FMO DATABASE

FMODB ID: 8561Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1428088.192755
FMO2-HF: Nuclear repulsion	1368790.857381
FMO2-HF: Total energy	-59297.335374
FMO2-MP2: Total energy	-59470.993562

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.
-4.829	-1.769	0.043	-1.227	-1.874	0.007

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 : 0.001 / q_NPA : -0.010

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	0.007	0.020	3.803	-1.257	0.141	-0.011	-0.560	-0.826	0.002
4	A	117	THR	0	-0.044	-0.036	6.290	0.353	0.353	0.000	0.000	0.000	0.000
5	A	118	GLN	0	0.024	0.016	9.148	-0.134	-0.134	0.000	0.000	0.000	0.000
6	A	119	SER	0	-0.031	-0.025	11.972	-0.110	-0.110	0.000	0.000	0.000	0.000
7	A	120	PRO	0	-0.022	0.012	15.572	0.004	0.004	0.000	0.000	0.000	0.000
8	A	121	ALA	0	-0.027	-0.012	18.676	-0.040	-0.040	0.000	0.000	0.000	0.000
9	A	122	SER	0	0.033	0.019	21.056	0.016	0.016	0.000	0.000	0.000	0.000
10	A	123	LEU	0	0.006	-0.010	20.016	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	124	SER	0	0.034	0.023	24.206	0.003	0.003	0.000	0.000	0.000	0.000
12	A	125	THR	0	0.019	-0.002	26.294	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	126	TYR	0	0.025	0.002	28.575	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	127	ASN	0	-0.057	-0.034	30.193	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	128	ASP	-1	-0.944	-0.953	32.087	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	129	GLN	0	-0.040	-0.015	31.701	0.004	0.004	0.000	0.000	0.000	0.000
17	A	130	SER	0	-0.014	-0.040	29.418	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	131	VAL	0	-0.019	-0.011	24.138	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	132	SER	0	-0.087	-0.042	26.851	0.007	0.007	0.000	0.000	0.000	0.000
20	A	133	PHE	0	-0.020	-0.019	20.952	0.002	0.002	0.000	0.000	0.000	0.000
21	A	134	VAL	0	-0.026	-0.001	26.421	0.003	0.003	0.000	0.000	0.000	0.000
22	A	135	LEU	0	0.015	-0.001	27.981	0.010	0.010	0.000	0.000	0.000	0.000
23	A	136	GLU	-1	-0.862	-0.918	29.349	0.151	0.151	0.000	0.000	0.000	0.000
24	A	137	ASN	0	-0.103	-0.059	31.000	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	138	GLY	0	0.049	0.013	30.134	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	139	SER	0	-0.069	-0.031	25.911	0.019	0.019	0.000	0.000	0.000	0.000
27	A	140	TYR	0	-0.075	-0.066	23.720	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	141	VAL	0	-0.032	0.003	26.691	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	142	ILE	0	0.001	0.005	24.238	0.008	0.008	0.000	0.000	0.000	0.000
30	A	143	ASN	0	-0.008	-0.012	26.996	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	144	VAL	0	0.015	0.010	28.122	0.004	0.004	0.000	0.000	0.000	0.000
32	A	145	ASP	-1	-0.863	-0.927	30.777	0.028	0.028	0.000	0.000	0.000	0.000
33	A	146	ASP	-1	-0.858	-0.901	33.298	0.021	0.021	0.000	0.000	0.000	0.000
34	A	147	SER	0	-0.049	-0.023	33.533	0.007	0.007	0.000	0.000	0.000	0.000
