FMO DATABASE

FMODB ID: 6NJNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1097925.38787
FMO2-HF: Nuclear repulsion	1047480.214406
FMO2-HF: Total energy	-50445.173464
FMO2-MP2: Total energy	-50589.743027

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.
-23.95	-23.429	13.62	-6.845	-7.295	-0.042

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 : -0.048 / q_NPA : -0.048

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	-0.013	-0.009	3.877	-0.731	1.359	-0.021	-0.994	-1.076	0.002
4	B	79	PRO	0	-0.016	-0.004	7.220	0.327	0.327	0.000	0.000	0.000	0.000
5	B	80	ASN	0	-0.009	-0.018	10.811	-0.192	-0.192	0.000	0.000	0.000	0.000
6	B	81	ASP	-1	-0.883	-0.951	13.264	-0.666	-0.666	0.000	0.000	0.000	0.000
7	B	82	TRP	0	-0.032	-0.005	8.775	-0.159	-0.159	0.000	0.000	0.000	0.000
8	B	83	LEU	0	0.002	0.008	9.179	-0.081	-0.081	0.000	0.000	0.000	0.000
9	B	84	LEU	0	-0.005	-0.024	3.329	-0.830	-0.410	0.022	-0.088	-0.353	-0.001
10	B	85	ASN	0	-0.012	-0.002	6.499	0.683	0.683	0.000	0.000	0.000	0.000
11	B	86	GLU	-1	-0.838	-0.921	6.448	-1.165	-1.165	0.000	0.000	0.000	0.000
12	B	87	GLY	0	-0.068	-0.031	3.205	-1.566	-0.666	0.241	-0.367	-0.774	0.003
13	B	88	LYS	1	0.809	0.914	2.685	-4.460	-2.650	0.640	-1.004	-1.445	-0.014
14	B	90	TYR	0	-0.012	-0.033	6.214	0.338	0.338	0.000	0.000	0.000	0.000
15	B	91	TRP	0	-0.033	-0.005	10.010	0.167	0.167	0.000	0.000	0.000	0.000
16	B	92	PHE	0	0.048	0.016	13.056	0.057	0.057	0.000	0.000	0.000	0.000
17	B	93	SER	0	0.040	0.022	16.690	0.123	0.123	0.000	0.000	0.000	0.000
18	B	94	THR	0	-0.009	-0.020	18.791	0.022	0.022	0.000	0.000	0.000	0.000
19	B	95	SER	0	-0.080	-0.026	22.106	0.049	0.049	0.000	0.000	0.000	0.000
20	B	96	PHE	0	0.008	0.003	23.795	-0.033	-0.033	0.000	0.000	0.000	0.000
21	B	97	LYS	1	0.824	0.894	23.223	0.372	0.372	0.000	0.000	0.000	0.000
22	B	98	THR	0	0.062	0.039	25.917	-0.018	-0.018	0.000	0.000	0.000	0.000
23	B	99	TRP	0	0.016	0.015	21.531	-0.010	-0.010	0.000	0.000	0.000	0.000
24	B	100	LYS	1	0.940	0.949	22.294	0.332	0.332	0.000	0.000	0.000	0.000
25	B	101	GLU	-1	-0.818	-0.893	22.953	-0.301	-0.301	0.000	0.000	0.000	0.000
26	B	102	SER	0	-0.002	0.002	20.282	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	103	GLN	0	0.086	0.049	18.197	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	104	ARG	1	0.782	0.888	18.097	0.278	0.278	0.000	0.000	0.000	0.000
29	B	105	ASP	-1	-0.807	-0.896	19.041	-0.400	-0.400	0.000	0.000	0.000	0.000
30	B	106	CYS	0	-0.043	-0.008	12.994	0.039	0.039	0.000	0.000	0.000	0.000
31	B	107	THR	0	0.003	-0.007	14.398	-0.068	-0.068	0.000	0.000	0.000	0.000
32	B	108	GLN	0	-0.059	-0.026	15.525	0.015	0.015	0.000	0.000	0.000	0.000
33	B	109	LEU	0	-0.038	-0.011	13.339	0.077	0.077	0.000	0.000	0.000	0.000
34	B	110	GLN	0	-0.047	-0.030	10.870	-0.191	-0.191	0.000	0.000	0.000	0.000
35	B	111	ALA	0	-0.030	0.001	9.902	-0.319	-0.319	0.000	0.000	0.000	0.000
36	B	112	HIS	0	0.016	0.001	9.205	0.173	0.173	0.000	0.000	0.000	0.000
37	B	113	LEU	0	-0.018	-0.020	13.077	-0.111	-0.111	0.000	0.000	0.000	0.000
