FMO DATABASE

FMODB ID: 2JZJR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1096821.810292
FMO2-HF: Nuclear repulsion	1046377.717758
FMO2-HF: Total energy	-50444.092534
FMO2-MP2: Total energy	-50588.839523

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.
-24.852	-22.966	15.844	-7.897	-9.835	-0.041

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 : -0.044 / q_NPA : -0.049

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	-0.038	-0.029	3.835	-1.799	0.991	-0.031	-1.426	-1.333	0.001
4	B	79	PRO	0	-0.028	-0.015	6.981	0.267	0.267	0.000	0.000	0.000	0.000
5	B	80	ASN	0	-0.026	-0.012	10.558	-0.143	-0.143	0.000	0.000	0.000	0.000
6	B	81	ASP	-1	-0.939	-0.955	13.230	-0.742	-0.742	0.000	0.000	0.000	0.000
7	B	82	TRP	0	0.004	-0.024	8.631	-0.137	-0.137	0.000	0.000	0.000	0.000
8	B	83	LEU	0	-0.006	0.008	8.440	-0.307	-0.307	0.000	0.000	0.000	0.000
9	B	84	LEU	0	0.001	-0.020	3.203	-1.014	-0.558	0.027	-0.084	-0.399	-0.001
10	B	85	ASN	0	-0.001	0.021	6.787	0.477	0.477	0.000	0.000	0.000	0.000
11	B	86	GLU	-1	-0.825	-0.923	6.393	-0.792	-0.792	0.000	0.000	0.000	0.000
12	B	87	GLY	0	-0.070	-0.028	3.163	-1.605	-0.637	0.620	-0.534	-1.055	0.004
13	B	88	LYS	1	0.833	0.907	2.509	-5.135	-3.715	1.537	-0.987	-1.970	-0.017
14	B	90	TYR	0	0.044	-0.001	6.158	0.439	0.439	0.000	0.000	0.000	0.000
15	B	91	TRP	0	0.020	0.035	9.982	0.203	0.203	0.000	0.000	0.000	0.000
16	B	92	PHE	0	-0.010	-0.021	12.833	0.080	0.080	0.000	0.000	0.000	0.000
17	B	93	SER	0	0.007	0.005	16.236	0.134	0.134	0.000	0.000	0.000	0.000
18	B	94	THR	0	0.003	-0.012	18.296	0.015	0.015	0.000	0.000	0.000	0.000
19	B	95	SER	0	-0.092	-0.033	21.574	0.047	0.047	0.000	0.000	0.000	0.000
20	B	96	PHE	0	0.011	-0.013	23.245	-0.032	-0.032	0.000	0.000	0.000	0.000
21	B	97	LYS	1	0.818	0.883	22.576	0.399	0.399	0.000	0.000	0.000	0.000
22	B	98	THR	0	0.052	0.038	24.874	-0.023	-0.023	0.000	0.000	0.000	0.000
23	B	99	TRP	0	0.040	0.033	21.274	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	100	LYS	1	0.929	0.944	22.427	0.301	0.301	0.000	0.000	0.000	0.000
25	B	101	GLU	-1	-0.835	-0.912	22.704	-0.300	-0.300	0.000	0.000	0.000	0.000
26	B	102	SER	0	0.008	0.018	19.452	-0.028	-0.028	0.000	0.000	0.000	0.000
27	B	103	GLN	0	0.078	0.041	18.112	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	104	ARG	1	0.784	0.890	17.815	0.283	0.283	0.000	0.000	0.000	0.000
29	B	105	ASP	-1	-0.800	-0.901	18.242	-0.456	-0.456	0.000	0.000	0.000	0.000
30	B	106	CYS	0	-0.103	-0.019	12.617	0.038	0.038	0.000	0.000	0.000	0.000
31	B	107	THR	0	0.067	0.031	13.796	-0.095	-0.095	0.000	0.000	0.000	0.000
32	B	108	GLN	0	-0.140	-0.061	15.122	0.018	0.018	0.000	0.000	0.000	0.000
33	B	109	LEU	0	-0.020	-0.017	12.886	0.071	0.071	0.000	0.000	0.000	0.000
34	B	110	GLN	0	-0.041	-0.015	10.367	-0.273	-0.273	0.000	0.000	0.000	0.000
35	B	111	ALA	0	0.000	0.004	9.427	-0.403	-0.403	0.000	0.000	0.000	0.000
36	B	112	HIS	0	0.000	-0.011	9.431	0.189	0.189	0.000	0.000	0.000	0.000
37	B	113	LEU	0	-0.015	-0.017	12.715	-0.130	-0.130	0.000	0.000	0.000	0.000
