FMO DATABASE

FMODB ID: 49KNN

Calculation Name: 4HG4-P-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4HG4

Chain ID: P

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	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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1423248.033404
FMO2-HF: Nuclear repulsion	1361907.391789
FMO2-HF: Total energy	-61340.641614
FMO2-MP2: Total energy	-61521.167395

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(P:1:GLU)

Summations of interaction energy for fragment #1(P:1:GLU)

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.
-15.555	-11.403	3.609	-2.87	-4.89	0.015

Interaction energy analysis for fragmet #1(P:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.933 / q_NPA : -0.979

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	P	3	GLN	0	-0.044	-0.017	3.137	-8.990	-7.303	0.023	-0.642	-1.067	0.002
4	P	4	LEU	0	0.000	-0.015	6.495	-0.097	-0.097	0.000	0.000	0.000	0.000
5	P	5	VAL	0	-0.024	-0.007	10.257	-0.687	-0.687	0.000	0.000	0.000	0.000
6	P	6	GLU	-1	-0.780	-0.892	13.226	16.319	16.319	0.000	0.000	0.000	0.000
7	P	7	SER	0	-0.028	-0.016	16.685	-0.101	-0.101	0.000	0.000	0.000	0.000
8	P	8	GLY	0	0.011	0.017	20.280	0.057	0.057	0.000	0.000	0.000	0.000
9	P	9	ALA	0	0.011	0.006	22.494	-0.090	-0.090	0.000	0.000	0.000	0.000
10	P	10	GLU	-1	-0.828	-0.921	24.933	10.667	10.667	0.000	0.000	0.000	0.000
11	P	11	VAL	0	-0.011	-0.004	28.270	-0.134	-0.134	0.000	0.000	0.000	0.000
12	P	12	LYS	1	0.793	0.903	30.033	-10.310	-10.310	0.000	0.000	0.000	0.000
13	P	13	LYS	1	0.880	0.940	34.372	-7.995	-7.995	0.000	0.000	0.000	0.000
14	P	14	PRO	0	0.023	0.006	37.318	0.154	0.154	0.000	0.000	0.000	0.000
15	P	15	GLY	0	-0.009	0.007	38.280	-0.171	-0.171	0.000	0.000	0.000	0.000
16	P	16	SER	0	-0.078	-0.047	35.712	0.128	0.128	0.000	0.000	0.000	0.000
17	P	17	SER	0	0.001	-0.034	31.275	0.055	0.055	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.037	-0.017	27.175	-0.072	-0.072	0.000	0.000	0.000	0.000
19	P	19	LYS	1	0.892	0.934	24.710	-11.617	-11.617	0.000	0.000	0.000	0.000
20	P	20	VAL	0	0.041	0.051	21.759	0.198	0.198	0.000	0.000	0.000	0.000
21	P	21	SER	0	0.021	-0.003	18.568	-0.164	-0.164	0.000	0.000	0.000	0.000
22	P	22	CYS	0	-0.081	-0.040	14.347	0.347	0.347	0.000	0.000	0.000	0.000
23	P	23	LYS	1	0.858	0.940	10.274	-27.098	-27.098	0.000	0.000	0.000	0.000
24	P	24	ALA	0	0.023	0.017	8.663	0.612	0.612	0.000	0.000	0.000	0.000
25	P	25	SER	0	-0.033	-0.034	6.781	-1.876	-1.876	0.000	0.000	0.000	0.000
26	P	26	GLY	0	0.070	0.049	2.512	-6.624	-4.024	2.027	-2.547	-2.080	0.026