38	B	114	LEU	0	0.004	0.003	12.987	-0.017	-0.017	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.036	-0.012	12.979	0.148	0.148	0.000	0.000	0.000	0.000
40	B	116	ILE	0	0.000	-0.003	13.206	-0.105	-0.105	0.000	0.000	0.000	0.000
41	B	117	GLN	0	0.024	0.018	11.154	-0.086	-0.086	0.000	0.000	0.000	0.000
42	B	118	ASN	0	-0.068	-0.038	14.139	0.169	0.169	0.000	0.000	0.000	0.000
43	B	119	LEU	0	0.041	0.015	15.757	-0.073	-0.073	0.000	0.000	0.000	0.000
44	B	120	ASP	-1	-0.848	-0.919	13.944	-0.704	-0.704	0.000	0.000	0.000	0.000
45	B	121	GLU	-1	-0.810	-0.908	10.134	-1.558	-1.558	0.000	0.000	0.000	0.000
46	B	122	LEU	0	-0.032	-0.010	13.567	-0.027	-0.027	0.000	0.000	0.000	0.000
47	B	123	GLU	-1	-0.972	-0.998	17.135	-0.449	-0.449	0.000	0.000	0.000	0.000
48	B	124	PHE	0	-0.017	0.016	11.134	-0.022	-0.022	0.000	0.000	0.000	0.000
49	B	125	ILE	0	-0.012	-0.022	12.766	0.037	0.037	0.000	0.000	0.000	0.000
50	B	126	GLN	0	0.001	0.007	16.039	0.047	0.047	0.000	0.000	0.000	0.000
51	B	127	ASN	0	-0.045	-0.041	17.603	0.068	0.068	0.000	0.000	0.000	0.000
52	B	128	SER	0	-0.036	-0.010	15.649	-0.021	-0.021	0.000	0.000	0.000	0.000
53	B	129	LEU	0	-0.060	-0.016	17.697	0.009	0.009	0.000	0.000	0.000	0.000
54	B	130	LYS	1	0.953	0.970	20.731	0.428	0.428	0.000	0.000	0.000	0.000
55	B	131	PRO	0	0.033	-0.004	23.605	0.001	0.001	0.000	0.000	0.000	0.000
56	B	132	GLY	0	0.007	0.011	27.040	0.016	0.016	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.103	-0.040	21.460	-0.006	-0.006	0.000	0.000	0.000	0.000
58	B	134	PHE	0	0.003	0.000	22.847	-0.005	-0.005	0.000	0.000	0.000	0.000
59	B	135	GLY	0	0.004	-0.004	21.211	0.000	0.000	0.000	0.000	0.000	0.000
60	B	136	TRP	0	-0.054	-0.035	20.937	-0.022	-0.022	0.000	0.000	0.000	0.000
61	B	137	ILE	0	0.049	0.018	18.116	-0.071	-0.071	0.000	0.000	0.000	0.000
62	B	138	GLY	0	-0.022	-0.003	17.598	0.068	0.068	0.000	0.000	0.000	0.000
63	B	139	LEU	0	-0.034	-0.014	18.739	0.015	0.015	0.000	0.000	0.000	0.000
64	B	140	TYR	0	-0.100	-0.073	21.961	0.026	0.026	0.000	0.000	0.000	0.000
65	B	141	VAL	0	0.027	0.024	25.262	0.004	0.004	0.000	0.000	0.000	0.000
66	B	142	THR	0	-0.050	-0.023	27.619	0.014	0.014	0.000	0.000	0.000	0.000
67	B	143	PHE	0	0.003	-0.014	29.145	0.016	0.016	0.000	0.000	0.000	0.000
68	B	144	GLN	0	-0.018	0.007	32.758	0.011	0.011	0.000	0.000	0.000	0.000
69	B	145	GLY	0	-0.027	-0.027	32.552	0.009	0.009	0.000	0.000	0.000	0.000
70	B	146	ASN	0	-0.057	-0.035	33.104	0.001	0.001	0.000	0.000	0.000	0.000
71	B	147	LEU	0	0.022	0.012	29.587	0.001	0.001	0.000	0.000	0.000	0.000
72	B	148	TRP	0	-0.004	0.004	25.600	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	149	MET	0	-0.039	-0.012	22.939	0.021	0.021	0.000	0.000	0.000	0.000
74	B	150	TRP	0	0.070	0.021	18.344	-0.010	-0.010	0.000	0.000	0.000	0.000
75	B	151	ILE	0	-0.034	-0.015	16.309	0.026	0.026	0.000	0.000	0.000	0.000
76	B	152	ASP	-1	-0.879	-0.936	14.775	-0.664	-0.664	0.000	0.000	0.000	0.000
77	B	153	GLU	-1	-0.895	-0.941	16.621	-0.315	-0.315	0.000	0.000	0.000	0.000
78	B	154	HIS	0	-0.028	-0.002	16.896	0.092	0.092	0.000	0.000	0.000	0.000
