FMO DATABASE

FMODB ID: N97RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1429589.044388
FMO2-HF: Nuclear repulsion	1370291.142969
FMO2-HF: Total energy	-59297.901419
FMO2-MP2: Total energy	-59471.574838

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.
-5.642	-1.991	0.325	-1.458	-2.519	0.013

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 : 0.015 / q_NPA : -0.008

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	0.010	0.012	3.853	-0.961	0.237	-0.003	-0.436	-0.760	0.002
4	A	117	THR	0	-0.045	-0.035	6.051	0.323	0.323	0.000	0.000	0.000	0.000
5	A	118	GLN	0	0.024	0.014	9.340	0.126	0.126	0.000	0.000	0.000	0.000
6	A	119	SER	0	-0.044	-0.032	11.819	-0.110	-0.110	0.000	0.000	0.000	0.000
7	A	120	PRO	0	-0.004	0.021	15.513	0.008	0.008	0.000	0.000	0.000	0.000
8	A	121	ALA	0	-0.027	-0.016	18.718	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	122	SER	0	0.031	0.026	20.948	0.016	0.016	0.000	0.000	0.000	0.000
10	A	123	LEU	0	-0.020	-0.024	19.784	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	124	SER	0	0.025	0.023	24.002	0.003	0.003	0.000	0.000	0.000	0.000
12	A	125	THR	0	0.045	0.014	25.805	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	126	TYR	0	0.000	-0.013	28.027	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	127	ASN	0	-0.039	-0.025	29.760	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	128	ASP	-1	-0.939	-0.962	31.544	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	129	GLN	0	-0.057	-0.012	31.490	0.005	0.005	0.000	0.000	0.000	0.000
17	A	130	SER	0	0.008	-0.011	29.162	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	131	VAL	0	-0.001	-0.001	23.783	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	132	SER	0	-0.103	-0.062	26.820	0.006	0.006	0.000	0.000	0.000	0.000
20	A	133	PHE	0	-0.028	-0.019	20.544	0.000	0.000	0.000	0.000	0.000	0.000
21	A	134	VAL	0	0.005	0.011	26.263	0.008	0.008	0.000	0.000	0.000	0.000
22	A	135	LEU	0	0.007	-0.008	27.525	0.009	0.009	0.000	0.000	0.000	0.000
23	A	136	GLU	-1	-0.800	-0.898	29.297	0.155	0.155	0.000	0.000	0.000	0.000
24	A	137	ASN	0	-0.107	-0.054	31.113	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	138	GLY	0	-0.001	-0.013	29.916	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	139	SER	0	-0.069	-0.023	25.500	0.020	0.020	0.000	0.000	0.000	0.000
27	A	140	TYR	0	-0.073	-0.079	23.498	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	141	VAL	0	-0.025	0.005	26.765	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	142	ILE	0	-0.027	-0.007	23.802	0.006	0.006	0.000	0.000	0.000	0.000
30	A	143	ASN	0	-0.005	-0.002	26.798	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	144	VAL	0	-0.036	-0.033	27.437	0.005	0.005	0.000	0.000	0.000	0.000
32	A	145	ASP	-1	-0.834	-0.908	30.120	0.031	0.031	0.000	0.000	0.000	0.000
33	A	146	ASP	-1	-0.869	-0.921	32.876	0.018	0.018	0.000	0.000	0.000	0.000
34	A	147	SER	0	-0.061	-0.034	33.175	0.007	0.007	0.000	0.000	0.000	0.000
