FMO DATABASE

FMODB ID: V5G41

Calculation Name: 4EDA-D-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4EDA

Chain ID: D

ChEMBL ID:

UniProt ID: C5MQE6

Base Structure: X-ray

Registration Date: 2023-09-19

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-902287.090819
FMO2-HF: Nuclear repulsion	850328.852094
FMO2-HF: Total energy	-51958.238725
FMO2-MP2: Total energy	-52106.606208

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(D:10:ILE)

Summations of interaction energy for fragment #1(D:10:ILE)

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.
-9.775	-3.144	2.549	-2.987	-6.191	-0.016

Interaction energy analysis for fragmet #1(D:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.026

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

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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	D	12	GLY	0	-0.041	-0.033	3.050	-1.483	0.738	0.188	-1.069	-1.340	-0.004
4	D	13	GLY	0	-0.031	-0.008	5.539	0.142	0.142	0.000	0.000	0.000	0.000
5	D	14	TRP	0	-0.010	0.005	8.985	-0.076	-0.076	0.000	0.000	0.000	0.000
6	D	15	THR	0	-0.047	-0.027	10.767	0.065	0.065	0.000	0.000	0.000	0.000
7	D	16	GLY	0	0.008	-0.015	14.263	0.037	0.037	0.000	0.000	0.000	0.000
8	D	17	MET	0	-0.016	0.006	12.848	-0.036	-0.036	0.000	0.000	0.000	0.000
9	D	18	VAL	0	-0.001	0.007	14.647	0.008	0.008	0.000	0.000	0.000	0.000
10	D	19	ASP	-1	-0.976	-0.986	17.705	0.167	0.167	0.000	0.000	0.000	0.000
11	D	35	ALA	0	0.015	0.007	14.780	-0.010	-0.010	0.000	0.000	0.000	0.000
12	D	36	ALA	0	-0.013	-0.004	13.465	0.006	0.006	0.000	0.000	0.000	0.000
13	D	37	ASP	-1	-0.778	-0.867	13.931	0.364	0.364	0.000	0.000	0.000	0.000
14	D	38	LEU	0	-0.005	-0.001	15.609	-0.001	-0.001	0.000	0.000	0.000	0.000
15	D	39	LYS	1	0.837	0.896	18.049	-0.214	-0.214	0.000	0.000	0.000	0.000
16	D	40	SER	0	-0.024	-0.036	14.595	0.018	0.018	0.000	0.000	0.000	0.000
17	D	41	THR	0	0.033	0.014	16.506	0.030	0.030	0.000	0.000	0.000	0.000
18	D	42	GLN	0	-0.015	-0.003	17.590	-0.039	-0.039	0.000	0.000	0.000	0.000
19	D	43	ASN	0	0.005	0.004	19.551	-0.042	-0.042	0.000	0.000	0.000	0.000
20	D	44	ALA	0	0.058	0.035	16.663	-0.014	-0.014	0.000	0.000	0.000	0.000
21	D	45	ILE	0	-0.006	-0.007	18.086	-0.012	-0.012	0.000	0.000	0.000	0.000
22	D	46	ASP	-1	-0.930	-0.946	20.678	0.206	0.206	0.000	0.000	0.000	0.000
23	D	47	GLU	-1	-0.841	-0.900	20.270	0.386	0.386	0.000	0.000	0.000	0.000
24	D	48	ILE	0	-0.001	0.001	17.931	-0.015	-0.015	0.000	0.000	0.000	0.000
