FMO DATABASE

FMODB ID: NNGLQ

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:

Apendix: None

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	33
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-105368.924708
FMO2-HF: Nuclear repulsion	93209.115628
FMO2-HF: Total energy	-12159.80908
FMO2-MP2: Total energy	-12196.245514

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.
-0.249	0.988	0.002	-0.465	-0.775	0.002

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 : -0.001 / 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	A	3	SER	0	0.015	0.009	3.746	-0.408	0.725	0.003	-0.459	-0.677	0.002
4	A	4	LYS	1	0.944	0.945	4.622	-1.234	-1.130	-0.001	-0.006	-0.098	0.000
5	A	5	LEU	0	0.022	0.032	7.971	0.127	0.127	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.033	0.025	7.465	0.097	0.097	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.028	-0.026	6.914	0.383	0.383	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.040	0.022	9.227	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.013	-0.005	12.429	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.018	-0.010	10.456	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.865	-0.924	10.947	0.942	0.942	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.003	-0.010	14.506	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.001	0.015	16.284	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.001	-0.004	16.229	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.015	0.004	18.160	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.007	-0.004	20.376	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.032	-0.013	19.462	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.930	-0.957	22.070	0.197	0.197	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.132	-0.072	23.948	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	20	DAL	0	0.005	0.002	26.362	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.058	-0.017	23.123	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.028	0.014	26.854	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.912	0.915	27.698	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.824	-0.898	28.774	0.049	0.049	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.018	0.020	27.769	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.002	0.000	22.678	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.020	-0.014	25.713	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.036	-0.019	28.368	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.023	0.015	24.023	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.026	-0.017	22.824	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.014	-0.007	25.168	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.978	-0.981	25.268	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.122	-0.047	19.558	-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)