35	A	148	GLY	0	-0.006	0.001	35.935	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	149	LYS	1	0.837	0.875	36.594	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	150	ASP	-1	-0.870	-0.919	35.981	0.044	0.044	0.000	0.000	0.000	0.000
38	A	151	GLN	0	-0.010	0.016	33.324	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	152	GLU	-1	-0.958	-0.973	29.041	0.135	0.135	0.000	0.000	0.000	0.000
40	A	153	GLN	0	0.005	0.005	29.055	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	154	ASP	-1	-0.774	-0.867	24.708	0.172	0.172	0.000	0.000	0.000	0.000
42	A	155	GLN	0	-0.015	-0.020	22.203	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	156	VAL	0	0.011	0.000	17.597	0.024	0.024	0.000	0.000	0.000	0.000
44	A	157	LEU	0	-0.018	-0.011	13.643	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	158	LEU	0	0.006	0.007	14.069	0.046	0.046	0.000	0.000	0.000	0.000
46	A	159	ARG	1	0.844	0.909	8.701	-0.975	-0.975	0.000	0.000	0.000	0.000
47	A	160	TYR	0	0.023	0.001	8.698	-0.076	-0.076	0.000	0.000	0.000	0.000
48	A	161	TYR	0	0.027	0.009	2.822	-3.151	-0.955	0.329	-0.997	-1.528	0.011
49	A	162	GLU	-1	-0.881	-0.945	3.860	-2.614	-2.357	-0.001	-0.025	-0.231	0.000
50	A	163	SER	0	-0.034	-0.016	5.300	-0.355	-0.355	0.000	0.000	0.000	0.000
51	A	164	PRO	0	0.037	0.002	7.495	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	165	SER	0	-0.001	-0.007	9.660	0.205	0.205	0.000	0.000	0.000	0.000
53	A	166	PRO	0	0.048	0.012	12.715	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	167	ALA	0	-0.043	-0.016	14.755	0.061	0.061	0.000	0.000	0.000	0.000
55	A	168	SER	0	-0.035	-0.034	16.030	0.024	0.024	0.000	0.000	0.000	0.000
56	A	169	GLN	0	0.005	0.008	19.463	0.018	0.018	0.000	0.000	0.000	0.000
57	A	170	SER	0	-0.017	-0.010	17.417	0.011	0.011	0.000	0.000	0.000	0.000
58	A	171	GLY	0	0.020	0.011	19.531	0.017	0.017	0.000	0.000	0.000	0.000
59	A	172	ASP	-1	-0.927	-0.962	21.697	-0.313	-0.313	0.000	0.000	0.000	0.000
60	A	173	GLY	0	-0.022	-0.007	22.167	0.012	0.012	0.000	0.000	0.000	0.000
61	A	174	VAL	0	-0.039	-0.016	17.538	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	175	ASP	-1	-0.812	-0.890	14.297	-0.882	-0.882	0.000	0.000	0.000	0.000
63	A	176	GLY	0	0.002	0.005	13.923	-0.118	-0.118	0.000	0.000	0.000	0.000
64	A	177	LYS	1	0.786	0.896	9.333	1.173	1.173	0.000	0.000	0.000	0.000
65	A	178	LYS	1	0.905	0.965	11.857	0.572	0.572	0.000	0.000	0.000	0.000
66	A	179	LEU	0	0.012	0.018	8.901	-0.236	-0.236	0.000	0.000	0.000	0.000
67	A	180	MET	0	-0.025	0.000	5.497	-0.188	-0.188	0.000	0.000	0.000	0.000
68	A	181	VAL	0	0.000	-0.012	8.373	0.055	0.055	0.000	0.000	0.000	0.000
69	A	182	ASN	0	0.031	0.037	7.958	-0.076	-0.076	0.000	0.000	0.000	0.000
70	A	183	MET	0	0.002	-0.011	11.384	0.000	0.000	0.000	0.000	0.000	0.000
71	A	184	SER	0	0.043	0.031	14.549	0.049	0.049	0.000	0.000	0.000	0.000
72	A	185	PRO	0	0.035	0.022	16.408	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	186	ILE	0	-0.056	-0.034	18.685	0.056	0.056	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.843	0.917	20.233	-0.171	-0.171	0.000	0.000	0.000	0.000
