FMO DATABASE

FMODB ID: LNG29

Calculation Name: 2CKX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CKX

Chain ID: A

ChEMBL ID:

UniProt ID: A0ZPR8

Base Structure: X-ray

Registration Date: 2023-09-23

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-584888.905108
FMO2-HF: Nuclear repulsion	551793.969122
FMO2-HF: Total energy	-33094.935986
FMO2-MP2: Total energy	-33193.768181

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(A:578:ARG)

Summations of interaction energy for fragment #1(A:578:ARG)

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.
-5.228	-1.514	0.087	-1.546	-2.256	0.003

Interaction energy analysis for fragmet #1(A:578:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.026 / q_NPA : 1.009

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

Sort

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	A	580	PHE	0	-0.004	0.005	3.834	-2.099	-0.029	-0.015	-0.982	-1.072	0.004
4	A	581	SER	0	0.061	0.025	6.495	1.719	1.719	0.000	0.000	0.000	0.000
5	A	582	VAL	0	0.090	0.020	8.301	0.833	0.833	0.000	0.000	0.000	0.000
6	A	583	ALA	0	0.036	0.031	11.688	0.982	0.982	0.000	0.000	0.000	0.000
7	A	584	GLU	-1	-0.727	-0.824	6.926	-30.781	-30.781	0.000	0.000	0.000	0.000
8	A	585	VAL	0	-0.032	-0.015	10.390	0.583	0.583	0.000	0.000	0.000	0.000
9	A	586	GLU	-1	-0.832	-0.901	12.373	-13.462	-13.462	0.000	0.000	0.000	0.000
10	A	587	ALA	0	0.013	0.013	13.073	0.876	0.876	0.000	0.000	0.000	0.000
11	A	588	LEU	0	-0.069	-0.034	10.940	0.587	0.587	0.000	0.000	0.000	0.000
12	A	589	VAL	0	-0.018	-0.020	14.030	0.727	0.727	0.000	0.000	0.000	0.000
13	A	590	GLU	-1	-0.752	-0.830	17.037	-12.136	-12.136	0.000	0.000	0.000	0.000
14	A	591	ALA	0	0.024	0.008	16.294	0.702	0.702	0.000	0.000	0.000	0.000
15	A	592	VAL	0	-0.028	-0.015	16.510	0.521	0.521	0.000	0.000	0.000	0.000
16	A	593	GLU	-1	-0.801	-0.880	19.124	-11.926	-11.926	0.000	0.000	0.000	0.000
17	A	594	HIS	0	-0.074	-0.046	21.666	0.968	0.968	0.000	0.000	0.000	0.000
18	A	595	LEU	0	-0.097	-0.052	19.391	0.422	0.422	0.000	0.000	0.000	0.000
19	A	596	GLY	0	0.027	0.008	21.846	0.289	0.289	0.000	0.000	0.000	0.000
20	A	597	THR	0	-0.026	-0.043	19.101	-0.489	-0.489	0.000	0.000	0.000	0.000
21	A	598	GLY	0	0.024	0.004	19.714	-0.263	-0.263	0.000	0.000	0.000	0.000
22	A	599	ARG	1	0.820	0.897	20.063	11.424	11.424	0.000	0.000	0.000	0.000
23	A	600	TRP	0	0.050	0.034	14.765	-0.430	-0.430	0.000	0.000	0.000	0.000
24	A	601	ARG	1	0.936	0.971	15.628	12.953	12.953	0.000	0.000	0.000	0.000
25	A	602	ASP	-1	-0.749	-0.849	17.340	-12.034	-12.034	0.000	0.000	0.000	0.000
26	A	603	VAL	0	-0.003	-0.001	14.181	-0.177	-0.177	0.000	0.000	0.000	0.000
27	A	604	LYS	1	0.828	0.890	10.439	19.415	19.415	0.000	0.000	0.000	0.000
28	A	605	MET	0	-0.008	-0.002	14.250	-0.258	-0.258	0.000	0.000	0.000	0.000
29	A	606	ARG	1	0.768	0.867	17.145	12.466	12.466	0.000	0.000	0.000	0.000
30	A	607	ALA	0	0.001	-0.006	14.165	0.155	0.155	0.000	0.000	0.000	0.000
31	A	608	PHE	0	-0.060	-0.051	8.588	-1.213	-1.213	0.000	0.000	0.000	0.000
32	A	609	ASP	-1	-0.885	-0.928	12.047	-15.411	-15.411	0.000	0.000	0.000	0.000
33	A	610	ASN	0	-0.012	0.004	13.375	-0.675	-0.675	0.000	0.000	0.000	0.000
34	A	611	ALA	0	0.011	0.005	8.136	-0.991	-0.991	0.000	0.000	0.000	0.000
35	A	612	ASP	-1	-0.897	-0.952	8.992	-20.157	-20.157	0.000	0.000	0.000	0.000
36	A	613	HIS	0	-0.083	-0.033	3.180	0.627	1.076	0.011	-0.093	-0.368	0.000
37	A	614	ARG	1	0.718	0.835	2.763	35.056	36.251	0.091	-0.471	-0.816	-0.001
