FMO DATABASE

FMODB ID: J3NJ9

Calculation Name: 3LK2-T-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LK2

Chain ID: T

ChEMBL ID:

UniProt ID: P14315

Base Structure: X-ray

Registration Date: 2023-06-19

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	-97059.706927
FMO2-HF: Nuclear repulsion	83860.270544
FMO2-HF: Total energy	-13199.436382
FMO2-MP2: Total energy	-13238.820743

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(T:970:PHE)

Summations of interaction energy for fragment #1(T:970:PHE)

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.
13.33	0.059	0.48	14.308	-1.516	-0.016

Interaction energy analysis for fragmet #1(T:970:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : 0.024

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	T	972	SER	0	0.019	-0.012	2.477	12.389	-1.028	0.481	14.319	-1.382	-0.016
4	T	973	GLU	-1	-0.988	-0.990	4.187	0.821	0.967	-0.001	-0.011	-0.134	0.000
5	T	974	LEU	0	-0.015	-0.005	5.301	0.137	0.137	0.000	0.000	0.000	0.000
6	T	975	PRO	0	0.010	0.005	8.448	-0.199	-0.199	0.000	0.000	0.000	0.000
7	T	976	SER	0	-0.024	-0.031	11.916	0.014	0.014	0.000	0.000	0.000	0.000
8	T	977	GLU	-1	-0.942	-0.971	15.255	0.396	0.396	0.000	0.000	0.000	0.000
9	T	978	GLU	-1	-0.900	-0.934	18.222	0.272	0.272	0.000	0.000	0.000	0.000
10	T	979	GLY	0	-0.024	0.003	19.970	-0.031	-0.031	0.000	0.000	0.000	0.000
11	T	980	LYS	1	0.892	0.927	21.753	-0.164	-0.164	0.000	0.000	0.000	0.000
12	T	981	LYS	1	0.961	0.985	17.084	-0.175	-0.175	0.000	0.000	0.000	0.000
13	T	982	LEU	0	0.076	0.044	22.005	-0.012	-0.012	0.000	0.000	0.000	0.000
14	T	983	GLU	-1	-0.928	-0.962	24.080	0.084	0.084	0.000	0.000	0.000	0.000
15	T	984	HIS	0	0.000	-0.012	22.806	-0.008	-0.008	0.000	0.000	0.000	0.000
16	T	985	PHE	0	0.078	0.029	28.053	-0.010	-0.010	0.000	0.000	0.000	0.000
17	T	986	THR	0	-0.030	-0.020	30.149	-0.007	-0.007	0.000	0.000	0.000	0.000
18	T	987	LYS	1	0.985	0.991	25.507	-0.063	-0.063	0.000	0.000	0.000	0.000
19	T	988	LEU	0	-0.008	-0.002	30.889	-0.008	-0.008	0.000	0.000	0.000	0.000
20	T	989	ARG	1	0.961	1.005	34.082	-0.054	-0.054	0.000	0.000	0.000	0.000
21	T	990	PRO	0	0.035	0.018	36.260	-0.002	-0.002	0.000	0.000	0.000	0.000
22	T	991	LYS	1	0.886	0.939	33.261	-0.027	-0.027	0.000	0.000	0.000	0.000
23	T	992	ARG	1	0.988	1.002	38.293	-0.017	-0.017	0.000	0.000	0.000	0.000
24	T	993	ASN	0	0.012	0.001	39.288	0.001	0.001	0.000	0.000	0.000	0.000
25	T	994	LYS	1	0.845	0.925	36.212	-0.010	-0.010	0.000	0.000	0.000	0.000
26	T	995	LYS	1	0.999	0.994	41.139	-0.001	-0.001	0.000	0.000	0.000	0.000
27	T	996	GLN	0	0.042	0.018	40.532	-0.002	-0.002	0.000	0.000	0.000	0.000
28	T	997	GLN	0	0.055	0.026	34.019	0.006	0.006	0.000	0.000	0.000	0.000
29	T	998	PRO	0	-0.009	-0.012	34.087	-0.001	-0.001	0.000	0.000	0.000	0.000
30	T	999	THR	0	0.047	0.035	34.845	-0.002	-0.002	0.000	0.000	0.000	0.000
31	T	1000	GLN	0	0.014	0.004	32.328	0.001	0.001	0.000	0.000	0.000	0.000
32	T	1001	ALA	0	-0.029	-0.014	29.991	0.001	0.001	0.000	0.000	0.000	0.000
33	T	1002	ALA	0	0.024	0.024	31.445	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(T:970:PHE)