FMO DATABASE

FMODB ID: LJVQ9

Calculation Name: 3DI3-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3DI3

Chain ID: A

ChEMBL ID:

UniProt ID: P16871

Base Structure: X-ray

Registration Date: 2023-03-14

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1030839.161155
FMO2-HF: Nuclear repulsion	981258.691598
FMO2-HF: Total energy	-49580.469557
FMO2-MP2: Total energy	-49719.446521

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
79.148	82.726	0.427	-1.576	-2.428	0.006

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.883

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	A	9	GLY	0	0.094	0.042	3.834	7.905	9.403	-0.019	-0.674	-0.805	0.000
4	A	10	LYS	1	0.962	0.975	2.893	30.529	32.349	0.441	-0.847	-1.414	0.006
5	A	11	GLN	0	-0.009	-0.021	3.591	-2.918	-2.658	0.005	-0.055	-0.209	0.000
6	A	12	TYR	0	0.061	0.032	5.685	2.234	2.234	0.000	0.000	0.000	0.000
7	A	13	GLU	-1	-0.898	-0.952	8.829	-19.470	-19.470	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.021	-0.013	7.404	1.179	1.179	0.000	0.000	0.000	0.000
9	A	15	VAL	0	-0.022	-0.004	8.848	0.816	0.816	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.025	0.002	10.477	1.371	1.371	0.000	0.000	0.000	0.000
11	A	17	MET	0	-0.036	-0.031	12.011	1.050	1.050	0.000	0.000	0.000	0.000
12	A	18	VAL	0	0.028	0.035	13.189	1.087	1.087	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.016	-0.034	15.624	0.579	0.579	0.000	0.000	0.000	0.000
14	A	20	ILE	0	-0.033	-0.018	15.692	0.697	0.697	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.803	-0.903	17.405	-13.899	-13.899	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.012	0.006	19.861	1.087	1.087	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.041	-0.012	21.225	0.569	0.569	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.016	-0.003	21.418	0.602	0.602	0.000	0.000	0.000	0.000
19	A	25	ASP	-1	-0.839	-0.917	24.038	-10.690	-10.690	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.074	-0.044	25.955	0.453	0.453	0.000	0.000	0.000	0.000
21	A	27	MET	0	-0.040	-0.021	26.293	0.423	0.423	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.851	0.929	26.901	10.112	10.112	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.897	-0.950	30.123	-8.197	-8.197	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.050	-0.005	31.256	0.229	0.229	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.005	-0.037	32.723	-0.218	-0.218	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.006	-0.013	34.689	-0.052	-0.052	0.000	0.000	0.000	0.000
27	A	33	ASN	0	0.025	-0.002	37.913	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	34	CYS	0	0.002	0.037	30.543	-0.168	-0.168	0.000	0.000	0.000	0.000
29	A	35	LEU	0	0.029	0.036	34.126	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	36	ASN	0	-0.027	-0.003	33.631	-0.458	-0.458	0.000	0.000	0.000	0.000
31	A	37	ASN	0	-0.007	-0.019	35.339	0.076	0.076	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.884	-0.912	34.258	-9.190	-9.190	0.000	0.000	0.000	0.000
33	A	39	PHE	0	0.043	0.011	32.657	0.042	0.042	0.000	0.000	0.000	0.000
34	A	40	ASN	0	0.021	-0.014	33.565	-0.145	-0.145	0.000	0.000	0.000	0.000
35	A	41	PHE	0	-0.076	-0.040	25.693	-0.079	-0.079	0.000	0.000	0.000	0.000
36	A	42	PHE	0	0.053	0.021	26.406	-0.233	-0.233	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.906	0.976	29.947	8.738	8.738	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.904	0.936	31.191	9.329	9.329	0.000	0.000	0.000	0.000
39	A	45	HIS	0	-0.020	-0.011	25.781	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	46	ILE	0	0.097	0.050	26.104	0.093	0.093	0.000	0.000	0.000	0.000
41	A	47	CYS	0	-0.086	-0.023	17.578	-1.333	-1.333	0.000	0.000	0.000	0.000
42	A	48	ASP	-1	-0.836	-0.926	22.956	-12.057	-12.057	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.035	-0.030	20.477	-0.574	-0.574	0.000	0.000	0.000	0.000
44	A	50	ASN	0	0.003	0.019	19.899	-0.912	-0.912	0.000	0.000	0.000	0.000
45	A	51	LYS	1	0.935	0.972	16.592	17.622	17.622	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.696	-0.853	16.931	-16.774	-16.774	0.000	0.000	0.000	0.000
47	A	53	GLY	0	0.056	0.012	15.912	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	54	MET	0	-0.135	-0.078	16.723	0.110	0.110	0.000	0.000	0.000	0.000
49	A	55	PHE	0	0.057	0.037	19.967	0.694	0.694	0.000	0.000	0.000	0.000
50	A	56	LEU	0	0.065	0.035	15.692	0.822	0.822	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.021	0.017	17.138	0.556	0.556	0.000	0.000	0.000	0.000