27	P	27	GLY	0	0.034	0.001	2.497	-0.424	-0.650	1.560	0.323	-1.657	-0.013
28	P	28	THR	0	-0.018	-0.002	5.136	-4.891	-4.800	-0.001	-0.004	-0.086	0.000
29	P	29	PHE	0	0.056	0.036	8.877	-0.403	-0.403	0.000	0.000	0.000	0.000
30	P	30	ILE	0	0.062	0.015	11.475	-0.282	-0.282	0.000	0.000	0.000	0.000
31	P	31	THR	0	-0.073	-0.037	8.706	-0.102	-0.102	0.000	0.000	0.000	0.000
32	P	32	HIS	0	0.015	0.030	7.122	-0.468	-0.468	0.000	0.000	0.000	0.000
33	P	33	VAL	0	-0.009	0.004	11.590	-1.491	-1.491	0.000	0.000	0.000	0.000
34	P	34	PHE	0	0.018	0.005	12.417	0.582	0.582	0.000	0.000	0.000	0.000
35	P	35	THR	0	-0.038	-0.034	15.477	-1.277	-1.277	0.000	0.000	0.000	0.000
36	P	36	TRP	0	0.028	0.010	17.900	0.516	0.516	0.000	0.000	0.000	0.000
37	P	37	VAL	0	0.004	0.003	19.858	-0.741	-0.741	0.000	0.000	0.000	0.000
38	P	38	ARG	1	0.804	0.888	21.985	-9.958	-9.958	0.000	0.000	0.000	0.000
39	P	39	GLN	0	0.015	0.010	24.424	0.231	0.231	0.000	0.000	0.000	0.000
40	P	40	ALA	0	0.030	0.025	26.498	-0.009	-0.009	0.000	0.000	0.000	0.000
41	P	41	PRO	0	-0.002	-0.021	29.424	0.021	0.021	0.000	0.000	0.000	0.000
42	P	42	GLY	0	0.019	0.026	29.753	-0.329	-0.329	0.000	0.000	0.000	0.000
43	P	43	GLN	0	-0.040	-0.014	30.698	-0.252	-0.252	0.000	0.000	0.000	0.000
44	P	44	GLY	0	0.024	0.007	27.945	0.300	0.300	0.000	0.000	0.000	0.000
45	P	45	LEU	0	-0.014	-0.005	21.935	-0.024	-0.024	0.000	0.000	0.000	0.000
46	P	46	GLU	-1	-0.773	-0.870	25.795	9.467	9.467	0.000	0.000	0.000	0.000
47	P	47	TRP	0	-0.016	-0.004	21.072	-0.044	-0.044	0.000	0.000	0.000	0.000
48	P	48	VAL	0	-0.012	-0.011	24.264	-0.481	-0.481	0.000	0.000	0.000	0.000
49	P	49	GLY	0	0.044	-0.002	23.581	-0.488	-0.488	0.000	0.000	0.000	0.000
50	P	50	GLY	0	-0.024	0.004	20.157	0.598	0.598	0.000	0.000	0.000	0.000
51	P	51	PHE	0	0.000	0.002	16.586	-0.662	-0.662	0.000	0.000	0.000	0.000
52	P	52	ILE	0	0.006	0.020	17.222	1.141	1.141	0.000	0.000	0.000	0.000
53	P	52	ALA	0	0.008	0.013	14.289	-0.698	-0.698	0.000	0.000	0.000	0.000
54	P	53	ILE	0	-0.032	-0.014	16.075	-0.506	-0.506	0.000	0.000	0.000	0.000
55	P	54	PHE	0	-0.040	-0.028	17.535	-0.613	-0.613	0.000	0.000	0.000	0.000
56	P	55	GLY	0	0.007	0.019	19.844	-0.652	-0.652	0.000	0.000	0.000	0.000
57	P	56	THR	0	-0.001	0.002	21.400	-0.410	-0.410	0.000	0.000	0.000	0.000
58	P	57	SER	0	-0.002	-0.003	21.654	0.478	0.478	0.000	0.000	0.000	0.000
59	P	58	ASN	0	-0.022	0.009	23.530	-0.054	-0.054	0.000	0.000	0.000	0.000
60	P	59	TYR	0	0.046	0.000	24.739	0.233	0.233	0.000	0.000	0.000	0.000
61	P	60	ALA	0	0.029	0.025	27.405	-0.228	-0.228	0.000	0.000	0.000	0.000
