FMO DATABASE

FMODB ID: JQY29

Calculation Name: 5JJZ-A-Xray372

Preferred Name: Chromodomain Y-like protein 2

Target Type: SINGLE PROTEIN

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 5JJZ

Chain ID: A

ChEMBL ID: CHEMBL3879857

UniProt ID: Q8N8U2

Base Structure: X-ray

Registration Date: 2023-09-22

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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-339464.495821
FMO2-HF: Nuclear repulsion	314499.860962
FMO2-HF: Total energy	-24964.634859
FMO2-MP2: Total energy	-25038.572234

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:-4:ASN)

Summations of interaction energy for fragment #1(A:-4:ASN)

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.
-18.839	-11.034	2.962	-4.334	-6.433	-0.036

Interaction energy analysis for fragmet #1(A:-4:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.018

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	-2	TYR	0	-0.012	-0.034	2.283	-4.575	-1.949	1.046	-1.460	-2.212	-0.005
4	A	-1	PHE	0	-0.022	-0.014	6.622	0.757	0.757	0.000	0.000	0.000	0.000
5	A	0	GLN	0	-0.026	-0.017	10.428	-0.217	-0.217	0.000	0.000	0.000	0.000
6	A	1	GLY	0	0.024	0.020	12.897	0.201	0.201	0.000	0.000	0.000	0.000
7	A	2	ALA	0	-0.028	-0.031	16.207	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.026	-0.010	17.899	0.025	0.025	0.000	0.000	0.000	0.000
9	A	4	GLY	0	-0.014	-0.001	16.551	0.007	0.007	0.000	0.000	0.000	0.000
10	A	5	ASP	-1	-0.839	-0.883	14.229	-1.445	-1.445	0.000	0.000	0.000	0.000
11	A	6	LEU	0	-0.015	-0.016	8.699	0.052	0.052	0.000	0.000	0.000	0.000
12	A	7	TYR	0	-0.078	-0.058	10.120	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	8	GLU	-1	-0.797	-0.887	4.702	-5.877	-5.754	-0.001	-0.008	-0.113	0.000
14	A	9	VAL	0	-0.038	-0.021	5.618	0.808	0.808	0.000	0.000	0.000	0.000
15	A	10	GLU	-1	-0.893	-0.934	5.032	1.313	1.355	-0.001	-0.001	-0.041	0.000
16	A	11	ARG	1	0.900	0.941	6.517	-0.319	-0.319	0.000	0.000	0.000	0.000
17	A	12	ILE	0	0.030	0.026	7.948	-0.640	-0.640	0.000	0.000	0.000	0.000
18	A	13	VAL	0	-0.072	-0.040	10.459	0.203	0.203	0.000	0.000	0.000	0.000
19	A	14	ASP	-1	-0.841	-0.925	13.778	0.559	0.559	0.000	0.000	0.000	0.000
20	A	15	LYS	1	0.811	0.915	14.994	-0.562	-0.562	0.000	0.000	0.000	0.000
21	A	16	ARG	1	0.873	0.943	17.292	-0.170	-0.170	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.860	0.932	20.033	-0.225	-0.225	0.000	0.000	0.000	0.000
23	A	18	ASN	0	0.024	0.004	22.718	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	19	LYS	1	0.989	0.979	24.742	0.018	0.018	0.000	0.000	0.000	0.000
25	A	20	LYS	1	0.894	0.942	25.940	0.002	0.002	0.000	0.000	0.000	0.000
26	A	21	GLY	0	0.030	0.033	25.594	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.860	0.934	17.261	0.026	0.026	0.000	0.000	0.000	0.000
28	A	23	TRP	0	0.001	-0.016	17.497	0.029	0.029	0.000	0.000	0.000	0.000
29	A	24	GLU	-1	-0.806	-0.884	17.417	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	25	TYR	0	0.024	-0.025	12.469	0.120	0.120	0.000	0.000	0.000	0.000
31	A	26	LEU	0	-0.003	0.018	15.213	-0.102	-0.102	0.000	0.000	0.000	0.000
32	A	27	ILE	0	0.002	-0.003	10.172	0.253	0.253	0.000	0.000	0.000	0.000
33	A	28	ARG	1	0.799	0.876	10.687	-0.575	-0.575	0.000	0.000	0.000	0.000
34	A	29	TRP	0	0.009	-0.008	9.786	0.043	0.043	0.000	0.000	0.000	0.000
35	A	30	LYS	1	0.818	0.906	6.319	0.303	0.303	0.000	0.000	0.000	0.000
36	A	31	GLY	0	0.006	0.007	9.744	-0.148	-0.148	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.022	0.002	13.067	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	33	GLY	0	0.013	-0.004	14.736	0.122	0.122	0.000	0.000	0.000	0.000
39	A	34	SER	0	-0.010	-0.028	17.128	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	35	THR	0	-0.121	-0.084	18.191	0.022	0.022	0.000	0.000	0.000	0.000
41	A	36	GLU	-1	-0.859	-0.898	16.798	-0.103	-0.103	0.000	0.000	0.000	0.000
42	A	37	ASP	-1	-0.764	-0.834	15.234	0.332	0.332	0.000	0.000	0.000	0.000
43	A	38	THR	0	-0.031	-0.033	15.766	0.015	0.015	0.000	0.000	0.000	0.000
44	A	39	TRP	0	-0.057	-0.042	15.857	0.068	0.068	0.000	0.000	0.000	0.000
45	A	40	GLU	-1	-0.762	-0.849	13.954	-0.309	-0.309	0.000	0.000	0.000	0.000
46	A	41	PRO	0	-0.052	-0.030	16.104	0.116	0.116	0.000	0.000	0.000	0.000
47	A	42	GLU	-1	-0.736	-0.877	13.833	0.206	0.206	0.000	0.000	0.000	0.000
48	A	43	HIS	0	-0.059	-0.032	13.531	0.024	0.024	0.000	0.000	0.000	0.000
49	A	44	HIS	0	0.035	0.028	14.481	-0.056	-0.056	0.000	0.000	0.000	0.000
50	A	45	LEU	0	-0.041	-0.008	9.742	-0.156	-0.156	0.000	0.000	0.000	0.000
51	A	46	LEU	0	-0.009	-0.001	8.072	0.130	0.130	0.000	0.000	0.000	0.000
52	A	47	HIS	0	-0.049	-0.046	2.548	-2.555	-1.165	0.690	-0.815	-1.265	-0.007
53	A	48	CYS	0	-0.058	-0.023	2.934	0.581	1.585	0.126	-0.244	-0.886	0.000
54	A	49	GLU	-1	-0.869	-0.920	2.512	-4.847	-2.306	1.103	-1.804	-1.841	-0.024
55	A	50	GLU	-1	-0.905	-0.947	4.956	-2.309	-2.230	-0.001	-0.002	-0.075	0.000
56	A	51	PHE	0	-0.048	-0.024	7.716	0.293	0.293	0.000	0.000	0.000	0.000
57	A	52	ILE	0	-0.029	-0.022	10.831	0.183	0.183	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.962	-0.974	13.659	-0.446	-0.446	0.000	0.000	0.000	0.000
59	A	54	GLU	-1	-1.022	-1.005	15.662	0.061	0.061	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:ASN)