FMO DATABASE

FMODB ID: 7282K

Calculation Name: 4IOP-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4IOP

Chain ID: B

ChEMBL ID:

UniProt ID: Q6UVW9

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1098550.749294
FMO2-HF: Nuclear repulsion	1048107.99513
FMO2-HF: Total energy	-50442.754163
FMO2-MP2: Total energy	-50587.75036

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(B:76:TYR)

Summations of interaction energy for fragment #1(B:76:TYR)

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.
-25.385	-21.393	13.365	-7.159	-10.199	-0.033

Interaction energy analysis for fragmet #1(B:76:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.037

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	B	78	CYS	0	-0.017	-0.022	3.835	-1.681	1.168	-0.028	-1.444	-1.377	0.001
4	B	79	PRO	0	-0.023	-0.013	6.758	0.275	0.275	0.000	0.000	0.000	0.000
5	B	80	ASN	0	-0.017	-0.006	10.352	-0.145	-0.145	0.000	0.000	0.000	0.000
6	B	81	ASP	-1	-0.945	-0.960	13.060	-0.739	-0.739	0.000	0.000	0.000	0.000
7	B	82	TRP	0	-0.006	-0.024	8.389	-0.144	-0.144	0.000	0.000	0.000	0.000
8	B	83	LEU	0	0.007	0.007	8.294	-0.317	-0.317	0.000	0.000	0.000	0.000
9	B	84	LEU	0	-0.004	-0.017	3.699	-0.829	-0.552	0.001	-0.034	-0.244	0.000
10	B	85	ASN	0	0.014	0.029	6.760	0.472	0.472	0.000	0.000	0.000	0.000
11	B	86	GLU	-1	-0.825	-0.921	6.575	-0.836	-0.836	0.000	0.000	0.000	0.000
12	B	87	GLY	0	-0.080	-0.027	3.155	-1.476	-0.485	0.625	-0.531	-1.085	0.004
13	B	88	LYS	1	0.884	0.953	2.558	-5.662	-4.183	1.519	-0.959	-2.039	-0.015
14	B	90	TYR	0	0.011	-0.014	6.053	0.430	0.430	0.000	0.000	0.000	0.000
15	B	91	TRP	0	0.023	0.047	9.878	0.213	0.213	0.000	0.000	0.000	0.000
16	B	92	PHE	0	-0.019	-0.030	12.777	0.083	0.083	0.000	0.000	0.000	0.000
17	B	93	SER	0	0.023	0.006	16.114	0.129	0.129	0.000	0.000	0.000	0.000
18	B	94	THR	0	-0.058	-0.027	18.172	0.027	0.027	0.000	0.000	0.000	0.000
19	B	95	SER	0	-0.030	-0.017	21.445	0.048	0.048	0.000	0.000	0.000	0.000
20	B	96	PHE	0	-0.009	-0.020	23.126	-0.035	-0.035	0.000	0.000	0.000	0.000
21	B	97	LYS	1	0.887	0.930	22.398	0.423	0.423	0.000	0.000	0.000	0.000
22	B	98	THR	0	0.077	0.047	24.775	-0.014	-0.014	0.000	0.000	0.000	0.000
23	B	99	TRP	0	0.045	0.043	21.132	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	100	LYS	1	0.864	0.906	22.344	0.330	0.330	0.000	0.000	0.000	0.000
25	B	101	GLU	-1	-1.009	-1.013	22.670	-0.326	-0.326	0.000	0.000	0.000	0.000
26	B	102	SER	0	0.035	0.032	19.417	-0.027	-0.027	0.000	0.000	0.000	0.000
27	B	103	GLN	0	0.133	0.074	18.047	-0.015	-0.015	0.000	0.000	0.000	0.000
28	B	104	ARG	1	0.883	0.949	17.790	0.295	0.295	0.000	0.000	0.000	0.000
29	B	105	ASP	-1	-0.856	-0.942	18.265	-0.493	-0.493	0.000	0.000	0.000	0.000
30	B	106	CYS	0	-0.084	-0.008	12.477	0.030	0.030	0.000	0.000	0.000	0.000
31	B	107	THR	0	0.069	0.040	13.825	-0.095	-0.095	0.000	0.000	0.000	0.000
32	B	108	GLN	0	-0.115	-0.056	15.195	0.010	0.010	0.000	0.000	0.000	0.000
33	B	109	LEU	0	-0.066	-0.034	12.803	0.080	0.080	0.000	0.000	0.000	0.000
34	B	110	GLN	0	-0.039	-0.011	10.335	-0.302	-0.302	0.000	0.000	0.000	0.000
35	B	111	ALA	0	-0.017	-0.004	9.493	-0.429	-0.429	0.000	0.000	0.000	0.000