62	P	61	GLN	0	0.040	0.011	29.458	0.059	0.059	0.000	0.000	0.000	0.000
63	P	62	LYS	1	0.837	0.907	32.140	-9.490	-9.490	0.000	0.000	0.000	0.000
64	P	63	PHE	0	-0.014	-0.010	28.937	-0.159	-0.159	0.000	0.000	0.000	0.000
65	P	64	GLN	0	-0.012	-0.007	32.375	0.205	0.205	0.000	0.000	0.000	0.000
66	P	65	GLY	0	-0.008	0.002	33.677	-0.240	-0.240	0.000	0.000	0.000	0.000
67	P	66	ARG	1	0.820	0.888	33.305	-9.115	-9.115	0.000	0.000	0.000	0.000
68	P	67	VAL	0	0.016	0.018	26.913	0.125	0.125	0.000	0.000	0.000	0.000
69	P	68	THR	0	-0.045	-0.023	27.373	-0.246	-0.246	0.000	0.000	0.000	0.000
70	P	69	ILE	0	-0.022	0.002	21.436	0.229	0.229	0.000	0.000	0.000	0.000
71	P	70	THR	0	-0.015	0.002	22.524	-0.184	-0.184	0.000	0.000	0.000	0.000
72	P	71	ALA	0	0.017	-0.001	17.382	0.532	0.532	0.000	0.000	0.000	0.000
73	P	72	ASP	-1	-0.796	-0.861	17.721	16.250	16.250	0.000	0.000	0.000	0.000
74	P	73	GLU	-1	-0.884	-0.939	14.786	20.337	20.337	0.000	0.000	0.000	0.000
75	P	74	SER	0	-0.089	-0.058	14.251	1.437	1.437	0.000	0.000	0.000	0.000
76	P	75	THR	0	-0.029	-0.042	14.397	0.951	0.951	0.000	0.000	0.000	0.000
77	P	76	SER	0	-0.020	-0.005	10.530	2.227	2.227	0.000	0.000	0.000	0.000
78	P	77	THR	0	-0.008	-0.010	12.246	1.801	1.801	0.000	0.000	0.000	0.000
79	P	78	ALA	0	0.024	0.031	14.983	-0.949	-0.949	0.000	0.000	0.000	0.000
80	P	79	TYR	0	-0.004	-0.024	17.303	0.193	0.193	0.000	0.000	0.000	0.000
81	P	80	MET	0	-0.039	-0.003	20.708	-0.450	-0.450	0.000	0.000	0.000	0.000
82	P	81	GLU	-1	-0.807	-0.883	23.246	10.548	10.548	0.000	0.000	0.000	0.000
83	P	82	LEU	0	-0.017	-0.010	26.918	-0.092	-0.092	0.000	0.000	0.000	0.000
84	P	82	THR	0	0.006	-0.006	29.691	-0.216	-0.216	0.000	0.000	0.000	0.000
85	P	82	SER	0	0.000	-0.014	33.331	-0.134	-0.134	0.000	0.000	0.000	0.000
86	P	82	LEU	0	-0.056	-0.001	31.237	-0.096	-0.096	0.000	0.000	0.000	0.000
87	P	83	THR	0	0.035	-0.012	35.322	-0.297	-0.297	0.000	0.000	0.000	0.000
88	P	84	SER	0	0.043	0.012	35.221	0.185	0.185	0.000	0.000	0.000	0.000
89	P	85	GLU	-1	-0.918	-0.937	35.122	8.250	8.250	0.000	0.000	0.000	0.000
90	P	86	ASP	-1	-0.779	-0.852	31.350	9.554	9.554	0.000	0.000	0.000	0.000
91	P	87	THR	0	-0.026	0.001	30.334	0.389	0.389	0.000	0.000	0.000	0.000
92	P	88	ALA	0	-0.016	-0.014	27.306	-0.152	-0.152	0.000	0.000	0.000	0.000
93	P	89	VAL	0	0.008	0.027	21.994	0.093	0.093	0.000	0.000	0.000	0.000
94	P	90	TYR	0	-0.024	-0.042	22.700	-0.066	-0.066	0.000	0.000	0.000	0.000
95	P	91	TYR	0	0.015	0.011	18.014	0.403	0.403	0.000	0.000	0.000	0.000
96	P	93	ALA	0	0.024	0.010	13.823	0.357	0.357	0.000	0.000	0.000	0.000
97	P	94	ARG	1	0.875	0.932	8.170	-29.993	-29.993	0.000	0.000	0.000	0.000
