FMO DATABASE

FMODB ID: YV752

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

Total energy (hartree)

FMO2-HF: Electronic energy	-273346.628846
FMO2-HF: Nuclear repulsion	251737.765358
FMO2-HF: Total energy	-21608.863488
FMO2-MP2: Total energy	-21672.617068

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.
-2.513	0.883	0.126	-1.469	-2.053	-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 : 0.002 / q_NPA : -0.009

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	0.029	0.018	3.563	-1.846	0.650	-0.019	-1.174	-1.303	0.001
4	I	14	THR	0	0.038	0.040	5.208	-0.182	-0.109	-0.001	-0.005	-0.066	0.000
5	I	15	LYS	1	0.846	0.914	6.718	0.231	0.231	0.000	0.000	0.000	0.000
6	I	16	TYR	0	0.041	-0.008	3.109	-0.786	0.041	0.146	-0.290	-0.684	-0.002
7	I	17	GLN	0	0.045	0.028	6.118	-0.053	-0.053	0.000	0.000	0.000	0.000
8	I	18	GLN	0	0.030	0.015	8.444	0.045	0.045	0.000	0.000	0.000	0.000
9	I	19	LEU	0	-0.006	-0.002	8.734	0.030	0.030	0.000	0.000	0.000	0.000
10	I	20	ALA	0	0.036	0.030	9.003	0.053	0.053	0.000	0.000	0.000	0.000
11	I	21	ARG	1	0.922	0.965	11.004	0.341	0.341	0.000	0.000	0.000	0.000
12	I	22	THR	0	0.021	0.001	13.800	0.078	0.078	0.000	0.000	0.000	0.000
13	I	23	ALA	0	0.026	0.010	13.676	0.044	0.044	0.000	0.000	0.000	0.000
14	I	24	VAL	0	-0.045	-0.020	14.244	0.044	0.044	0.000	0.000	0.000	0.000
15	I	25	ALA	0	-0.033	-0.009	16.823	0.043	0.043	0.000	0.000	0.000	0.000
16	I	26	ILE	0	0.024	0.005	18.910	0.030	0.030	0.000	0.000	0.000	0.000
17	I	27	TYR	0	0.012	0.014	19.115	0.019	0.019	0.000	0.000	0.000	0.000
18	I	28	ASN	0	-0.007	-0.013	20.549	0.008	0.008	0.000	0.000	0.000	0.000
19	I	29	TYR	0	-0.057	-0.007	22.995	0.022	0.022	0.000	0.000	0.000	0.000
20	I	30	HIS	0	-0.019	-0.006	23.932	0.018	0.018	0.000	0.000	0.000	0.000
21	I	31	GLU	-1	-0.914	-0.972	23.680	-0.201	-0.201	0.000	0.000	0.000	0.000
22	I	32	GLN	0	-0.110	-0.046	26.278	0.019	0.019	0.000	0.000	0.000	0.000
23	I	33	ALA	0	-0.006	0.014	23.691	0.009	0.009	0.000	0.000	0.000	0.000
24	I	34	HIS	0	-0.004	-0.018	23.884	0.001	0.001	0.000	0.000	0.000	0.000
25	I	35	LEU	0	-0.012	0.003	18.489	0.001	0.001	0.000	0.000	0.000	0.000
26	I	36	THR	0	-0.016	-0.032	17.918	0.024	0.024	0.000	0.000	0.000	0.000
27	I	37	PHE	0	-0.028	-0.018	8.949	-0.002	-0.002	0.000	0.000	0.000	0.000
28	I	38	VAL	0	0.014	0.020	12.654	0.071	0.071	0.000	0.000	0.000	0.000
29	I	39	GLU	-1	-0.962	-0.979	7.467	-0.007	-0.007	0.000	0.000	0.000	0.000
30	I	48	ASN	0	0.044	0.005	15.148	0.004	0.004	0.000	0.000	0.000	0.000
31	I	49	TYR	0	-0.058	-0.024	14.048	-0.009	-0.009	0.000	0.000	0.000	0.000
32	I	50	TYR	0	-0.003	0.001	8.243	0.010	0.010	0.000	0.000	0.000	0.000
33	I	51	TYR	0	0.034	0.014	9.180	0.043	0.043	0.000	0.000	0.000	0.000
34	I	52	ILE	0	-0.013	-0.008	6.309	-0.294	-0.294	0.000	0.000	0.000	0.000
35	I	53	THR	0	-0.012	-0.004	7.285	0.253	0.253	0.000	0.000	0.000	0.000
36	I	54	LEU	0	-0.026	-0.006	7.935	-0.308	-0.308	0.000	0.000	0.000	0.000
37	I	55	ALA	0	0.049	0.030	10.231	0.111	0.111	0.000	0.000	0.000	0.000
38	I	56	ALA	0	-0.007	-0.006	13.185	0.025	0.025	0.000	0.000	0.000	0.000
39	I	69	LYS	1	0.760	0.874	12.899	0.295	0.295	0.000	0.000	0.000	0.000
40	I	70	ILE	0	-0.017	-0.014	11.066	0.054	0.054	0.000	0.000	0.000	0.000
41	I	71	GLY	0	0.014	0.009	13.648	-0.016	-0.016	0.000	0.000	0.000	0.000
42	I	72	VAL	0	-0.028	-0.025	13.792	-0.001	-0.001	0.000	0.000	0.000	0.000
43	I	73	VAL	0	0.000	0.013	16.698	0.013	0.013	0.000	0.000	0.000	0.000
44	I	74	GLU	-1	-0.922	-0.971	15.315	-0.079	-0.079	0.000	0.000	0.000	0.000
45	I	75	SER	0	-0.061	-0.028	19.731	0.008	0.008	0.000	0.000	0.000	0.000
46	I	76	ALA	0	0.014	0.003	23.160	0.007	0.007	0.000	0.000	0.000	0.000
47	I	77	GLY	0	0.000	0.013	20.903	0.003	0.003	0.000	0.000	0.000	0.000
48	I	78	TRP	0	-0.018	0.004	19.330	-0.009	-0.009	0.000	0.000	0.000	0.000
49	I	79	THR	0	-0.008	-0.033	15.599	-0.018	-0.018	0.000	0.000	0.000	0.000
50	I	80	GLY	0	-0.004	0.015	17.866	0.021	0.021	0.000	0.000	0.000	0.000
51	I	81	VAL	0	-0.020	-0.019	15.777	-0.040	-0.040	0.000	0.000	0.000	0.000
52	I	82	GLU	-1	-0.865	-0.914	17.600	-0.254	-0.254	0.000	0.000	0.000	0.000
53	I	83	GLU	-1	-0.787	-0.895	17.299	-0.333	-0.333	0.000	0.000	0.000	0.000
54	I	84	PHE	0	-0.003	-0.003	14.199	-0.053	-0.053	0.000	0.000	0.000	0.000

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