36	B	112	HIS	0	0.007	-0.013	9.403	0.260	0.260	0.000	0.000	0.000	0.000
37	B	113	LEU	0	0.004	-0.015	12.641	-0.132	-0.132	0.000	0.000	0.000	0.000
38	B	114	LEU	0	0.014	0.013	12.741	-0.033	-0.033	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.018	0.002	12.534	0.119	0.119	0.000	0.000	0.000	0.000
40	B	116	ILE	0	-0.009	-0.015	13.316	-0.082	-0.082	0.000	0.000	0.000	0.000
41	B	117	GLN	0	0.037	0.034	11.091	-0.102	-0.102	0.000	0.000	0.000	0.000
42	B	118	ASN	0	-0.009	-0.020	14.273	0.116	0.116	0.000	0.000	0.000	0.000
43	B	119	LEU	0	0.063	0.032	15.706	-0.062	-0.062	0.000	0.000	0.000	0.000
44	B	120	ASP	-1	-0.811	-0.872	14.150	-0.511	-0.511	0.000	0.000	0.000	0.000
45	B	121	GLU	-1	-0.916	-0.983	10.476	-0.950	-0.950	0.000	0.000	0.000	0.000
46	B	122	LEU	0	-0.052	-0.019	13.625	-0.065	-0.065	0.000	0.000	0.000	0.000
47	B	123	GLU	-1	-1.011	-1.012	17.009	-0.376	-0.376	0.000	0.000	0.000	0.000
48	B	124	PHE	0	-0.034	-0.019	10.637	-0.051	-0.051	0.000	0.000	0.000	0.000
49	B	125	ILE	0	-0.008	-0.023	12.380	-0.012	-0.012	0.000	0.000	0.000	0.000
50	B	126	GLN	0	0.089	0.054	15.864	0.018	0.018	0.000	0.000	0.000	0.000
51	B	127	ASN	0	-0.031	-0.021	18.244	0.019	0.019	0.000	0.000	0.000	0.000
52	B	128	SER	0	-0.043	-0.006	15.410	-0.037	-0.037	0.000	0.000	0.000	0.000
53	B	129	LEU	0	-0.082	-0.027	17.559	-0.015	-0.015	0.000	0.000	0.000	0.000
54	B	130	LYS	1	0.936	0.961	20.356	0.422	0.422	0.000	0.000	0.000	0.000
55	B	131	PRO	0	0.022	-0.009	23.302	0.003	0.003	0.000	0.000	0.000	0.000
56	B	132	GLY	0	0.033	0.033	26.689	0.013	0.013	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.145	-0.069	21.420	-0.015	-0.015	0.000	0.000	0.000	0.000
58	B	134	PHE	0	0.026	0.001	22.278	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	135	GLY	0	0.023	-0.001	20.466	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	136	TRP	0	-0.017	0.007	20.276	-0.006	-0.006	0.000	0.000	0.000	0.000
61	B	137	ILE	0	0.056	0.010	17.487	-0.064	-0.064	0.000	0.000	0.000	0.000
62	B	138	GLY	0	-0.033	-0.010	17.332	0.054	0.054	0.000	0.000	0.000	0.000
63	B	139	LEU	0	-0.029	-0.004	18.421	0.038	0.038	0.000	0.000	0.000	0.000
64	B	140	TYR	0	-0.056	-0.033	21.717	0.013	0.013	0.000	0.000	0.000	0.000
65	B	141	VAL	0	0.040	0.026	24.949	0.007	0.007	0.000	0.000	0.000	0.000
66	B	142	THR	0	-0.073	0.011	27.682	0.002	0.002	0.000	0.000	0.000	0.000
67	B	143	PHE	0	0.007	-0.017	29.339	0.009	0.009	0.000	0.000	0.000	0.000
68	B	144	GLN	0	0.025	0.006	32.331	0.010	0.010	0.000	0.000	0.000	0.000
69	B	145	GLY	0	-0.051	-0.025	32.805	0.004	0.004	0.000	0.000	0.000	0.000
70	B	146	ASN	0	-0.043	-0.046	32.560	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	147	LEU	0	-0.006	-0.022	28.793	0.002	0.002	0.000	0.000	0.000	0.000
72	B	148	TRP	0	-0.005	0.016	25.431	-0.012	-0.012	0.000	0.000	0.000	0.000
73	B	149	MET	0	-0.024	-0.002	22.182	0.011	0.011	0.000	0.000	0.000	0.000
74	B	150	TRP	0	0.087	0.028	17.827	-0.027	-0.027	0.000	0.000	0.000	0.000
75	B	151	ILE	0	-0.056	-0.013	15.973	0.019	0.019	0.000	0.000	0.000	0.000
76	B	152	ASP	-1	-0.895	-0.976	14.997	-0.512	-0.512	0.000	0.000	0.000	0.000
77	B	153	GLU	-1	-0.957	-0.978	16.452	-0.272	-0.272	0.000	0.000	0.000	0.000
