FMO DATABASE

FMODB ID: 9GRL2

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	OptHSide
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	-1030257.064549
FMO2-HF: Nuclear repulsion	980675.819925
FMO2-HF: Total energy	-49581.244624
FMO2-MP2: Total energy	-49720.148232

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.
80.571	84.193	0.347	-1.603	-2.363	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 : 0.821 / q_NPA : 0.874

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	0.095	0.044	3.834	7.781	9.281	-0.018	-0.671	-0.810	0.000
4	A	10	LYS	1	0.977	0.984	2.912	30.990	32.872	0.360	-0.876	-1.365	0.006
5	A	11	GLN	0	-0.007	-0.013	3.585	-2.652	-2.412	0.005	-0.056	-0.188	0.000
6	A	12	TYR	0	0.051	0.025	5.697	2.320	2.320	0.000	0.000	0.000	0.000
7	A	13	GLU	-1	-0.913	-0.956	8.841	-19.904	-19.904	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.016	-0.013	7.101	1.402	1.402	0.000	0.000	0.000	0.000
9	A	15	VAL	0	-0.028	-0.013	8.772	0.837	0.837	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.024	0.007	10.490	1.420	1.420	0.000	0.000	0.000	0.000
11	A	17	MET	0	-0.019	-0.007	12.017	1.460	1.460	0.000	0.000	0.000	0.000
12	A	18	VAL	0	0.035	0.029	13.206	1.134	1.134	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.027	-0.040	15.630	0.664	0.664	0.000	0.000	0.000	0.000
14	A	20	ILE	0	-0.022	-0.013	15.640	0.708	0.708	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.759	-0.867	18.093	-13.658	-13.658	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.024	0.000	19.872	1.013	1.013	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.042	-0.014	21.007	0.558	0.558	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.018	-0.011	21.279	0.593	0.593	0.000	0.000	0.000	0.000
19	A	25	ASP	-1	-0.801	-0.881	24.062	-10.158	-10.158	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.066	-0.028	25.960	0.468	0.468	0.000	0.000	0.000	0.000
21	A	27	MET	0	-0.026	-0.019	26.398	0.415	0.415	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.844	0.918	27.596	9.974	9.974	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.894	-0.946	30.130	-8.295	-8.295	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.053	-0.012	31.286	0.228	0.228	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.041	-0.010	32.732	-0.220	-0.220	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.001	-0.001	34.698	-0.045	-0.045	0.000	0.000	0.000	0.000
27	A	33	ASN	0	0.012	-0.006	37.922	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	34	CYS	0	-0.007	0.030	30.556	-0.163	-0.163	0.000	0.000	0.000	0.000
29	A	35	LEU	0	0.026	0.019	33.781	-0.074	-0.074	0.000	0.000	0.000	0.000
30	A	36	ASN	0	-0.021	-0.002	33.687	-0.445	-0.445	0.000	0.000	0.000	0.000
31	A	37	ASN	0	-0.001	-0.010	35.330	0.116	0.116	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.877	-0.923	34.089	-9.221	-9.221	0.000	0.000	0.000	0.000
33	A	39	PHE	0	0.055	0.021	32.654	0.056	0.056	0.000	0.000	0.000	0.000
34	A	40	ASN	0	0.025	-0.013	33.583	-0.179	-0.179	0.000	0.000	0.000	0.000
35	A	41	PHE	0	-0.073	-0.036	25.480	-0.094	-0.094	0.000	0.000	0.000	0.000
36	A	42	PHE	0	0.060	0.025	26.440	-0.228	-0.228	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.907	0.971	29.965	8.794	8.794	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.911	0.942	31.410	9.296	9.296	0.000	0.000	0.000	0.000
39	A	45	HIS	0	-0.029	-0.007	25.867	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	46	ILE	0	0.096	0.047	26.081	0.087	0.087	0.000	0.000	0.000	0.000
41	A	47	CYS	0	-0.073	-0.020	17.591	-1.295	-1.295	0.000	0.000	0.000	0.000
42	A	48	ASP	-1	-0.827	-0.927	22.932	-12.066	-12.066	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.024	-0.020	20.453	-0.560	-0.560	0.000	0.000	0.000	0.000
44	A	50	ASN	0	-0.009	0.011	19.888	-0.916	-0.916	0.000	0.000	0.000	0.000
45	A	51	LYS	1	0.935	0.969	16.591	17.569	17.569	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.686	-0.838	16.943	-16.872	-16.872	0.000	0.000	0.000	0.000
47	A	53	GLY	0	0.071	0.022	15.909	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	54	MET	0	-0.140	-0.079	16.717	0.136	0.136	0.000	0.000	0.000	0.000
49	A	55	PHE	0	0.043	0.030	19.955	0.664	0.664	0.000	0.000	0.000	0.000
50	A	56	LEU	0	0.072	0.039	15.534	0.819	0.819	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.029	0.017	17.111	0.554	0.554	0.000	0.000	0.000	0.000
52	A	58	ARG	1	0.902	0.948	19.457	12.920	12.920	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.030	0.007	21.338	0.467	0.467	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.045	0.035	19.133	0.362	0.362	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.854	0.913	19.481	15.830	15.830	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.854	0.943	24.019	11.110	11.110	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.075	0.043	20.814	0.557	0.557	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.823	0.894	22.305	13.416	13.416	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.034	-0.012	26.093	0.247	0.247	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.033	0.022	27.698	0.424	0.424	0.000	0.000	0.000	0.000
