FMO DATABASE

FMODB ID: QV6NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-257289.526151
FMO2-HF: Nuclear repulsion	236379.336824
FMO2-HF: Total energy	-20910.189328
FMO2-MP2: Total energy	-20973.323653

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.
-5.904	-1.071	0.889	-2.197	-3.526	-0.006

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 : 0.052 / q_NPA : 0.014

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	0.024	0.019	2.589	-1.484	1.052	0.444	-1.082	-1.898	0.000
4	A	14	GLU	-1	-0.852	-0.922	2.964	0.020	1.219	0.390	-0.716	-0.873	-0.007
5	A	15	SER	0	-0.015	-0.033	5.571	0.159	0.159	0.000	0.000	0.000	0.000
6	A	16	ILE	0	0.000	0.005	7.320	-0.118	-0.118	0.000	0.000	0.000	0.000
7	A	17	GLU	-1	-0.818	-0.889	10.026	0.216	0.216	0.000	0.000	0.000	0.000
8	A	18	LYS	1	0.895	0.935	13.392	-0.109	-0.109	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.983	1.000	14.361	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	20	ARG	1	0.813	0.900	16.625	0.028	0.028	0.000	0.000	0.000	0.000
11	A	21	ILE	0	0.043	0.024	19.007	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	22	ARG	1	0.842	0.901	20.566	0.056	0.056	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.926	0.956	22.277	0.049	0.049	0.000	0.000	0.000	0.000
14	A	24	GLY	0	0.039	0.023	24.166	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	25	ARG	1	0.837	0.912	18.061	0.113	0.113	0.000	0.000	0.000	0.000
16	A	26	VAL	0	-0.022	-0.016	16.202	0.014	0.014	0.000	0.000	0.000	0.000
17	A	27	GLU	-1	-0.750	-0.840	15.238	-0.071	-0.071	0.000	0.000	0.000	0.000
18	A	28	TYR	0	0.038	-0.012	11.500	0.042	0.042	0.000	0.000	0.000	0.000
19	A	29	LEU	0	-0.061	-0.019	12.519	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	30	VAL	0	0.022	0.012	7.118	0.058	0.058	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.800	0.917	9.250	-0.283	-0.283	0.000	0.000	0.000	0.000
22	A	32	TRP	0	0.010	-0.018	5.976	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	33	ARG	1	0.860	0.917	2.823	-3.744	-2.646	0.055	-0.399	-0.755	0.001
24	A	34	GLY	0	-0.012	0.007	7.807	-0.097	-0.097	0.000	0.000	0.000	0.000
25	A	35	TRP	0	-0.013	0.007	10.356	0.000	0.000	0.000	0.000	0.000	0.000
26	A	36	SER	0	0.016	-0.004	13.138	0.030	0.030	0.000	0.000	0.000	0.000
27	A	37	PRO	0	0.090	0.015	14.909	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	38	LYS	1	0.854	0.944	15.931	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	39	TYR	0	-0.002	-0.005	14.478	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	40	ASN	0	0.019	0.011	12.509	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	41	THR	0	-0.029	-0.030	12.274	0.002	0.002	0.000	0.000	0.000	0.000
32	A	42	TRP	0	-0.047	-0.032	12.786	0.013	0.013	0.000	0.000	0.000	0.000
33	A	43	GLU	-1	-0.764	-0.839	9.912	-0.194	-0.194	0.000	0.000	0.000	0.000
34	A	44	PRO	0	-0.003	-0.006	12.972	0.025	0.025	0.000	0.000	0.000	0.000
35	A	45	GLU	-1	-0.814	-0.914	11.970	-0.123	-0.123	0.000	0.000	0.000	0.000
36	A	46	GLU	-1	-0.836	-0.896	10.956	-0.186	-0.186	0.000	0.000	0.000	0.000
37	A	47	ASN	0	-0.053	-0.034	10.496	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	48	ILE	0	-0.055	-0.032	6.603	-0.073	-0.073	0.000	0.000	0.000	0.000
39	A	49	LEU	0	-0.038	-0.001	6.051	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	50	ASP	-1	-0.817	-0.912	5.567	-1.034	-1.034	0.000	0.000	0.000	0.000
41	A	51	PRO	0	0.035	0.003	7.053	0.150	0.150	0.000	0.000	0.000	0.000
42	A	52	ARG	1	0.886	0.943	8.806	0.667	0.667	0.000	0.000	0.000	0.000
43	A	53	LEU	0	-0.036	-0.013	8.677	0.053	0.053	0.000	0.000	0.000	0.000
44	A	54	LEU	0	-0.052	-0.011	12.168	0.053	0.053	0.000	0.000	0.000	0.000
45	A	55	ILE	0	-0.004	-0.001	14.926	0.002	0.002	0.000	0.000	0.000	0.000
46	A	56	ALA	0	0.024	0.009	18.322	0.005	0.005	0.000	0.000	0.000	0.000
47	A	57	PHE	0	-0.013	-0.025	20.369	0.009	0.009	0.000	0.000	0.000	0.000
48	A	58	GLN	0	0.048	0.043	20.753	0.017	0.017	0.000	0.000	0.000	0.000
49	A	59	ASN	0	0.047	0.028	23.739	0.000	0.000	0.000	0.000	0.000	0.000
50	A	60	ARG	1	0.873	0.942	24.963	0.092	0.092	0.000	0.000	0.000	0.000

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