FMO DATABASE

FMODB ID: R82Y8

Calculation Name: 3I8Z-A-Xray372

Preferred Name: E3 SUMO-protein ligase CBX4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3I8Z

Chain ID: A

ChEMBL ID: CHEMBL3232685

UniProt ID: O00257

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	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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-257781.856754
FMO2-HF: Nuclear repulsion	236871.7687
FMO2-HF: Total energy	-20910.088054
FMO2-MP2: Total energy	-20973.24848

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:11:PHE)

Summations of interaction energy for fragment #1(A:11:PHE)

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.
-9.582	-4.197	0.995	-2.405	-3.974	0.004

Interaction energy analysis for fragmet #1(A:11:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.012

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	13	VAL	0	0.029	0.020	2.339	-1.428	1.045	0.651	-1.098	-2.025	0.001
4	A	14	GLU	-1	-0.895	-0.937	3.118	0.643	1.715	0.157	-0.503	-0.727	-0.004
5	A	15	SER	0	-0.011	-0.029	5.411	0.158	0.158	0.000	0.000	0.000	0.000
6	A	16	ILE	0	-0.007	0.009	7.407	-0.139	-0.139	0.000	0.000	0.000	0.000
7	A	17	GLU	-1	-0.852	-0.920	9.808	0.322	0.322	0.000	0.000	0.000	0.000
8	A	18	LYS	1	0.911	0.942	13.232	-0.156	-0.156	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.982	1.000	14.457	-0.056	-0.056	0.000	0.000	0.000	0.000
10	A	20	ARG	1	0.817	0.905	16.724	0.004	0.004	0.000	0.000	0.000	0.000
11	A	21	ILE	0	0.030	0.023	19.020	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	22	ARG	1	0.851	0.903	20.235	0.044	0.044	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.927	0.958	22.530	0.045	0.045	0.000	0.000	0.000	0.000
14	A	24	GLY	0	0.030	0.011	24.467	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	25	ARG	1	0.873	0.941	18.525	0.102	0.102	0.000	0.000	0.000	0.000
16	A	26	VAL	0	-0.001	0.005	16.242	0.016	0.016	0.000	0.000	0.000	0.000
17	A	27	GLU	-1	-0.738	-0.834	15.197	-0.054	-0.054	0.000	0.000	0.000	0.000
18	A	28	TYR	0	0.046	-0.008	11.341	0.043	0.043	0.000	0.000	0.000	0.000
19	A	29	LEU	0	-0.055	-0.013	12.437	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	30	VAL	0	0.021	0.015	7.245	0.064	0.064	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.838	0.933	9.483	-0.477	-0.477	0.000	0.000	0.000	0.000
22	A	32	TRP	0	-0.003	-0.026	5.880	0.045	0.045	0.000	0.000	0.000	0.000
23	A	33	ARG	1	0.875	0.932	2.855	-7.822	-5.982	0.187	-0.804	-1.222	0.007
24	A	34	GLY	0	-0.002	-0.002	7.538	-0.164	-0.164	0.000	0.000	0.000	0.000
25	A	35	TRP	0	-0.016	0.009	10.082	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	36	SER	0	0.008	-0.010	12.797	0.030	0.030	0.000	0.000	0.000	0.000
27	A	37	PRO	0	0.111	0.027	14.690	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	38	LYS	1	0.848	0.949	15.723	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	39	TYR	0	-0.017	-0.024	14.194	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	40	ASN	0	0.024	0.023	12.656	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	41	THR	0	-0.016	-0.022	11.820	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	42	TRP	0	-0.054	-0.032	12.631	0.017	0.017	0.000	0.000	0.000	0.000
33	A	43	GLU	-1	-0.756	-0.850	9.751	-0.170	-0.170	0.000	0.000	0.000	0.000
34	A	44	PRO	0	-0.004	-0.003	12.896	0.024	0.024	0.000	0.000	0.000	0.000
35	A	45	GLU	-1	-0.835	-0.930	12.129	-0.114	-0.114	0.000	0.000	0.000	0.000
36	A	46	GLU	-1	-0.877	-0.925	11.018	-0.190	-0.190	0.000	0.000	0.000	0.000
37	A	47	ASN	0	-0.062	-0.039	10.520	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	48	ILE	0	-0.049	-0.032	6.723	-0.074	-0.074	0.000	0.000	0.000	0.000
39	A	49	LEU	0	-0.055	-0.011	6.155	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	50	ASP	-1	-0.802	-0.909	5.897	-1.117	-1.117	0.000	0.000	0.000	0.000
41	A	51	PRO	0	0.041	0.013	7.276	0.148	0.148	0.000	0.000	0.000	0.000
42	A	52	ARG	1	0.879	0.939	8.957	0.735	0.735	0.000	0.000	0.000	0.000
43	A	53	LEU	0	-0.051	-0.022	9.077	0.058	0.058	0.000	0.000	0.000	0.000
44	A	54	LEU	0	-0.039	-0.005	12.368	0.059	0.059	0.000	0.000	0.000	0.000
45	A	55	ILE	0	-0.004	0.002	15.051	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	56	ALA	0	-0.002	-0.003	18.475	0.004	0.004	0.000	0.000	0.000	0.000
47	A	57	PHE	0	-0.003	-0.019	20.637	0.011	0.011	0.000	0.000	0.000	0.000
48	A	58	GLN	0	0.048	0.040	21.230	0.018	0.018	0.000	0.000	0.000	0.000
49	A	59	ASN	0	0.037	0.021	24.290	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	60	ARG	1	0.895	0.952	25.321	0.102	0.102	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:PHE)