61	A	67	LEU	0	0.015	0.020	24.909	0.176	0.176	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.946	0.980	29.216	9.484	9.484	0.000	0.000	0.000	0.000
63	A	69	MET	0	-0.003	0.016	32.299	-0.218	-0.218	0.000	0.000	0.000	0.000
64	A	70	ASN	0	-0.047	-0.040	29.901	-0.113	-0.113	0.000	0.000	0.000	0.000
65	A	71	SER	0	0.009	-0.010	30.843	0.141	0.141	0.000	0.000	0.000	0.000
66	A	72	THR	0	-0.005	-0.014	28.304	-0.382	-0.382	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.033	0.039	28.533	0.021	0.021	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.871	-0.950	24.779	-11.112	-11.112	0.000	0.000	0.000	0.000
69	A	75	PHE	0	-0.020	-0.015	24.094	-0.526	-0.526	0.000	0.000	0.000	0.000
70	A	76	ASP	-1	-0.800	-0.895	24.762	-10.577	-10.577	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.036	0.020	22.378	-0.629	-0.629	0.000	0.000	0.000	0.000
72	A	78	HIS	0	0.035	0.033	20.054	-1.304	-1.304	0.000	0.000	0.000	0.000
73	A	79	LEU	0	0.035	0.025	19.890	-0.684	-0.684	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.014	0.001	21.014	-0.491	-0.491	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.955	0.983	16.456	13.430	13.430	0.000	0.000	0.000	0.000
76	A	82	VAL	0	0.036	0.027	16.222	-1.103	-1.103	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.031	-0.012	16.932	-0.673	-0.673	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.821	-0.879	17.364	-15.488	-15.488	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.061	0.022	13.844	-1.135	-1.135	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.024	-0.027	12.979	-2.040	-2.040	0.000	0.000	0.000	0.000
81	A	87	THR	0	-0.128	-0.088	14.317	-0.250	-0.250	0.000	0.000	0.000	0.000
82	A	88	ILE	0	0.019	0.004	10.965	-0.650	-0.650	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.003	0.021	7.187	-2.329	-2.329	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.014	0.011	9.746	-2.047	-2.047	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.006	0.006	10.901	0.245	0.245	0.000	0.000	0.000	0.000
86	A	92	CYS	0	-0.050	-0.023	6.289	-0.517	-0.517	0.000	0.000	0.000	0.000
87	A	93	THR	0	-0.054	-0.048	5.969	-5.050	-5.050	0.000	0.000	0.000	0.000
88	A	94	GLY	0	0.061	0.041	7.441	1.921	1.921	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.098	-0.048	9.685	3.607	3.607	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.035	0.019	12.923	-0.326	-0.326	0.000	0.000	0.000	0.000
91	A	97	LYS	1	0.891	0.935	15.259	15.008	15.008	0.000	0.000	0.000	0.000
92	A	98	GLY	0	0.050	0.043	18.365	-0.222	-0.222	0.000	0.000	0.000	0.000
93	A	122	GLN	0	-0.016	-0.017	27.733	0.110	0.110	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.973	0.981	32.977	8.502	8.502	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.883	0.931	31.655	9.395	9.395	0.000	0.000	0.000	0.000
96	A	125	LEU	0	-0.033	-0.012	30.168	0.217	0.217	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.026	-0.012	32.831	-0.260	-0.260	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.803	-0.906	34.173	-8.842	-8.842	0.000	0.000	0.000	0.000
99	A	128	LEU	0	0.067	0.022	30.310	-0.332	-0.332	0.000	0.000	0.000	0.000
100	A	130	PHE	0	-0.039	-0.013	28.792	-0.370	-0.370	0.000	0.000	0.000	0.000
101	A	131	LEU	0	-0.020	-0.015	25.578	-0.348	-0.348	0.000	0.000	0.000	0.000
102	A	132	LYS	1	0.895	0.951	25.981	9.289	9.289	0.000	0.000	0.000	0.000
103	A	133	ARG	1	0.911	0.953	25.586	9.933	9.933	0.000	0.000	0.000	0.000
104	A	134	LEU	0	-0.093	-0.046	23.994	-0.400	-0.400	0.000	0.000	0.000	0.000
105	A	135	LEU	0	0.016	-0.005	20.821	-0.678	-0.678	0.000	0.000	0.000	0.000
106	A	136	GLN	0	0.004	0.006	21.018	-0.391	-0.391	0.000	0.000	0.000	0.000
107	A	137	GLU	-1	-0.816	-0.895	21.182	-12.419	-12.419	0.000	0.000	0.000	0.000
108	A	138	ILE	0	-0.062	-0.041	17.814	-0.711	-0.711	0.000	0.000	0.000	0.000
109	A	139	LYS	1	0.801	0.869	16.763	13.687	13.687	0.000	0.000	0.000	0.000
110	A	140	THR	0	0.001	-0.014	16.843	-0.867	-0.867	0.000	0.000	0.000	0.000
111	A	142	TRP	0	0.006	-0.003	11.144	-1.160	-1.160	0.000	0.000	0.000	0.000
112	A	143	ASN	0	0.017	0.006	12.996	-1.144	-1.144	0.000	0.000	0.000	0.000
113	A	144	LYS	1	0.834	0.917	14.058	15.129	15.129	0.000	0.000	0.000	0.000
114	A	145	ILE	0	-0.065	-0.028	12.189	-0.110	-0.110	0.000	0.000	0.000	0.000
115	A	146	LEU	0	-0.073	-0.028	8.539	-2.032	-2.032	0.000	0.000	0.000	0.000
116	A	147	MET	0	-0.044	-0.011	10.951	-0.023	-0.023	0.000	0.000	0.000	0.000

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