FMO DATABASE

FMODB ID: 1N8GZ

Calculation Name: 4DOH-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4DOH

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UHF4

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1568816.682992
FMO2-HF: Nuclear repulsion	1506117.42266
FMO2-HF: Total energy	-62699.260332
FMO2-MP2: Total energy	-62878.64169

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(A:24:DAL)

Summations of interaction energy for fragment #1(A:24:DAL)

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.
-0.334	1.872	-0.02	-1.14	-1.046	0.005

Interaction energy analysis for fragmet #1(A:24:DAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.017

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	A	26	LYS	1	0.874	0.959	3.837	-0.093	2.018	-0.019	-1.133	-0.959	0.005
4	A	27	THR	0	0.005	-0.005	6.512	0.100	0.100	0.000	0.000	0.000	0.000
5	A	28	LEU	0	-0.013	-0.002	8.924	0.122	0.122	0.000	0.000	0.000	0.000
6	A	29	ASN	0	0.017	0.010	12.283	0.047	0.047	0.000	0.000	0.000	0.000
7	A	30	LEU	0	-0.021	-0.030	15.306	0.023	0.023	0.000	0.000	0.000	0.000
8	A	31	GLY	0	0.024	0.000	18.363	0.018	0.018	0.000	0.000	0.000	0.000
9	A	32	SER	0	-0.010	-0.015	19.649	0.000	0.000	0.000	0.000	0.000	0.000
10	A	33	CYS	0	-0.032	0.021	18.658	0.004	0.004	0.000	0.000	0.000	0.000
11	A	34	VAL	0	0.019	0.004	13.059	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	35	ILE	0	0.010	0.009	12.997	0.009	0.009	0.000	0.000	0.000	0.000
13	A	36	ALA	0	0.036	0.020	7.822	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	37	THR	0	0.002	0.003	8.590	0.025	0.025	0.000	0.000	0.000	0.000
15	A	38	ASN	0	0.074	0.018	6.140	-1.273	-1.273	0.000	0.000	0.000	0.000
16	A	39	LEU	0	0.034	0.009	7.481	0.277	0.277	0.000	0.000	0.000	0.000
17	A	40	GLN	0	-0.020	-0.004	4.711	0.268	0.363	-0.001	-0.007	-0.087	0.000
18	A	41	GLU	-1	-0.949	-0.968	6.828	-0.606	-0.606	0.000	0.000	0.000	0.000
19	A	42	ILE	0	0.022	0.003	9.083	0.295	0.295	0.000	0.000	0.000	0.000
20	A	43	ARG	1	0.913	0.957	9.232	0.929	0.929	0.000	0.000	0.000	0.000
21	A	44	ASN	0	0.025	0.016	8.206	0.216	0.216	0.000	0.000	0.000	0.000
22	A	45	GLY	0	0.005	0.008	12.089	0.112	0.112	0.000	0.000	0.000	0.000
23	A	46	PHE	0	0.032	-0.001	14.634	0.075	0.075	0.000	0.000	0.000	0.000
24	A	47	SER	0	-0.085	-0.030	14.940	0.074	0.074	0.000	0.000	0.000	0.000
25	A	48	GLU	-1	-0.915	-0.962	16.507	-0.206	-0.206	0.000	0.000	0.000	0.000
26	A	49	ILE	0	-0.040	-0.030	18.920	0.029	0.029	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.924	0.991	17.212	0.231	0.231	0.000	0.000	0.000	0.000
28	A	51	GLY	0	0.041	0.018	21.335	0.014	0.014	0.000	0.000	0.000	0.000
29	A	52	SER	0	-0.022	-0.014	24.222	0.013	0.013	0.000	0.000	0.000	0.000
30	A	53	VAL	0	0.018	0.005	23.516	0.010	0.010	0.000	0.000	0.000	0.000
31	A	54	GLN	0	0.000	-0.022	22.202	0.026	0.026	0.000	0.000	0.000	0.000
32	A	55	ALA	0	-0.022	0.008	26.494	0.010	0.010	0.000	0.000	0.000	0.000
33	A	56	LYS	1	0.837	0.918	29.180	0.123	0.123	0.000	0.000	0.000	0.000
