FMO DATABASE

FMODB ID: JLQ99

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

Total energy (hartree)

FMO2-HF: Electronic energy	-157247.199089
FMO2-HF: Nuclear repulsion	138131.083332
FMO2-HF: Total energy	-19116.115758
FMO2-MP2: Total energy	-19170.63392

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.
-2.902	1.3	0.22	-2.184	-2.236	0.006

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 : 0.030 / q_NPA : 0.013

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	-0.052	-0.014	3.804	-0.593	2.134	-0.025	-1.494	-1.208	0.004
4	4	18	THR	0	0.011	0.009	2.669	-1.612	-0.190	0.246	-0.677	-0.990	0.002
5	4	19	GLY	0	0.024	0.003	4.526	-0.627	-0.574	-0.001	-0.013	-0.038	0.000
6	4	20	SER	0	-0.036	0.003	6.990	0.111	0.111	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.020	0.000	7.997	-0.121	-0.121	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.030	-0.015	10.548	0.036	0.036	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.036	0.019	10.207	-0.080	-0.080	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.015	0.002	8.216	0.094	0.094	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.015	0.017	10.857	0.048	0.048	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.012	0.002	12.867	0.031	0.031	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.030	0.010	12.440	-0.001	-0.001	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.076	0.015	9.438	0.044	0.044	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.009	-0.008	11.773	0.054	0.054	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.053	-0.023	13.885	-0.018	-0.018	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.065	-0.024	8.639	0.025	0.025	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.029	-0.011	7.192	0.035	0.035	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.041	0.033	10.914	-0.072	-0.072	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.011	-0.012	12.244	0.097	0.097	0.000	0.000	0.000	0.000
21	4	35	SER	0	-0.005	0.000	11.253	-0.049	-0.049	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.007	0.001	14.065	-0.037	-0.037	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.018	-0.020	14.755	0.057	0.057	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.028	0.010	18.683	-0.018	-0.018	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.005	0.015	21.797	-0.006	-0.006	0.000	0.000	0.000	0.000
26	4	62	THR	0	0.015	-0.001	7.418	-0.053	-0.053	0.000	0.000	0.000	0.000
27	4	63	GLN	0	0.020	0.008	10.674	-0.008	-0.008	0.000	0.000	0.000	0.000
28	4	64	ASN	0	0.061	0.028	12.225	-0.020	-0.020	0.000	0.000	0.000	0.000
29	4	65	ASN	0	-0.013	-0.003	13.601	-0.033	-0.033	0.000	0.000	0.000	0.000
30	4	66	ASP	-1	-0.829	-0.919	12.462	-0.217	-0.217	0.000	0.000	0.000	0.000
31	4	67	TRP	0	-0.007	-0.011	14.624	-0.019	-0.019	0.000	0.000	0.000	0.000
32	4	68	PHE	0	0.081	0.017	16.490	-0.002	-0.002	0.000	0.000	0.000	0.000
33	4	69	SER	0	0.001	0.035	14.104	0.001	0.001	0.000	0.000	0.000	0.000
34	4	70	LYS	1	0.846	0.912	16.255	0.034	0.034	0.000	0.000	0.000	0.000
35	4	71	LEU	0	-0.010	-0.001	19.188	0.002	0.002	0.000	0.000	0.000	0.000
36	4	72	ALA	0	0.014	0.017	18.788	0.005	0.005	0.000	0.000	0.000	0.000
37	4	73	SER	0	-0.040	-0.032	18.466	-0.007	-0.007	0.000	0.000	0.000	0.000
38	4	74	SER	0	-0.109	-0.053	21.080	0.012	0.012	0.000	0.000	0.000	0.000
39	4	75	ALA	0	0.001	0.012	24.017	0.012	0.012	0.000	0.000	0.000	0.000
40	4	76	PHE	0	-0.002	-0.005	26.004	-0.002	-0.002	0.000	0.000	0.000	0.000
41	4	77	THR	0	-0.007	-0.020	27.296	-0.006	-0.006	0.000	0.000	0.000	0.000
42	4	78	GLY	0	-0.046	-0.006	29.745	0.000	0.000	0.000	0.000	0.000	0.000
43	4	79	LEU	0	0.037	0.013	33.202	-0.002	-0.002	0.000	0.000	0.000	0.000
44	4	80	PHE	0	-0.011	-0.003	36.586	0.002	0.002	0.000	0.000	0.000	0.000
45	4	81	GLY	0	0.005	0.005	38.800	0.001	0.001	0.000	0.000	0.000	0.000
46	4	82	ALA	0	-0.020	-0.007	41.601	-0.002	-0.002	0.000	0.000	0.000	0.000
47	4	83	LEU	0	0.007	0.001	40.421	0.000	0.000	0.000	0.000	0.000	0.000
48	4	84	LEU	0	0.005	0.000	43.539	0.002	0.002	0.000	0.000	0.000	0.000
49	4	85	ALA	0	-0.001	0.011	42.459	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)