FMO DATABASE

FMODB ID: M3LRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1034053.547543
FMO2-HF: Nuclear repulsion	984471.568108
FMO2-HF: Total energy	-49581.979435
FMO2-MP2: Total energy	-49720.782335

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.
84.644	87.095	0.02	-0.964	-1.507	0.004

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 : 0.838 / q_NPA : 0.884

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	9	GLY	0	0.075	0.028	3.869	10.521	11.790	-0.012	-0.529	-0.728	0.001
4	A	10	LYS	1	0.976	0.972	3.651	31.676	32.700	0.033	-0.416	-0.641	0.003
5	A	11	GLN	0	0.011	0.014	4.127	-1.251	-1.093	-0.001	-0.019	-0.138	0.000
6	A	12	TYR	0	0.027	-0.007	6.417	2.859	2.859	0.000	0.000	0.000	0.000
7	A	13	GLU	-1	-0.932	-0.973	9.073	-20.913	-20.913	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.025	-0.021	7.336	1.573	1.573	0.000	0.000	0.000	0.000
9	A	15	VAL	0	-0.033	-0.015	9.357	0.839	0.839	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.046	-0.002	11.215	1.325	1.325	0.000	0.000	0.000	0.000
11	A	17	MET	0	0.018	0.006	12.839	1.623	1.623	0.000	0.000	0.000	0.000
12	A	18	VAL	0	0.049	0.039	13.715	1.096	1.096	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.005	-0.019	16.327	0.700	0.700	0.000	0.000	0.000	0.000
14	A	20	ILE	0	-0.032	-0.018	16.598	0.677	0.677	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.770	-0.873	18.825	-13.611	-13.611	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.016	0.002	20.419	1.013	1.013	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.030	-0.006	21.862	0.577	0.577	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.031	-0.013	21.924	0.557	0.557	0.000	0.000	0.000	0.000
19	A	25	ASP	-1	-0.815	-0.884	24.549	-9.991	-9.991	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.048	-0.035	26.327	0.466	0.466	0.000	0.000	0.000	0.000
21	A	27	MET	0	-0.007	0.000	26.960	0.413	0.413	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.833	0.913	28.526	9.928	9.928	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.884	-0.950	30.457	-8.490	-8.490	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.052	-0.012	32.042	0.238	0.238	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.063	0.011	33.106	-0.283	-0.283	0.000	0.000	0.000	0.000
26	A	32	SER	0	0.008	-0.002	35.343	0.002	0.002	0.000	0.000	0.000	0.000
27	A	33	ASN	0	0.002	-0.001	38.714	-0.042	-0.042	0.000	0.000	0.000	0.000
28	A	34	CYS	0	-0.062	-0.003	31.090	-0.179	-0.179	0.000	0.000	0.000	0.000
29	A	35	LEU	0	0.018	0.001	34.421	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	36	ASN	0	0.008	0.004	34.294	-0.488	-0.488	0.000	0.000	0.000	0.000
31	A	37	ASN	0	0.003	0.005	35.935	0.063	0.063	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.842	-0.900	34.290	-9.385	-9.385	0.000	0.000	0.000	0.000
33	A	39	PHE	0	0.070	0.017	33.079	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	40	ASN	0	0.018	-0.007	33.363	-0.261	-0.261	0.000	0.000	0.000	0.000
35	A	41	PHE	0	-0.066	-0.016	24.832	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	42	PHE	0	0.086	0.026	27.098	-0.169	-0.169	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.899	0.969	29.702	8.887	8.887	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.903	0.946	30.794	9.603	9.603	0.000	0.000	0.000	0.000
39	A	45	HIS	0	-0.059	-0.028	25.401	-0.197	-0.197	0.000	0.000	0.000	0.000
40	A	46	ILE	0	0.111	0.055	25.609	0.039	0.039	0.000	0.000	0.000	0.000
41	A	47	CYS	0	-0.079	-0.019	18.370	-1.266	-1.266	0.000	0.000	0.000	0.000
42	A	48	ASP	-1	-0.826	-0.930	22.198	-12.412	-12.412	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.025	-0.017	20.031	-0.640	-0.640	0.000	0.000	0.000	0.000
44	A	50	ASN	0	0.002	0.020	19.889	-0.670	-0.670	0.000	0.000	0.000	0.000
45	A	51	LYS	1	0.952	0.979	15.830	18.158	18.158	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.708	-0.852	16.379	-17.177	-17.177	0.000	0.000	0.000	0.000
47	A	53	GLY	0	0.057	0.015	15.393	0.142	0.142	0.000	0.000	0.000	0.000
48	A	54	MET	0	-0.123	-0.062	16.209	0.212	0.212	0.000	0.000	0.000	0.000
49	A	55	PHE	0	0.031	0.018	19.574	0.531	0.531	0.000	0.000	0.000	0.000
50	A	56	LEU	0	0.057	0.032	15.054	0.670	0.670	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.028	0.018	16.683	0.607	0.607	0.000	0.000	0.000	0.000
52	A	58	ARG	1	0.913	0.953	18.979	13.171	13.171	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.038	0.013	21.050	0.519	0.519	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.043	0.027	18.767	0.450	0.450	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.832	0.908	19.357	15.998	15.998	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.829	0.932	23.913	11.282	11.282	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.072	0.034	21.142	0.538	0.538	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.843	0.906	22.126	13.736	13.736	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.025	-0.022	25.942	0.271	0.271	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.023	0.004	28.024	0.460	0.460	0.000	0.000	0.000	0.000