34	A	57	ASP	-1	-0.814	-0.901	29.161	-0.130	-0.130	0.000	0.000	0.000	0.000
35	A	58	GLY	0	0.019	0.019	31.120	0.003	0.003	0.000	0.000	0.000	0.000
36	A	59	ASN	0	-0.006	0.007	33.335	0.003	0.003	0.000	0.000	0.000	0.000
37	A	60	ILE	0	-0.004	-0.010	31.775	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	61	ASP	-1	-0.916	-0.957	32.642	-0.083	-0.083	0.000	0.000	0.000	0.000
39	A	62	ILE	0	-0.042	-0.009	31.910	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	63	ARG	1	0.879	0.926	23.600	0.147	0.147	0.000	0.000	0.000	0.000
41	A	64	ILE	0	-0.004	-0.007	27.001	0.006	0.006	0.000	0.000	0.000	0.000
42	A	65	LEU	0	-0.006	0.004	21.596	0.002	0.002	0.000	0.000	0.000	0.000
43	A	66	ARG	1	0.918	0.959	25.098	0.112	0.112	0.000	0.000	0.000	0.000
44	A	67	ARG	1	0.927	0.949	24.684	0.103	0.103	0.000	0.000	0.000	0.000
45	A	68	THR	0	0.004	0.007	25.736	0.004	0.004	0.000	0.000	0.000	0.000
46	A	69	GLU	-1	-0.903	-0.976	26.247	-0.140	-0.140	0.000	0.000	0.000	0.000
47	A	70	SER	0	0.012	0.030	20.724	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	71	LEU	0	0.055	0.005	17.453	0.016	0.016	0.000	0.000	0.000	0.000
49	A	72	GLN	0	0.029	0.016	18.517	0.009	0.009	0.000	0.000	0.000	0.000
50	A	73	ASP	-1	-0.900	-0.931	20.130	-0.107	-0.107	0.000	0.000	0.000	0.000
51	A	74	THR	0	-0.134	-0.061	22.755	0.018	0.018	0.000	0.000	0.000	0.000
52	A	75	LYS	1	0.949	0.972	23.101	0.089	0.089	0.000	0.000	0.000	0.000
53	A	76	PRO	0	0.063	0.029	20.935	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	77	ALA	0	0.005	-0.006	22.387	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	78	ASN	0	-0.009	-0.026	24.909	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.793	0.927	18.098	0.202	0.202	0.000	0.000	0.000	0.000
57	A	80	CYS	0	-0.039	-0.007	20.343	-0.045	-0.045	0.000	0.000	0.000	0.000
58	A	81	CYS	0	-0.030	-0.014	21.285	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	82	LEU	0	0.031	0.004	23.012	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.028	0.020	16.632	0.000	0.000	0.000	0.000	0.000	0.000
61	A	84	ARG	1	0.950	0.981	21.216	0.217	0.217	0.000	0.000	0.000	0.000
62	A	85	HIS	0	-0.014	-0.013	22.695	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	86	LEU	0	0.043	0.030	21.973	0.005	0.005	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.001	0.002	17.525	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.912	0.965	21.856	0.213	0.213	0.000	0.000	0.000	0.000
66	A	89	LEU	0	-0.031	0.003	25.304	0.011	0.011	0.000	0.000	0.000	0.000
67	A	90	TYR	0	-0.005	-0.045	22.271	0.009	0.009	0.000	0.000	0.000	0.000
68	A	91	LEU	0	-0.060	-0.043	21.030	0.007	0.007	0.000	0.000	0.000	0.000
69	A	92	ASP	-1	-0.915	-0.958	24.655	-0.192	-0.192	0.000	0.000	0.000	0.000
70	A	93	ARG	1	0.802	0.888	27.808	0.170	0.170	0.000	0.000	0.000	0.000
71	A	94	VAL	0	0.010	0.036	24.881	0.010	0.010	0.000	0.000	0.000	0.000
72	A	95	PHE	0	0.028	0.003	19.641	0.010	0.010	0.000	0.000	0.000	0.000
73	A	96	LYS	1	0.916	0.964	25.084	0.184	0.184	0.000	0.000	0.000	0.000
