FMO DATABASE

FMODB ID: 39JVL

Calculation Name: 1ZBA-4-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose

ligand 3-letter code: SGN

PDB ID: 1ZBA

Chain ID: 4

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-22

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	49
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157387.630973
FMO2-HF: Nuclear repulsion	138271.360703
FMO2-HF: Total energy	-19116.27027
FMO2-MP2: Total energy	-19170.767082

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15: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.
-3.123	1.62	0.524	-2.584	-2.682	0.002

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.019

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	4	17	ASN	0	-0.045	-0.020	3.676	0.886	3.451	0.020	-1.465	-1.119	0.005
4	4	18	THR	0	0.012	0.007	2.674	-3.409	-1.283	0.505	-1.108	-1.523	-0.003
5	4	19	GLY	0	0.027	0.006	4.608	-0.653	-0.601	-0.001	-0.011	-0.040	0.000
6	4	20	SER	0	-0.052	-0.014	6.853	0.165	0.165	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.027	0.008	8.113	-0.091	-0.091	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.028	-0.004	10.378	0.091	0.091	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.035	0.009	9.969	-0.081	-0.081	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.012	0.006	7.822	0.100	0.100	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.018	0.013	10.543	0.064	0.064	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.015	0.001	12.562	0.035	0.035	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.026	0.010	12.160	0.023	0.023	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.057	0.012	8.554	-0.020	-0.020	0.000	0.000	0.000	0.000
15	4	29	GLN	0	0.002	-0.012	11.657	0.062	0.062	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.042	-0.018	13.905	-0.036	-0.036	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.048	-0.014	8.504	-0.011	-0.011	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.032	-0.021	6.846	0.085	0.085	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.020	0.020	10.781	-0.112	-0.112	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.018	-0.005	12.106	0.155	0.155	0.000	0.000	0.000	0.000
21	4	35	SER	0	0.010	0.006	10.908	-0.070	-0.070	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.017	-0.005	13.721	-0.063	-0.063	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.011	-0.012	14.440	0.079	0.079	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.013	0.008	18.367	-0.025	-0.025	0.000	0.000	0.000	0.000
25	4	39	GLY	0	0.006	0.016	21.171	-0.001	-0.001	0.000	0.000	0.000	0.000
26	4	62	THR	0	0.010	-0.007	7.467	-0.026	-0.026	0.000	0.000	0.000	0.000
27	4	63	GLN	0	0.031	0.017	10.363	-0.058	-0.058	0.000	0.000	0.000	0.000
28	4	64	ASN	0	0.051	0.023	12.389	0.008	0.008	0.000	0.000	0.000	0.000
29	4	65	ASN	0	0.008	0.002	13.413	-0.048	-0.048	0.000	0.000	0.000	0.000
30	4	66	ASP	-1	-0.825	-0.904	12.661	-0.142	-0.142	0.000	0.000	0.000	0.000
31	4	67	TRP	0	0.021	0.008	14.689	-0.014	-0.014	0.000	0.000	0.000	0.000
32	4	68	PHE	0	0.052	0.017	16.578	-0.007	-0.007	0.000	0.000	0.000	0.000
33	4	69	SER	0	0.003	0.017	14.292	-0.006	-0.006	0.000	0.000	0.000	0.000
34	4	70	LYS	1	0.821	0.903	16.402	-0.006	-0.006	0.000	0.000	0.000	0.000
35	4	71	LEU	0	0.007	0.011	19.386	-0.001	-0.001	0.000	0.000	0.000	0.000
36	4	72	ALA	0	0.009	0.012	19.036	0.002	0.002	0.000	0.000	0.000	0.000
37	4	73	SER	0	-0.044	-0.041	18.792	-0.009	-0.009	0.000	0.000	0.000	0.000
38	4	74	SER	0	-0.101	-0.052	21.422	0.011	0.011	0.000	0.000	0.000	0.000
39	4	75	ALA	0	0.010	0.013	24.427	0.011	0.011	0.000	0.000	0.000	0.000
40	4	76	PHE	0	-0.017	-0.008	26.358	-0.005	-0.005	0.000	0.000	0.000	0.000
41	4	77	THR	0	-0.009	-0.011	27.519	-0.005	-0.005	0.000	0.000	0.000	0.000
42	4	78	GLY	0	-0.014	0.008	29.963	-0.003	-0.003	0.000	0.000	0.000	0.000
43	4	79	LEU	0	0.004	-0.007	33.503	0.000	0.000	0.000	0.000	0.000	0.000
44	4	80	PHE	0	-0.018	-0.011	37.050	0.002	0.002	0.000	0.000	0.000	0.000
45	4	81	GLY	0	0.020	0.003	39.274	0.002	0.002	0.000	0.000	0.000	0.000
46	4	82	ALA	0	-0.021	0.000	42.280	-0.002	-0.002	0.000	0.000	0.000	0.000
47	4	83	LEU	0	-0.003	-0.004	40.983	-0.001	-0.001	0.000	0.000	0.000	0.000
48	4	84	LEU	0	-0.009	-0.004	44.104	0.002	0.002	0.000	0.000	0.000	0.000
49	4	85	ALA	0	0.016	0.016	43.353	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)