38	A	615	THR	0	0.038	-0.018	6.996	3.352	3.352	0.000	0.000	0.000	0.000
39	A	616	TYR	0	0.077	0.011	9.830	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	617	VAL	0	-0.013	-0.004	10.867	0.633	0.633	0.000	0.000	0.000	0.000
41	A	618	ASP	-1	-0.763	-0.838	6.099	-27.910	-27.910	0.000	0.000	0.000	0.000
42	A	619	LEU	0	-0.039	0.004	8.310	-0.357	-0.357	0.000	0.000	0.000	0.000
43	A	620	LYS	1	0.838	0.921	10.687	18.555	18.555	0.000	0.000	0.000	0.000
44	A	621	ASP	-1	-0.826	-0.923	9.468	-19.233	-19.233	0.000	0.000	0.000	0.000
45	A	622	LYS	1	0.901	0.971	7.810	26.116	26.116	0.000	0.000	0.000	0.000
46	A	623	TRP	0	0.080	0.036	10.017	0.369	0.369	0.000	0.000	0.000	0.000
47	A	624	LYS	1	0.977	0.999	13.547	15.380	15.380	0.000	0.000	0.000	0.000
48	A	625	THR	0	-0.065	-0.051	10.431	0.031	0.031	0.000	0.000	0.000	0.000
49	A	626	LEU	0	0.004	0.022	12.321	0.214	0.214	0.000	0.000	0.000	0.000
50	A	627	VAL	0	0.060	0.034	14.620	0.687	0.687	0.000	0.000	0.000	0.000
51	A	628	HIS	0	-0.040	-0.002	16.118	0.952	0.952	0.000	0.000	0.000	0.000
52	A	629	THR	0	-0.032	-0.049	14.654	0.229	0.229	0.000	0.000	0.000	0.000
53	A	630	ALA	0	-0.033	-0.015	17.223	0.462	0.462	0.000	0.000	0.000	0.000
54	A	631	SER	0	-0.021	-0.023	19.840	0.835	0.835	0.000	0.000	0.000	0.000
55	A	632	ILE	0	-0.087	-0.017	18.067	0.569	0.569	0.000	0.000	0.000	0.000
56	A	633	ALA	0	0.041	0.015	22.293	-0.054	-0.054	0.000	0.000	0.000	0.000
57	A	634	PRO	0	0.085	0.015	21.170	-0.587	-0.587	0.000	0.000	0.000	0.000
58	A	635	GLN	0	0.005	0.005	20.545	-0.396	-0.396	0.000	0.000	0.000	0.000
59	A	636	GLN	0	-0.018	-0.004	20.760	-0.134	-0.134	0.000	0.000	0.000	0.000
60	A	637	ARG	1	0.848	0.957	16.711	13.516	13.516	0.000	0.000	0.000	0.000
61	A	638	ARG	1	0.857	0.913	13.281	17.029	17.029	0.000	0.000	0.000	0.000
62	A	639	GLY	0	0.003	0.004	10.352	-0.457	-0.457	0.000	0.000	0.000	0.000
63	A	640	GLU	-1	-0.948	-0.973	9.045	-25.364	-25.364	0.000	0.000	0.000	0.000
64	A	641	PRO	0	-0.006	-0.010	11.703	0.476	0.476	0.000	0.000	0.000	0.000
65	A	642	VAL	0	0.003	0.005	13.175	-0.551	-0.551	0.000	0.000	0.000	0.000
66	A	643	PRO	0	0.033	0.021	15.304	0.687	0.687	0.000	0.000	0.000	0.000
67	A	644	GLN	0	0.014	-0.025	18.386	-0.448	-0.448	0.000	0.000	0.000	0.000
68	A	645	ASP	-1	-0.828	-0.908	21.142	-13.423	-13.423	0.000	0.000	0.000	0.000
69	A	646	LEU	0	0.034	0.009	15.995	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	647	LEU	0	-0.064	-0.030	16.809	-0.095	-0.095	0.000	0.000	0.000	0.000
71	A	648	ASP	-1	-0.830	-0.911	19.884	-11.563	-11.563	0.000	0.000	0.000	0.000
72	A	649	ARG	1	0.778	0.847	20.565	13.376	13.376	0.000	0.000	0.000	0.000
73	A	650	VAL	0	-0.040	-0.002	17.024	0.075	0.075	0.000	0.000	0.000	0.000
74	A	651	LEU	0	-0.018	-0.012	19.989	0.269	0.269	0.000	0.000	0.000	0.000
75	A	652	ALA	0	0.015	0.019	22.941	0.366	0.366	0.000	0.000	0.000	0.000
76	A	653	ALA	0	0.031	0.015	21.351	0.330	0.330	0.000	0.000	0.000	0.000
77	A	654	HIS	0	-0.008	-0.013	21.068	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	655	ALA	0	-0.021	-0.003	22.777	0.291	0.291	0.000	0.000	0.000	0.000
79	A	656	TYR	0	-0.004	0.001	26.261	0.432	0.432	0.000	0.000	0.000	0.000
80	A	657	TRP	0	0.016	0.006	23.136	0.413	0.413	0.000	0.000	0.000	0.000
81	A	658	SER	0	-0.105	-0.049	24.594	0.072	0.072	0.000	0.000	0.000	0.000
82	A	659	GLN	0	-0.128	-0.066	26.565	0.479	0.479	0.000	0.000	0.000	0.000
83	A	660	GLN	0	-0.063	-0.010	28.270	0.445	0.445	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:578:ARG)