FMO DATABASE

FMODB ID: P765K

Calculation Name: 2GYP-A-Xray19

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: 2018-06-04

Reference:

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	49
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-120251.350425
FMO2-HF: Nuclear repulsion	106876.589477
FMO2-HF: Total energy	-13374.760948
FMO2-MP2: Total energy	-13414.394042

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.
9.634	-20.726	49.614	-10.359	-8.896	-0.025

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 : -0.038 / q_NPA : -0.007

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

Sort

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	-0.009	0.013	2.890	2.193	1.420	0.031	1.626	-0.884	0.003
4	A	4	LYS	1	1.026	0.986	5.935	-2.669	-2.669	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.040	0.027	7.955	-0.202	-0.202	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.044	0.015	6.689	-0.127	-0.127	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.039	0.045	4.266	-0.162	-0.053	-0.001	-0.009	-0.098	0.000
8	A	8	LEU	0	0.051	0.019	8.273	-0.084	-0.084	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.037	0.007	11.578	-0.077	-0.077	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.029	0.027	10.299	-0.063	-0.063	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.889	-0.899	10.261	0.219	0.219	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.007	-0.015	13.396	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.008	0.017	16.058	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.004	-0.001	16.181	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.042	0.020	17.527	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.022	0.029	19.373	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.007	-0.002	19.788	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.974	-0.959	21.389	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.095	-0.041	23.344	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	DAL	0	0.007	-0.006	25.449	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.060	-0.015	23.512	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.013	0.007	26.928	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.947	0.924	27.893	0.019	0.019	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.825	-0.895	28.841	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.047	0.036	27.659	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.052	0.074	22.433	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.030	-0.019	25.627	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.005	0.042	28.212	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.014	-0.005	23.400	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.028	-0.011	22.449	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.021	0.008	24.889	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.962	-0.925	24.942	0.044	0.044	0.000	0.000	0.000	0.000
33	A	33	TRP	-1	-0.999	-0.986	19.290	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	67	HOH	0	-0.038	-0.040	22.096	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	HOH	0	-0.062	-0.076	14.543	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	69	HOH	0	-0.048	-0.026	9.881	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	70	HOH	0	-0.037	-0.070	7.847	0.015	0.015	0.000	0.000	0.000	0.000
38	A	71	HOH	0	0.005	0.006	7.949	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	72	HOH	0	-0.050	-0.042	25.595	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	91	HOH	0	-0.079	-0.060	22.848	0.005	0.005	0.000	0.000	0.000	0.000
41	A	94	HOH	0	-0.088	-0.096	26.890	0.000	0.000	0.000	0.000	0.000	0.000
42	A	96	HOH	0	0.039	0.003	1.411	9.065	-12.212	33.498	-8.851	-3.371	-0.004
43	A	99	HOH	0	0.034	0.020	3.740	-0.386	-0.179	0.000	-0.115	-0.093	0.000
44	A	101	HOH	0	0.045	0.039	2.394	1.846	-2.435	6.278	-0.519	-1.478	-0.011
45	A	105	HOH	0	-0.016	-0.028	1.952	0.148	-4.197	9.808	-2.491	-2.972	-0.013
46	A	107	HOH	0	-0.061	-0.046	29.902	0.000	0.000	0.000	0.000	0.000	0.000
47	A	108	HOH	0	-0.003	-0.002	9.187	0.036	0.036	0.000	0.000	0.000	0.000
48	A	109	HOH	0	-0.042	-0.061	31.189	0.000	0.000	0.000	0.000	0.000	0.000
49	A	119	HOH	0	-0.045	-0.030	7.941	-0.055	-0.055	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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