FMO DATABASE

FMODB ID: 859KY

Calculation Name: 1QQP-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: 1QQP

Chain ID: 4

ChEMBL ID:

UniProt ID: P03305

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-139916.152005
FMO2-HF: Nuclear repulsion	121953.240836
FMO2-HF: Total energy	-17962.911168
FMO2-MP2: Total energy	-18014.112487

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.
0.123	1.696	-0.016	-0.629	-0.926	0.003

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 : -0.001 / q_NPA : -0.014

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	4	17	ASN	0	-0.041	-0.023	3.805	0.479	1.795	-0.015	-0.595	-0.705	0.003
4	4	18	THR	0	0.025	0.004	3.767	-0.321	-0.144	0.000	-0.031	-0.146	0.000
5	4	19	GLY	0	0.016	0.002	4.962	0.950	1.030	-0.001	-0.003	-0.075	0.000
6	4	20	SER	0	-0.035	0.001	7.306	0.001	0.001	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.040	0.009	7.915	-0.076	-0.076	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.073	-0.021	10.262	-0.071	-0.071	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.041	0.002	10.758	-0.195	-0.195	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.012	-0.010	10.148	0.197	0.197	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.012	0.001	11.944	0.044	0.044	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.006	0.009	14.536	0.062	0.062	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.019	-0.004	13.986	-0.100	-0.100	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.055	0.013	9.695	-0.030	-0.030	0.000	0.000	0.000	0.000
15	4	29	GLN	0	0.010	-0.010	12.347	-0.003	-0.003	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.052	-0.012	14.990	0.072	0.072	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.016	0.012	10.230	0.101	0.101	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.029	-0.017	8.436	-0.194	-0.194	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.038	0.029	11.512	0.096	0.096	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.039	-0.023	11.765	-0.166	-0.166	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.898	-0.934	9.579	-1.023	-1.023	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.047	-0.031	13.019	0.032	0.032	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.011	-0.008	13.442	-0.087	-0.087	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.007	0.009	17.175	0.025	0.025	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.010	-0.006	19.990	-0.008	-0.008	0.000	0.000	0.000	0.000
26	4	65	ASN	0	-0.005	-0.025	12.827	0.021	0.021	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.838	-0.914	11.622	0.496	0.496	0.000	0.000	0.000	0.000
28	4	67	TRP	0	-0.025	-0.022	13.593	0.010	0.010	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.071	0.013	15.822	-0.007	-0.007	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.024	0.047	13.843	-0.014	-0.014	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.947	0.965	15.962	-0.110	-0.110	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.008	-0.001	18.814	-0.011	-0.011	0.000	0.000	0.000	0.000
33	4	72	ALA	0	0.005	0.006	18.776	-0.014	-0.014	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.028	-0.020	18.606	-0.003	-0.003	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.114	-0.051	21.235	-0.023	-0.023	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.003	0.013	24.077	-0.019	-0.019	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.006	-0.004	26.074	-0.001	-0.001	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.008	-0.010	27.243	0.012	0.012	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.038	-0.005	29.816	0.001	0.001	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.025	0.002	33.313	0.003	0.003	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.005	-0.021	36.802	-0.003	-0.003	0.000	0.000	0.000	0.000
42	4	81	GLY	0	0.020	0.032	38.896	-0.005	-0.005	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.029	-0.006	41.854	0.002	0.002	0.000	0.000	0.000	0.000
44	4	83	LEU	0	0.010	0.003	39.625	0.002	0.002	0.000	0.000	0.000	0.000
45	4	84	LEU	0	-0.018	-0.012	43.348	-0.003	-0.003	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.001	0.009	42.738	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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