FMO DATABASE

FMODB ID: 1NV1Z

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	OptAll
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	-273593.190907
FMO2-HF: Nuclear repulsion	251983.664009
FMO2-HF: Total energy	-21609.526898
FMO2-MP2: Total energy	-21673.210037

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.
0.677	3.849	0.034	-1.456	-1.75	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 : 0.033 / 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	I	13	THR	0	-0.004	-0.003	3.285	-1.609	1.132	0.026	-1.373	-1.394	0.001
4	I	14	THR	0	0.057	0.012	4.905	-0.042	0.013	-0.001	-0.008	-0.046	0.000
5	I	15	LYS	1	0.895	0.960	7.194	0.857	0.857	0.000	0.000	0.000	0.000
6	I	16	TYR	0	0.046	0.013	3.564	0.282	0.658	0.009	-0.075	-0.310	0.000
7	I	17	GLN	0	0.065	0.037	6.825	0.277	0.277	0.000	0.000	0.000	0.000
8	I	18	GLN	0	0.009	0.012	8.609	0.269	0.269	0.000	0.000	0.000	0.000
9	I	19	LEU	0	-0.007	0.008	9.703	0.140	0.140	0.000	0.000	0.000	0.000
10	I	20	ALA	0	0.035	0.023	8.664	0.168	0.168	0.000	0.000	0.000	0.000
11	I	21	ARG	1	0.866	0.931	10.753	0.500	0.500	0.000	0.000	0.000	0.000
12	I	22	THR	0	0.008	-0.015	13.839	0.113	0.113	0.000	0.000	0.000	0.000
13	I	23	ALA	0	0.021	0.008	13.407	0.070	0.070	0.000	0.000	0.000	0.000
14	I	24	VAL	0	-0.035	-0.016	13.973	0.059	0.059	0.000	0.000	0.000	0.000
15	I	25	ALA	0	-0.036	-0.007	16.570	0.048	0.048	0.000	0.000	0.000	0.000
16	I	26	ILE	0	0.014	-0.001	18.649	0.035	0.035	0.000	0.000	0.000	0.000
17	I	27	TYR	0	0.019	0.011	18.807	0.029	0.029	0.000	0.000	0.000	0.000
18	I	28	ASN	0	-0.018	-0.024	20.577	0.025	0.025	0.000	0.000	0.000	0.000
19	I	29	TYR	0	-0.035	-0.009	22.616	0.019	0.019	0.000	0.000	0.000	0.000
20	I	30	HIS	0	-0.081	-0.049	23.787	0.019	0.019	0.000	0.000	0.000	0.000
21	I	31	GLU	-1	-0.884	-0.935	23.407	-0.107	-0.107	0.000	0.000	0.000	0.000
22	I	32	GLN	0	-0.090	-0.045	26.068	0.015	0.015	0.000	0.000	0.000	0.000
23	I	33	ALA	0	-0.005	0.019	23.327	0.007	0.007	0.000	0.000	0.000	0.000
24	I	34	HIS	0	-0.008	-0.018	23.809	-0.016	-0.016	0.000	0.000	0.000	0.000
25	I	35	LEU	0	-0.003	0.014	18.199	0.002	0.002	0.000	0.000	0.000	0.000
26	I	36	THR	0	-0.007	-0.018	17.481	-0.023	-0.023	0.000	0.000	0.000	0.000
27	I	37	PHE	0	0.003	-0.002	8.398	0.036	0.036	0.000	0.000	0.000	0.000
28	I	38	VAL	0	0.003	0.012	12.201	0.030	0.030	0.000	0.000	0.000	0.000
29	I	39	GLU	-1	-0.910	-0.953	7.318	-0.017	-0.017	0.000	0.000	0.000	0.000
30	I	48	ASN	0	0.016	-0.003	15.765	0.018	0.018	0.000	0.000	0.000	0.000
31	I	49	TYR	0	-0.085	-0.059	14.004	-0.024	-0.024	0.000	0.000	0.000	0.000
32	I	50	TYR	0	0.018	0.020	8.473	-0.024	-0.024	0.000	0.000	0.000	0.000
33	I	51	TYR	0	0.033	0.008	8.747	0.004	0.004	0.000	0.000	0.000	0.000
34	I	52	ILE	0	-0.018	-0.013	5.822	-0.045	-0.045	0.000	0.000	0.000	0.000
35	I	53	THR	0	0.001	0.016	7.251	0.175	0.175	0.000	0.000	0.000	0.000
36	I	54	LEU	0	-0.040	-0.026	7.717	-0.214	-0.214	0.000	0.000	0.000	0.000
37	I	55	ALA	0	0.040	0.024	10.165	0.116	0.116	0.000	0.000	0.000	0.000
38	I	56	ALA	0	0.003	0.008	12.998	-0.043	-0.043	0.000	0.000	0.000	0.000
39	I	69	LYS	1	0.756	0.869	13.095	0.081	0.081	0.000	0.000	0.000	0.000
40	I	70	ILE	0	0.001	-0.011	10.571	-0.016	-0.016	0.000	0.000	0.000	0.000
41	I	71	GLY	0	0.029	0.010	13.573	0.011	0.011	0.000	0.000	0.000	0.000
42	I	72	VAL	0	-0.038	-0.036	14.018	-0.033	-0.033	0.000	0.000	0.000	0.000
43	I	73	VAL	0	-0.011	-0.007	17.133	0.032	0.032	0.000	0.000	0.000	0.000
44	I	74	GLU	-1	-0.895	-0.948	15.151	-0.254	-0.254	0.000	0.000	0.000	0.000
45	I	75	SER	0	-0.045	-0.019	19.803	-0.001	-0.001	0.000	0.000	0.000	0.000
46	I	76	ALA	0	-0.012	-0.008	23.019	0.010	0.010	0.000	0.000	0.000	0.000
47	I	77	GLY	0	-0.016	-0.004	21.388	0.000	0.000	0.000	0.000	0.000	0.000
48	I	78	TRP	0	-0.009	0.012	19.369	-0.022	-0.022	0.000	0.000	0.000	0.000
49	I	79	THR	0	-0.018	-0.036	15.733	-0.037	-0.037	0.000	0.000	0.000	0.000
50	I	80	GLY	0	0.000	0.017	17.592	0.017	0.017	0.000	0.000	0.000	0.000
51	I	81	VAL	0	-0.028	-0.023	15.567	-0.037	-0.037	0.000	0.000	0.000	0.000
52	I	82	GLU	-1	-0.825	-0.867	17.490	-0.108	-0.108	0.000	0.000	0.000	0.000
53	I	83	GLU	-1	-0.792	-0.892	17.211	-0.081	-0.081	0.000	0.000	0.000	0.000
54	I	84	PHE	0	-0.007	-0.004	14.415	-0.034	-0.034	0.000	0.000	0.000	0.000

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