FMO DATABASE

FMODB ID: G64M1

Calculation Name: 5VI4-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5VI4

Chain ID: A

ChEMBL ID:

UniProt ID: Q61730

Base Structure: X-ray

Registration Date: 2023-06-26

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1427494.05059
FMO2-HF: Nuclear repulsion	1368197.944028
FMO2-HF: Total energy	-59296.106561
FMO2-MP2: Total energy	-59469.796467

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:114:SER)

Summations of interaction energy for fragment #1(A:114:SER)

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.
-4.297	-1.648	0.001	-1.022	-1.628	0.005

Interaction energy analysis for fragmet #1(A:114:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.004

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	116	LEU	0	0.000	0.019	3.803	-1.383	0.048	-0.013	-0.591	-0.827	0.003
4	A	117	THR	0	-0.051	-0.040	6.275	0.333	0.333	0.000	0.000	0.000	0.000
5	A	118	GLN	0	0.015	0.009	9.567	-0.138	-0.138	0.000	0.000	0.000	0.000
6	A	119	SER	0	0.016	-0.011	11.972	-0.083	-0.083	0.000	0.000	0.000	0.000
7	A	120	PRO	0	-0.041	0.007	15.572	0.002	0.002	0.000	0.000	0.000	0.000
8	A	121	ALA	0	-0.009	-0.002	18.676	-0.040	-0.040	0.000	0.000	0.000	0.000
9	A	122	SER	0	0.039	0.021	21.056	0.016	0.016	0.000	0.000	0.000	0.000
10	A	123	LEU	0	-0.002	-0.011	20.023	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	124	SER	0	0.018	0.021	24.171	0.004	0.004	0.000	0.000	0.000	0.000
12	A	125	THR	0	0.025	0.000	26.177	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	126	TYR	0	0.018	0.003	28.462	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	127	ASN	0	-0.047	-0.034	30.070	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	128	ASP	-1	-0.953	-0.959	32.006	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	129	GLN	0	-0.033	-0.001	31.581	0.005	0.005	0.000	0.000	0.000	0.000
17	A	130	SER	0	-0.004	-0.025	29.378	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	131	VAL	0	-0.024	-0.012	24.189	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	132	SER	0	-0.078	-0.035	26.907	0.008	0.008	0.000	0.000	0.000	0.000
20	A	133	PHE	0	-0.037	-0.025	21.036	0.003	0.003	0.000	0.000	0.000	0.000
21	A	134	VAL	0	-0.028	0.000	26.475	0.004	0.004	0.000	0.000	0.000	0.000
22	A	135	LEU	0	0.014	-0.009	28.456	0.011	0.011	0.000	0.000	0.000	0.000
23	A	136	GLU	-1	-0.913	-0.937	29.394	0.149	0.149	0.000	0.000	0.000	0.000
24	A	137	ASN	0	-0.082	-0.060	31.048	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	138	GLY	0	0.039	0.014	29.824	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	139	SER	0	-0.039	-0.014	26.023	0.018	0.018	0.000	0.000	0.000	0.000
27	A	140	TYR	0	-0.031	-0.028	24.015	0.011	0.011	0.000	0.000	0.000	0.000
28	A	141	VAL	0	-0.022	0.012	26.734	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	142	ILE	0	-0.004	-0.005	24.126	0.008	0.008	0.000	0.000	0.000	0.000
30	A	143	ASN	0	0.001	-0.008	27.043	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	144	VAL	0	0.008	0.011	28.128	0.004	0.004	0.000	0.000	0.000	0.000
32	A	145	ASP	-1	-0.865	-0.922	30.708	0.027	0.027	0.000	0.000	0.000	0.000