38	B	114	LEU	0	0.032	0.023	12.806	-0.023	-0.023	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.010	-0.001	12.650	0.123	0.123	0.000	0.000	0.000	0.000
40	B	116	ILE	0	-0.036	-0.022	13.309	-0.067	-0.067	0.000	0.000	0.000	0.000
41	B	117	GLN	0	0.040	0.043	11.336	-0.068	-0.068	0.000	0.000	0.000	0.000
42	B	118	ASN	0	-0.023	-0.028	14.229	0.123	0.123	0.000	0.000	0.000	0.000
43	B	119	LEU	0	0.049	0.026	15.661	-0.067	-0.067	0.000	0.000	0.000	0.000
44	B	120	ASP	-1	-0.829	-0.894	14.431	-0.463	-0.463	0.000	0.000	0.000	0.000
45	B	121	GLU	-1	-0.905	-0.966	10.338	-1.002	-1.002	0.000	0.000	0.000	0.000
46	B	122	LEU	0	-0.028	-0.006	13.603	-0.067	-0.067	0.000	0.000	0.000	0.000
47	B	123	GLU	-1	-1.009	-1.012	17.002	-0.369	-0.369	0.000	0.000	0.000	0.000
48	B	124	PHE	0	-0.045	-0.029	11.019	-0.047	-0.047	0.000	0.000	0.000	0.000
49	B	125	ILE	0	-0.008	-0.018	12.312	-0.010	-0.010	0.000	0.000	0.000	0.000
50	B	126	GLN	0	0.050	0.034	15.852	0.028	0.028	0.000	0.000	0.000	0.000
51	B	127	ASN	0	-0.030	-0.015	17.745	0.045	0.045	0.000	0.000	0.000	0.000
52	B	128	SER	0	-0.034	-0.016	15.526	-0.037	-0.037	0.000	0.000	0.000	0.000
53	B	129	LEU	0	-0.077	-0.017	17.575	-0.014	-0.014	0.000	0.000	0.000	0.000
54	B	130	LYS	1	0.948	0.965	20.391	0.418	0.418	0.000	0.000	0.000	0.000
55	B	131	PRO	0	0.013	-0.010	23.349	0.003	0.003	0.000	0.000	0.000	0.000
56	B	132	GLY	0	0.019	0.019	26.731	0.012	0.012	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.123	-0.050	21.146	-0.016	-0.016	0.000	0.000	0.000	0.000
58	B	134	PHE	0	0.007	-0.004	22.378	0.002	0.002	0.000	0.000	0.000	0.000
59	B	135	GLY	0	0.021	-0.002	20.552	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	136	TRP	0	-0.058	-0.017	20.447	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	137	ILE	0	0.057	0.009	17.598	-0.060	-0.060	0.000	0.000	0.000	0.000
62	B	138	GLY	0	-0.033	-0.012	17.361	0.053	0.053	0.000	0.000	0.000	0.000
63	B	139	LEU	0	-0.036	0.002	18.456	0.037	0.037	0.000	0.000	0.000	0.000
64	B	140	TYR	0	-0.098	-0.045	21.741	0.010	0.010	0.000	0.000	0.000	0.000
65	B	141	VAL	0	0.041	0.017	24.980	0.008	0.008	0.000	0.000	0.000	0.000
66	B	142	THR	0	-0.056	-0.018	27.829	0.003	0.003	0.000	0.000	0.000	0.000
67	B	143	PHE	0	-0.013	-0.009	29.490	0.009	0.009	0.000	0.000	0.000	0.000
68	B	144	GLN	0	0.009	-0.004	32.470	0.010	0.010	0.000	0.000	0.000	0.000
69	B	145	GLY	0	-0.052	-0.024	32.972	0.004	0.004	0.000	0.000	0.000	0.000
70	B	146	ASN	0	-0.054	-0.034	32.629	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	147	LEU	0	0.016	-0.004	29.244	0.002	0.002	0.000	0.000	0.000	0.000
72	B	148	TRP	0	0.021	0.023	25.459	-0.012	-0.012	0.000	0.000	0.000	0.000
73	B	149	MET	0	-0.042	-0.021	22.608	0.019	0.019	0.000	0.000	0.000	0.000
74	B	150	TRP	0	0.111	0.036	18.047	-0.023	-0.023	0.000	0.000	0.000	0.000
75	B	151	ILE	0	-0.049	-0.011	16.131	0.019	0.019	0.000	0.000	0.000	0.000
76	B	152	ASP	-1	-0.887	-0.967	14.992	-0.477	-0.477	0.000	0.000	0.000	0.000
77	B	153	GLU	-1	-0.966	-0.991	16.607	-0.243	-0.243	0.000	0.000	0.000	0.000
78	B	154	HIS	0	-0.001	0.003	16.884	0.083	0.083	0.000	0.000	0.000	0.000