35	A	148	GLY	0	-0.017	-0.002	36.129	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	149	LYS	1	0.854	0.884	36.875	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	150	ASP	-1	-0.888	-0.927	35.967	0.048	0.048	0.000	0.000	0.000	0.000
38	A	151	GLN	0	0.029	0.034	34.517	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	152	GLU	-1	-0.996	-1.004	29.460	0.137	0.137	0.000	0.000	0.000	0.000
40	A	153	GLN	0	0.016	0.025	28.906	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	154	ASP	-1	-0.807	-0.895	25.075	0.167	0.167	0.000	0.000	0.000	0.000
42	A	155	GLN	0	-0.027	-0.027	22.134	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	156	VAL	0	0.005	-0.011	17.846	0.018	0.018	0.000	0.000	0.000	0.000
44	A	157	LEU	0	-0.027	-0.010	13.575	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	158	LEU	0	0.002	0.002	14.011	0.032	0.032	0.000	0.000	0.000	0.000
46	A	159	ARG	1	0.849	0.917	8.490	-0.987	-0.987	0.000	0.000	0.000	0.000
47	A	160	TYR	0	0.025	0.002	9.161	-0.114	-0.114	0.000	0.000	0.000	0.000
48	A	161	TYR	0	0.021	-0.008	3.244	-1.916	-0.445	0.055	-0.657	-0.869	0.005
49	A	162	GLU	-1	-0.889	-0.946	4.417	-2.534	-2.343	-0.001	-0.010	-0.179	0.000
50	A	163	SER	0	-0.038	-0.017	5.654	-0.445	-0.445	0.000	0.000	0.000	0.000
51	A	164	PRO	0	0.031	-0.005	8.220	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	165	SER	0	-0.003	0.000	9.967	0.198	0.198	0.000	0.000	0.000	0.000
53	A	166	PRO	0	0.037	0.008	13.072	-0.080	-0.080	0.000	0.000	0.000	0.000
54	A	167	ALA	0	-0.032	-0.014	15.059	0.053	0.053	0.000	0.000	0.000	0.000
55	A	168	SER	0	-0.037	-0.019	16.397	0.023	0.023	0.000	0.000	0.000	0.000
56	A	169	GLN	0	0.017	-0.001	19.775	0.008	0.008	0.000	0.000	0.000	0.000
57	A	170	SER	0	0.007	0.013	17.745	0.006	0.006	0.000	0.000	0.000	0.000
58	A	171	GLY	0	-0.004	0.000	19.865	0.012	0.012	0.000	0.000	0.000	0.000
59	A	172	ASP	-1	-0.934	-0.967	22.139	-0.303	-0.303	0.000	0.000	0.000	0.000
60	A	173	GLY	0	-0.019	-0.008	22.633	0.013	0.013	0.000	0.000	0.000	0.000
61	A	174	VAL	0	-0.045	-0.017	17.415	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	175	ASP	-1	-0.824	-0.907	14.177	-0.877	-0.877	0.000	0.000	0.000	0.000
63	A	176	GLY	0	0.011	0.005	14.011	-0.110	-0.110	0.000	0.000	0.000	0.000
64	A	177	LYS	1	0.833	0.913	9.746	1.129	1.129	0.000	0.000	0.000	0.000
65	A	178	LYS	1	0.850	0.939	12.384	0.537	0.537	0.000	0.000	0.000	0.000
66	A	179	LEU	0	0.017	0.017	9.105	-0.217	-0.217	0.000	0.000	0.000	0.000
67	A	180	MET	0	-0.028	-0.003	6.050	-0.084	-0.084	0.000	0.000	0.000	0.000
68	A	181	VAL	0	0.020	0.004	9.128	0.034	0.034	0.000	0.000	0.000	0.000
69	A	182	ASN	0	0.025	0.026	8.292	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	183	MET	0	0.010	0.005	11.946	0.041	0.041	0.000	0.000	0.000	0.000
71	A	184	SER	0	0.022	0.008	14.684	0.067	0.067	0.000	0.000	0.000	0.000
72	A	185	PRO	0	0.056	0.037	16.521	-0.037	-0.037	0.000	0.000	0.000	0.000
73	A	186	ILE	0	-0.052	-0.026	18.962	0.049	0.049	0.000	0.000	0.000	0.000
74	A	187	LYS	1	0.856	0.930	20.402	-0.166	-0.166	0.000	0.000	0.000	0.000
75	A	188	ASP	-1	-0.789	-0.892	20.580	0.334	0.334	0.000	0.000	0.000	0.000