78	B	154	HIS	0	-0.055	-0.025	17.394	0.081	0.081	0.000	0.000	0.000	0.000
79	B	155	PHE	0	-0.055	-0.035	20.931	-0.022	-0.022	0.000	0.000	0.000	0.000
80	B	156	LEU	0	-0.001	0.029	22.657	-0.011	-0.011	0.000	0.000	0.000	0.000
81	B	157	VAL	0	-0.001	-0.019	22.825	0.025	0.025	0.000	0.000	0.000	0.000
82	B	158	PRO	0	-0.007	-0.010	24.833	-0.019	-0.019	0.000	0.000	0.000	0.000
83	B	159	GLU	-1	-0.911	-0.959	24.499	-0.199	-0.199	0.000	0.000	0.000	0.000
84	B	160	LEU	0	-0.058	-0.012	18.806	-0.013	-0.013	0.000	0.000	0.000	0.000
85	B	161	PHE	0	-0.017	-0.029	20.100	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	162	SER	0	-0.011	-0.018	24.982	0.015	0.015	0.000	0.000	0.000	0.000
87	B	163	VAL	0	-0.037	-0.002	25.770	0.007	0.007	0.000	0.000	0.000	0.000
88	B	164	ILE	0	-0.019	0.005	28.027	0.022	0.022	0.000	0.000	0.000	0.000
89	B	165	GLY	0	0.029	-0.010	31.064	-0.009	-0.009	0.000	0.000	0.000	0.000
90	B	166	PRO	0	-0.049	-0.003	33.211	0.003	0.003	0.000	0.000	0.000	0.000
91	B	167	THR	0	0.038	-0.001	31.358	-0.012	-0.012	0.000	0.000	0.000	0.000
92	B	168	ASP	-1	-0.873	-0.921	33.008	-0.189	-0.189	0.000	0.000	0.000	0.000
93	B	169	ASP	-1	-0.835	-0.946	32.176	-0.194	-0.194	0.000	0.000	0.000	0.000
94	B	170	ARG	1	0.861	0.942	31.516	0.209	0.209	0.000	0.000	0.000	0.000
95	B	171	SER	0	-0.035	-0.004	30.042	-0.010	-0.010	0.000	0.000	0.000	0.000
96	B	172	CYS	0	-0.053	-0.038	24.617	-0.016	-0.016	0.000	0.000	0.000	0.000
97	B	173	ALA	0	0.046	0.026	22.808	0.018	0.018	0.000	0.000	0.000	0.000
98	B	174	VAL	0	-0.027	-0.022	22.449	-0.036	-0.036	0.000	0.000	0.000	0.000
99	B	175	ILE	0	-0.023	-0.005	18.823	0.032	0.032	0.000	0.000	0.000	0.000
100	B	176	THR	0	-0.035	-0.006	22.264	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	177	GLY	0	0.060	0.026	22.215	-0.016	-0.016	0.000	0.000	0.000	0.000
102	B	178	ASN	0	-0.076	-0.035	23.297	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	179	TRP	0	0.012	-0.008	25.460	0.009	0.009	0.000	0.000	0.000	0.000
104	B	180	VAL	0	0.043	0.018	22.590	-0.024	-0.024	0.000	0.000	0.000	0.000
105	B	181	TYR	0	0.018	0.023	25.207	0.022	0.022	0.000	0.000	0.000	0.000
106	B	182	SER	0	0.008	-0.008	26.621	-0.029	-0.029	0.000	0.000	0.000	0.000
107	B	183	GLU	-1	-0.924	-0.966	27.813	-0.255	-0.255	0.000	0.000	0.000	0.000
108	B	184	ASP	-1	-0.785	-0.880	29.453	-0.227	-0.227	0.000	0.000	0.000	0.000
109	B	186	SER	0	-0.098	-0.048	28.398	-0.012	-0.012	0.000	0.000	0.000	0.000
110	B	187	SER	0	0.011	0.000	29.782	0.015	0.015	0.000	0.000	0.000	0.000
111	B	188	THR	0	-0.030	-0.016	27.547	-0.017	-0.017	0.000	0.000	0.000	0.000
112	B	189	PHE	0	0.027	-0.003	24.757	0.012	0.012	0.000	0.000	0.000	0.000
113	B	190	LYS	1	0.965	1.013	21.117	0.479	0.479	0.000	0.000	0.000	0.000
114	B	191	GLY	0	0.001	0.002	18.799	0.004	0.004	0.000	0.000	0.000	0.000
115	B	192	ILE	0	0.042	0.021	14.487	0.005	0.005	0.000	0.000	0.000	0.000
116	B	194	GLN	0	0.068	0.033	8.597	-0.169	-0.169	0.000	0.000	0.000	0.000
117	B	195	ARG	1	0.934	0.965	5.269	3.435	3.435	0.000	0.000	0.000	0.000
118	B	196	ASP	-1	-0.880	-0.905	1.851	-15.347	-16.951	11.248	-4.191	-5.454	-0.023

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Interactive mode: IFIE and PIEDA for fragment #1(B:76:TYR)