74	A	97	ASN	0	-0.010	-0.011	28.054	0.015	0.015	0.000	0.000	0.000	0.000
75	A	98	TYR	0	0.015	0.015	27.097	0.012	0.012	0.000	0.000	0.000	0.000
76	A	99	GLN	0	-0.020	0.000	29.085	0.005	0.005	0.000	0.000	0.000	0.000
77	A	100	THR	0	0.002	-0.016	27.666	0.007	0.007	0.000	0.000	0.000	0.000
78	A	101	PRO	0	0.009	0.011	31.051	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	102	ASP	-1	-0.814	-0.907	27.702	-0.143	-0.143	0.000	0.000	0.000	0.000
80	A	103	HIS	0	0.086	0.011	27.919	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	104	TYR	0	-0.043	-0.019	19.984	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	105	THR	0	-0.026	-0.014	23.350	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	106	LEU	0	0.016	0.005	23.329	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	107	ARG	1	0.948	0.986	21.996	0.162	0.162	0.000	0.000	0.000	0.000
85	A	108	LYS	1	0.952	0.994	16.377	0.311	0.311	0.000	0.000	0.000	0.000
86	A	109	ILE	0	0.021	0.018	19.180	-0.048	-0.048	0.000	0.000	0.000	0.000
87	A	110	SER	0	0.010	0.010	20.981	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	111	SER	0	-0.032	0.004	16.073	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	112	LEU	0	0.007	0.002	15.638	-0.059	-0.059	0.000	0.000	0.000	0.000
90	A	113	ALA	0	0.026	0.020	17.404	-0.040	-0.040	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.038	-0.046	18.375	0.005	0.005	0.000	0.000	0.000	0.000
92	A	115	SER	0	0.041	0.019	13.518	-0.058	-0.058	0.000	0.000	0.000	0.000
93	A	116	PHE	0	0.002	-0.016	15.160	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	117	LEU	0	-0.011	0.005	17.236	0.019	0.019	0.000	0.000	0.000	0.000
95	A	118	THR	0	-0.083	-0.045	14.301	0.003	0.003	0.000	0.000	0.000	0.000
96	A	119	ILE	0	0.091	0.051	13.099	0.022	0.022	0.000	0.000	0.000	0.000
97	A	120	LYN	0	0.017	0.009	15.925	0.069	0.069	0.000	0.000	0.000	0.000
98	A	121	LYS	1	0.889	0.930	18.458	0.421	0.421	0.000	0.000	0.000	0.000
99	A	122	ASP	-1	-0.816	-0.893	14.090	-0.543	-0.543	0.000	0.000	0.000	0.000
100	A	123	LEU	0	-0.003	-0.007	17.665	0.054	0.054	0.000	0.000	0.000	0.000
101	A	124	ARG	1	0.825	0.909	19.860	0.284	0.284	0.000	0.000	0.000	0.000
102	A	125	LEU	0	0.037	0.035	18.607	0.032	0.032	0.000	0.000	0.000	0.000
103	A	127	HIS	0	-0.018	-0.025	21.711	0.020	0.020	0.000	0.000	0.000	0.000
104	A	128	ALA	0	-0.016	-0.007	24.745	0.018	0.018	0.000	0.000	0.000	0.000
105	A	129	HIS	0	-0.023	-0.004	21.584	0.023	0.023	0.000	0.000	0.000	0.000
106	A	130	MET	0	-0.029	-0.016	25.527	0.008	0.008	0.000	0.000	0.000	0.000
107	A	131	THR	0	-0.028	-0.014	22.514	0.000	0.000	0.000	0.000	0.000	0.000
108	A	133	HIS	0	0.045	0.025	24.692	0.001	0.001	0.000	0.000	0.000	0.000
109	A	135	GLY	0	0.051	0.043	29.148	0.011	0.011	0.000	0.000	0.000	0.000
110	A	136	GLU	-1	-0.861	-0.964	30.893	-0.095	-0.095	0.000	0.000	0.000	0.000
111	A	137	GLU	-1	-0.836	-0.913	27.707	-0.127	-0.127	0.000	0.000	0.000	0.000
