FMO DATABASE

FMODB ID: N9NGQ

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:

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157116.328537
FMO2-HF: Nuclear repulsion	138000.571897
FMO2-HF: Total energy	-19115.75664
FMO2-MP2: Total energy	-19170.313677

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.
-3.459	0.922	0.413	-2.349	-2.446	0.008

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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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	-0.047	-0.012	3.804	-0.783	2.008	-0.024	-1.524	-1.244	0.004
4	4	18	THR	0	0.014	0.014	2.499	-2.092	-0.564	0.438	-0.809	-1.157	0.004
5	4	19	GLY	0	0.019	0.000	4.475	-0.578	-0.516	-0.001	-0.016	-0.045	0.000
6	4	20	SER	0	-0.035	0.001	6.971	0.123	0.123	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.032	0.008	8.030	-0.101	-0.101	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.033	-0.017	10.577	0.041	0.041	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.013	0.010	10.312	-0.067	-0.067	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.020	0.000	8.837	0.076	0.076	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.014	0.014	10.972	0.047	0.047	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.008	0.008	12.991	0.028	0.028	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.032	0.010	12.578	0.000	0.000	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.069	0.012	9.387	0.093	0.093	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.006	-0.002	11.924	0.050	0.050	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.056	-0.022	14.008	-0.018	-0.018	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.069	-0.029	8.565	0.021	0.021	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.011	-0.001	7.422	-0.006	-0.006	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.005	0.017	11.022	-0.036	-0.036	0.000	0.000	0.000	0.000
20	4	34	MET	0	0.024	0.001	12.296	0.086	0.086	0.000	0.000	0.000	0.000
21	4	35	SER	0	-0.010	-0.001	11.427	-0.045	-0.045	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.005	0.000	14.065	-0.019	-0.019	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.012	-0.015	14.586	0.066	0.066	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.023	0.006	18.700	-0.015	-0.015	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.008	0.012	21.822	-0.007	-0.007	0.000	0.000	0.000	0.000
26	4	62	THR	0	-0.007	-0.005	7.465	-0.079	-0.079	0.000	0.000	0.000	0.000
27	4	63	GLN	0	0.040	0.012	10.591	0.004	0.004	0.000	0.000	0.000	0.000
28	4	64	ASN	0	0.034	0.014	12.164	-0.037	-0.037	0.000	0.000	0.000	0.000
29	4	65	ASN	0	-0.066	-0.045	13.544	-0.016	-0.016	0.000	0.000	0.000	0.000
30	4	66	ASP	-1	-0.820	-0.906	12.168	-0.252	-0.252	0.000	0.000	0.000	0.000
31	4	67	TRP	0	-0.025	-0.019	14.603	-0.015	-0.015	0.000	0.000	0.000	0.000
32	4	68	PHE	0	0.084	0.016	16.626	0.001	0.001	0.000	0.000	0.000	0.000
33	4	69	SER	0	0.028	0.045	13.871	0.001	0.001	0.000	0.000	0.000	0.000
34	4	70	LYS	1	0.905	0.947	16.273	0.043	0.043	0.000	0.000	0.000	0.000
35	4	71	LEU	0	-0.020	-0.010	19.194	0.004	0.004	0.000	0.000	0.000	0.000
36	4	72	ALA	0	0.019	0.013	18.843	0.007	0.007	0.000	0.000	0.000	0.000
37	4	73	SER	0	-0.029	-0.019	18.428	-0.003	-0.003	0.000	0.000	0.000	0.000
38	4	74	SER	0	-0.115	-0.045	21.112	0.013	0.013	0.000	0.000	0.000	0.000
39	4	75	ALA	0	0.004	0.012	24.050	0.012	0.012	0.000	0.000	0.000	0.000
40	4	76	PHE	0	-0.009	-0.009	26.040	-0.002	-0.002	0.000	0.000	0.000	0.000
41	4	77	THR	0	0.020	-0.007	27.220	-0.006	-0.006	0.000	0.000	0.000	0.000
42	4	78	GLY	0	-0.064	-0.015	29.796	0.000	0.000	0.000	0.000	0.000	0.000
43	4	79	LEU	0	0.045	0.016	33.252	-0.001	-0.001	0.000	0.000	0.000	0.000
44	4	80	PHE	0	-0.015	-0.005	36.639	0.002	0.002	0.000	0.000	0.000	0.000
45	4	81	GLY	0	0.000	0.005	38.844	0.001	0.001	0.000	0.000	0.000	0.000
46	4	82	ALA	0	-0.016	-0.005	41.649	-0.002	-0.002	0.000	0.000	0.000	0.000
47	4	83	LEU	0	0.020	0.005	40.521	0.000	0.000	0.000	0.000	0.000	0.000
48	4	84	LEU	0	0.006	-0.002	43.599	0.002	0.002	0.000	0.000	0.000	0.000
49	4	85	ALA	0	-0.018	0.006	42.519	0.000	0.000	0.000	0.000	0.000	0.000

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