FMO DATABASE

FMODB ID: 98762

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

Total energy (hartree)

FMO2-HF: Electronic energy	-579672.42655
FMO2-HF: Nuclear repulsion	546577.199427
FMO2-HF: Total energy	-33095.227123
FMO2-MP2: Total energy	-33193.906965

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.
-8.632	-5.952	0.007	-1.167	-1.521	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 : 1.025 / q_NPA : 1.008

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	0.001	0.015	3.898	-2.902	-1.191	-0.007	-0.870	-0.835	0.003
4	A	581	SER	0	0.033	0.006	6.729	2.075	2.075	0.000	0.000	0.000	0.000
5	A	582	VAL	0	0.050	0.006	8.365	1.093	1.093	0.000	0.000	0.000	0.000
6	A	583	ALA	0	0.016	0.019	11.792	0.986	0.986	0.000	0.000	0.000	0.000
7	A	584	GLU	-1	-0.739	-0.835	6.900	-30.831	-30.831	0.000	0.000	0.000	0.000
8	A	585	VAL	0	-0.049	-0.032	10.546	0.601	0.601	0.000	0.000	0.000	0.000
9	A	586	GLU	-1	-0.808	-0.890	12.748	-13.144	-13.144	0.000	0.000	0.000	0.000
10	A	587	ALA	0	0.002	0.008	13.426	0.765	0.765	0.000	0.000	0.000	0.000
11	A	588	LEU	0	-0.062	-0.032	11.407	0.520	0.520	0.000	0.000	0.000	0.000
12	A	589	VAL	0	-0.033	-0.016	14.531	0.700	0.700	0.000	0.000	0.000	0.000
13	A	590	GLU	-1	-0.740	-0.829	17.661	-11.966	-11.966	0.000	0.000	0.000	0.000
14	A	591	ALA	0	0.025	0.014	16.856	0.687	0.687	0.000	0.000	0.000	0.000
15	A	592	VAL	0	-0.034	-0.028	17.095	0.504	0.504	0.000	0.000	0.000	0.000
16	A	593	GLU	-1	-0.792	-0.887	19.771	-11.852	-11.852	0.000	0.000	0.000	0.000
17	A	594	HIS	0	-0.065	-0.035	22.371	0.945	0.945	0.000	0.000	0.000	0.000
18	A	595	LEU	0	-0.098	-0.042	20.006	0.412	0.412	0.000	0.000	0.000	0.000
19	A	596	GLY	0	0.057	0.026	22.542	0.195	0.195	0.000	0.000	0.000	0.000
20	A	597	THR	0	-0.024	-0.032	19.714	-0.398	-0.398	0.000	0.000	0.000	0.000
21	A	598	GLY	0	0.013	-0.001	20.332	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	599	ARG	1	0.852	0.934	20.933	10.920	10.920	0.000	0.000	0.000	0.000
23	A	600	TRP	0	0.025	0.004	15.310	-0.484	-0.484	0.000	0.000	0.000	0.000
24	A	601	ARG	1	0.906	0.948	15.906	12.668	12.668	0.000	0.000	0.000	0.000
25	A	602	ASP	-1	-0.766	-0.879	17.654	-12.186	-12.186	0.000	0.000	0.000	0.000
26	A	603	VAL	0	-0.009	-0.002	14.792	-0.136	-0.136	0.000	0.000	0.000	0.000
27	A	604	LYS	1	0.815	0.908	11.173	18.896	18.896	0.000	0.000	0.000	0.000
28	A	605	MET	0	-0.016	-0.016	14.854	-0.104	-0.104	0.000	0.000	0.000	0.000
29	A	606	ARG	1	0.772	0.867	18.016	12.357	12.357	0.000	0.000	0.000	0.000
30	A	607	ALA	0	0.002	0.005	15.068	0.246	0.246	0.000	0.000	0.000	0.000
31	A	608	PHE	0	-0.044	-0.032	9.515	-1.139	-1.139	0.000	0.000	0.000	0.000
32	A	609	ASP	-1	-0.892	-0.928	12.543	-15.362	-15.362	0.000	0.000	0.000	0.000
33	A	610	ASN	0	0.011	-0.001	14.232	-0.709	-0.709	0.000	0.000	0.000	0.000
34	A	611	ALA	0	-0.009	0.001	9.122	-0.863	-0.863	0.000	0.000	0.000	0.000
35	A	612	ASP	-1	-0.861	-0.947	9.471	-19.994	-19.994	0.000	0.000	0.000	0.000
36	A	613	HIS	0	-0.123	-0.049	3.974	0.339	0.585	0.000	-0.029	-0.216	0.000
37	A	614	ARG	1	0.753	0.846	3.090	34.383	35.106	0.014	-0.268	-0.470	0.000
38	A	615	THR	0	0.040	-0.006	7.644	3.065	3.065	0.000	0.000	0.000	0.000
39	A	616	TYR	0	0.070	0.008	10.467	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	617	VAL	0	-0.023	-0.005	10.997	0.701	0.701	0.000	0.000	0.000	0.000
