FMO DATABASE

FMODB ID: N2QJQ

Calculation Name: 1VIT-L-Xray540

Preferred Name:

Target Type:

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

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VIT

Chain ID: L

ChEMBL ID:

UniProt ID: P28507

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-130225.223162
FMO2-HF: Nuclear repulsion	115712.881546
FMO2-HF: Total energy	-14512.341616
FMO2-MP2: Total energy	-14554.324663

3D Structure Molmil

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(L:1:THR)

Summations of interaction energy for fragment #1(L:1:THR)

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.
-1.751	0.612	-0.007	-0.85	-1.508	0.005

Interaction energy analysis for fragmet #1(L:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.038

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].
4	L	1	PHE	0	-0.063	0.084	4.126	-0.257	0.145	0.001	-0.139	-0.264	0.000
5	L	1	GLY	0	0.044	-0.073	2.782	1.240	3.076	-0.008	-0.678	-1.150	0.005
6	L	1	ALA	0	0.033	-0.036	4.355	-1.027	-0.902	0.000	-0.033	-0.094	0.000
7	L	1	ALA	0	-0.073	0.118	6.829	0.155	0.155	0.000	0.000	0.000	0.000
8	L	1	GLY	0	-0.022	-0.128	6.433	0.728	0.728	0.000	0.000	0.000	0.000
9	L	1	GLU	0	0.043	-0.011	8.642	0.338	0.338	0.000	0.000	0.000	0.000
10	L	1	GLU	-1	-0.938	-0.831	7.412	-2.833	-2.833	0.000	0.000	0.000	0.000
11	L	1	ALA	0	0.087	-0.097	10.137	0.228	0.228	0.000	0.000	0.000	0.000
12	L	1	ALA	0	-0.067	0.105	11.611	0.018	0.018	0.000	0.000	0.000	0.000
13	L	1	ASP	0	0.048	-0.085	9.312	0.180	0.180	0.000	0.000	0.000	0.000
14	L	1	ASP	-1	-0.901	-0.822	8.817	-1.953	-1.953	0.000	0.000	0.000	0.000
15	L	1	CYS	0	0.078	-0.123	10.827	0.095	0.095	0.000	0.000	0.000	0.000
16	L	1	CYS	0	-0.093	0.114	12.634	0.017	0.017	0.000	0.000	0.000	0.000
17	L	2	GLY	0	-0.001	-0.105	12.886	0.051	0.051	0.000	0.000	0.000	0.000
18	L	3	LEU	0	0.064	-0.002	13.975	0.127	0.127	0.000	0.000	0.000	0.000
19	L	3	LEU	0	-0.071	0.105	12.300	0.004	0.004	0.000	0.000	0.000	0.000
20	L	4	ARG	0	0.083	-0.103	13.705	-0.088	-0.088	0.000	0.000	0.000	0.000
21	L	4	ARG	1	0.715	0.959	17.575	0.321	0.321	0.000	0.000	0.000	0.000
22	L	5	PRO	0	0.005	-0.114	11.951	0.030	0.030	0.000	0.000	0.000	0.000
23	L	6	LEU	0	0.042	0.003	13.806	0.030	0.030	0.000	0.000	0.000	0.000
24	L	6	LEU	0	-0.043	0.100	16.304	0.006	0.006	0.000	0.000	0.000	0.000
25	L	7	PHE	0	0.075	-0.059	17.110	0.050	0.050	0.000	0.000	0.000	0.000
26	L	7	PHE	0	-0.119	0.057	19.220	0.001	0.001	0.000	0.000	0.000	0.000
27	L	8	GLU	0	0.157	-0.087	16.854	0.044	0.044	0.000	0.000	0.000	0.000
28	L	8	GLU	-1	-0.813	-0.783	16.188	-0.410	-0.410	0.000	0.000	0.000	0.000
29	L	9	LYS	0	0.032	-0.087	12.905	0.011	0.011	0.000	0.000	0.000	0.000
30	L	9	LYS	1	0.713	0.977	9.126	1.372	1.372	0.000	0.000	0.000	0.000