25	D	49	THR	0	-0.072	-0.047	21.679	-0.030	-0.030	0.000	0.000	0.000	0.000
26	D	50	ASN	0	-0.043	-0.022	25.189	-0.012	-0.012	0.000	0.000	0.000	0.000
27	D	51	LYS	1	0.840	0.901	21.642	-0.344	-0.344	0.000	0.000	0.000	0.000
28	D	52	VAL	0	0.002	0.005	24.114	-0.018	-0.018	0.000	0.000	0.000	0.000
29	D	53	ASN	0	0.016	0.001	25.881	-0.010	-0.010	0.000	0.000	0.000	0.000
30	D	54	SER	0	0.051	0.009	28.867	-0.014	-0.014	0.000	0.000	0.000	0.000
31	D	55	VAL	0	-0.037	-0.017	26.384	-0.009	-0.009	0.000	0.000	0.000	0.000
32	D	56	ILE	0	0.018	0.007	29.636	-0.011	-0.011	0.000	0.000	0.000	0.000
33	D	57	GLU	-1	-0.922	-0.942	32.789	0.143	0.143	0.000	0.000	0.000	0.000
34	D	58	LYS	1	0.781	0.892	30.791	-0.165	-0.165	0.000	0.000	0.000	0.000
35	D	59	MET	0	-0.009	0.019	31.415	-0.005	-0.005	0.000	0.000	0.000	0.000
36	D	60	ASN	0	-0.034	-0.017	36.261	-0.006	-0.006	0.000	0.000	0.000	0.000
37	D	61	THR	0	-0.038	-0.012	39.801	-0.007	-0.007	0.000	0.000	0.000	0.000
38	D	83	LYS	1	0.867	0.912	46.271	-0.061	-0.061	0.000	0.000	0.000	0.000
39	D	84	VAL	0	-0.049	-0.036	48.459	0.002	0.002	0.000	0.000	0.000	0.000
40	D	85	ASP	-1	-0.891	-0.927	46.424	0.062	0.062	0.000	0.000	0.000	0.000
41	D	86	ASP	-1	-0.729	-0.866	44.594	0.057	0.057	0.000	0.000	0.000	0.000
42	D	87	GLY	0	-0.035	-0.021	43.553	0.003	0.003	0.000	0.000	0.000	0.000
43	D	88	PHE	0	-0.089	-0.036	41.968	0.001	0.001	0.000	0.000	0.000	0.000
44	D	89	LEU	0	0.061	0.022	40.342	0.005	0.005	0.000	0.000	0.000	0.000
45	D	90	ASP	-1	-0.874	-0.918	39.272	0.075	0.075	0.000	0.000	0.000	0.000
46	D	91	ILE	0	-0.040	-0.023	37.585	0.005	0.005	0.000	0.000	0.000	0.000
47	D	92	TRP	0	-0.017	-0.010	36.628	0.008	0.008	0.000	0.000	0.000	0.000
48	D	93	THR	0	-0.028	-0.028	34.699	0.007	0.007	0.000	0.000	0.000	0.000
49	D	94	TYR	0	0.038	0.023	31.759	0.009	0.009	0.000	0.000	0.000	0.000
50	D	95	ASN	0	-0.037	-0.021	31.892	0.012	0.012	0.000	0.000	0.000	0.000
51	D	96	ALA	0	0.008	0.006	31.084	0.011	0.011	0.000	0.000	0.000	0.000
52	D	97	GLU	-1	-0.915	-0.966	29.104	0.123	0.123	0.000	0.000	0.000	0.000
53	D	98	LEU	0	-0.005	-0.009	27.329	0.014	0.014	0.000	0.000	0.000	0.000
54	D	99	LEU	0	-0.022	-0.014	26.296	0.019	0.019	0.000	0.000	0.000	0.000
55	D	100	VAL	0	-0.016	-0.002	24.736	0.021	0.021	0.000	0.000	0.000	0.000
56	D	101	LEU	0	-0.003	0.007	22.757	0.023	0.023	0.000	0.000	0.000	0.000
57	D	102	LEU	0	-0.016	-0.011	21.403	0.029	0.029	0.000	0.000	0.000	0.000
58	D	103	GLU	-1	-0.823	-0.907	20.954	0.365	0.365	0.000	0.000	0.000	0.000
