FMO DATABASE

FMODB ID: YV562

Calculation Name: 4LX3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LX3

Chain ID: B

ChEMBL ID:

UniProt ID: B2J066

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

Total energy (hartree)

FMO2-HF: Electronic energy	-120284.803929
FMO2-HF: Nuclear repulsion	105929.397562
FMO2-HF: Total energy	-14355.406367
FMO2-MP2: Total energy	-14397.350598

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
2.203	3.583	-0.005	-0.502	-0.873	0.002

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.003

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	B	3	LYS	1	0.941	0.977	3.863	2.036	3.416	-0.005	-0.502	-0.873	0.002
4	B	4	ILE	0	0.032	0.012	5.673	0.374	0.374	0.000	0.000	0.000	0.000
5	B	5	ALA	0	-0.010	0.007	9.181	-0.143	-0.143	0.000	0.000	0.000	0.000
6	B	6	THR	0	0.008	-0.007	11.229	-0.005	-0.005	0.000	0.000	0.000	0.000
7	B	7	ARG	1	0.992	0.996	14.507	0.113	0.113	0.000	0.000	0.000	0.000
8	B	8	LYS	1	0.965	0.984	16.775	-0.049	-0.049	0.000	0.000	0.000	0.000
9	B	9	TYR	0	0.008	0.007	20.355	0.014	0.014	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.020	-0.003	22.054	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.032	0.025	25.284	0.002	0.002	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.918	0.955	27.120	-0.024	-0.024	0.000	0.000	0.000	0.000
13	B	13	GLN	0	0.021	0.009	25.467	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.012	0.006	29.248	-0.007	-0.007	0.000	0.000	0.000	0.000
15	B	15	VAL	0	-0.036	-0.018	25.446	0.009	0.009	0.000	0.000	0.000	0.000
16	B	16	TYR	0	-0.019	-0.017	26.272	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	17	ASP	-1	-0.833	-0.897	24.605	0.135	0.135	0.000	0.000	0.000	0.000
18	B	18	ILE	0	-0.049	-0.017	24.382	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	19	GLY	0	0.020	0.006	25.953	0.002	0.002	0.000	0.000	0.000	0.000
20	B	20	VAL	0	-0.029	-0.001	24.363	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	21	GLU	-1	-0.804	-0.911	27.122	0.094	0.094	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.893	0.929	25.088	-0.136	-0.136	0.000	0.000	0.000	0.000
23	B	23	ASP	-1	-0.873	-0.943	21.328	0.160	0.160	0.000	0.000	0.000	0.000
24	B	24	HIS	1	0.769	0.904	21.880	-0.113	-0.113	0.000	0.000	0.000	0.000
25	B	25	ASN	0	0.008	0.006	18.392	0.031	0.031	0.000	0.000	0.000	0.000
26	B	26	PHE	0	0.052	0.017	19.326	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	27	ALA	0	0.020	0.013	17.343	0.030	0.030	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.016	0.003	16.186	-0.048	-0.048	0.000	0.000	0.000	0.000
29	B	29	LYS	1	1.011	0.990	16.682	-0.346	-0.346	0.000	0.000	0.000	0.000
30	B	30	ASN	0	-0.073	-0.060	12.364	-0.032	-0.032	0.000	0.000	0.000	0.000
31	B	31	GLY	0	0.030	0.027	11.842	0.170	0.170	0.000	0.000	0.000	0.000
32	B	32	PHE	0	-0.031	0.001	9.656	0.053	0.053	0.000	0.000	0.000	0.000
33	B	33	ILE	0	0.021	0.012	12.976	-0.080	-0.080	0.000	0.000	0.000	0.000
34	B	34	ALA	0	-0.025	0.001	14.599	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	35	SER	0	0.030	-0.009	17.148	-0.012	-0.012	0.000	0.000	0.000	0.000
36	B	36	ASN	0	-0.047	-0.013	19.537	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)