FMO DATABASE

FMODB ID: 897NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-340261.599747
FMO2-HF: Nuclear repulsion	315297.358103
FMO2-HF: Total energy	-24964.241644
FMO2-MP2: Total energy	-25038.140604

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.
-16.709	-9.008	1.894	-3.729	-5.863	-0.028

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 : -0.030 / q_NPA : -0.019

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	-2	TYR	0	0.039	0.011	2.881	-2.858	-0.743	0.046	-0.754	-1.406	0.003
4	A	-1	PHE	0	0.002	-0.003	6.830	0.456	0.456	0.000	0.000	0.000	0.000
5	A	0	GLN	0	-0.025	-0.011	10.382	-0.235	-0.235	0.000	0.000	0.000	0.000
6	A	1	GLY	0	0.004	0.003	12.890	0.184	0.184	0.000	0.000	0.000	0.000
7	A	2	ALA	0	-0.019	-0.025	16.204	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.047	-0.033	18.288	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	4	GLY	0	0.012	0.014	16.777	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	5	ASP	-1	-0.904	-0.937	13.981	-1.213	-1.213	0.000	0.000	0.000	0.000
11	A	6	LEU	0	-0.018	-0.011	8.094	0.071	0.071	0.000	0.000	0.000	0.000
12	A	7	TYR	0	-0.027	-0.011	10.361	-0.076	-0.076	0.000	0.000	0.000	0.000
13	A	8	GLU	-1	-0.898	-0.956	5.021	-2.733	-2.733	0.000	0.000	0.000	0.000
14	A	9	VAL	0	-0.046	-0.013	5.359	0.570	0.570	0.000	0.000	0.000	0.000
15	A	10	GLU	-1	-0.903	-0.936	4.692	2.032	2.121	-0.001	-0.003	-0.085	0.000
16	A	11	ARG	1	0.940	0.956	6.253	-0.514	-0.514	0.000	0.000	0.000	0.000
17	A	12	ILE	0	0.018	0.019	7.833	-0.727	-0.727	0.000	0.000	0.000	0.000
18	A	13	VAL	0	-0.106	-0.064	10.298	0.091	0.091	0.000	0.000	0.000	0.000
19	A	14	ASP	-1	-0.838	-0.921	13.703	0.744	0.744	0.000	0.000	0.000	0.000
20	A	15	LYS	1	0.877	0.947	14.590	-0.904	-0.904	0.000	0.000	0.000	0.000
21	A	16	ARG	1	0.862	0.948	16.771	-0.449	-0.449	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.931	0.981	19.566	-0.380	-0.380	0.000	0.000	0.000	0.000
23	A	18	ASN	0	0.018	0.008	22.058	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	19	LYS	1	0.996	0.980	23.953	-0.136	-0.136	0.000	0.000	0.000	0.000
25	A	20	LYS	1	0.899	0.944	25.209	-0.109	-0.109	0.000	0.000	0.000	0.000
26	A	21	GLY	0	0.014	0.022	24.999	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.874	0.937	17.351	-0.230	-0.230	0.000	0.000	0.000	0.000
28	A	23	TRP	0	0.002	-0.011	16.757	0.021	0.021	0.000	0.000	0.000	0.000
29	A	24	GLU	-1	-0.818	-0.909	16.704	0.232	0.232	0.000	0.000	0.000	0.000
30	A	25	TYR	0	-0.029	-0.054	12.560	0.140	0.140	0.000	0.000	0.000	0.000
31	A	26	LEU	0	0.009	0.023	14.569	-0.115	-0.115	0.000	0.000	0.000	0.000
32	A	27	ILE	0	-0.002	0.008	9.657	0.347	0.347	0.000	0.000	0.000	0.000
33	A	28	ARG	1	0.793	0.879	10.450	-1.038	-1.038	0.000	0.000	0.000	0.000
34	A	29	TRP	0	0.043	0.007	9.404	0.263	0.263	0.000	0.000	0.000	0.000
35	A	30	LYS	1	0.876	0.928	6.910	-0.225	-0.225	0.000	0.000	0.000	0.000
36	A	31	GLY	0	-0.019	-0.011	9.681	-0.196	-0.196	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.016	0.011	12.990	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	33	GLY	0	-0.001	-0.010	14.249	0.120	0.120	0.000	0.000	0.000	0.000
39	A	34	SER	0	-0.032	-0.037	16.566	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	35	THR	0	-0.053	-0.029	17.671	0.008	0.008	0.000	0.000	0.000	0.000
41	A	36	GLU	-1	-0.915	-0.954	16.761	0.053	0.053	0.000	0.000	0.000	0.000
42	A	37	ASP	-1	-0.738	-0.827	15.142	0.721	0.721	0.000	0.000	0.000	0.000
43	A	38	THR	0	-0.025	-0.031	15.254	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	39	TRP	0	-0.057	-0.035	15.308	0.098	0.098	0.000	0.000	0.000	0.000
45	A	40	GLU	-1	-0.771	-0.872	13.604	0.016	0.016	0.000	0.000	0.000	0.000
46	A	41	PRO	0	-0.051	-0.019	15.516	0.124	0.124	0.000	0.000	0.000	0.000
47	A	42	GLU	-1	-0.785	-0.910	13.128	0.485	0.485	0.000	0.000	0.000	0.000
48	A	43	HIS	0	-0.075	-0.029	12.913	0.034	0.034	0.000	0.000	0.000	0.000
49	A	44	HIS	0	0.018	0.024	13.886	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	45	LEU	0	-0.034	-0.006	9.101	-0.111	-0.111	0.000	0.000	0.000	0.000
51	A	46	LEU	0	-0.011	0.000	7.646	0.113	0.113	0.000	0.000	0.000	0.000
52	A	47	HIS	0	0.013	-0.004	2.653	-3.498	-1.658	0.403	-0.877	-1.366	-0.007
53	A	48	CYS	0	-0.050	-0.019	2.771	0.679	1.826	0.209	-0.324	-1.032	0.000
54	A	49	GLU	-1	-0.937	-0.976	2.479	-5.278	-2.848	1.238	-1.769	-1.898	-0.024
55	A	50	GLU	-1	-0.939	-0.956	5.107	-3.091	-3.011	-0.001	-0.002	-0.076	0.000
56	A	51	PHE	0	-0.013	-0.010	7.516	0.489	0.489	0.000	0.000	0.000	0.000
57	A	52	ILE	0	-0.033	-0.023	10.806	0.140	0.140	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.983	-0.979	13.554	-0.522	-0.522	0.000	0.000	0.000	0.000
59	A	54	GLU	-1	-1.009	-1.003	15.677	-0.059	-0.059	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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