59	D	104	ASN	0	-0.041	-0.017	19.248	0.046	0.046	0.000	0.000	0.000	0.000
60	D	105	GLU	-1	-0.908	-0.944	15.660	0.454	0.454	0.000	0.000	0.000	0.000
61	D	106	ARG	1	0.907	0.951	15.807	-0.251	-0.251	0.000	0.000	0.000	0.000
62	D	107	THR	0	-0.017	-0.006	16.184	0.051	0.051	0.000	0.000	0.000	0.000
63	D	108	LEU	0	-0.018	-0.009	10.761	0.079	0.079	0.000	0.000	0.000	0.000
64	D	109	ASP	-1	-0.846	-0.919	11.514	1.040	1.040	0.000	0.000	0.000	0.000
65	D	110	TYR	0	-0.084	-0.060	12.055	0.155	0.155	0.000	0.000	0.000	0.000
66	D	111	HIS	0	-0.009	-0.012	11.085	0.136	0.136	0.000	0.000	0.000	0.000
67	D	112	ASP	-1	-0.814	-0.901	5.745	3.363	3.363	0.000	0.000	0.000	0.000
68	D	113	SER	0	-0.020	-0.026	7.423	0.652	0.652	0.000	0.000	0.000	0.000
69	D	114	ASN	0	-0.036	-0.027	9.576	0.146	0.146	0.000	0.000	0.000	0.000
70	D	115	VAL	0	-0.031	-0.004	5.913	-0.046	-0.046	0.000	0.000	0.000	0.000
71	D	116	LYS	1	0.796	0.889	3.687	-4.182	-3.926	0.000	-0.029	-0.226	0.000
72	D	117	ASN	0	-0.005	-0.005	7.197	-0.487	-0.487	0.000	0.000	0.000	0.000
73	D	118	LEU	0	-0.006	0.009	5.936	-0.322	-0.322	0.000	0.000	0.000	0.000
74	D	119	TYR	0	0.064	0.015	3.060	-2.211	-1.034	0.214	-0.447	-0.944	-0.002
75	D	120	GLU	-1	-0.815	-0.880	7.508	0.133	0.133	0.000	0.000	0.000	0.000
76	D	121	LYS	1	0.910	0.988	10.774	-0.314	-0.314	0.000	0.000	0.000	0.000
77	D	122	VAL	0	0.000	0.006	8.410	-0.118	-0.118	0.000	0.000	0.000	0.000
78	D	123	ARG	1	0.837	0.885	10.008	-0.315	-0.315	0.000	0.000	0.000	0.000
79	D	124	SER	0	-0.057	-0.047	11.969	-0.019	-0.019	0.000	0.000	0.000	0.000
80	D	125	GLN	0	-0.053	-0.033	14.371	0.027	0.027	0.000	0.000	0.000	0.000
81	D	126	LEU	0	-0.040	0.015	12.700	-0.017	-0.017	0.000	0.000	0.000	0.000
82	D	127	LYN	0	0.018	0.000	14.905	-0.054	-0.054	0.000	0.000	0.000	0.000
83	D	128	ASN	0	-0.100	-0.042	15.592	-0.034	-0.034	0.000	0.000	0.000	0.000
84	D	129	ASN	0	-0.148	-0.084	15.602	0.017	0.017	0.000	0.000	0.000	0.000
85	D	130	ALA	0	0.027	0.016	10.836	-0.048	-0.048	0.000	0.000	0.000	0.000
86	D	131	LYS	1	0.859	0.932	10.779	0.627	0.627	0.000	0.000	0.000	0.000
87	D	132	GLU	-1	-0.796	-0.890	2.998	-8.944	-6.680	0.188	-1.152	-1.300	-0.011
88	D	133	ILE	0	-0.079	-0.036	7.708	0.243	0.243	0.000	0.000	0.000	0.000
89	D	134	GLY	0	0.016	0.002	4.420	0.106	0.200	-0.001	-0.011	-0.082	0.000
90	D	135	ASN	0	-0.055	-0.037	2.215	-0.262	0.151	1.852	-0.943	-1.321	0.003
91	D	136	GLY	0	0.048	0.045	3.116	-0.450	-0.513	0.102	0.708	-0.747	-0.002
92	D	137	CYS	0	-0.126	-0.067	3.886	1.279	1.548	0.006	-0.044	-0.231	0.000