61	A	67	LEU	0	0.022	0.033	25.291	0.289	0.289	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.927	0.972	29.548	9.687	9.687	0.000	0.000	0.000	0.000
63	A	69	MET	0	-0.027	-0.018	33.023	-0.176	-0.176	0.000	0.000	0.000	0.000
64	A	70	ASN	0	-0.043	-0.026	30.432	-0.090	-0.090	0.000	0.000	0.000	0.000
65	A	71	SER	0	-0.017	-0.024	31.086	0.099	0.099	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.021	-0.006	28.426	-0.401	-0.401	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.035	0.037	28.846	0.042	0.042	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.835	-0.929	24.570	-11.641	-11.641	0.000	0.000	0.000	0.000
69	A	75	PHE	0	-0.005	-0.006	24.649	-0.501	-0.501	0.000	0.000	0.000	0.000
70	A	76	ASP	-1	-0.787	-0.877	25.441	-10.575	-10.575	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.028	0.010	22.855	-0.621	-0.621	0.000	0.000	0.000	0.000
72	A	78	HIS	0	-0.005	0.003	20.544	-1.410	-1.410	0.000	0.000	0.000	0.000
73	A	79	LEU	0	0.034	0.017	20.488	-0.662	-0.662	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.027	0.000	21.603	-0.470	-0.470	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.922	0.971	16.810	13.300	13.300	0.000	0.000	0.000	0.000
76	A	82	VAL	0	0.035	0.022	16.482	-1.134	-1.134	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.045	-0.024	17.414	-0.798	-0.798	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.817	-0.889	17.554	-15.448	-15.448	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.060	0.033	13.762	-1.093	-1.093	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.039	-0.023	12.864	-1.989	-1.989	0.000	0.000	0.000	0.000
81	A	87	THR	0	-0.080	-0.062	13.918	-0.679	-0.679	0.000	0.000	0.000	0.000
82	A	88	ILE	0	0.025	0.013	10.845	-0.565	-0.565	0.000	0.000	0.000	0.000
83	A	89	LEU	0	0.034	0.035	7.229	-2.388	-2.388	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.028	0.003	9.102	-2.636	-2.636	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.025	0.011	10.268	0.268	0.268	0.000	0.000	0.000	0.000
86	A	92	CYS	0	-0.085	-0.039	6.138	-0.514	-0.514	0.000	0.000	0.000	0.000
87	A	93	THR	0	-0.042	-0.036	5.397	-6.672	-6.672	0.000	0.000	0.000	0.000
88	A	94	GLY	0	0.035	0.032	6.878	1.925	1.925	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.101	-0.051	9.267	4.427	4.427	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.044	0.011	12.839	0.052	0.052	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.894	0.945	14.787	15.020	15.020	0.000	0.000	0.000	0.000
92	A	98	GLY	0	0.049	0.036	18.446	0.070	0.070	0.000	0.000	0.000	0.000
93	A	122	GLN	0	0.021	0.011	27.566	0.112	0.112	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.935	0.957	32.716	8.996	8.996	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.893	0.957	31.319	9.449	9.449	0.000	0.000	0.000	0.000
96	A	125	LEU	0	-0.031	-0.015	30.648	0.216	0.216	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.035	-0.006	33.408	-0.246	-0.246	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.778	-0.868	34.589	-8.872	-8.872	0.000	0.000	0.000	0.000
99	A	128	LEU	0	0.056	0.012	30.804	-0.342	-0.342	0.000	0.000	0.000	0.000
100	A	130	PHE	0	-0.054	-0.026	29.494	-0.379	-0.379	0.000	0.000	0.000	0.000
101	A	131	LEU	0	-0.028	-0.013	25.991	-0.389	-0.389	0.000	0.000	0.000	0.000
102	A	132	LYS	1	0.862	0.931	26.620	9.300	9.300	0.000	0.000	0.000	0.000
103	A	133	ARG	1	0.876	0.915	26.343	10.009	10.009	0.000	0.000	0.000	0.000
104	A	134	LEU	0	-0.063	-0.028	24.516	-0.464	-0.464	0.000	0.000	0.000	0.000
105	A	135	LEU	0	0.016	0.000	21.638	-0.707	-0.707	0.000	0.000	0.000	0.000
106	A	136	GLN	0	0.034	0.018	21.494	-0.439	-0.439	0.000	0.000	0.000	0.000
107	A	137	GLU	-1	-0.834	-0.901	22.114	-12.312	-12.312	0.000	0.000	0.000	0.000
108	A	138	ILE	0	-0.043	-0.031	18.002	-0.718	-0.718	0.000	0.000	0.000	0.000
109	A	139	LYS	1	0.829	0.892	17.418	13.814	13.814	0.000	0.000	0.000	0.000
110	A	140	THR	0	-0.001	-0.008	17.286	-0.855	-0.855	0.000	0.000	0.000	0.000
111	A	142	TRP	0	0.004	-0.022	10.600	-1.152	-1.152	0.000	0.000	0.000	0.000
112	A	143	ASN	0	-0.027	-0.010	13.627	-1.307	-1.307	0.000	0.000	0.000	0.000
113	A	144	LYS	1	0.842	0.904	14.707	14.890	14.890	0.000	0.000	0.000	0.000
114	A	145	ILE	0	-0.063	-0.028	11.932	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	146	LEU	0	-0.061	-0.019	8.763	-2.692	-2.692	0.000	0.000	0.000	0.000
116	A	147	MET	0	-0.041	0.006	11.246	0.146	0.146	0.000	0.000	0.000	0.000

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