FMO DATABASE

FMODB ID: NN82Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-340442.475908
FMO2-HF: Nuclear repulsion	315477.980613
FMO2-HF: Total energy	-24964.495295
FMO2-MP2: Total energy	-25038.435563

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.
-17.574	-10.279	1.809	-3.53	-5.574	-0.031

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 : -0.036 / 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	-0.018	-0.032	2.633	-3.094	-0.838	0.184	-0.832	-1.607	0.001
4	A	-1	PHE	0	0.000	-0.001	6.830	0.478	0.478	0.000	0.000	0.000	0.000
5	A	0	GLN	0	-0.027	-0.020	10.384	-0.227	-0.227	0.000	0.000	0.000	0.000
6	A	1	GLY	0	0.009	0.006	12.770	0.193	0.193	0.000	0.000	0.000	0.000
7	A	2	ALA	0	-0.023	-0.026	16.103	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.037	-0.028	18.255	0.001	0.001	0.000	0.000	0.000	0.000
9	A	4	GLY	0	0.009	0.013	16.644	0.004	0.004	0.000	0.000	0.000	0.000
10	A	5	ASP	-1	-0.874	-0.903	14.025	-1.265	-1.265	0.000	0.000	0.000	0.000
11	A	6	LEU	0	0.007	0.003	8.324	0.067	0.067	0.000	0.000	0.000	0.000
12	A	7	TYR	0	-0.065	-0.049	10.303	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	8	GLU	-1	-0.820	-0.906	4.960	-3.789	-3.789	0.000	0.000	0.000	0.000
14	A	9	VAL	0	-0.047	-0.020	5.368	0.665	0.665	0.000	0.000	0.000	0.000
15	A	10	GLU	-1	-0.908	-0.933	4.684	2.065	2.148	-0.001	-0.003	-0.078	0.000
16	A	11	ARG	1	0.935	0.957	6.232	-0.463	-0.463	0.000	0.000	0.000	0.000
17	A	12	ILE	0	0.013	0.020	7.807	-0.713	-0.713	0.000	0.000	0.000	0.000
18	A	13	VAL	0	-0.091	-0.065	10.273	0.123	0.123	0.000	0.000	0.000	0.000
19	A	14	ASP	-1	-0.829	-0.916	13.675	0.647	0.647	0.000	0.000	0.000	0.000
20	A	15	LYS	1	0.846	0.923	14.633	-0.682	-0.682	0.000	0.000	0.000	0.000
21	A	16	ARG	1	0.862	0.937	16.771	-0.330	-0.330	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.913	0.972	19.639	-0.292	-0.292	0.000	0.000	0.000	0.000
23	A	18	ASN	0	0.002	-0.011	22.130	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	19	LYS	1	1.000	0.982	24.028	-0.072	-0.072	0.000	0.000	0.000	0.000
25	A	20	LYS	1	0.906	0.950	25.358	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	21	GLY	0	0.011	0.019	25.070	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.851	0.915	17.133	-0.072	-0.072	0.000	0.000	0.000	0.000
28	A	23	TRP	0	-0.009	-0.013	16.770	0.032	0.032	0.000	0.000	0.000	0.000
29	A	24	GLU	-1	-0.804	-0.878	16.771	0.122	0.122	0.000	0.000	0.000	0.000
30	A	25	TYR	0	0.006	-0.039	12.557	0.134	0.134	0.000	0.000	0.000	0.000
31	A	26	LEU	0	0.015	0.028	14.549	-0.110	-0.110	0.000	0.000	0.000	0.000
32	A	27	ILE	0	-0.005	0.004	9.698	0.321	0.321	0.000	0.000	0.000	0.000
33	A	28	ARG	1	0.808	0.875	10.463	-0.939	-0.939	0.000	0.000	0.000	0.000
34	A	29	TRP	0	0.016	-0.004	9.391	0.215	0.215	0.000	0.000	0.000	0.000
35	A	30	LYS	1	0.844	0.915	6.694	-0.547	-0.547	0.000	0.000	0.000	0.000
36	A	31	GLY	0	-0.009	-0.005	9.682	-0.204	-0.204	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.024	0.000	12.989	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	33	GLY	0	0.011	-0.001	14.242	0.126	0.126	0.000	0.000	0.000	0.000
39	A	34	SER	0	-0.010	-0.030	16.555	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	35	THR	0	-0.121	-0.079	17.656	0.014	0.014	0.000	0.000	0.000	0.000
41	A	36	GLU	-1	-0.859	-0.904	16.557	0.050	0.050	0.000	0.000	0.000	0.000
42	A	37	ASP	-1	-0.748	-0.823	14.897	0.654	0.654	0.000	0.000	0.000	0.000
43	A	38	THR	0	-0.021	-0.030	15.239	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	39	TRP	0	-0.078	-0.043	15.293	0.079	0.079	0.000	0.000	0.000	0.000
45	A	40	GLU	-1	-0.768	-0.866	13.611	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	41	PRO	0	-0.049	-0.021	15.513	0.112	0.112	0.000	0.000	0.000	0.000
47	A	42	GLU	-1	-0.760	-0.878	13.241	0.304	0.304	0.000	0.000	0.000	0.000
48	A	43	HIS	0	-0.064	-0.033	12.984	0.008	0.008	0.000	0.000	0.000	0.000
49	A	44	HIS	0	0.022	0.029	13.886	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	45	LEU	0	-0.042	-0.007	9.237	-0.115	-0.115	0.000	0.000	0.000	0.000
51	A	46	LEU	0	-0.013	0.001	7.862	0.130	0.130	0.000	0.000	0.000	0.000
52	A	47	HIS	0	-0.048	-0.050	2.986	-3.171	-1.577	0.225	-0.767	-1.053	-0.008
53	A	48	CYS	0	-0.054	-0.015	2.963	0.841	1.921	0.142	-0.290	-0.932	0.000
54	A	49	GLU	-1	-0.875	-0.933	2.453	-5.876	-3.666	1.260	-1.636	-1.835	-0.024
55	A	50	GLU	-1	-0.924	-0.958	5.055	-2.501	-2.429	-0.001	-0.002	-0.069	0.000
56	A	51	PHE	0	-0.031	-0.011	7.817	0.348	0.348	0.000	0.000	0.000	0.000
57	A	52	ILE	0	-0.033	-0.021	10.792	0.174	0.174	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.967	-0.978	13.494	-0.544	-0.544	0.000	0.000	0.000	0.000
59	A	54	GLU	-1	-1.014	-1.002	15.570	-0.076	-0.076	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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