FMO DATABASE

FMODB ID: XN2MQ

Calculation Name: 3I8Z-A-Xray40

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: 2019-02-15

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	89
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-312706.661198
FMO2-HF: Nuclear repulsion	288812.73377
FMO2-HF: Total energy	-23893.927428
FMO2-MP2: Total energy	-23964.776428

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:10:ACE)

Summations of interaction energy for fragment #1(A:10:ACE)

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.
1.885	2.895	0.185	-0.301	-0.894	-0.004

Interaction energy analysis for fragmet #1(A:10:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / 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	12	ALA	0	0.069	0.054	3.870	1.258	1.939	-0.010	-0.291	-0.380	0.000
4	A	13	VAL	0	0.022	0.019	7.142	0.379	0.379	0.000	0.000	0.000	0.000
5	A	14	GLU	-1	-0.894	-0.932	6.436	0.109	0.109	0.000	0.000	0.000	0.000
6	A	15	SER	0	-0.006	-0.030	7.648	0.119	0.119	0.000	0.000	0.000	0.000
7	A	16	ILE	0	-0.003	0.008	10.431	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.823	-0.889	13.016	0.026	0.026	0.000	0.000	0.000	0.000
9	A	18	LYS	1	0.912	0.949	16.140	0.062	0.062	0.000	0.000	0.000	0.000
10	A	19	LYS	1	0.956	0.976	18.334	0.053	0.053	0.000	0.000	0.000	0.000
11	A	20	ARG	1	0.821	0.908	20.718	0.122	0.122	0.000	0.000	0.000	0.000
12	A	21	ILE	0	0.038	0.034	23.617	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	22	ARG	1	0.870	0.918	25.165	0.121	0.121	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.932	0.966	27.756	0.088	0.088	0.000	0.000	0.000	0.000
15	A	24	GLY	0	0.025	0.010	29.592	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	25	ARG	1	0.947	0.997	24.727	0.125	0.125	0.000	0.000	0.000	0.000
17	A	26	VAL	0	0.033	0.017	20.253	0.009	0.009	0.000	0.000	0.000	0.000
18	A	27	GLU	-1	-0.737	-0.842	20.217	-0.151	-0.151	0.000	0.000	0.000	0.000
19	A	28	TYR	0	0.016	-0.031	15.758	0.032	0.032	0.000	0.000	0.000	0.000
20	A	29	LEU	0	-0.058	-0.016	17.215	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.019	0.013	11.526	0.009	0.009	0.000	0.000	0.000	0.000
22	A	31	LYS	1	0.827	0.936	11.763	0.005	0.005	0.000	0.000	0.000	0.000
23	A	32	TRP	0	-0.028	-0.033	10.557	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	33	ARG	1	0.864	0.912	4.220	-0.146	-0.009	0.004	-0.050	-0.091	0.000
25	A	34	GLY	0	0.005	-0.012	8.905	-0.059	-0.059	0.000	0.000	0.000	0.000
26	A	35	TRP	0	-0.020	0.007	11.441	0.016	0.016	0.000	0.000	0.000	0.000
27	A	36	SER	0	-0.003	-0.022	14.359	0.005	0.005	0.000	0.000	0.000	0.000
28	A	37	PRO	0	0.090	0.018	17.117	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	38	LYS	1	0.900	0.979	18.030	0.031	0.031	0.000	0.000	0.000	0.000
30	A	39	TYR	0	-0.043	-0.018	16.960	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	40	ASN	0	0.054	0.033	16.136	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	41	THR	0	-0.024	0.011	16.553	0.014	0.014	0.000	0.000	0.000	0.000
33	A	42	TRP	0	-0.027	-0.020	17.304	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.763	-0.890	15.009	-0.291	-0.291	0.000	0.000	0.000	0.000
35	A	44	PRO	0	-0.018	-0.005	18.171	0.009	0.009	0.000	0.000	0.000	0.000
36	A	45	GLU	-1	-0.762	-0.862	17.456	-0.203	-0.203	0.000	0.000	0.000	0.000
37	A	46	GLU	-1	-0.891	-0.928	16.837	-0.233	-0.233	0.000	0.000	0.000	0.000
38	A	47	ASN	0	-0.007	0.001	16.380	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	48	ILE	0	-0.034	-0.018	11.961	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.057	-0.010	12.065	-0.090	-0.090	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.729	-0.871	12.601	-0.446	-0.446	0.000	0.000	0.000	0.000