98	P	95	GLY	0	0.034	0.016	12.284	-0.116	-0.116	0.000	0.000	0.000	0.000
99	P	96	ILE	0	-0.023	-0.013	12.116	1.496	1.496	0.000	0.000	0.000	0.000
100	P	97	SER	0	-0.003	-0.008	14.159	-1.666	-1.666	0.000	0.000	0.000	0.000
101	P	98	GLY	0	0.041	0.003	17.179	0.143	0.143	0.000	0.000	0.000	0.000
102	P	99	SER	0	-0.047	-0.028	19.806	-0.714	-0.714	0.000	0.000	0.000	0.000
103	P	100	TYR	0	-0.068	-0.047	18.037	-0.155	-0.155	0.000	0.000	0.000	0.000
104	P	100	GLY	0	0.011	0.019	17.952	-0.209	-0.209	0.000	0.000	0.000	0.000
105	P	100	TRP	0	0.021	0.003	12.433	-1.127	-1.127	0.000	0.000	0.000	0.000
106	P	100	PHE	0	-0.028	-0.026	14.079	0.680	0.680	0.000	0.000	0.000	0.000
107	P	101	ASP	-1	-0.901	-0.938	8.623	25.057	25.057	0.000	0.000	0.000	0.000
108	P	102	PRO	0	0.007	0.009	7.235	-0.222	-0.222	0.000	0.000	0.000	0.000
109	P	103	TRP	0	-0.040	-0.038	9.779	-1.909	-1.909	0.000	0.000	0.000	0.000
110	P	104	GLY	0	0.003	0.009	12.054	1.129	1.129	0.000	0.000	0.000	0.000
111	P	105	GLN	0	-0.017	-0.020	14.253	-0.073	-0.073	0.000	0.000	0.000	0.000
112	P	106	GLY	0	-0.012	-0.019	16.403	-0.813	-0.813	0.000	0.000	0.000	0.000
113	P	107	THR	0	-0.042	-0.016	19.470	-0.240	-0.240	0.000	0.000	0.000	0.000
114	P	108	LEU	0	-0.028	-0.006	21.630	-0.404	-0.404	0.000	0.000	0.000	0.000
115	P	109	VAL	0	0.019	0.013	25.156	-0.023	-0.023	0.000	0.000	0.000	0.000
116	P	110	THR	0	-0.011	-0.017	27.979	-0.302	-0.302	0.000	0.000	0.000	0.000
117	P	111	VAL	0	-0.003	0.007	31.586	-0.057	-0.057	0.000	0.000	0.000	0.000
118	P	112	SER	0	0.030	0.007	34.764	-0.286	-0.286	0.000	0.000	0.000	0.000
119	P	113	SER	0	0.034	0.007	38.000	0.088	0.088	0.000	0.000	0.000	0.000
120	P	114	ALA	0	0.016	0.029	39.107	-0.102	-0.102	0.000	0.000	0.000	0.000
121	P	115	SER	0	-0.001	-0.012	39.513	0.181	0.181	0.000	0.000	0.000	0.000
122	P	116	THR	0	0.020	0.011	35.102	-0.018	-0.018	0.000	0.000	0.000	0.000
123	P	117	LYS	1	0.861	0.946	37.365	-7.114	-7.114	0.000	0.000	0.000	0.000
124	P	118	GLY	0	0.107	0.055	37.906	0.127	0.127	0.000	0.000	0.000	0.000
125	P	119	PRO	0	-0.056	-0.031	38.146	-0.364	-0.364	0.000	0.000	0.000	0.000
126	P	142	VAL	0	0.003	-0.005	37.875	-0.082	-0.082	0.000	0.000	0.000	0.000
127	P	143	LYS	1	0.887	0.928	39.799	-6.535	-6.535	0.000	0.000	0.000	0.000
128	P	144	ASP	-1	-0.808	-0.898	41.838	6.839	6.839	0.000	0.000	0.000	0.000
129	P	145	TYR	0	-0.083	-0.050	33.981	-0.187	-0.187	0.000	0.000	0.000	0.000
130	P	146	PHE	0	0.019	0.008	35.422	0.014	0.014	0.000	0.000	0.000	0.000
131	P	147	PRO	0	-0.046	-0.004	31.130	-0.051	-0.051	0.000	0.000	0.000	0.000