41	A	618	ASP	-1	-0.777	-0.857	6.204	-27.334	-27.334	0.000	0.000	0.000	0.000
42	A	619	LEU	0	-0.018	0.011	8.558	-0.495	-0.495	0.000	0.000	0.000	0.000
43	A	620	LYS	1	0.860	0.933	11.159	18.368	18.368	0.000	0.000	0.000	0.000
44	A	621	ASP	-1	-0.838	-0.922	9.608	-19.059	-19.059	0.000	0.000	0.000	0.000
45	A	622	LYS	1	0.876	0.962	8.029	24.832	24.832	0.000	0.000	0.000	0.000
46	A	623	TRP	0	0.105	0.051	10.149	0.365	0.365	0.000	0.000	0.000	0.000
47	A	624	LYS	1	0.969	0.995	13.811	15.265	15.265	0.000	0.000	0.000	0.000
48	A	625	THR	0	-0.064	-0.058	10.178	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	626	LEU	0	0.008	0.029	12.740	0.231	0.231	0.000	0.000	0.000	0.000
50	A	627	VAL	0	0.057	0.028	15.003	0.652	0.652	0.000	0.000	0.000	0.000
51	A	628	HIS	0	-0.046	-0.003	16.174	0.907	0.907	0.000	0.000	0.000	0.000
52	A	629	THR	0	-0.033	-0.048	14.789	0.238	0.238	0.000	0.000	0.000	0.000
53	A	630	ALA	0	-0.001	-0.002	17.317	0.388	0.388	0.000	0.000	0.000	0.000
54	A	631	SER	0	-0.018	-0.020	20.220	0.756	0.756	0.000	0.000	0.000	0.000
55	A	632	ILE	0	-0.078	-0.018	17.942	0.515	0.515	0.000	0.000	0.000	0.000
56	A	633	ALA	0	0.062	0.025	22.084	-0.157	-0.157	0.000	0.000	0.000	0.000
57	A	634	PRO	0	0.055	0.003	21.197	-0.509	-0.509	0.000	0.000	0.000	0.000
58	A	635	GLN	0	0.008	0.007	20.598	-0.348	-0.348	0.000	0.000	0.000	0.000
59	A	636	GLN	0	-0.003	0.006	20.479	-0.149	-0.149	0.000	0.000	0.000	0.000
60	A	637	ARG	1	0.843	0.947	16.816	13.251	13.251	0.000	0.000	0.000	0.000
61	A	638	ARG	1	0.838	0.901	13.455	16.686	16.686	0.000	0.000	0.000	0.000
62	A	639	GLY	0	0.010	0.010	10.228	-0.635	-0.635	0.000	0.000	0.000	0.000
63	A	640	GLU	-1	-0.873	-0.947	8.631	-25.341	-25.341	0.000	0.000	0.000	0.000
64	A	641	PRO	0	-0.025	-0.024	11.181	0.603	0.603	0.000	0.000	0.000	0.000
65	A	642	VAL	0	-0.004	0.010	13.135	0.120	0.120	0.000	0.000	0.000	0.000
66	A	643	PRO	0	0.029	0.019	15.275	0.627	0.627	0.000	0.000	0.000	0.000
67	A	644	GLN	0	0.011	-0.010	18.539	-0.519	-0.519	0.000	0.000	0.000	0.000
68	A	645	ASP	-1	-0.820	-0.909	21.437	-13.159	-13.159	0.000	0.000	0.000	0.000
69	A	646	LEU	0	0.037	0.013	16.260	0.061	0.061	0.000	0.000	0.000	0.000
70	A	647	LEU	0	-0.062	-0.031	16.730	-0.170	-0.170	0.000	0.000	0.000	0.000
71	A	648	ASP	-1	-0.838	-0.910	20.197	-11.349	-11.349	0.000	0.000	0.000	0.000
72	A	649	ARG	1	0.751	0.838	21.127	13.174	13.174	0.000	0.000	0.000	0.000
73	A	650	VAL	0	-0.036	-0.010	17.531	0.085	0.085	0.000	0.000	0.000	0.000
74	A	651	LEU	0	-0.038	-0.020	20.562	0.252	0.252	0.000	0.000	0.000	0.000
75	A	652	ALA	0	0.006	0.010	23.598	0.351	0.351	0.000	0.000	0.000	0.000
76	A	653	ALA	0	0.039	0.017	22.099	0.322	0.322	0.000	0.000	0.000	0.000
77	A	654	HIS	0	0.008	-0.004	21.448	-0.123	-0.123	0.000	0.000	0.000	0.000
78	A	655	ALA	0	-0.019	0.002	23.259	0.267	0.267	0.000	0.000	0.000	0.000
79	A	656	TYR	0	-0.013	0.000	26.845	0.289	0.289	0.000	0.000	0.000	0.000
80	A	657	TRP	0	0.029	0.014	23.723	0.388	0.388	0.000	0.000	0.000	0.000
81	A	658	SER	0	-0.098	-0.052	25.014	0.094	0.094	0.000	0.000	0.000	0.000
82	A	659	GLN	0	-0.109	-0.053	27.116	0.484	0.484	0.000	0.000	0.000	0.000
83	A	660	GLN	0	-0.060	-0.014	28.612	0.374	0.374	0.000	0.000	0.000	0.000

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