76	A	189	THR	0	-0.023	-0.020	14.646	0.000	0.000	0.000	0.000	0.000	0.000
77	A	190	ASP	-1	-0.904	-0.962	14.722	0.859	0.859	0.000	0.000	0.000	0.000
78	A	191	ILE	0	-0.032	0.010	16.146	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	192	TRP	0	-0.014	-0.004	11.115	0.004	0.004	0.000	0.000	0.000	0.000
80	A	193	LEU	0	-0.009	-0.004	16.145	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	194	HIS	1	0.823	0.894	16.127	-0.133	-0.133	0.000	0.000	0.000	0.000
82	A	195	ALA	0	0.024	0.006	17.427	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	196	ASN	0	-0.069	-0.045	19.128	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	197	ASP	-1	-0.813	-0.902	20.299	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	198	LYS	1	0.810	0.883	21.887	-0.034	-0.034	0.000	0.000	0.000	0.000
86	A	199	ASP	-1	-0.894	-0.913	25.290	0.029	0.029	0.000	0.000	0.000	0.000
87	A	200	TYR	0	-0.036	-0.008	24.376	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	201	SER	0	-0.005	-0.020	24.691	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	202	VAL	0	-0.020	-0.024	20.527	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	203	GLU	-1	-0.839	-0.900	21.685	0.108	0.108	0.000	0.000	0.000	0.000
91	A	204	LEU	0	0.007	-0.001	19.774	0.016	0.016	0.000	0.000	0.000	0.000
92	A	205	GLN	0	-0.034	-0.018	18.669	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	206	ARG	1	0.982	0.982	18.186	-0.284	-0.284	0.000	0.000	0.000	0.000
94	A	207	GLY	0	-0.029	-0.028	15.779	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	208	ASP	-1	-0.815	-0.883	14.479	0.774	0.774	0.000	0.000	0.000	0.000
96	A	209	VAL	0	-0.055	-0.035	8.877	0.069	0.069	0.000	0.000	0.000	0.000
97	A	210	SER	0	-0.091	-0.054	8.780	0.356	0.356	0.000	0.000	0.000	0.000
98	A	211	PRO	0	0.011	0.043	8.102	-0.203	-0.203	0.000	0.000	0.000	0.000
99	A	212	PRO	0	0.043	0.010	10.060	0.011	0.011	0.000	0.000	0.000	0.000
100	A	213	GLU	-1	-0.801	-0.912	8.754	-0.404	-0.404	0.000	0.000	0.000	0.000
101	A	214	GLN	0	-0.014	0.006	11.615	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	215	ALA	0	0.014	0.016	12.729	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	216	PHE	0	-0.048	-0.011	6.673	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	217	PHE	0	0.005	-0.001	11.330	-0.070	-0.070	0.000	0.000	0.000	0.000
105	A	218	VAL	0	-0.022	-0.004	11.667	-0.056	-0.056	0.000	0.000	0.000	0.000
106	A	219	LEU	0	-0.003	0.007	13.231	0.097	0.097	0.000	0.000	0.000	0.000
107	A	220	HIS	0	-0.032	-0.031	15.181	-0.070	-0.070	0.000	0.000	0.000	0.000
108	A	221	LYS	1	0.827	0.898	18.332	0.203	0.203	0.000	0.000	0.000	0.000
109	A	222	LYS	1	0.844	0.909	20.511	0.181	0.181	0.000	0.000	0.000	0.000
110	A	223	SER	0	0.048	0.022	24.034	0.008	0.008	0.000	0.000	0.000	0.000
111	A	224	SER	0	-0.013	-0.029	24.642	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	225	ASP	-1	-0.830	-0.881	25.260	-0.060	-0.060	0.000	0.000	0.000	0.000
113	A	226	PHE	0	0.037	0.030	24.622	0.010	0.010	0.000	0.000	0.000	0.000