75	A	188	ASP	-1	-0.792	-0.887	20.462	0.337	0.337	0.000	0.000	0.000	0.000
76	A	189	THR	0	0.006	-0.007	15.080	0.007	0.007	0.000	0.000	0.000	0.000
77	A	190	ASP	-1	-0.804	-0.890	14.771	0.662	0.662	0.000	0.000	0.000	0.000
78	A	191	ILE	0	-0.007	0.017	16.385	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	192	TRP	0	-0.036	-0.024	10.817	0.044	0.044	0.000	0.000	0.000	0.000
80	A	193	LEU	0	-0.003	0.004	16.230	-0.049	-0.049	0.000	0.000	0.000	0.000
81	A	194	HIS	1	0.825	0.896	16.027	-0.138	-0.138	0.000	0.000	0.000	0.000
82	A	195	ALA	0	0.037	0.019	17.010	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	196	ASN	0	-0.044	-0.028	18.655	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	197	ASP	-1	-0.814	-0.910	19.464	0.001	0.001	0.000	0.000	0.000	0.000
85	A	198	LYS	1	0.769	0.865	21.248	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	199	ASP	-1	-0.854	-0.887	25.096	0.033	0.033	0.000	0.000	0.000	0.000
87	A	200	TYR	0	-0.042	-0.012	24.061	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	201	SER	0	0.018	-0.011	24.907	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	202	VAL	0	-0.039	-0.031	19.851	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	203	GLU	-1	-0.788	-0.861	21.374	0.131	0.131	0.000	0.000	0.000	0.000
91	A	204	LEU	0	-0.002	-0.007	19.874	0.015	0.015	0.000	0.000	0.000	0.000
92	A	205	GLN	0	-0.064	-0.043	18.610	0.010	0.010	0.000	0.000	0.000	0.000
93	A	206	ARG	1	0.853	0.912	17.768	-0.356	-0.356	0.000	0.000	0.000	0.000
94	A	207	GLY	0	-0.051	-0.026	16.216	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	208	ASP	-1	-0.804	-0.881	14.006	0.824	0.824	0.000	0.000	0.000	0.000
96	A	209	VAL	0	-0.079	-0.037	8.864	0.050	0.050	0.000	0.000	0.000	0.000
97	A	210	SER	0	-0.065	-0.052	8.580	0.431	0.431	0.000	0.000	0.000	0.000
98	A	211	PRO	0	0.007	0.030	8.062	-0.224	-0.224	0.000	0.000	0.000	0.000
99	A	212	PRO	0	0.043	0.015	9.742	0.029	0.029	0.000	0.000	0.000	0.000
100	A	213	GLU	-1	-0.775	-0.898	8.696	-0.549	-0.549	0.000	0.000	0.000	0.000
101	A	214	GLN	0	-0.019	0.008	11.292	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	215	ALA	0	-0.025	-0.003	12.653	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	216	PHE	0	-0.048	-0.014	6.346	0.053	0.053	0.000	0.000	0.000	0.000
104	A	217	PHE	0	-0.010	-0.011	10.978	-0.081	-0.081	0.000	0.000	0.000	0.000
105	A	218	VAL	0	-0.009	0.002	11.115	-0.073	-0.073	0.000	0.000	0.000	0.000
106	A	219	LEU	0	-0.014	-0.004	12.536	0.101	0.101	0.000	0.000	0.000	0.000
107	A	220	HIS	0	-0.045	-0.047	14.506	-0.068	-0.068	0.000	0.000	0.000	0.000
108	A	221	LYS	1	0.803	0.888	17.834	0.208	0.208	0.000	0.000	0.000	0.000
109	A	222	LYS	1	0.841	0.903	20.100	0.180	0.180	0.000	0.000	0.000	0.000
110	A	223	SER	0	0.038	0.029	23.727	0.010	0.010	0.000	0.000	0.000	0.000
111	A	224	SER	0	0.020	-0.019	24.317	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	225	ASP	-1	-0.857	-0.885	24.874	-0.067	-0.067	0.000	0.000	0.000	0.000
113	A	226	PHE	0	0.037	0.020	24.229	0.006	0.006	0.000	0.000	0.000	0.000
