FMO DATABASE

FMODB ID: VQZ31

Calculation Name: 5KUY-I-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5KUY

Chain ID: I

ChEMBL ID:

UniProt ID: Q91MA7

Base Structure: X-ray

Registration Date: 2023-09-23

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-273171.292536
FMO2-HF: Nuclear repulsion	251562.132027
FMO2-HF: Total energy	-21609.160509
FMO2-MP2: Total energy	-21672.88501

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(I:11:CYS)

Summations of interaction energy for fragment #1(I:11:CYS)

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.
-1.35	2.375	0.077	-1.65	-2.15	-0.001

Interaction energy analysis for fragmet #1(I:11:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.010

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	I	13	THR	0	0.058	0.044	3.308	-2.140	0.840	0.000	-1.426	-1.553	0.000
4	I	14	THR	0	-0.008	-0.003	4.917	0.167	0.240	-0.001	-0.006	-0.065	0.000
5	I	15	LYS	1	0.891	0.940	6.843	0.464	0.464	0.000	0.000	0.000	0.000
6	I	16	TYR	0	0.033	-0.006	3.198	-0.435	0.237	0.078	-0.218	-0.532	-0.001
7	I	17	GLN	0	0.049	0.036	6.134	0.060	0.060	0.000	0.000	0.000	0.000
8	I	18	GLN	0	0.034	0.016	8.458	0.162	0.162	0.000	0.000	0.000	0.000
9	I	19	LEU	0	-0.005	0.006	8.994	0.090	0.090	0.000	0.000	0.000	0.000
10	I	20	ALA	0	0.032	0.027	8.946	0.110	0.110	0.000	0.000	0.000	0.000
11	I	21	ARG	1	0.916	0.963	10.992	0.450	0.450	0.000	0.000	0.000	0.000
12	I	22	THR	0	0.010	-0.012	13.820	0.100	0.100	0.000	0.000	0.000	0.000
13	I	23	ALA	0	0.024	0.007	13.639	0.060	0.060	0.000	0.000	0.000	0.000
14	I	24	VAL	0	-0.042	-0.017	14.216	0.051	0.051	0.000	0.000	0.000	0.000
15	I	25	ALA	0	-0.039	-0.012	16.811	0.046	0.046	0.000	0.000	0.000	0.000
16	I	26	ILE	0	0.026	0.005	18.896	0.034	0.034	0.000	0.000	0.000	0.000
17	I	27	TYR	0	0.021	0.015	19.061	0.025	0.025	0.000	0.000	0.000	0.000
18	I	28	ASN	0	-0.011	-0.009	20.850	0.015	0.015	0.000	0.000	0.000	0.000
19	I	29	TYR	0	-0.051	-0.007	22.984	0.020	0.020	0.000	0.000	0.000	0.000
20	I	30	HIS	0	-0.080	-0.050	23.922	0.021	0.021	0.000	0.000	0.000	0.000
21	I	31	GLU	-1	-0.865	-0.925	23.720	-0.141	-0.141	0.000	0.000	0.000	0.000
22	I	32	GLN	0	-0.109	-0.053	26.264	0.015	0.015	0.000	0.000	0.000	0.000
23	I	33	ALA	0	-0.001	0.019	23.669	0.007	0.007	0.000	0.000	0.000	0.000
24	I	34	HIS	0	-0.010	-0.021	23.870	-0.009	-0.009	0.000	0.000	0.000	0.000
25	I	35	LEU	0	-0.003	0.004	18.370	0.001	0.001	0.000	0.000	0.000	0.000
26	I	36	THR	0	-0.013	-0.030	17.940	0.006	0.006	0.000	0.000	0.000	0.000
27	I	37	PHE	0	-0.019	-0.015	8.879	0.013	0.013	0.000	0.000	0.000	0.000
28	I	38	VAL	0	0.011	0.016	12.601	0.052	0.052	0.000	0.000	0.000	0.000
29	I	39	GLU	-1	-0.949	-0.973	7.298	-0.209	-0.209	0.000	0.000	0.000	0.000
30	I	48	ASN	0	0.024	-0.001	15.170	0.014	0.014	0.000	0.000	0.000	0.000
31	I	49	TYR	0	-0.083	-0.059	14.030	-0.023	-0.023	0.000	0.000	0.000	0.000
32	I	50	TYR	0	-0.006	0.001	8.267	0.011	0.011	0.000	0.000	0.000	0.000
33	I	51	TYR	0	0.039	0.014	9.166	-0.013	-0.013	0.000	0.000	0.000	0.000
34	I	52	ILE	0	-0.018	-0.010	6.206	-0.124	-0.124	0.000	0.000	0.000	0.000
35	I	53	THR	0	-0.002	0.010	7.282	0.249	0.249	0.000	0.000	0.000	0.000
36	I	54	LEU	0	-0.029	-0.015	7.925	-0.264	-0.264	0.000	0.000	0.000	0.000
37	I	55	ALA	0	0.035	0.022	10.222	0.132	0.132	0.000	0.000	0.000	0.000
38	I	56	ALA	0	0.006	0.001	13.164	-0.016	-0.016	0.000	0.000	0.000	0.000
39	I	69	LYS	1	0.760	0.871	12.873	0.141	0.141	0.000	0.000	0.000	0.000
40	I	70	ILE	0	-0.017	-0.014	10.972	0.012	0.012	0.000	0.000	0.000	0.000
41	I	71	GLY	0	0.032	0.019	13.629	0.008	0.008	0.000	0.000	0.000	0.000
42	I	72	VAL	0	-0.029	-0.027	13.679	-0.022	-0.022	0.000	0.000	0.000	0.000
43	I	73	VAL	0	-0.007	0.007	16.713	0.026	0.026	0.000	0.000	0.000	0.000
44	I	74	GLU	-1	-0.919	-0.972	15.185	-0.124	-0.124	0.000	0.000	0.000	0.000
45	I	75	SER	0	-0.046	-0.014	19.739	0.001	0.001	0.000	0.000	0.000	0.000
46	I	76	ALA	0	-0.005	-0.010	23.155	0.004	0.004	0.000	0.000	0.000	0.000
47	I	77	GLY	0	0.004	0.016	20.913	0.000	0.000	0.000	0.000	0.000	0.000
48	I	78	TRP	0	-0.027	0.000	19.306	-0.014	-0.014	0.000	0.000	0.000	0.000
49	I	79	THR	0	-0.017	-0.039	15.509	-0.022	-0.022	0.000	0.000	0.000	0.000
50	I	80	GLY	0	0.010	0.025	17.881	0.013	0.013	0.000	0.000	0.000	0.000
51	I	81	VAL	0	-0.020	-0.018	15.821	-0.030	-0.030	0.000	0.000	0.000	0.000
52	I	82	GLU	-1	-0.824	-0.877	17.580	-0.137	-0.137	0.000	0.000	0.000	0.000
53	I	83	GLU	-1	-0.788	-0.895	17.304	-0.160	-0.160	0.000	0.000	0.000	0.000
54	I	84	PHE	0	-0.009	-0.003	14.485	-0.047	-0.047	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:11:CYS)