52	A	58	ARG	1	0.898	0.944	19.461	12.954	12.954	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.030	0.007	21.233	0.476	0.476	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.036	0.031	19.110	0.363	0.363	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.853	0.917	19.206	15.932	15.932	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.896	0.959	23.971	11.133	11.133	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.068	0.040	20.812	0.572	0.572	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.916	0.968	22.569	13.246	13.246	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.046	-0.019	26.074	0.123	0.123	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.010	0.009	27.738	0.429	0.429	0.000	0.000	0.000	0.000
61	A	67	LEU	0	0.008	0.015	24.934	0.151	0.151	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.944	0.975	29.199	9.435	9.435	0.000	0.000	0.000	0.000
63	A	69	MET	0	-0.015	0.008	32.283	-0.212	-0.212	0.000	0.000	0.000	0.000
64	A	70	ASN	0	-0.031	-0.033	29.881	-0.111	-0.111	0.000	0.000	0.000	0.000
65	A	71	SER	0	0.019	0.019	30.828	0.078	0.078	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.022	-0.022	28.300	-0.374	-0.374	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.028	0.055	28.523	0.023	0.023	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.852	-0.945	24.739	-10.992	-10.992	0.000	0.000	0.000	0.000
69	A	75	PHE	0	-0.015	-0.012	24.084	-0.518	-0.518	0.000	0.000	0.000	0.000
70	A	76	ASP	-1	-0.859	-0.946	24.749	-10.653	-10.653	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.034	0.021	22.354	-0.632	-0.632	0.000	0.000	0.000	0.000
72	A	78	HIS	0	0.036	0.028	19.469	-1.253	-1.253	0.000	0.000	0.000	0.000
73	A	79	LEU	0	0.012	0.013	19.876	-0.702	-0.702	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.008	-0.004	20.998	-0.488	-0.488	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.991	1.000	16.471	13.796	13.796	0.000	0.000	0.000	0.000
76	A	82	VAL	0	0.040	0.032	16.205	-1.111	-1.111	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.053	-0.021	16.913	-0.627	-0.627	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.944	-0.969	17.344	-15.837	-15.837	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.076	0.023	13.824	-1.154	-1.154	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.010	-0.031	12.959	-2.029	-2.029	0.000	0.000	0.000	0.000
81	A	87	THR	0	-0.115	-0.078	14.270	-0.258	-0.258	0.000	0.000	0.000	0.000
82	A	88	ILE	0	-0.021	-0.007	10.634	-0.634	-0.634	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.007	0.014	7.145	-2.309	-2.309	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.020	0.023	9.700	-2.038	-2.038	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.023	0.009	10.888	0.243	0.243	0.000	0.000	0.000	0.000
86	A	92	CYS	0	-0.041	-0.022	6.139	-0.128	-0.128	0.000	0.000	0.000	0.000
87	A	93	THR	0	-0.058	-0.057	6.088	-5.267	-5.267	0.000	0.000	0.000	0.000
88	A	94	GLY	0	0.064	0.042	7.435	1.910	1.910	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.093	-0.046	9.656	3.596	3.596	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.028	0.009	12.779	-0.279	-0.279	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.889	0.952	15.230	15.065	15.065	0.000	0.000	0.000	0.000
92	A	98	GLY	0	0.049	0.037	18.329	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	122	GLN	0	-0.003	-0.013	27.668	0.123	0.123	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.951	0.973	32.929	8.570	8.570	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.970	0.977	32.279	9.115	9.115	0.000	0.000	0.000	0.000
96	A	125	LEU	0	-0.044	-0.022	30.184	0.216	0.216	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.000	-0.018	32.814	-0.217	-0.217	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.830	-0.922	33.946	-8.734	-8.734	0.000	0.000	0.000	0.000
99	A	128	LEU	0	0.087	0.029	30.179	-0.339	-0.339	0.000	0.000	0.000	0.000
100	A	130	PHE	0	-0.034	-0.012	28.308	-0.333	-0.333	0.000	0.000	0.000	0.000
101	A	131	LEU	0	-0.001	-0.008	25.427	-0.334	-0.334	0.000	0.000	0.000	0.000
102	A	132	LYS	1	0.972	1.005	25.966	9.306	9.306	0.000	0.000	0.000	0.000
103	A	133	ARG	1	0.956	0.989	25.572	9.992	9.992	0.000	0.000	0.000	0.000
104	A	134	LEU	0	-0.082	-0.039	23.973	-0.361	-0.361	0.000	0.000	0.000	0.000
105	A	135	LEU	0	0.030	-0.003	21.010	-0.661	-0.661	0.000	0.000	0.000	0.000
106	A	136	GLN	0	0.004	0.008	21.004	-0.484	-0.484	0.000	0.000	0.000	0.000
107	A	137	GLU	-1	-0.860	-0.935	21.169	-12.716	-12.716	0.000	0.000	0.000	0.000
108	A	138	ILE	0	-0.055	-0.036	17.611	-0.688	-0.688	0.000	0.000	0.000	0.000
109	A	139	LYS	1	0.835	0.925	17.092	13.499	13.499	0.000	0.000	0.000	0.000
110	A	140	THR	0	0.006	-0.004	16.830	-0.835	-0.835	0.000	0.000	0.000	0.000
111	A	142	TRP	0	0.005	0.005	11.447	-1.284	-1.284	0.000	0.000	0.000	0.000
112	A	143	ASN	0	0.035	0.009	12.985	-1.247	-1.247	0.000	0.000	0.000	0.000
113	A	144	LYS	1	0.857	0.940	14.047	15.431	15.431	0.000	0.000	0.000	0.000
114	A	145	ILE	0	-0.072	-0.033	12.156	-0.065	-0.065	0.000	0.000	0.000	0.000
115	A	146	LEU	0	-0.071	-0.023	8.543	-2.048	-2.048	0.000	0.000	0.000	0.000
116	A	147	MET	0	-0.046	-0.013	11.153	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)