79	B	155	PHE	0	-0.055	-0.034	21.124	-0.023	-0.023	0.000	0.000	0.000	0.000
80	B	156	LEU	0	-0.002	0.022	22.176	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	157	VAL	0	0.003	-0.010	22.705	0.023	0.023	0.000	0.000	0.000	0.000
82	B	158	PRO	0	-0.007	-0.005	24.798	-0.019	-0.019	0.000	0.000	0.000	0.000
83	B	159	GLU	-1	-0.917	-0.966	24.459	-0.183	-0.183	0.000	0.000	0.000	0.000
84	B	160	LEU	0	-0.067	-0.015	18.636	-0.013	-0.013	0.000	0.000	0.000	0.000
85	B	161	PHE	0	0.003	-0.019	19.776	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	162	SER	0	-0.019	-0.025	24.965	0.016	0.016	0.000	0.000	0.000	0.000
87	B	163	VAL	0	-0.037	-0.001	25.694	0.006	0.006	0.000	0.000	0.000	0.000
88	B	164	ILE	0	-0.014	0.009	28.042	0.021	0.021	0.000	0.000	0.000	0.000
89	B	165	GLY	0	0.031	-0.008	31.087	-0.008	-0.008	0.000	0.000	0.000	0.000
90	B	166	PRO	0	-0.040	-0.004	33.235	0.003	0.003	0.000	0.000	0.000	0.000
91	B	167	THR	0	0.024	-0.003	31.512	-0.011	-0.011	0.000	0.000	0.000	0.000
92	B	168	ASP	-1	-0.856	-0.889	33.029	-0.177	-0.177	0.000	0.000	0.000	0.000
93	B	169	ASP	-1	-0.819	-0.932	32.281	-0.180	-0.180	0.000	0.000	0.000	0.000
94	B	170	ARG	1	0.795	0.878	31.457	0.194	0.194	0.000	0.000	0.000	0.000
95	B	171	SER	0	-0.023	-0.005	30.088	-0.009	-0.009	0.000	0.000	0.000	0.000
96	B	172	CYS	0	-0.048	-0.034	24.694	-0.015	-0.015	0.000	0.000	0.000	0.000
97	B	173	ALA	0	0.048	0.020	22.977	0.016	0.016	0.000	0.000	0.000	0.000
98	B	174	VAL	0	-0.033	-0.016	22.501	-0.033	-0.033	0.000	0.000	0.000	0.000
99	B	175	ILE	0	-0.009	0.002	18.795	0.027	0.027	0.000	0.000	0.000	0.000
100	B	176	THR	0	-0.035	-0.010	22.315	-0.015	-0.015	0.000	0.000	0.000	0.000
101	B	177	GLY	0	0.055	0.025	22.215	-0.016	-0.016	0.000	0.000	0.000	0.000
102	B	178	ASN	0	-0.073	-0.034	23.298	0.002	0.002	0.000	0.000	0.000	0.000
103	B	179	TRP	0	0.043	0.009	25.481	0.011	0.011	0.000	0.000	0.000	0.000
104	B	180	VAL	0	0.035	0.019	22.407	-0.022	-0.022	0.000	0.000	0.000	0.000
105	B	181	TYR	0	0.013	0.022	25.236	0.022	0.022	0.000	0.000	0.000	0.000
106	B	182	SER	0	-0.009	-0.014	26.662	-0.026	-0.026	0.000	0.000	0.000	0.000
107	B	183	GLU	-1	-0.907	-0.967	27.758	-0.240	-0.240	0.000	0.000	0.000	0.000
108	B	184	ASP	-1	-0.746	-0.819	29.510	-0.210	-0.210	0.000	0.000	0.000	0.000
109	B	186	SER	0	-0.120	-0.075	28.479	-0.010	-0.010	0.000	0.000	0.000	0.000
110	B	187	SER	0	0.010	-0.001	29.693	0.015	0.015	0.000	0.000	0.000	0.000
111	B	188	THR	0	-0.057	-0.035	27.643	-0.016	-0.016	0.000	0.000	0.000	0.000
112	B	189	PHE	0	0.053	0.016	24.972	0.010	0.010	0.000	0.000	0.000	0.000
113	B	190	LYS	1	0.965	1.015	21.135	0.485	0.485	0.000	0.000	0.000	0.000
114	B	191	GLY	0	0.022	0.008	18.904	0.002	0.002	0.000	0.000	0.000	0.000
115	B	192	ILE	0	0.033	0.010	14.367	0.003	0.003	0.000	0.000	0.000	0.000
116	B	194	GLN	0	0.094	0.042	8.755	-0.087	-0.087	0.000	0.000	0.000	0.000
117	B	195	ARG	1	0.895	0.958	5.716	3.244	3.244	0.000	0.000	0.000	0.000
118	B	196	ASP	-1	-0.807	-0.850	1.760	-15.081	-18.829	13.691	-4.866	-5.078	-0.028

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