FMO DATABASE

FMODB ID: 82R3Y

Calculation Name: 3LK3-T-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LK3

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	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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-170437.723034
FMO2-HF: Nuclear repulsion	150647.615624
FMO2-HF: Total energy	-19790.10741
FMO2-MP2: Total energy	-19847.98867

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:971:ILE)

Summations of interaction energy for fragment #1(T:971:ILE)

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.
-2.696	0.558	-0.012	-1.757	-1.486	0.004

Interaction energy analysis for fragmet #1(T:971:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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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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	973	GLU	-1	-0.938	-0.965	3.795	-3.203	0.051	-0.012	-1.757	-1.486	0.004
4	T	974	LEU	0	-0.022	-0.010	5.465	0.148	0.148	0.000	0.000	0.000	0.000
5	T	975	PRO	0	0.004	-0.006	8.177	0.010	0.010	0.000	0.000	0.000	0.000
6	T	976	SER	0	-0.026	-0.028	12.048	0.049	0.049	0.000	0.000	0.000	0.000
7	T	977	GLU	-1	-0.912	-0.953	14.595	-0.151	-0.151	0.000	0.000	0.000	0.000
8	T	978	GLU	-1	-0.912	-0.936	16.527	-0.177	-0.177	0.000	0.000	0.000	0.000
9	T	979	GLY	0	-0.017	0.007	19.502	0.011	0.011	0.000	0.000	0.000	0.000
10	T	980	LYS	1	0.891	0.920	20.603	0.114	0.114	0.000	0.000	0.000	0.000
11	T	981	LYS	1	0.940	0.988	17.903	0.202	0.202	0.000	0.000	0.000	0.000
12	T	982	LEU	0	0.081	0.045	19.333	0.016	0.016	0.000	0.000	0.000	0.000
13	T	983	GLU	-1	-0.974	-0.997	20.991	-0.137	-0.137	0.000	0.000	0.000	0.000
14	T	984	HIS	0	0.077	0.028	19.240	0.008	0.008	0.000	0.000	0.000	0.000
15	T	985	PHE	0	0.087	0.042	24.702	0.000	0.000	0.000	0.000	0.000	0.000
16	T	986	THR	0	-0.024	-0.013	25.755	0.001	0.001	0.000	0.000	0.000	0.000
17	T	987	LYS	1	0.863	0.917	21.172	0.182	0.182	0.000	0.000	0.000	0.000
18	T	988	LEU	0	0.008	0.017	27.035	-0.002	-0.002	0.000	0.000	0.000	0.000
19	T	989	ARG	1	0.939	0.983	30.370	0.074	0.074	0.000	0.000	0.000	0.000
20	T	990	PRO	0	0.037	0.014	32.544	-0.004	-0.004	0.000	0.000	0.000	0.000
21	T	991	LYS	1	0.947	0.983	30.509	0.090	0.090	0.000	0.000	0.000	0.000
22	T	992	ARG	1	0.973	0.992	33.722	0.049	0.049	0.000	0.000	0.000	0.000
23	T	993	ASN	0	0.009	0.001	33.918	-0.005	-0.005	0.000	0.000	0.000	0.000
24	T	994	LYS	1	0.892	0.941	30.567	0.063	0.063	0.000	0.000	0.000	0.000
25	T	995	LYS	1	0.979	0.983	36.420	0.041	0.041	0.000	0.000	0.000	0.000
26	T	996	GLN	0	0.081	0.050	35.244	-0.003	-0.003	0.000	0.000	0.000	0.000
27	T	997	GLN	0	0.023	0.001	30.343	-0.001	-0.001	0.000	0.000	0.000	0.000
28	T	998	PRO	0	-0.012	-0.011	29.308	0.003	0.003	0.000	0.000	0.000	0.000
29	T	999	THR	0	0.048	0.031	29.697	-0.003	-0.003	0.000	0.000	0.000	0.000
30	T	1000	GLN	0	0.004	0.004	27.973	0.001	0.001	0.000	0.000	0.000	0.000
31	T	1001	ALA	0	-0.024	-0.014	25.001	-0.003	-0.003	0.000	0.000	0.000	0.000
32	T	1002	ALA	0	0.006	0.010	27.134	-0.002	-0.002	0.000	0.000	0.000	0.000
33	T	1003	VAL	0	0.003	-0.004	30.148	0.001	0.001	0.000	0.000	0.000	0.000
34	T	1004	CYS	0	0.015	0.020	33.788	0.002	0.002	0.000	0.000	0.000	0.000
35	T	1021	ARG	1	0.838	0.884	33.305	-0.023	-0.023	0.000	0.000	0.000	0.000
36	T	1022	VAL	0	-0.046	-0.034	29.963	-0.002	-0.002	0.000	0.000	0.000	0.000
37	T	1023	ASP	-1	-0.928	-0.967	28.824	0.022	0.022	0.000	0.000	0.000	0.000
38	T	1024	GLU	-1	-0.816	-0.881	29.707	0.032	0.032	0.000	0.000	0.000	0.000
39	T	1025	GLY	0	0.027	0.022	30.798	-0.003	-0.003	0.000	0.000	0.000	0.000
40	T	1026	VAL	0	-0.053	-0.031	24.931	0.006	0.006	0.000	0.000	0.000	0.000
41	T	1027	ASP	-1	-0.882	-0.938	24.951	0.080	0.080	0.000	0.000	0.000	0.000
42	T	1028	GLU	-1	-0.857	-0.928	25.299	0.068	0.068	0.000	0.000	0.000	0.000
43	T	1029	PHE	0	-0.070	-0.019	22.620	0.010	0.010	0.000	0.000	0.000	0.000
44	T	1030	PHE	0	-0.032	-0.011	20.088	0.007	0.007	0.000	0.000	0.000	0.000
45	T	1031	THR	0	-0.030	-0.029	21.535	0.017	0.017	0.000	0.000	0.000	0.000
46	T	1032	LYS	1	0.839	0.926	24.033	-0.096	-0.096	0.000	0.000	0.000	0.000
47	T	1033	LYS	1	0.954	0.971	22.939	-0.180	-0.180	0.000	0.000	0.000	0.000
48	T	1034	VAL	0	0.019	0.000	26.514	-0.006	-0.006	0.000	0.000	0.000	0.000
49	T	1035	THR	0	0.037	0.036	26.958	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(T:971:ILE)