33	A	146	ASP	-1	-0.863	-0.925	33.272	0.018	0.018	0.000	0.000	0.000	0.000
34	A	147	SER	0	-0.036	-0.012	33.680	0.006	0.006	0.000	0.000	0.000	0.000
35	A	148	GLY	0	-0.027	-0.007	36.186	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	149	LYS	1	0.964	0.958	36.934	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	150	ASP	-1	-0.973	-0.988	35.983	0.049	0.049	0.000	0.000	0.000	0.000
38	A	151	GLN	0	-0.003	0.015	34.208	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	152	GLU	-1	-1.023	-1.019	29.795	0.134	0.134	0.000	0.000	0.000	0.000
40	A	153	GLN	0	0.030	0.018	28.905	0.001	0.001	0.000	0.000	0.000	0.000
41	A	154	ASP	-1	-0.843	-0.916	25.259	0.155	0.155	0.000	0.000	0.000	0.000
42	A	155	GLN	0	-0.017	-0.028	22.145	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	156	VAL	0	-0.001	-0.010	18.285	0.020	0.020	0.000	0.000	0.000	0.000
44	A	157	LEU	0	-0.040	-0.017	13.076	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	158	LEU	0	-0.002	0.001	14.037	0.030	0.030	0.000	0.000	0.000	0.000
46	A	159	ARG	1	0.826	0.889	8.570	-0.994	-0.994	0.000	0.000	0.000	0.000
47	A	160	TYR	0	0.002	-0.002	9.136	-0.090	-0.090	0.000	0.000	0.000	0.000
48	A	161	TYR	0	0.036	0.004	3.571	-1.072	-0.059	0.015	-0.419	-0.609	0.002
49	A	162	GLU	-1	-0.903	-0.947	4.400	-2.710	-2.505	-0.001	-0.012	-0.192	0.000
50	A	163	SER	0	-0.041	-0.018	5.530	-0.514	-0.514	0.000	0.000	0.000	0.000
51	A	164	PRO	0	0.028	-0.007	7.826	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	165	SER	0	-0.005	0.001	9.892	0.222	0.222	0.000	0.000	0.000	0.000
53	A	166	PRO	0	0.015	-0.002	12.957	-0.085	-0.085	0.000	0.000	0.000	0.000
54	A	167	ALA	0	-0.017	-0.005	15.070	0.052	0.052	0.000	0.000	0.000	0.000
55	A	168	SER	0	-0.031	-0.007	16.381	0.019	0.019	0.000	0.000	0.000	0.000
56	A	169	GLN	0	0.025	-0.009	19.756	0.004	0.004	0.000	0.000	0.000	0.000
57	A	170	SER	0	-0.002	0.009	17.724	0.012	0.012	0.000	0.000	0.000	0.000
58	A	171	GLY	0	-0.004	0.001	19.840	0.013	0.013	0.000	0.000	0.000	0.000
59	A	172	ASP	-1	-0.928	-0.965	22.118	-0.310	-0.310	0.000	0.000	0.000	0.000
60	A	173	GLY	0	-0.029	-0.013	22.612	0.013	0.013	0.000	0.000	0.000	0.000
61	A	174	VAL	0	-0.043	-0.017	17.515	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	175	ASP	-1	-0.902	-0.953	14.293	-0.915	-0.915	0.000	0.000	0.000	0.000
63	A	176	GLY	0	0.018	0.013	13.991	-0.103	-0.103	0.000	0.000	0.000	0.000
64	A	177	LYS	1	0.919	0.954	9.988	1.188	1.188	0.000	0.000	0.000	0.000
65	A	178	LYS	1	0.871	0.958	12.366	0.590	0.590	0.000	0.000	0.000	0.000
66	A	179	LEU	0	0.019	0.017	8.863	-0.231	-0.231	0.000	0.000	0.000	0.000
67	A	180	MET	0	-0.027	-0.007	6.394	-0.092	-0.092	0.000	0.000	0.000	0.000
68	A	181	VAL	0	0.029	0.010	9.000	0.023	0.023	0.000	0.000	0.000	0.000
69	A	182	ASN	0	0.012	0.035	8.631	-0.060	-0.060	0.000	0.000	0.000	0.000
70	A	183	MET	0	0.023	0.006	11.931	0.046	0.046	0.000	0.000	0.000	0.000
71	A	184	SER	0	0.038	0.034	14.596	0.070	0.070	0.000	0.000	0.000	0.000
72	A	185	PRO	0	0.050	0.032	16.577	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	186	ILE	0	-0.051	-0.020	19.022	0.048	0.048	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.913	0.963	20.465	-0.188	-0.188	0.000	0.000	0.000	0.000
