FMO DATABASE

FMODB ID: 89VQY

Calculation Name: 2GYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name: norleucine

ligand 3-letter code: NLE

PDB ID: 2GYP

Chain ID: A

ChEMBL ID:

UniProt ID: P20823

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

Total energy (hartree)

FMO2-HF: Electronic energy	-105332.090784
FMO2-HF: Nuclear repulsion	93172.401678
FMO2-HF: Total energy	-12159.689106
FMO2-MP2: Total energy	-12196.165668

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(A:1:NLE)

Summations of interaction energy for fragment #1(A:1:NLE)

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.
-0.01	1.11	0.017	-0.328	-0.809	0.004

Interaction energy analysis for fragmet #1(A:1:NLE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.020

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	A	3	SER	0	0.018	0.016	3.600	-0.631	0.397	0.018	-0.321	-0.725	0.004
4	A	4	LYS	1	1.012	0.985	4.747	-0.888	-0.796	-0.001	-0.007	-0.084	0.000
5	A	5	LEU	0	-0.016	0.012	7.570	0.191	0.191	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.018	0.003	7.301	0.117	0.117	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.006	0.001	6.526	0.252	0.252	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.022	0.002	8.887	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.015	-0.004	11.958	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.020	-0.010	10.265	-0.056	-0.056	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.885	-0.938	10.375	1.169	1.169	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.001	-0.009	14.003	-0.059	-0.059	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.008	0.008	16.295	-0.041	-0.041	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.003	0.000	16.192	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.023	0.004	18.011	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.005	0.001	19.957	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.017	-0.006	19.693	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.959	-0.967	21.670	0.224	0.224	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.120	-0.058	23.593	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	20	DAL	0	0.001	-0.010	25.971	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.060	-0.014	23.456	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.017	0.011	27.008	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.923	0.919	27.942	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.808	-0.895	28.887	0.068	0.068	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.016	0.017	27.844	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.010	0.007	22.651	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.037	-0.023	25.763	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.048	-0.023	28.315	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.011	0.007	23.710	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.015	-0.012	22.809	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.015	0.000	25.152	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-1.028	-0.991	25.505	0.016	0.016	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.091	-0.033	19.907	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:NLE)