FMO DATABASE

FMODB ID: 14MZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-170178.835025
FMO2-HF: Nuclear repulsion	150389.414306
FMO2-HF: Total energy	-19789.420719
FMO2-MP2: Total energy	-19847.34523

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.
-0.889	1.129	-0.028	-0.855	-1.135	0

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 : -0.020 / 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].
3	T	973	GLU	-1	-0.920	-0.959	3.475	-1.762	0.256	-0.028	-0.855	-1.135
4	T	974	LEU	0	-0.051	-0.021	5.224	0.349	0.349	0.000	0.000	0.000
5	T	975	PRO	0	0.021	0.000	8.290	-0.049	-0.049	0.000	0.000	0.000
6	T	976	SER	0	0.006	0.009	12.127	0.004	0.004	0.000	0.000	0.000
7	T	977	GLU	-1	-0.936	-0.970	14.429	0.013	0.013	0.000	0.000	0.000
8	T	978	GLU	-1	-0.925	-0.959	17.418	-0.140	-0.140	0.000	0.000	0.000
9	T	979	GLY	0	-0.034	0.001	19.487	0.006	0.006	0.000	0.000	0.000
10	T	980	LYS	1	0.905	0.929	21.008	0.074	0.074	0.000	0.000	0.000
11	T	981	LYS	1	0.952	0.995	17.597	0.190	0.190	0.000	0.000	0.000
12	T	982	LEU	0	0.066	0.034	18.954	0.015	0.015	0.000	0.000	0.000
13	T	983	GLU	-1	-0.932	-0.973	21.151	-0.122	-0.122	0.000	0.000	0.000
14	T	984	HIS	0	0.007	-0.011	18.955	0.006	0.006	0.000	0.000	0.000
15	T	985	PHE	0	0.069	0.026	24.353	-0.002	-0.002	0.000	0.000	0.000
16	T	986	THR	0	-0.067	-0.036	26.024	0.002	0.002	0.000	0.000	0.000
17	T	987	LYS	1	0.946	0.970	21.754	0.191	0.191	0.000	0.000	0.000
18	T	988	LEU	0	0.003	0.003	26.711	0.000	0.000	0.000	0.000	0.000
19	T	989	ARG	1	0.942	0.994	29.507	0.115	0.115	0.000	0.000	0.000
20	T	990	PRO	0	0.052	0.024	32.119	-0.004	-0.004	0.000	0.000	0.000
21	T	991	LYS	1	0.972	0.999	29.123	0.127	0.127	0.000	0.000	0.000
22	T	992	ARG	1	0.982	0.987	33.644	0.089	0.089	0.000	0.000	0.000
23	T	993	ASN	0	0.000	-0.011	34.259	-0.009	-0.009	0.000	0.000	0.000
24	T	994	LYS	1	0.944	0.976	31.262	0.116	0.116	0.000	0.000	0.000
25	T	995	LYS	1	0.972	0.984	36.001	0.070	0.070	0.000	0.000	0.000
26	T	996	GLN	0	0.086	0.047	35.937	-0.004	-0.004	0.000	0.000	0.000
27	T	997	GLN	0	-0.029	-0.027	29.373	-0.006	-0.006	0.000	0.000	0.000
28	T	998	PRO	0	-0.038	-0.022	28.909	0.005	0.005	0.000	0.000	0.000
29	T	999	THR	0	0.051	0.045	29.959	-0.003	-0.003	0.000	0.000	0.000
30	T	1000	GLN	0	0.019	-0.004	27.969	-0.002	-0.002	0.000	0.000	0.000
31	T	1001	ALA	0	-0.021	-0.004	25.107	0.003	0.003	0.000	0.000	0.000
32	T	1002	ALA	0	0.008	0.017	27.242	0.003	0.003	0.000	0.000	0.000
33	T	1003	VAL	0	0.007	-0.014	29.943	0.000	0.000	0.000	0.000	0.000
34	T	1004	CYS	0	0.000	0.014	33.578	0.005	0.005	0.000	0.000	0.000
35	T	1021	ARG	1	0.881	0.910	33.112	0.047	0.047	0.000	0.000	0.000
36	T	1022	VAL	0	-0.008	-0.005	29.772	0.003	0.003	0.000	0.000	0.000
37	T	1023	ASP	-1	-0.886	-0.945	29.036	-0.069	-0.069	0.000	0.000	0.000
38	T	1024	GLU	-1	-0.917	-0.943	30.326	-0.037	-0.037	0.000	0.000	0.000
39	T	1025	GLY	0	0.007	0.012	31.414	0.001	0.001	0.000	0.000	0.000
40	T	1026	VAL	0	-0.041	-0.031	25.485	0.002	0.002	0.000	0.000	0.000
41	T	1027	ASP	-1	-0.846	-0.918	25.615	-0.073	-0.073	0.000	0.000	0.000
42	T	1028	GLU	-1	-0.912	-0.972	25.448	-0.037	-0.037	0.000	0.000	0.000
43	T	1029	PHE	0	-0.050	-0.009	23.147	0.010	0.010	0.000	0.000	0.000
44	T	1030	PHE	0	-0.032	-0.016	20.261	0.004	0.004	0.000	0.000	0.000
45	T	1031	THR	0	-0.023	-0.008	21.900	0.003	0.003	0.000	0.000	0.000
46	T	1032	LYS	1	0.871	0.953	24.388	0.011	0.011	0.000	0.000	0.000
47	T	1033	LYS	1	0.961	0.975	23.935	-0.034	-0.034	0.000	0.000	0.000
48	T	1034	VAL	0	-0.018	-0.014	27.071	-0.001	-0.001	0.000	0.000	0.000
49	T	1035	THR	0	0.015	0.011	26.743	0.001	0.001	0.000	0.000	0.000

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