75	A	188	ASP	-1	-0.821	-0.925	20.665	0.341	0.341	0.000	0.000	0.000	0.000
76	A	189	THR	0	-0.044	-0.021	14.390	0.005	0.005	0.000	0.000	0.000	0.000
77	A	190	ASP	-1	-0.900	-0.964	14.806	0.897	0.897	0.000	0.000	0.000	0.000
78	A	191	ILE	0	-0.037	0.009	16.194	-0.037	-0.037	0.000	0.000	0.000	0.000
79	A	192	TRP	0	0.000	-0.009	11.212	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	193	LEU	0	-0.001	-0.005	16.189	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	194	HIS	1	0.857	0.934	16.097	-0.139	-0.139	0.000	0.000	0.000	0.000
82	A	195	ALA	0	0.032	0.010	17.416	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	196	ASN	0	-0.034	-0.020	19.128	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	197	ASP	-1	-0.827	-0.917	20.767	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	198	LYS	1	0.821	0.897	21.898	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	199	ASP	-1	-0.899	-0.903	25.279	0.028	0.028	0.000	0.000	0.000	0.000
87	A	200	TYR	0	-0.012	0.001	24.377	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	201	SER	0	-0.008	-0.034	24.712	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	202	VAL	0	-0.022	-0.021	20.361	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	203	GLU	-1	-0.878	-0.938	21.672	0.109	0.109	0.000	0.000	0.000	0.000
91	A	204	LEU	0	0.000	-0.007	19.882	0.016	0.016	0.000	0.000	0.000	0.000
92	A	205	GLN	0	-0.010	-0.014	18.708	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	206	ARG	1	0.974	0.980	18.224	-0.279	-0.279	0.000	0.000	0.000	0.000
94	A	207	GLY	0	-0.038	-0.030	15.969	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	208	ASP	-1	-0.809	-0.881	14.599	0.778	0.778	0.000	0.000	0.000	0.000
96	A	209	VAL	0	-0.048	-0.009	8.940	0.073	0.073	0.000	0.000	0.000	0.000
97	A	210	SER	0	-0.115	-0.085	8.802	0.344	0.344	0.000	0.000	0.000	0.000
98	A	211	PRO	0	0.020	0.043	8.255	-0.207	-0.207	0.000	0.000	0.000	0.000
99	A	212	PRO	0	0.050	0.017	10.071	0.019	0.019	0.000	0.000	0.000	0.000
100	A	213	GLU	-1	-0.809	-0.921	8.713	-0.350	-0.350	0.000	0.000	0.000	0.000
101	A	214	GLN	0	-0.036	-0.014	11.640	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	215	ALA	0	0.009	0.014	12.624	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	216	PHE	0	-0.049	-0.016	6.784	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	217	PHE	0	0.013	0.002	11.283	-0.066	-0.066	0.000	0.000	0.000	0.000
105	A	218	VAL	0	-0.024	-0.007	11.492	-0.071	-0.071	0.000	0.000	0.000	0.000
106	A	219	LEU	0	-0.007	0.007	13.123	0.105	0.105	0.000	0.000	0.000	0.000
107	A	220	HIS	0	-0.040	-0.036	15.050	-0.069	-0.069	0.000	0.000	0.000	0.000
108	A	221	LYS	1	0.923	0.958	18.196	0.238	0.238	0.000	0.000	0.000	0.000
109	A	222	LYS	1	0.898	0.943	20.489	0.183	0.183	0.000	0.000	0.000	0.000
110	A	223	SER	0	0.023	0.010	23.951	0.008	0.008	0.000	0.000	0.000	0.000
111	A	224	SER	0	-0.065	-0.037	24.614	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	225	ASP	-1	-0.910	-0.962	25.227	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	226	PHE	0	0.023	0.018	24.547	0.011	0.011	0.000	0.000	0.000	0.000
