FMO DATABASE

FMODB ID: VR4K1

Calculation Name: 1OQO-C-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1OQO

Chain ID: C

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	33
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-150322.932166
FMO2-HF: Nuclear repulsion	135008.856259
FMO2-HF: Total energy	-15314.075907
FMO2-MP2: Total energy	-15356.640321

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(C:6:PHE)

Summations of interaction energy for fragment #1(C:6:PHE)

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.
-4.333	1.49	3.107	-2.722	-6.208	0.004

Interaction energy analysis for fragmet #1(C:6:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.026

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	C	8	MET	0	0.051	0.016	2.745	-4.304	0.000	0.917	-2.153	-3.069	-0.002
4	C	9	GLN	0	0.023	0.002	3.612	0.418	0.542	0.014	0.158	-0.295	0.000
5	C	39	CYS	0	-0.115	-0.052	4.480	-0.080	0.145	-0.001	-0.012	-0.212	0.000
6	C	11	GLN	0	0.033	0.014	2.470	-1.420	-0.354	2.178	-0.710	-2.534	0.006
7	C	12	ARG	1	0.941	0.977	4.923	0.989	1.093	-0.001	-0.005	-0.098	0.000
8	C	13	ARG	1	0.858	0.906	7.338	0.472	0.472	0.000	0.000	0.000	0.000
9	C	14	PHE	0	0.002	0.008	7.690	0.088	0.088	0.000	0.000	0.000	0.000
10	C	15	TYR	0	0.019	0.007	8.389	0.047	0.047	0.000	0.000	0.000	0.000
11	C	16	GLU	-1	-0.879	-0.935	10.281	-0.184	-0.184	0.000	0.000	0.000	0.000
12	C	17	ALA	0	0.006	-0.005	12.922	0.027	0.027	0.000	0.000	0.000	0.000
13	C	18	LEU	0	-0.053	-0.030	12.605	0.023	0.023	0.000	0.000	0.000	0.000
14	C	19	HIS	0	-0.074	-0.053	12.850	0.024	0.024	0.000	0.000	0.000	0.000
15	C	20	ASP	-1	-0.823	-0.903	16.486	-0.093	-0.093	0.000	0.000	0.000	0.000
16	C	21	PRO	0	-0.024	-0.016	18.569	0.014	0.014	0.000	0.000	0.000	0.000
17	C	22	ASN	0	-0.073	-0.039	21.675	0.011	0.011	0.000	0.000	0.000	0.000
18	C	23	LEU	0	-0.063	-0.003	18.440	0.005	0.005	0.000	0.000	0.000	0.000
19	C	24	ASN	0	0.048	0.029	22.620	0.008	0.008	0.000	0.000	0.000	0.000
20	C	25	GLU	-1	-0.916	-0.981	22.396	0.061	0.061	0.000	0.000	0.000	0.000
21	C	26	GLU	-1	-0.891	-0.947	22.098	0.020	0.020	0.000	0.000	0.000	0.000
22	C	27	GLN	0	0.031	0.012	22.584	0.001	0.001	0.000	0.000	0.000	0.000
23	C	28	ARG	1	0.904	0.965	17.272	-0.018	-0.018	0.000	0.000	0.000	0.000
24	C	29	ASN	0	0.006	0.000	17.680	0.008	0.008	0.000	0.000	0.000	0.000
25	C	30	ALA	0	0.003	0.016	18.011	0.011	0.011	0.000	0.000	0.000	0.000
26	C	31	LYS	1	0.862	0.933	15.739	0.113	0.113	0.000	0.000	0.000	0.000
27	C	32	ILE	0	0.005	-0.015	12.590	-0.018	-0.018	0.000	0.000	0.000	0.000
28	C	33	LYS	1	0.806	0.897	13.332	-0.094	-0.094	0.000	0.000	0.000	0.000
29	C	34	SER	0	0.001	-0.004	14.700	0.010	0.010	0.000	0.000	0.000	0.000
30	C	35	ILE	0	-0.047	-0.018	9.708	-0.026	-0.026	0.000	0.000	0.000	0.000
31	C	36	ARG	1	0.930	0.955	10.039	-0.416	-0.416	0.000	0.000	0.000	0.000
32	C	37	ASP	-1	-0.823	-0.904	10.871	0.151	0.151	0.000	0.000	0.000	0.000
33	C	38	ASP	-1	-0.853	-0.866	12.132	-0.181	-0.181	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:6:PHE)