FMO DATABASE

FMODB ID: 3JZ5L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-586221.322759
FMO2-HF: Nuclear repulsion	553126.77734
FMO2-HF: Total energy	-33094.545419
FMO2-MP2: Total energy	-33193.457527

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.
-7.065	-3.96	0.203	-1.247	-2.061	0.002

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 : 1.018 / q_NPA : 0.990

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	A	580	PHE	0	0.021	0.018	3.800	-0.281	1.116	-0.005	-0.600	-0.793	0.000
4	A	581	SER	0	0.054	0.036	6.401	1.135	1.135	0.000	0.000	0.000	0.000
5	A	582	VAL	0	0.111	0.029	8.082	0.848	0.848	0.000	0.000	0.000	0.000
6	A	583	ALA	0	0.040	0.035	11.445	1.029	1.029	0.000	0.000	0.000	0.000
7	A	584	GLU	-1	-0.744	-0.821	6.609	-28.566	-28.566	0.000	0.000	0.000	0.000
8	A	585	VAL	0	-0.032	-0.014	10.357	0.582	0.582	0.000	0.000	0.000	0.000
9	A	586	GLU	-1	-0.841	-0.917	12.431	-13.489	-13.489	0.000	0.000	0.000	0.000
10	A	587	ALA	0	0.009	0.009	13.443	0.856	0.856	0.000	0.000	0.000	0.000
11	A	588	LEU	0	-0.059	-0.034	11.029	0.588	0.588	0.000	0.000	0.000	0.000
12	A	589	VAL	0	-0.028	-0.019	14.277	0.681	0.681	0.000	0.000	0.000	0.000
13	A	590	GLU	-1	-0.754	-0.824	17.110	-11.968	-11.968	0.000	0.000	0.000	0.000
14	A	591	ALA	0	0.023	-0.004	16.632	0.656	0.656	0.000	0.000	0.000	0.000
15	A	592	VAL	0	-0.040	-0.017	16.449	0.505	0.505	0.000	0.000	0.000	0.000
16	A	593	GLU	-1	-0.785	-0.866	19.135	-11.796	-11.796	0.000	0.000	0.000	0.000
17	A	594	HIS	0	-0.052	-0.032	21.892	0.885	0.885	0.000	0.000	0.000	0.000
18	A	595	LEU	0	-0.096	-0.048	19.736	0.414	0.414	0.000	0.000	0.000	0.000
19	A	596	GLY	0	0.030	-0.001	21.850	0.282	0.282	0.000	0.000	0.000	0.000
20	A	597	THR	0	-0.033	-0.041	19.045	-0.448	-0.448	0.000	0.000	0.000	0.000
21	A	598	GLY	0	0.017	0.003	19.663	-0.276	-0.276	0.000	0.000	0.000	0.000
22	A	599	ARG	1	0.845	0.922	20.018	11.223	11.223	0.000	0.000	0.000	0.000
23	A	600	TRP	0	0.058	0.036	14.712	-0.330	-0.330	0.000	0.000	0.000	0.000
24	A	601	ARG	1	0.943	0.975	15.802	12.806	12.806	0.000	0.000	0.000	0.000
25	A	602	ASP	-1	-0.765	-0.870	17.564	-11.835	-11.835	0.000	0.000	0.000	0.000
26	A	603	VAL	0	-0.014	-0.005	14.349	-0.128	-0.128	0.000	0.000	0.000	0.000
27	A	604	LYS	1	0.798	0.862	11.066	18.621	18.621	0.000	0.000	0.000	0.000
28	A	605	MET	0	0.009	0.000	14.770	-0.258	-0.258	0.000	0.000	0.000	0.000
29	A	606	ARG	1	0.755	0.856	17.870	12.290	12.290	0.000	0.000	0.000	0.000
30	A	607	ALA	0	0.007	-0.004	14.727	0.147	0.147	0.000	0.000	0.000	0.000
31	A	608	PHE	0	-0.069	-0.052	9.603	-0.969	-0.969	0.000	0.000	0.000	0.000
32	A	609	ASP	-1	-0.898	-0.935	12.875	-14.881	-14.881	0.000	0.000	0.000	0.000
33	A	610	ASN	0	-0.025	0.005	12.910	-0.781	-0.781	0.000	0.000	0.000	0.000
34	A	611	ALA	0	0.026	0.010	8.501	-0.888	-0.888	0.000	0.000	0.000	0.000
35	A	612	ASP	-1	-0.897	-0.952	9.921	-19.374	-19.374	0.000	0.000	0.000	0.000
36	A	613	HIS	0	-0.072	-0.035	3.999	-0.354	-0.059	0.000	-0.062	-0.233	0.000
37	A	614	ARG	1	0.727	0.824	2.813	30.988	32.401	0.208	-0.585	-1.035	0.002
38	A	615	THR	0	0.060	0.036	7.624	2.754	2.754	0.000	0.000	0.000	0.000
39	A	616	TYR	0	0.061	0.000	10.016	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	617	VAL	0	-0.034	-0.019	10.792	0.722	0.722	0.000	0.000	0.000	0.000