114	A	227	VAL	0	-0.056	-0.042	19.226	-0.031	-0.031	0.000	0.000	0.000	0.000
115	A	228	SER	0	0.024	0.000	19.819	0.024	0.024	0.000	0.000	0.000	0.000
116	A	229	PHE	0	0.023	-0.002	15.971	-0.045	-0.045	0.000	0.000	0.000	0.000
117	A	230	GLU	-1	-0.807	-0.898	16.626	-0.361	-0.361	0.000	0.000	0.000	0.000
118	A	231	SER	0	-0.009	-0.024	15.379	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	232	LYS	1	0.855	0.912	8.648	0.796	0.796	0.000	0.000	0.000	0.000
120	A	233	ASN	0	-0.037	-0.026	13.701	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	234	LEU	0	-0.038	-0.003	15.528	0.006	0.006	0.000	0.000	0.000	0.000
122	A	235	PRO	0	0.023	0.004	16.452	0.008	0.008	0.000	0.000	0.000	0.000
123	A	236	GLY	0	-0.006	0.007	18.581	0.030	0.030	0.000	0.000	0.000	0.000
124	A	237	THR	0	-0.062	-0.017	20.437	0.034	0.034	0.000	0.000	0.000	0.000
125	A	238	TYR	0	0.028	0.001	19.799	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	239	ILE	0	-0.012	0.003	17.883	0.020	0.020	0.000	0.000	0.000	0.000
127	A	240	GLY	0	0.010	0.002	21.858	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	241	VAL	0	-0.015	0.004	25.499	0.014	0.014	0.000	0.000	0.000	0.000
129	A	242	LYS	1	0.923	0.955	28.358	0.020	0.020	0.000	0.000	0.000	0.000
130	A	243	ASP	-1	-0.934	-0.962	31.056	0.007	0.007	0.000	0.000	0.000	0.000
131	A	244	ASN	0	-0.036	-0.024	32.227	0.004	0.004	0.000	0.000	0.000	0.000
132	A	245	GLN	0	0.012	0.012	29.079	0.021	0.021	0.000	0.000	0.000	0.000
133	A	246	LEU	0	-0.014	0.002	22.596	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	247	ALA	0	-0.023	-0.017	25.632	0.008	0.008	0.000	0.000	0.000	0.000
135	A	248	LEU	0	-0.008	-0.004	20.082	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	249	VAL	0	-0.035	-0.024	24.089	0.005	0.005	0.000	0.000	0.000	0.000
137	A	250	GLU	-1	-0.894	-0.955	24.514	-0.135	-0.135	0.000	0.000	0.000	0.000
138	A	251	GLU	-1	-0.889	-0.929	24.729	-0.179	-0.179	0.000	0.000	0.000	0.000
139	A	252	LYS	1	0.925	0.952	26.693	0.116	0.116	0.000	0.000	0.000	0.000
140	A	253	ASP	-1	-0.913	-0.962	30.370	-0.125	-0.125	0.000	0.000	0.000	0.000
141	A	254	GLU	-1	-1.023	-1.010	32.368	-0.057	-0.057	0.000	0.000	0.000	0.000
142	A	255	SER	0	0.065	0.042	32.089	0.002	0.002	0.000	0.000	0.000	0.000
143	A	256	SER	0	0.011	0.009	28.823	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	257	ASN	0	-0.034	-0.020	28.071	-0.009	-0.009	0.000	0.000	0.000	0.000
145	A	258	ASN	0	0.001	-0.007	28.287	0.011	0.011	0.000	0.000	0.000	0.000
146	A	259	ILE	0	-0.015	-0.009	23.261	0.008	0.008	0.000	0.000	0.000	0.000
147	A	260	MET	0	-0.095	-0.012	23.521	-0.017	-0.017	0.000	0.000	0.000	0.000
148	A	261	PHE	0	0.033	0.012	22.291	0.020	0.020	0.000	0.000	0.000	0.000
149	A	262	LYS	1	0.943	0.996	23.390	0.000	0.000	0.000	0.000	0.000	0.000
150	A	263	LEU	0	-0.031	-0.005	18.246	0.019	0.019	0.000	0.000	0.000	0.000
151	A	264	SER	0	0.000	-0.010	22.579	-0.021	-0.021	0.000	0.000	0.000	0.000
152	A	265	LYS	1	0.991	1.006	21.999	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:114:SER)