FMO DATABASE

FMODB ID: GNJ91

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

Total energy (hartree)

FMO2-HF: Electronic energy	-170102.182559
FMO2-HF: Nuclear repulsion	150312.358297
FMO2-HF: Total energy	-19789.824262
FMO2-MP2: Total energy	-19847.700264

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.
-2.819	0.891	-0.025	-2.02	-1.666	0.007

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 : 0.015 / 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

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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	-0.968	3.847	-3.461	0.249	-0.025	-2.020	-1.666	0.007
4	T	974	LEU	0	-0.027	-0.007	5.437	0.202	0.202	0.000	0.000	0.000	0.000
5	T	975	PRO	0	0.014	-0.004	8.224	-0.018	-0.018	0.000	0.000	0.000	0.000
6	T	976	SER	0	0.000	0.008	12.068	0.054	0.054	0.000	0.000	0.000	0.000
7	T	977	GLU	-1	-0.932	-0.966	14.562	-0.097	-0.097	0.000	0.000	0.000	0.000
8	T	978	GLU	-1	-0.926	-0.961	16.917	-0.129	-0.129	0.000	0.000	0.000	0.000
9	T	979	GLY	0	-0.033	-0.001	19.740	0.011	0.011	0.000	0.000	0.000	0.000
10	T	980	LYS	1	0.907	0.930	21.186	0.092	0.092	0.000	0.000	0.000	0.000
11	T	981	LYS	1	0.949	0.995	17.881	0.195	0.195	0.000	0.000	0.000	0.000
12	T	982	LEU	0	0.070	0.037	19.193	0.015	0.015	0.000	0.000	0.000	0.000
13	T	983	GLU	-1	-0.948	-0.981	21.316	-0.122	-0.122	0.000	0.000	0.000	0.000
14	T	984	HIS	0	0.018	-0.007	19.143	0.009	0.009	0.000	0.000	0.000	0.000
15	T	985	PHE	0	0.079	0.028	24.489	-0.003	-0.003	0.000	0.000	0.000	0.000
16	T	986	THR	0	-0.062	-0.031	25.973	0.000	0.000	0.000	0.000	0.000	0.000
17	T	987	LYS	1	0.935	0.962	21.175	0.177	0.177	0.000	0.000	0.000	0.000
18	T	988	LEU	0	0.010	0.010	26.780	0.000	0.000	0.000	0.000	0.000	0.000
19	T	989	ARG	1	0.936	0.991	30.123	0.075	0.075	0.000	0.000	0.000	0.000
20	T	990	PRO	0	0.047	0.021	32.183	-0.004	-0.004	0.000	0.000	0.000	0.000
21	T	991	LYS	1	0.968	0.998	29.628	0.097	0.097	0.000	0.000	0.000	0.000
22	T	992	ARG	1	0.982	0.982	33.863	0.053	0.053	0.000	0.000	0.000	0.000
23	T	993	ASN	0	-0.005	-0.012	34.430	-0.005	-0.005	0.000	0.000	0.000	0.000
24	T	994	LYS	1	0.941	0.982	30.869	0.068	0.068	0.000	0.000	0.000	0.000
25	T	995	LYS	1	0.966	0.982	36.109	0.045	0.045	0.000	0.000	0.000	0.000
26	T	996	GLN	0	0.079	0.039	35.646	-0.004	-0.004	0.000	0.000	0.000	0.000
27	T	997	GLN	0	-0.004	-0.015	30.364	0.000	0.000	0.000	0.000	0.000	0.000
28	T	998	PRO	0	-0.032	-0.022	28.937	0.003	0.003	0.000	0.000	0.000	0.000
29	T	999	THR	0	0.044	0.037	29.919	-0.002	-0.002	0.000	0.000	0.000	0.000
30	T	1000	GLN	0	0.008	-0.001	27.901	0.000	0.000	0.000	0.000	0.000	0.000
31	T	1001	ALA	0	-0.017	-0.005	25.092	-0.002	-0.002	0.000	0.000	0.000	0.000
32	T	1002	ALA	0	0.009	0.018	27.237	0.000	0.000	0.000	0.000	0.000	0.000
33	T	1003	VAL	0	-0.003	-0.017	29.929	-0.001	-0.001	0.000	0.000	0.000	0.000
34	T	1004	CYS	0	0.017	0.020	33.548	0.003	0.003	0.000	0.000	0.000	0.000
35	T	1021	ARG	1	0.820	0.872	33.260	-0.017	-0.017	0.000	0.000	0.000	0.000
36	T	1022	VAL	0	-0.033	-0.036	30.022	0.000	0.000	0.000	0.000	0.000	0.000
37	T	1023	ASP	-1	-0.910	-0.944	28.562	0.014	0.014	0.000	0.000	0.000	0.000
38	T	1024	GLU	-1	-0.840	-0.893	30.359	0.026	0.026	0.000	0.000	0.000	0.000
39	T	1025	GLY	0	0.021	0.020	31.266	-0.001	-0.001	0.000	0.000	0.000	0.000
40	T	1026	VAL	0	-0.042	-0.030	25.379	0.006	0.006	0.000	0.000	0.000	0.000
41	T	1027	ASP	-1	-0.845	-0.922	25.510	0.059	0.059	0.000	0.000	0.000	0.000
42	T	1028	GLU	-1	-0.912	-0.970	25.312	0.064	0.064	0.000	0.000	0.000	0.000
43	T	1029	PHE	0	-0.044	-0.007	22.789	0.009	0.009	0.000	0.000	0.000	0.000
44	T	1030	PHE	0	-0.033	-0.014	20.195	0.009	0.009	0.000	0.000	0.000	0.000
45	T	1031	THR	0	-0.020	-0.004	21.734	0.013	0.013	0.000	0.000	0.000	0.000
46	T	1032	LYS	1	0.856	0.935	24.225	-0.086	-0.086	0.000	0.000	0.000	0.000
47	T	1033	LYS	1	0.961	0.964	23.635	-0.159	-0.159	0.000	0.000	0.000	0.000
48	T	1034	VAL	0	-0.009	0.003	26.843	-0.005	-0.005	0.000	0.000	0.000	0.000
49	T	1035	THR	0	0.031	0.027	26.473	-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)