114	A	227	VAL	0	-0.058	-0.041	19.337	-0.029	-0.029	0.000	0.000	0.000	0.000
115	A	228	SER	0	0.016	-0.005	19.953	0.022	0.022	0.000	0.000	0.000	0.000
116	A	229	PHE	0	0.031	0.004	16.002	-0.040	-0.040	0.000	0.000	0.000	0.000
117	A	230	GLU	-1	-0.798	-0.883	16.546	-0.329	-0.329	0.000	0.000	0.000	0.000
118	A	231	SER	0	0.004	-0.013	15.458	-0.032	-0.032	0.000	0.000	0.000	0.000
119	A	232	LYS	1	0.853	0.903	8.155	0.809	0.809	0.000	0.000	0.000	0.000
120	A	233	ASN	0	-0.030	-0.022	13.744	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	234	LEU	0	-0.036	-0.006	15.534	0.003	0.003	0.000	0.000	0.000	0.000
122	A	235	PRO	0	0.017	0.006	16.361	0.010	0.010	0.000	0.000	0.000	0.000
123	A	236	GLY	0	-0.005	0.005	18.627	0.028	0.028	0.000	0.000	0.000	0.000
124	A	237	THR	0	-0.072	-0.027	20.491	0.033	0.033	0.000	0.000	0.000	0.000
125	A	238	TYR	0	-0.007	-0.030	19.867	-0.034	-0.034	0.000	0.000	0.000	0.000
126	A	239	ILE	0	-0.013	0.005	18.041	0.019	0.019	0.000	0.000	0.000	0.000
127	A	240	GLY	0	0.007	-0.002	21.936	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	241	VAL	0	-0.023	-0.002	25.583	0.013	0.013	0.000	0.000	0.000	0.000
129	A	242	LYS	1	0.907	0.955	28.440	0.014	0.014	0.000	0.000	0.000	0.000
130	A	243	ASP	-1	-0.904	-0.953	31.125	0.008	0.008	0.000	0.000	0.000	0.000
131	A	244	ASN	0	-0.030	-0.023	32.299	0.002	0.002	0.000	0.000	0.000	0.000
132	A	245	GLN	0	0.002	0.006	29.186	0.018	0.018	0.000	0.000	0.000	0.000
133	A	246	LEU	0	-0.011	-0.004	22.872	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	247	ALA	0	-0.025	-0.017	25.685	0.007	0.007	0.000	0.000	0.000	0.000
135	A	248	LEU	0	-0.006	0.003	20.376	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	249	VAL	0	-0.019	-0.020	24.142	0.004	0.004	0.000	0.000	0.000	0.000
137	A	250	GLU	-1	-0.834	-0.912	24.584	-0.133	-0.133	0.000	0.000	0.000	0.000
138	A	251	GLU	-1	-0.808	-0.876	24.464	-0.174	-0.174	0.000	0.000	0.000	0.000
139	A	252	LYS	1	0.841	0.902	26.786	0.115	0.115	0.000	0.000	0.000	0.000
140	A	253	ASP	-1	-0.884	-0.947	30.467	-0.118	-0.118	0.000	0.000	0.000	0.000
141	A	254	GLU	-1	-0.975	-0.969	32.477	-0.055	-0.055	0.000	0.000	0.000	0.000
142	A	255	SER	0	0.045	0.008	32.273	0.003	0.003	0.000	0.000	0.000	0.000
143	A	256	SER	0	-0.010	0.002	28.868	0.002	0.002	0.000	0.000	0.000	0.000
144	A	257	ASN	0	-0.030	-0.025	28.184	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	258	ASN	0	0.008	-0.004	28.614	0.012	0.012	0.000	0.000	0.000	0.000
146	A	259	ILE	0	-0.017	-0.009	23.245	0.008	0.008	0.000	0.000	0.000	0.000
147	A	260	MET	0	-0.110	-0.014	23.632	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	261	PHE	0	0.035	0.013	22.401	0.020	0.020	0.000	0.000	0.000	0.000
149	A	262	LYS	1	0.863	0.940	23.521	0.004	0.004	0.000	0.000	0.000	0.000
150	A	263	LEU	0	-0.011	0.007	18.355	0.018	0.018	0.000	0.000	0.000	0.000
151	A	264	SER	0	-0.023	-0.015	22.604	-0.019	-0.019	0.000	0.000	0.000	0.000
152	A	265	LYS	1	1.000	1.006	21.913	0.006	0.006	0.000	0.000	0.000	0.000

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