FMO DATABASE

FMODB ID: YY2N2

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-149958.934942
FMO2-HF: Nuclear repulsion	134645.244076
FMO2-HF: Total energy	-15313.690866
FMO2-MP2: Total energy	-15356.262571

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.
-4.647	0.231	3.776	-2.143	-6.513	0

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 : 0.018 / q_NPA : -0.002

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	C	8	MET	0	0.077	0.068	2.430	-4.254	-1.009	1.921	-1.917	-3.249	-0.006
4	C	9	GLN	0	0.005	0.000	3.430	0.316	0.192	0.022	0.440	-0.339	0.001
5	C	39	CYS	0	-0.106	-0.062	4.190	-0.083	0.192	-0.001	-0.022	-0.252	0.000
6	C	11	GLN	0	0.032	0.014	2.440	-1.556	-0.203	1.835	-0.636	-2.552	0.005
7	C	12	ARG	1	0.900	0.919	4.824	0.567	0.696	-0.001	-0.008	-0.121	0.000
8	C	13	ARG	1	0.937	0.976	7.011	0.277	0.277	0.000	0.000	0.000	0.000
9	C	14	PHE	0	-0.003	0.008	7.801	0.072	0.072	0.000	0.000	0.000	0.000
10	C	15	TYR	0	0.009	-0.001	8.160	0.043	0.043	0.000	0.000	0.000	0.000
11	C	16	GLU	-1	-0.943	-0.980	10.012	-0.148	-0.148	0.000	0.000	0.000	0.000
12	C	17	ALA	0	-0.006	-0.009	12.622	0.026	0.026	0.000	0.000	0.000	0.000
13	C	18	LEU	0	-0.060	-0.033	12.401	0.021	0.021	0.000	0.000	0.000	0.000
14	C	19	HIS	0	-0.060	-0.038	12.987	0.016	0.016	0.000	0.000	0.000	0.000
15	C	20	ASP	-1	-0.866	-0.924	16.238	-0.090	-0.090	0.000	0.000	0.000	0.000
16	C	21	PRO	0	-0.033	-0.019	18.279	0.009	0.009	0.000	0.000	0.000	0.000
17	C	22	ASN	0	-0.049	-0.016	21.668	0.012	0.012	0.000	0.000	0.000	0.000
18	C	23	LEU	0	-0.069	-0.018	18.218	0.007	0.007	0.000	0.000	0.000	0.000
19	C	24	ASN	0	0.075	0.031	22.416	-0.004	-0.004	0.000	0.000	0.000	0.000
20	C	25	GLU	-1	-0.942	-0.999	22.276	-0.033	-0.033	0.000	0.000	0.000	0.000
21	C	26	GLU	-1	-0.925	-0.962	21.966	-0.016	-0.016	0.000	0.000	0.000	0.000
22	C	27	GLN	0	0.045	0.032	22.437	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	28	ARG	1	0.948	0.995	17.308	0.062	0.062	0.000	0.000	0.000	0.000
24	C	29	ASN	0	-0.004	-0.005	17.534	-0.008	-0.008	0.000	0.000	0.000	0.000
25	C	30	ALA	0	-0.007	0.008	18.009	0.005	0.005	0.000	0.000	0.000	0.000
26	C	31	LYS	1	0.957	0.978	15.541	0.110	0.110	0.000	0.000	0.000	0.000
27	C	32	ILE	0	0.007	-0.014	12.542	-0.010	-0.010	0.000	0.000	0.000	0.000
28	C	33	LYS	1	0.913	0.968	13.330	-0.043	-0.043	0.000	0.000	0.000	0.000
29	C	34	SER	0	0.013	-0.001	14.697	0.017	0.017	0.000	0.000	0.000	0.000
30	C	35	ILE	0	-0.061	-0.015	9.487	0.000	0.000	0.000	0.000	0.000	0.000
31	C	36	ARG	1	0.937	0.957	10.036	-0.094	-0.094	0.000	0.000	0.000	0.000
32	C	37	ASP	-1	-0.892	-0.954	10.865	0.112	0.112	0.000	0.000	0.000	0.000
33	C	38	ASP	-1	-0.923	-0.930	12.109	0.021	0.021	0.000	0.000	0.000	0.000

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