132	P	148	GLU	-1	-0.769	-0.898	30.317	9.121	9.121	0.000	0.000	0.000	0.000
133	P	149	PRO	0	0.000	0.002	25.897	0.185	0.185	0.000	0.000	0.000	0.000
134	P	150	VAL	0	-0.019	-0.010	27.762	0.259	0.259	0.000	0.000	0.000	0.000
135	P	151	THR	0	0.017	0.009	27.667	-0.323	-0.323	0.000	0.000	0.000	0.000
136	P	152	VAL	0	-0.009	-0.005	29.971	0.138	0.138	0.000	0.000	0.000	0.000
137	P	153	SER	0	0.031	0.015	31.209	-0.022	-0.022	0.000	0.000	0.000	0.000
138	P	154	TRP	0	0.039	0.015	33.020	0.050	0.050	0.000	0.000	0.000	0.000
139	P	155	ASN	0	-0.016	-0.018	36.057	0.084	0.084	0.000	0.000	0.000	0.000
140	P	156	SER	0	-0.019	-0.015	34.491	-0.020	-0.020	0.000	0.000	0.000	0.000
141	P	157	GLY	0	0.044	0.033	32.578	0.223	0.223	0.000	0.000	0.000	0.000
142	P	158	ALA	0	-0.044	-0.009	33.369	0.041	0.041	0.000	0.000	0.000	0.000
143	P	159	LEU	0	-0.045	-0.013	36.419	-0.107	-0.107	0.000	0.000	0.000	0.000
144	P	160	THR	0	0.069	0.025	31.883	0.147	0.147	0.000	0.000	0.000	0.000
145	P	161	SER	0	-0.006	-0.021	33.491	-0.176	-0.176	0.000	0.000	0.000	0.000
146	P	162	GLY	0	0.051	0.031	34.983	-0.168	-0.168	0.000	0.000	0.000	0.000
147	P	163	VAL	0	-0.068	-0.022	33.820	-0.154	-0.154	0.000	0.000	0.000	0.000
148	P	164	HIS	0	-0.036	-0.034	35.580	0.034	0.034	0.000	0.000	0.000	0.000
149	P	165	THR	0	-0.012	-0.003	32.086	-0.244	-0.244	0.000	0.000	0.000	0.000
150	P	166	PHE	0	-0.027	-0.006	34.805	0.016	0.016	0.000	0.000	0.000	0.000
151	P	167	PRO	0	0.017	-0.002	32.879	0.124	0.124	0.000	0.000	0.000	0.000
152	P	168	ALA	0	0.011	0.025	33.501	-0.269	-0.269	0.000	0.000	0.000	0.000
153	P	169	VAL	0	-0.008	-0.002	35.411	0.057	0.057	0.000	0.000	0.000	0.000
154	P	170	LEU	0	0.015	-0.001	37.580	-0.022	-0.022	0.000	0.000	0.000	0.000
155	P	171	GLN	0	0.023	0.012	39.744	-0.209	-0.209	0.000	0.000	0.000	0.000
156	P	172	SER	0	-0.006	-0.019	43.032	0.068	0.068	0.000	0.000	0.000	0.000
157	P	173	SER	0	-0.004	0.006	44.555	-0.024	-0.024	0.000	0.000	0.000	0.000
158	P	174	GLY	0	0.004	0.006	41.060	0.009	0.009	0.000	0.000	0.000	0.000
159	P	175	LEU	0	-0.081	-0.026	39.666	0.180	0.180	0.000	0.000	0.000	0.000
160	P	176	TYR	0	0.015	0.002	34.058	-0.036	-0.036	0.000	0.000	0.000	0.000
161	P	177	SER	0	-0.061	-0.037	38.552	-0.202	-0.202	0.000	0.000	0.000	0.000
162	P	178	LEU	0	0.036	0.036	33.933	0.007	0.007	0.000	0.000	0.000	0.000
163	P	179	SER	0	-0.022	-0.028	37.632	-0.323	-0.323	0.000	0.000	0.000	0.000
164	P	180	SER	0	-0.003	-0.009	37.370	0.253	0.253	0.000	0.000	0.000	0.000
165	P	181	VAL	0	0.015	0.028	38.849	-0.074	-0.074	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:1:GLU)