93	D	138	PHE	0	0.014	-0.009	6.750	0.168	0.168	0.000	0.000	0.000	0.000
94	D	139	GLU	-1	-0.820	-0.907	9.482	0.006	0.006	0.000	0.000	0.000	0.000
95	D	140	PHE	0	0.044	0.010	12.140	0.011	0.011	0.000	0.000	0.000	0.000
96	D	141	TYR	0	0.031	0.015	11.501	0.049	0.049	0.000	0.000	0.000	0.000
97	D	142	HIS	0	-0.002	-0.019	13.710	0.020	0.020	0.000	0.000	0.000	0.000
98	D	143	LYN	0	-0.043	-0.009	17.081	0.029	0.029	0.000	0.000	0.000	0.000
99	D	144	CYS	0	-0.151	-0.066	18.962	0.045	0.045	0.000	0.000	0.000	0.000
100	D	145	ASP	-1	-0.858	-0.905	19.183	-0.146	-0.146	0.000	0.000	0.000	0.000
101	D	146	ASN	0	-0.059	-0.052	19.426	-0.007	-0.007	0.000	0.000	0.000	0.000
102	D	147	THR	0	0.004	-0.020	19.910	-0.005	-0.005	0.000	0.000	0.000	0.000
103	D	149	MET	0	0.034	0.028	15.656	-0.005	-0.005	0.000	0.000	0.000	0.000
104	D	150	GLU	-1	-0.844	-0.910	18.417	-0.001	-0.001	0.000	0.000	0.000	0.000
105	D	151	SER	0	-0.017	-0.026	19.771	0.017	0.017	0.000	0.000	0.000	0.000
106	D	152	VAL	0	0.007	0.015	15.047	0.021	0.021	0.000	0.000	0.000	0.000
107	D	153	LYS	1	0.812	0.886	14.939	-0.031	-0.031	0.000	0.000	0.000	0.000
108	D	154	ASN	0	-0.098	-0.045	17.917	0.004	0.004	0.000	0.000	0.000	0.000
109	D	155	GLY	0	0.012	-0.004	21.056	0.000	0.000	0.000	0.000	0.000	0.000
110	D	156	THR	0	-0.049	0.002	21.874	-0.003	-0.003	0.000	0.000	0.000	0.000
111	D	157	TYR	0	-0.017	-0.009	18.378	0.006	0.006	0.000	0.000	0.000	0.000
112	D	158	ASP	-1	-0.829	-0.931	20.514	-0.072	-0.072	0.000	0.000	0.000	0.000
113	D	159	TYR	0	0.026	0.013	20.716	-0.010	-0.010	0.000	0.000	0.000	0.000
114	D	160	PRO	0	-0.025	-0.020	22.838	-0.012	-0.012	0.000	0.000	0.000	0.000
115	D	161	LYS	1	0.813	0.910	23.540	0.136	0.136	0.000	0.000	0.000	0.000
116	D	162	TYR	0	0.027	0.012	20.647	-0.020	-0.020	0.000	0.000	0.000	0.000
117	D	163	SER	-1	-0.628	-0.829	20.788	-0.205	-0.205	0.000	0.000	0.000	0.000
118	D	164	GLU	-1	-0.964	-0.975	22.717	-0.102	-0.102	0.000	0.000	0.000	0.000
119	D	165	GLU	-1	-0.843	-0.908	23.405	-0.159	-0.159	0.000	0.000	0.000	0.000
120	D	166	ALA	0	0.041	0.016	21.353	-0.008	-0.008	0.000	0.000	0.000	0.000
121	D	167	LYS	1	0.806	0.892	22.965	0.114	0.114	0.000	0.000	0.000	0.000
122	D	168	LEU	0	-0.048	-0.019	22.200	0.002	0.002	0.000	0.000	0.000	0.000
123	D	169	ASN	0	-0.068	-0.033	21.179	0.012	0.012	0.000	0.000	0.000	0.000
124	D	170	ARG	1	0.887	0.947	19.493	0.218	0.218	0.000	0.000	0.000	0.000
125	D	171	GLU	-1	-0.865	-0.906	24.956	-0.116	-0.116	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:ILE)