112	A	138	ALA	0	-0.005	-0.003	27.019	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	139	MET	0	0.014	0.003	28.491	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	140	LYS	1	0.930	0.984	31.317	0.091	0.091	0.000	0.000	0.000	0.000
115	A	141	LYS	1	0.938	0.958	26.257	0.144	0.144	0.000	0.000	0.000	0.000
116	A	142	TYR	0	0.028	0.016	27.110	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	143	SER	0	0.010	0.005	29.096	0.000	0.000	0.000	0.000	0.000	0.000
118	A	144	GLN	0	-0.079	-0.033	30.954	0.010	0.010	0.000	0.000	0.000	0.000
119	A	145	ILE	0	0.006	0.011	25.357	0.000	0.000	0.000	0.000	0.000	0.000
120	A	146	LEU	0	-0.043	-0.035	29.516	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	147	SER	0	0.020	0.010	31.350	0.007	0.007	0.000	0.000	0.000	0.000
122	A	148	HIS	0	0.011	0.005	30.137	0.002	0.002	0.000	0.000	0.000	0.000
123	A	149	PHE	0	-0.047	-0.027	29.116	0.001	0.001	0.000	0.000	0.000	0.000
124	A	150	GLU	-1	-0.890	-0.961	31.825	-0.122	-0.122	0.000	0.000	0.000	0.000
125	A	151	LYN	0	-0.034	0.007	34.105	0.005	0.005	0.000	0.000	0.000	0.000
126	A	152	LEU	0	-0.041	-0.010	32.443	0.005	0.005	0.000	0.000	0.000	0.000
127	A	153	GLU	-1	-0.873	-0.933	36.138	-0.089	-0.089	0.000	0.000	0.000	0.000
128	A	154	PRO	0	0.055	0.007	35.104	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	155	GLN	0	0.002	-0.001	32.243	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	156	ALA	0	0.060	0.036	32.340	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	157	ALA	0	0.015	0.018	31.532	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	158	VAL	0	-0.048	-0.033	28.524	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	159	VAL	0	-0.041	-0.019	27.423	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	160	LYS	1	0.849	0.929	27.137	0.121	0.121	0.000	0.000	0.000	0.000
135	A	161	ALA	0	0.000	0.005	25.269	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	162	LEU	0	-0.038	-0.005	21.706	-0.030	-0.030	0.000	0.000	0.000	0.000
137	A	163	GLY	0	0.017	-0.006	21.985	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	164	GLU	-1	-0.762	-0.886	22.255	-0.180	-0.180	0.000	0.000	0.000	0.000
139	A	165	LEU	0	0.005	-0.001	17.242	-0.023	-0.023	0.000	0.000	0.000	0.000
140	A	166	ASP	-1	-0.916	-0.957	16.547	-0.293	-0.293	0.000	0.000	0.000	0.000
141	A	167	ILE	0	-0.010	0.005	16.825	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	168	LEU	0	0.027	0.010	17.536	-0.016	-0.016	0.000	0.000	0.000	0.000
143	A	169	LEU	0	-0.021	-0.030	12.358	-0.043	-0.043	0.000	0.000	0.000	0.000
144	A	170	GLN	0	0.011	0.012	13.165	-0.100	-0.100	0.000	0.000	0.000	0.000
145	A	171	TRP	0	-0.020	-0.002	14.885	0.012	0.012	0.000	0.000	0.000	0.000
146	A	172	MET	0	-0.049	-0.030	13.151	0.001	0.001	0.000	0.000	0.000	0.000
147	A	173	GLU	-1	-0.926	-0.971	8.359	-1.027	-1.027	0.000	0.000	0.000	0.000
148	A	174	GLU	-1	-0.902	-0.967	11.735	-0.167	-0.167	0.000	0.000	0.000	0.000
149	A	175	THR	0	-0.099	-0.037	13.991	0.036	0.036	0.000	0.000	0.000	0.000
150	A	176	GLU	-1	-0.844	-0.922	11.462	-0.322	-0.322	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:24:DAL)