0.022	30.691	0.373	0.373	0.000	0.000	0.000	0.000
134	Q	165	GLU	-1	-0.919	-0.988	27.175	11.690	11.690	0.000	0.000	0.000	0.000
135	Q	166	GLN	0	0.007	0.003	30.977	-0.419	-0.419	0.000	0.000	0.000	0.000
136	Q	167	ASP	-1	-0.828	-0.895	32.899	8.442	8.442	0.000	0.000	0.000	0.000
137	Q	168	SER	0	-0.051	-0.051	35.369	0.031	0.031	0.000	0.000	0.000	0.000
138	Q	169	LYS	1	0.842	0.919	36.550	-8.000	-8.000	0.000	0.000	0.000	0.000
139	Q	170	ASP	-1	-0.812	-0.917	39.944	7.702	7.702	0.000	0.000	0.000	0.000
140	Q	171	SER	0	-0.059	-0.024	36.027	-0.072	-0.072	0.000	0.000	0.000	0.000
141	Q	172	THR	0	-0.070	-0.030	36.898	0.020	0.020	0.000	0.000	0.000	0.000
142	Q	173	TYR	0	-0.106	-0.129	30.393	0.378	0.378	0.000	0.000	0.000	0.000
143	Q	174	SER	0	0.032	-0.005	35.618	-0.253	-0.253	0.000	0.000	0.000	0.000
144	Q	175	LEU	0	-0.065	-0.004	33.599	0.181	0.181	0.000	0.000	0.000	0.000
145	Q	176	SER	0	0.016	-0.012	35.424	-0.336	-0.336	0.000	0.000	0.000	0.000
146	Q	177	SER	0	0.008	0.032	35.660	0.190	0.190	0.000	0.000	0.000	0.000
147	Q	178	THR	0	-0.007	-0.003	36.667	-0.221	-0.221	0.000	0.000	0.000	0.000
148	Q	196	VAL	0	-0.009	-0.013	40.681	0.068	0.068	0.000	0.000	0.000	0.000
149	Q	197	THR	0	0.019	-0.003	39.767	-0.156	-0.156	0.000	0.000	0.000	0.000
150	Q	198	HIS	0	0.032	0.011	37.594	0.022	0.022	0.000	0.000	0.000	0.000
151	Q	199	GLN	0	0.032	0.001	36.089	-0.216	-0.216	0.000	0.000	0.000	0.000
152	Q	200	GLY	0	-0.042	0.003	41.054	-0.142	-0.142	0.000	0.000	0.000	0.000
153	Q	201	LEU	0	-0.052	-0.016	42.633	-0.177	-0.177	0.000	0.000	0.000	0.000
154	Q	202	SER	0	-0.016	-0.012	45.536	-0.022	-0.022	0.000	0.000	0.000	0.000
155	Q	203	SER	0	-0.016	-0.016	46.720	-0.002	-0.002	0.000	0.000	0.000	0.000
156	Q	204	PRO	0	0.004	0.023	44.483	-0.050	-0.050	0.000	0.000	0.000	0.000

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