FMO DATABASE

FMODB ID: ZV8NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-257154.585757
FMO2-HF: Nuclear repulsion	236244.815692
FMO2-HF: Total energy	-20909.770065
FMO2-MP2: Total energy	-20972.920464

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.
-4.866	0.755	1.056	-2.578	-4.099	-0.003

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 : 0.045 / 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

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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	0.030	0.020	2.335	-2.341	0.439	0.658	-1.276	-2.162	0.003
4	A	14	GLU	-1	-0.955	-0.969	3.181	-1.975	-0.891	0.149	-0.501	-0.732	-0.004
5	A	15	SER	0	-0.017	-0.033	5.460	-0.028	-0.028	0.000	0.000	0.000	0.000
6	A	16	ILE	0	-0.010	0.004	7.505	0.080	0.080	0.000	0.000	0.000	0.000
7	A	17	GLU	-1	-0.869	-0.917	9.763	-0.260	-0.260	0.000	0.000	0.000	0.000
8	A	18	LYS	1	0.908	0.945	13.280	0.171	0.171	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.988	1.000	14.428	0.194	0.194	0.000	0.000	0.000	0.000
10	A	20	ARG	1	0.834	0.928	16.702	0.130	0.130	0.000	0.000	0.000	0.000
11	A	21	ILE	0	0.035	0.029	19.015	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	22	ARG	1	0.839	0.896	19.922	0.112	0.112	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.918	0.953	22.606	0.077	0.077	0.000	0.000	0.000	0.000
14	A	24	GLY	0	0.032	0.013	24.579	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	25	ARG	1	0.993	1.009	19.306	0.122	0.122	0.000	0.000	0.000	0.000
16	A	26	VAL	0	0.040	0.024	15.719	0.014	0.014	0.000	0.000	0.000	0.000
17	A	27	GLU	-1	-0.751	-0.857	15.208	-0.133	-0.133	0.000	0.000	0.000	0.000
18	A	28	TYR	0	0.054	-0.002	11.256	0.010	0.010	0.000	0.000	0.000	0.000
19	A	29	LEU	0	-0.065	-0.021	12.425	0.008	0.008	0.000	0.000	0.000	0.000
20	A	30	VAL	0	0.025	0.016	7.158	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.862	0.950	9.410	0.175	0.175	0.000	0.000	0.000	0.000
22	A	32	TRP	0	-0.028	-0.028	6.029	-0.201	-0.201	0.000	0.000	0.000	0.000
23	A	33	ARG	1	0.919	0.939	2.717	-0.083	1.674	0.249	-0.801	-1.205	-0.002
24	A	34	GLY	0	-0.011	-0.008	7.419	0.207	0.207	0.000	0.000	0.000	0.000
25	A	35	TRP	0	-0.012	0.011	10.148	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	36	SER	0	0.001	-0.014	12.797	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	37	PRO	0	0.104	0.024	14.646	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	38	LYS	1	0.891	0.970	15.671	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	39	TYR	0	-0.029	-0.025	14.159	0.007	0.007	0.000	0.000	0.000	0.000
30	A	40	ASN	0	0.050	0.027	12.620	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	41	THR	0	-0.023	0.003	11.705	0.012	0.012	0.000	0.000	0.000	0.000
32	A	42	TRP	0	-0.044	-0.026	12.615	-0.035	-0.035	0.000	0.000	0.000	0.000
33	A	43	GLU	-1	-0.753	-0.885	9.747	-0.140	-0.140	0.000	0.000	0.000	0.000
34	A	44	PRO	0	-0.012	-0.005	12.905	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	45	GLU	-1	-0.891	-0.957	12.225	-0.267	-0.267	0.000	0.000	0.000	0.000
36	A	46	GLU	-1	-0.972	-0.985	11.131	-0.226	-0.226	0.000	0.000	0.000	0.000
37	A	47	ASN	0	-0.062	-0.037	10.537	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	48	ILE	0	-0.053	-0.036	6.653	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	49	LEU	0	-0.063	-0.017	6.266	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	50	ASP	-1	-0.819	-0.916	6.240	-1.177	-1.177	0.000	0.000	0.000	0.000
41	A	51	PRO	0	0.043	0.017	7.379	0.132	0.132	0.000	0.000	0.000	0.000
42	A	52	ARG	1	0.889	0.941	9.143	0.670	0.670	0.000	0.000	0.000	0.000
43	A	53	LEU	0	-0.046	-0.019	9.386	0.046	0.046	0.000	0.000	0.000	0.000
44	A	54	LEU	0	-0.030	-0.001	12.559	0.050	0.050	0.000	0.000	0.000	0.000
45	A	55	ILE	0	-0.008	0.001	15.175	0.002	0.002	0.000	0.000	0.000	0.000
46	A	56	ALA	0	-0.006	-0.004	18.633	0.014	0.014	0.000	0.000	0.000	0.000
47	A	57	PHE	0	-0.012	-0.024	20.770	0.008	0.008	0.000	0.000	0.000	0.000
48	A	58	GLN	0	0.029	0.026	21.362	0.012	0.012	0.000	0.000	0.000	0.000
49	A	59	ASN	0	0.007	0.005	24.376	0.004	0.004	0.000	0.000	0.000	0.000
50	A	60	ARG	1	0.954	0.987	24.896	0.105	0.105	0.000	0.000	0.000	0.000

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