41	A	618	ASP	-1	-0.758	-0.865	6.353	-27.196	-27.196	0.000	0.000	0.000	0.000
42	A	619	LEU	0	-0.045	-0.006	8.262	-0.316	-0.316	0.000	0.000	0.000	0.000
43	A	620	LYS	1	0.931	0.975	10.626	16.505	16.505	0.000	0.000	0.000	0.000
44	A	621	ASP	-1	-0.896	-0.959	9.235	-20.120	-20.120	0.000	0.000	0.000	0.000
45	A	622	LYS	1	0.903	0.966	7.850	26.896	26.896	0.000	0.000	0.000	0.000
46	A	623	TRP	0	0.085	0.049	9.976	0.263	0.263	0.000	0.000	0.000	0.000
47	A	624	LYS	1	0.969	0.995	13.512	15.465	15.465	0.000	0.000	0.000	0.000
48	A	625	THR	0	-0.084	-0.071	10.281	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	626	LEU	0	0.016	0.020	12.295	0.190	0.190	0.000	0.000	0.000	0.000
50	A	627	VAL	0	0.051	0.032	14.587	0.656	0.656	0.000	0.000	0.000	0.000
51	A	628	HIS	0	-0.027	0.007	16.123	1.024	1.024	0.000	0.000	0.000	0.000
52	A	629	THR	0	-0.028	-0.039	14.607	0.215	0.215	0.000	0.000	0.000	0.000
53	A	630	ALA	0	-0.032	-0.017	17.194	0.456	0.456	0.000	0.000	0.000	0.000
54	A	631	SER	0	-0.030	-0.026	19.814	0.848	0.848	0.000	0.000	0.000	0.000
55	A	632	ILE	0	-0.084	-0.016	18.000	0.551	0.551	0.000	0.000	0.000	0.000
56	A	633	ALA	0	0.041	0.012	22.204	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	634	PRO	0	0.080	0.012	21.105	-0.632	-0.632	0.000	0.000	0.000	0.000
58	A	635	GLN	0	0.030	0.029	20.110	-0.526	-0.526	0.000	0.000	0.000	0.000
59	A	636	GLN	0	-0.035	-0.011	20.276	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	637	ARG	1	0.874	0.964	16.629	13.746	13.746	0.000	0.000	0.000	0.000
61	A	638	ARG	1	0.843	0.900	12.827	17.510	17.510	0.000	0.000	0.000	0.000
62	A	639	GLY	0	0.003	0.005	9.855	-0.456	-0.456	0.000	0.000	0.000	0.000
63	A	640	GLU	-1	-0.947	-0.977	9.094	-25.000	-25.000	0.000	0.000	0.000	0.000
64	A	641	PRO	0	-0.018	-0.012	11.491	0.536	0.536	0.000	0.000	0.000	0.000
65	A	642	VAL	0	0.016	0.014	13.294	-0.530	-0.530	0.000	0.000	0.000	0.000
66	A	643	PRO	0	0.026	0.017	15.029	0.717	0.717	0.000	0.000	0.000	0.000
67	A	644	GLN	0	0.001	-0.035	18.201	-0.361	-0.361	0.000	0.000	0.000	0.000
68	A	645	ASP	-1	-0.839	-0.914	20.860	-13.281	-13.281	0.000	0.000	0.000	0.000
69	A	646	LEU	0	0.040	0.012	15.548	0.010	0.010	0.000	0.000	0.000	0.000
70	A	647	LEU	0	-0.075	-0.035	17.046	-0.082	-0.082	0.000	0.000	0.000	0.000
71	A	648	ASP	-1	-0.820	-0.905	19.884	-11.647	-11.647	0.000	0.000	0.000	0.000
72	A	649	ARG	1	0.769	0.853	20.562	13.264	13.264	0.000	0.000	0.000	0.000
73	A	650	VAL	0	-0.035	-0.001	17.036	0.089	0.089	0.000	0.000	0.000	0.000
74	A	651	LEU	0	-0.022	-0.017	19.941	0.275	0.275	0.000	0.000	0.000	0.000
75	A	652	ALA	0	0.018	0.022	22.899	0.367	0.367	0.000	0.000	0.000	0.000
76	A	653	ALA	0	0.030	0.014	21.314	0.331	0.331	0.000	0.000	0.000	0.000
77	A	654	HIS	0	-0.013	-0.013	21.062	-0.064	-0.064	0.000	0.000	0.000	0.000
78	A	655	ALA	0	-0.016	0.005	22.730	0.284	0.284	0.000	0.000	0.000	0.000
79	A	656	TYR	0	-0.010	-0.008	26.188	0.453	0.453	0.000	0.000	0.000	0.000
80	A	657	TRP	0	-0.018	-0.005	22.775	0.416	0.416	0.000	0.000	0.000	0.000
81	A	658	SER	0	-0.124	-0.067	24.547	0.037	0.037	0.000	0.000	0.000	0.000
82	A	659	GLN	0	-0.115	-0.057	26.521	0.467	0.467	0.000	0.000	0.000	0.000
83	A	660	GLN	0	-0.018	0.015	28.254	0.330	0.330	0.000	0.000	0.000	0.000

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