114	A	227	VAL	0	-0.029	-0.025	18.710	-0.032	-0.032	0.000	0.000	0.000	0.000
115	A	228	SER	0	0.024	-0.004	19.568	0.024	0.024	0.000	0.000	0.000	0.000
116	A	229	PHE	0	0.020	-0.007	15.585	-0.041	-0.041	0.000	0.000	0.000	0.000
117	A	230	GLU	-1	-0.789	-0.865	15.944	-0.349	-0.349	0.000	0.000	0.000	0.000
118	A	231	SER	0	0.015	-0.001	14.822	-0.025	-0.025	0.000	0.000	0.000	0.000
119	A	232	LYS	1	0.834	0.899	7.415	0.844	0.844	0.000	0.000	0.000	0.000
120	A	233	ASN	0	-0.045	-0.034	13.084	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	234	LEU	0	-0.037	-0.013	15.340	0.015	0.015	0.000	0.000	0.000	0.000
122	A	235	PRO	0	0.047	0.026	15.590	0.012	0.012	0.000	0.000	0.000	0.000
123	A	236	GLY	0	-0.015	0.002	18.015	0.029	0.029	0.000	0.000	0.000	0.000
124	A	237	THR	0	-0.075	-0.040	20.053	0.036	0.036	0.000	0.000	0.000	0.000
125	A	238	TYR	0	-0.005	-0.036	19.272	-0.040	-0.040	0.000	0.000	0.000	0.000
126	A	239	ILE	0	-0.012	-0.004	17.500	0.020	0.020	0.000	0.000	0.000	0.000
127	A	240	GLY	0	0.005	-0.005	21.195	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	241	VAL	0	-0.029	-0.009	24.837	0.015	0.015	0.000	0.000	0.000	0.000
129	A	242	LYS	1	0.863	0.933	27.732	0.014	0.014	0.000	0.000	0.000	0.000
130	A	243	ASP	-1	-0.889	-0.945	30.386	0.010	0.010	0.000	0.000	0.000	0.000
131	A	244	ASN	0	-0.014	-0.007	32.217	0.001	0.001	0.000	0.000	0.000	0.000
132	A	245	GLN	0	-0.039	-0.011	28.646	0.018	0.018	0.000	0.000	0.000	0.000
133	A	246	LEU	0	-0.006	-0.005	22.589	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	247	ALA	0	-0.022	-0.025	24.698	0.010	0.010	0.000	0.000	0.000	0.000
135	A	248	LEU	0	-0.005	0.004	19.742	-0.013	-0.013	0.000	0.000	0.000	0.000
136	A	249	VAL	0	-0.009	-0.011	23.582	0.009	0.009	0.000	0.000	0.000	0.000
137	A	250	GLU	-1	-0.836	-0.901	23.892	-0.137	-0.137	0.000	0.000	0.000	0.000
138	A	251	GLU	-1	-0.781	-0.851	24.262	-0.170	-0.170	0.000	0.000	0.000	0.000
139	A	252	LYS	1	0.822	0.874	26.248	0.122	0.122	0.000	0.000	0.000	0.000
140	A	253	ASP	-1	-0.884	-0.936	30.035	-0.123	-0.123	0.000	0.000	0.000	0.000
141	A	254	GLU	-1	-0.965	-0.958	31.712	-0.060	-0.060	0.000	0.000	0.000	0.000
142	A	255	SER	0	-0.001	-0.020	31.903	0.005	0.005	0.000	0.000	0.000	0.000
143	A	256	SER	0	-0.015	-0.024	27.694	0.005	0.005	0.000	0.000	0.000	0.000
144	A	257	ASN	0	-0.024	-0.021	27.457	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	258	ASN	0	0.030	0.017	28.384	0.011	0.011	0.000	0.000	0.000	0.000
146	A	259	ILE	0	0.009	0.018	22.906	0.010	0.010	0.000	0.000	0.000	0.000
147	A	260	MET	0	-0.106	-0.004	23.136	-0.018	-0.018	0.000	0.000	0.000	0.000
148	A	261	PHE	0	0.022	0.012	22.099	0.020	0.020	0.000	0.000	0.000	0.000
149	A	262	LYS	1	0.873	0.928	23.396	0.006	0.006	0.000	0.000	0.000	0.000
150	A	263	LEU	0	0.020	0.023	18.186	0.019	0.019	0.000	0.000	0.000	0.000
151	A	264	SER	0	0.011	0.008	22.385	-0.020	-0.020	0.000	0.000	0.000	0.000
152	A	265	LYS	1	0.936	0.974	21.430	0.013	0.013	0.000	0.000	0.000	0.000

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