FMO DATABASE

FMODB ID: N1K5Q

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	OptH
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	-96821.653579
FMO2-HF: Nuclear repulsion	83622.513521
FMO2-HF: Total energy	-13199.140059
FMO2-MP2: Total energy	-13238.524924

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.
13.595	-0.228	0.527	14.773	-1.478	-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 : -0.024 / 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	T	972	SER	0	0.022	-0.015	2.463	12.750	-1.223	0.528	14.786	-1.342	-0.016
4	T	973	GLU	-1	-0.997	-0.992	4.189	0.681	0.831	-0.001	-0.013	-0.136	0.000
5	T	974	LEU	0	-0.007	-0.003	5.498	0.080	0.080	0.000	0.000	0.000	0.000
6	T	975	PRO	0	0.023	0.012	8.451	-0.170	-0.170	0.000	0.000	0.000	0.000
7	T	976	SER	0	0.007	-0.003	11.921	0.023	0.023	0.000	0.000	0.000	0.000
8	T	977	GLU	-1	-0.932	-0.969	15.258	0.333	0.333	0.000	0.000	0.000	0.000
9	T	978	GLU	-1	-0.950	-0.967	18.590	0.201	0.201	0.000	0.000	0.000	0.000
10	T	979	GLY	0	-0.030	0.002	19.983	-0.026	-0.026	0.000	0.000	0.000	0.000
11	T	980	LYS	1	0.895	0.926	21.757	-0.127	-0.127	0.000	0.000	0.000	0.000
12	T	981	LYS	1	0.966	0.988	17.033	-0.088	-0.088	0.000	0.000	0.000	0.000
13	T	982	LEU	0	0.069	0.043	22.010	-0.008	-0.008	0.000	0.000	0.000	0.000
14	T	983	GLU	-1	-0.934	-0.960	24.078	0.058	0.058	0.000	0.000	0.000	0.000
15	T	984	HIS	0	0.001	-0.014	22.638	-0.001	-0.001	0.000	0.000	0.000	0.000
16	T	985	PHE	0	0.082	0.028	28.048	-0.009	-0.009	0.000	0.000	0.000	0.000
17	T	986	THR	0	-0.045	-0.028	30.305	-0.006	-0.006	0.000	0.000	0.000	0.000
18	T	987	LYS	1	0.969	0.977	26.044	-0.030	-0.030	0.000	0.000	0.000	0.000
19	T	988	LEU	0	-0.030	-0.010	30.882	-0.006	-0.006	0.000	0.000	0.000	0.000
20	T	989	ARG	1	0.938	0.993	34.076	-0.039	-0.039	0.000	0.000	0.000	0.000
21	T	990	PRO	0	0.022	0.017	36.252	-0.002	-0.002	0.000	0.000	0.000	0.000
22	T	991	LYS	1	0.976	0.983	32.081	-0.004	-0.004	0.000	0.000	0.000	0.000
23	T	992	ARG	1	0.998	1.007	38.284	-0.011	-0.011	0.000	0.000	0.000	0.000
24	T	993	ASN	0	0.000	-0.005	39.278	0.000	0.000	0.000	0.000	0.000	0.000
25	T	994	LYS	1	0.939	0.966	36.437	-0.007	-0.007	0.000	0.000	0.000	0.000
26	T	995	LYS	1	0.984	0.988	41.115	0.003	0.003	0.000	0.000	0.000	0.000
27	T	996	GLN	0	0.053	0.022	40.513	-0.003	-0.003	0.000	0.000	0.000	0.000
28	T	997	GLN	0	-0.028	-0.010	33.957	0.004	0.004	0.000	0.000	0.000	0.000
29	T	998	PRO	0	-0.013	-0.013	34.064	-0.001	-0.001	0.000	0.000	0.000	0.000
30	T	999	THR	0	0.048	0.035	34.882	-0.002	-0.002	0.000	0.000	0.000	0.000
31	T	1000	GLN	0	0.025	0.007	32.145	0.001	0.001	0.000	0.000	0.000	0.000
32	T	1001	ALA	0	-0.038	-0.016	30.042	0.000	0.000	0.000	0.000	0.000	0.000
33	T	1002	ALA	0	0.019	0.021	31.616	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)