79	B	155	PHE	0	-0.016	-0.024	21.182	-0.017	-0.017	0.000	0.000	0.000	0.000
80	B	156	LEU	0	-0.023	0.001	22.286	-0.015	-0.015	0.000	0.000	0.000	0.000
81	B	157	VAL	0	0.016	0.015	22.320	0.027	0.027	0.000	0.000	0.000	0.000
82	B	158	PRO	0	-0.006	-0.018	24.512	-0.021	-0.021	0.000	0.000	0.000	0.000
83	B	159	GLU	-1	-0.949	-0.979	24.416	-0.258	-0.258	0.000	0.000	0.000	0.000
84	B	160	LEU	0	-0.039	0.002	18.329	-0.015	-0.015	0.000	0.000	0.000	0.000
85	B	161	PHE	0	0.011	-0.013	19.689	-0.011	-0.011	0.000	0.000	0.000	0.000
86	B	162	SER	0	-0.005	-0.005	24.874	0.014	0.014	0.000	0.000	0.000	0.000
87	B	163	VAL	0	-0.033	-0.003	25.350	0.000	0.000	0.000	0.000	0.000	0.000
88	B	164	ILE	0	-0.013	0.001	27.807	0.025	0.025	0.000	0.000	0.000	0.000
89	B	165	GLY	0	0.031	-0.007	30.839	-0.009	-0.009	0.000	0.000	0.000	0.000
90	B	166	PRO	0	-0.021	0.011	33.141	0.005	0.005	0.000	0.000	0.000	0.000
91	B	167	THR	0	0.020	0.000	31.447	-0.013	-0.013	0.000	0.000	0.000	0.000
92	B	168	ASP	-1	-0.835	-0.868	33.001	-0.206	-0.206	0.000	0.000	0.000	0.000
93	B	169	ASP	-1	-0.826	-0.934	32.711	-0.202	-0.202	0.000	0.000	0.000	0.000
94	B	170	ARG	1	0.801	0.873	31.735	0.214	0.214	0.000	0.000	0.000	0.000
95	B	171	SER	0	-0.037	-0.019	30.433	-0.009	-0.009	0.000	0.000	0.000	0.000
96	B	172	CYS	0	-0.081	-0.053	25.183	-0.021	-0.021	0.000	0.000	0.000	0.000
97	B	173	ALA	0	0.049	0.026	23.021	0.018	0.018	0.000	0.000	0.000	0.000
98	B	174	VAL	0	-0.034	-0.014	22.942	-0.037	-0.037	0.000	0.000	0.000	0.000
99	B	175	ILE	0	0.022	0.014	18.761	0.023	0.023	0.000	0.000	0.000	0.000
100	B	176	THR	0	0.023	-0.006	22.406	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	177	GLY	0	0.051	0.032	22.286	-0.021	-0.021	0.000	0.000	0.000	0.000
102	B	178	ASN	0	-0.131	-0.065	23.344	0.023	0.023	0.000	0.000	0.000	0.000
103	B	179	TRP	0	0.033	0.017	25.464	0.015	0.015	0.000	0.000	0.000	0.000
104	B	180	VAL	0	0.040	0.026	22.222	-0.023	-0.023	0.000	0.000	0.000	0.000
105	B	181	TYR	0	-0.017	-0.005	25.031	0.027	0.027	0.000	0.000	0.000	0.000
106	B	182	SER	0	-0.025	-0.031	26.826	-0.030	-0.030	0.000	0.000	0.000	0.000
107	B	183	GLU	-1	-0.886	-0.960	27.923	-0.253	-0.253	0.000	0.000	0.000	0.000
108	B	184	ASP	-1	-0.763	-0.824	29.445	-0.230	-0.230	0.000	0.000	0.000	0.000
109	B	186	SER	0	-0.081	-0.067	28.463	-0.009	-0.009	0.000	0.000	0.000	0.000
110	B	187	SER	0	0.031	0.017	29.921	0.017	0.017	0.000	0.000	0.000	0.000
111	B	188	THR	0	-0.051	-0.025	28.283	-0.013	-0.013	0.000	0.000	0.000	0.000
112	B	189	PHE	0	0.023	0.003	25.526	0.012	0.012	0.000	0.000	0.000	0.000
113	B	190	LYS	1	0.898	0.969	20.604	0.503	0.503	0.000	0.000	0.000	0.000
114	B	191	GLY	0	0.012	0.011	19.614	0.008	0.008	0.000	0.000	0.000	0.000
115	B	192	ILE	0	-0.007	0.006	14.439	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	194	GLN	0	0.070	0.025	9.190	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	195	ARG	1	0.858	0.934	5.946	2.636	2.636	0.000	0.000	0.000	0.000
118	B	196	ASP	-1	-0.772	-0.846	1.717	-14.872	-19.571	12.738	-4.392	-3.647	-0.032

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