42	A	51	PRO	0	0.064	0.034	14.177	0.061	0.061	0.000	0.000	0.000	0.000
43	A	52	ARG	1	0.901	0.961	15.045	0.331	0.331	0.000	0.000	0.000	0.000
44	A	53	LEU	0	-0.025	-0.008	14.999	0.033	0.033	0.000	0.000	0.000	0.000
45	A	54	LEU	0	-0.034	0.002	18.722	0.021	0.021	0.000	0.000	0.000	0.000
46	A	55	ILE	0	0.021	0.020	21.784	0.007	0.007	0.000	0.000	0.000	0.000
47	A	56	ALA	0	0.038	0.024	24.974	0.000	0.000	0.000	0.000	0.000	0.000
48	A	57	PHE	0	0.012	-0.002	27.214	0.006	0.006	0.000	0.000	0.000	0.000
49	A	58	GLN	0	0.025	0.038	28.259	0.012	0.012	0.000	0.000	0.000	0.000
50	A	59	ASN	0	0.037	0.017	31.155	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	60	ARG	1	0.879	0.940	31.888	0.085	0.085	0.000	0.000	0.000	0.000
52	A	61	NME	0	0.039	0.032	35.746	0.004	0.004	0.000	0.000	0.000	0.000
53	A	1	HOH	0	0.013	0.009	19.104	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	2	HOH	0	0.035	0.020	21.734	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	3	HOH	0	0.013	0.003	14.924	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	4	HOH	0	-0.012	-0.003	10.556	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	5	HOH	0	-0.042	-0.028	23.100	0.004	0.004	0.000	0.000	0.000	0.000
58	A	6	HOH	0	-0.024	-0.023	25.368	0.002	0.002	0.000	0.000	0.000	0.000
59	A	7	HOH	0	-0.016	-0.019	18.533	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	HOH	0	-0.003	0.001	5.171	0.139	0.139	0.000	0.000	0.000	0.000
61	A	64	HOH	0	-0.018	-0.026	21.757	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	66	HOH	0	-0.023	-0.010	3.084	0.573	0.765	0.191	0.040	-0.423	-0.004
63	A	67	HOH	0	0.031	0.023	20.809	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	68	HOH	0	-0.013	-0.010	22.307	0.006	0.006	0.000	0.000	0.000	0.000
65	A	69	HOH	0	-0.009	-0.010	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	70	HOH	0	-0.053	-0.040	16.465	0.015	0.015	0.000	0.000	0.000	0.000
67	A	71	HOH	0	-0.035	-0.024	24.291	0.001	0.001	0.000	0.000	0.000	0.000
68	A	75	HOH	0	0.020	0.020	25.704	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	78	HOH	0	0.048	0.035	22.452	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	79	HOH	0	-0.033	-0.020	12.112	0.016	0.016	0.000	0.000	0.000	0.000
71	A	80	HOH	0	-0.022	-0.018	16.487	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	82	HOH	0	-0.033	-0.020	13.956	0.025	0.025	0.000	0.000	0.000	0.000
73	A	83	HOH	0	-0.051	-0.046	26.075	0.002	0.002	0.000	0.000	0.000	0.000
74	A	86	HOH	0	-0.016	-0.016	20.701	0.008	0.008	0.000	0.000	0.000	0.000
75	A	87	HOH	0	-0.038	-0.023	20.829	0.007	0.007	0.000	0.000	0.000	0.000
76	A	88	HOH	0	-0.038	-0.031	33.683	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	89	HOH	0	-0.034	-0.024	14.060	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	90	HOH	0	-0.009	-0.011	22.727	0.001	0.001	0.000	0.000	0.000	0.000
79	A	91	HOH	0	-0.076	-0.059	20.558	0.000	0.000	0.000	0.000	0.000	0.000
80	A	92	HOH	0	0.036	0.021	22.230	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	95	HOH	0	-0.011	-0.013	23.734	0.005	0.005	0.000	0.000	0.000	0.000
82	A	97	HOH	0	0.027	0.019	25.560	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	100	HOH	0	-0.042	-0.029	20.200	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	101	HOH	0	-0.005	-0.010	23.415	0.003	0.003	0.000	0.000	0.000	0.000
85	A	108	HOH	0	-0.018	-0.015	33.242	0.001	0.001	0.000	0.000	0.000	0.000
86	A	110	HOH	0	0.029	0.022	36.282	0.000	0.000	0.000	0.000	0.000	0.000
87	A	111	HOH	0	-0.015	-0.012	9.628	-0.069	-0.069	0.000	0.000	0.000	0.000
88	A	112	HOH	0	-0.012	-0.018	30.766	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	113	HOH	0	-0.043	-0.025	22.841	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ACE)