31	L	10	LYS	0	0.089	-0.087	14.202	0.022	0.022	0.000	0.000	0.000	0.000
32	L	10	LYS	1	0.689	0.990	15.911	0.173	0.173	0.000	0.000	0.000	0.000
33	L	11	GLN	0	0.094	-0.053	16.877	0.040	0.040	0.000	0.000	0.000	0.000
34	L	11	GLN	0	-0.112	0.074	19.059	-0.002	-0.002	0.000	0.000	0.000	0.000
35	L	12	VAL	0	0.084	-0.105	19.789	0.026	0.026	0.000	0.000	0.000	0.000
36	L	12	VAL	0	-0.126	0.078	20.612	0.006	0.006	0.000	0.000	0.000	0.000
37	L	13	GLN	0	0.149	-0.097	21.543	-0.030	-0.030	0.000	0.000	0.000	0.000
38	L	13	GLN	0	-0.061	0.095	24.621	0.022	0.022	0.000	0.000	0.000	0.000
39	L	14	ASP	0	0.002	-0.068	24.178	0.019	0.019	0.000	0.000	0.000	0.000
40	L	14	ASP	-1	-0.872	-0.807	24.074	-0.206	-0.206	0.000	0.000	0.000	0.000
41	L	14	GLN	0	0.077	-0.116	25.543	-0.002	-0.002	0.000	0.000	0.000	0.000
42	L	14	GLN	0	-0.081	0.090	28.964	0.008	0.008	0.000	0.000	0.000	0.000
43	L	14	THR	0	0.032	-0.093	28.868	0.008	0.008	0.000	0.000	0.000	0.000
44	L	14	THR	0	-0.014	0.086	29.748	0.002	0.002	0.000	0.000	0.000	0.000
45	L	14	GLU	0	0.153	-0.092	26.697	0.005	0.005	0.000	0.000	0.000	0.000
46	L	14	GLU	-1	-0.873	-0.765	23.931	-0.256	-0.256	0.000	0.000	0.000	0.000
47	L	14	LYS	0	-0.020	-0.116	27.878	-0.013	-0.013	0.000	0.000	0.000	0.000
48	L	14	LYS	1	0.812	1.013	28.170	0.163	0.163	0.000	0.000	0.000	0.000
49	L	14	GLU	0	0.164	-0.061	30.615	-0.002	-0.002	0.000	0.000	0.000	0.000
50	L	14	GLU	-1	-1.015	-0.863	32.261	-0.133	-0.133	0.000	0.000	0.000	0.000
51	L	14	LEU	0	0.025	-0.101	29.114	0.010	0.010	0.000	0.000	0.000	0.000
52	L	14	LEU	0	-0.080	0.088	26.842	-0.004	-0.004	0.000	0.000	0.000	0.000
53	L	14	PHE	0	0.111	-0.057	29.762	0.001	0.001	0.000	0.000	0.000	0.000
54	L	14	PHE	0	-0.127	0.055	24.360	-0.003	-0.003	0.000	0.000	0.000	0.000
55	L	14	GLU	0	0.146	-0.091	30.459	-0.003	-0.003	0.000	0.000	0.000	0.000
56	L	14	GLU	-1	-1.044	-0.852	34.299	-0.124	-0.124	0.000	0.000	0.000	0.000
57	L	14	SER	0	-0.015	-0.120	33.806	0.008	0.008	0.000	0.000	0.000	0.000
58	L	14	SER	0	-0.084	0.047	32.659	-0.001	-0.001	0.000	0.000	0.000	0.000
59	L	14	TYR	0	0.045	-0.109	32.256	0.007	0.007	0.000	0.000	0.000	0.000
60	L	14	TYR	0	-0.085	0.090	27.817	-0.011	-0.011	0.000	0.000	0.000	0.000
61	L	14	ILE	0	-0.008	-0.067	33.683	-0.003	-0.003	0.000	0.000	0.000	0.000
62	L	14	ILE	0	-0.101	0.082	37.412	0.002	0.002	0.000	0.000	0.000	0.000
63	L	14	GLU	0	0.208	-0.090	34.228	0.008	0.008	0.000	0.000	0.000	0.000
64	L	14	GLU	-1	-1.081	-0.874	33.327	-0.168	-0.168	0.000	0.000	0.000	0.000
65	L	14	GLY	0	0.058	-0.074	32.520	-0.016	-0.016	0.000	0.000	0.000	0.000
66	L	15	ARG	0	-0.083	-0.042	30.622	0.003	0.003	0.000	0.000	0.000	0.000
67	L	15	ARG	1	0.879	0.942	28.892	0.215	0.215	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:1:THR)