FMO DATABASE

FMODB ID: Q1RZY

Calculation Name: 1VIT-L-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1VIT

Chain ID: L

ChEMBL ID:

UniProt ID: P28507

Base Structure: X-ray

Registration Date: 2023-06-20

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-130020.590916
FMO2-HF: Nuclear repulsion	115501.836002
FMO2-HF: Total energy	-14518.754914
FMO2-MP2: Total energy	-14560.924871

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(L:1:THR)

Summations of interaction energy for fragment #1(L:1:THR)

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.
-4.016	0.11	0.587	-2.106	-2.607	0.005

Interaction energy analysis for fragmet #1(L:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / 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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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	L	1	GLY	0	0.100	0.047	2.618	-3.835	-0.412	0.562	-1.894	-2.091	0.006
4	L	1	ALA	0	-0.088	-0.034	3.654	0.247	0.914	0.026	-0.211	-0.482	-0.001
5	L	1	GLY	0	0.001	-0.003	5.606	-0.745	-0.709	-0.001	-0.001	-0.034	0.000
6	L	1	GLU	-1	-0.932	-0.976	5.929	0.665	0.665	0.000	0.000	0.000	0.000
7	L	1	ALA	0	0.045	0.024	9.315	-0.119	-0.119	0.000	0.000	0.000	0.000
8	L	1	ASP	-1	-0.869	-0.906	7.972	-0.221	-0.221	0.000	0.000	0.000	0.000
9	L	1	CYS	0	0.011	0.011	10.005	-0.002	-0.002	0.000	0.000	0.000	0.000
10	L	2	GLY	0	-0.020	-0.011	12.306	-0.062	-0.062	0.000	0.000	0.000	0.000
11	L	3	LEU	0	-0.001	-0.001	11.867	-0.029	-0.029	0.000	0.000	0.000	0.000
12	L	4	ARG	1	0.826	0.886	12.611	0.014	0.014	0.000	0.000	0.000	0.000
13	L	5	PRO	0	0.010	-0.003	11.153	-0.038	-0.038	0.000	0.000	0.000	0.000
14	L	6	LEU	0	-0.048	-0.026	13.465	-0.029	-0.029	0.000	0.000	0.000	0.000
15	L	7	PHE	0	-0.012	-0.023	16.591	0.005	0.005	0.000	0.000	0.000	0.000
16	L	8	GLU	-1	-0.725	-0.836	15.882	-0.063	-0.063	0.000	0.000	0.000	0.000
17	L	9	LYS	1	0.766	0.864	8.266	0.152	0.152	0.000	0.000	0.000	0.000
18	L	10	LYS	1	0.878	0.940	14.553	0.028	0.028	0.000	0.000	0.000	0.000
19	L	11	GLN	0	-0.032	-0.018	17.248	0.025	0.025	0.000	0.000	0.000	0.000
20	L	12	VAL	0	-0.040	0.002	20.018	0.011	0.011	0.000	0.000	0.000	0.000
21	L	13	GLN	0	0.013	-0.002	21.356	0.006	0.006	0.000	0.000	0.000	0.000
22	L	14	ASP	-1	-0.853	-0.932	23.512	0.007	0.007	0.000	0.000	0.000	0.000
23	L	14	GLN	0	-0.044	-0.035	25.328	-0.006	-0.006	0.000	0.000	0.000	0.000
24	L	14	THR	0	0.036	0.013	28.122	-0.001	-0.001	0.000	0.000	0.000	0.000
25	L	14	GLU	-1	-0.809	-0.879	23.226	-0.040	-0.040	0.000	0.000	0.000	0.000
26	L	14	LYS	1	0.879	0.922	27.262	0.031	0.031	0.000	0.000	0.000	0.000
27	L	14	GLU	-1	-0.882	-0.924	30.130	0.001	0.001	0.000	0.000	0.000	0.000
28	L	14	LEU	0	-0.018	-0.007	26.197	0.001	0.001	0.000	0.000	0.000	0.000
29	L	14	PHE	0	-0.010	-0.003	23.965	-0.001	-0.001	0.000	0.000	0.000	0.000
30	L	14	GLU	-1	-0.957	-0.961	30.094	-0.027	-0.027	0.000	0.000	0.000	0.000
31	L	14	SER	0	-0.058	-0.047	32.167	0.002	0.002	0.000	0.000	0.000	0.000
32	L	14	TYR	0	-0.048	-0.035	27.060	0.000	0.000	0.000	0.000	0.000	0.000
33	L	14	ILE	0	-0.011	0.014	32.937	-0.002	-0.002	0.000	0.000	0.000	0.000
34	L	14	GLU	-1	-0.944	-0.969	32.845	-0.049	-0.049	0.000	0.000	0.000	0.000
35	L	14	GLY	0	0.057	0.051	32.144	-0.002	-0.002	0.000	0.000	0.000	0.000
36	L	15	ARG	1	0.829	0.894	28.220	0.060	0.060	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:1:THR)