FMO DATABASE

FMODB ID: MLRLZ

Calculation Name: 2FAZ-A-Xray547

Preferred Name: E3 ubiquitin-protein ligase UHRF1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FAZ

Chain ID: A

ChEMBL ID: CHEMBL2424510

UniProt ID: Q96T88

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-562074.593381
FMO2-HF: Nuclear repulsion	529459.0466
FMO2-HF: Total energy	-32615.54678
FMO2-MP2: Total energy	-32710.435642

3D Structure Molmil

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
22.526	26.709	3.589	-3.931	-3.842	-0.032

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.902

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	TRP	0	0.076	0.035	3.841	0.260	2.159	-0.024	-0.881	-0.995	-0.002
19	A	18	SER	0	-0.032	-0.019	3.365	-0.240	0.246	0.033	-0.174	-0.346	0.001
20	A	19	LEU	0	0.006	0.029	3.922	2.199	2.530	0.001	-0.094	-0.237	0.000
21	A	20	SER	0	-0.019	-0.026	2.232	-22.077	-20.690	3.579	-2.758	-2.208	-0.031
22	A	21	ARG	1	1.055	1.026	4.200	40.421	40.501	0.000	-0.024	-0.056	0.000
4	A	3	ILE	0	0.006	0.009	6.813	-0.126	-0.126	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.013	-0.002	10.537	1.785	1.785	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.041	0.026	13.800	0.084	0.084	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.893	0.934	16.161	15.805	15.805	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.018	-0.001	19.836	-0.161	-0.161	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.016	-0.015	23.144	-0.127	-0.127	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.811	-0.878	25.659	-10.875	-10.875	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.025	-0.012	24.602	0.281	0.281	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.863	0.924	24.636	9.688	9.688	0.000	0.000	0.000	0.000
13	A	12	GLN	0	0.044	0.029	21.468	-0.414	-0.414	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.003	-0.001	17.251	-0.279	-0.279	0.000	0.000	0.000	0.000
15	A	14	HIS	1	0.892	0.945	15.231	15.853	15.853	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.013	0.011	9.639	0.311	0.311	0.000	0.000	0.000	0.000
17	A	16	VAL	0	0.026	0.027	9.191	0.710	0.710	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.854	-0.944	5.500	-32.071	-32.071	0.000	0.000	0.000	0.000
23	A	22	LEU	0	0.006	0.000	6.968	3.850	3.850	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.052	-0.035	6.691	1.415	1.415	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.850	0.929	9.120	19.171	19.171	0.000	0.000	0.000	0.000
26	A	25	VAL	0	0.021	0.018	12.835	-0.772	-0.772	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.723	-0.864	15.198	-17.419	-17.419	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.894	-0.938	10.826	-21.664	-21.664	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.012	-0.005	11.607	-0.177	-0.177	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.813	0.866	13.390	15.297	15.297	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.865	0.940	14.583	18.921	18.921	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.939	0.982	8.258	28.070	28.070	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.022	-0.012	14.002	0.383	0.383	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.023	-0.007	16.657	0.350	0.350	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.914	-0.964	14.315	-18.143	-18.143	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.059	-0.022	12.994	0.282	0.282	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.096	-0.065	16.513	0.441	0.441	0.000	0.000	0.000	0.000
38	A	37	HIS	0	-0.025	0.008	20.714	0.804	0.804	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.026	0.017	22.128	0.496	0.496	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.817	-0.910	22.307	-12.282	-12.282	0.000	0.000	0.000	0.000
41	A	40	PRO	0	0.003	-0.009	20.221	0.149	0.149	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.013	0.013	22.315	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.009	0.017	25.654	0.224	0.224	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.030	-0.030	19.368	-0.408	-0.408	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.818	0.901	23.142	11.728	11.728	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.037	0.023	16.587	0.010	0.010	0.000	0.000	0.000	0.000
47	A	46	PHE	0	0.005	-0.005	20.088	0.331	0.331	0.000	0.000	0.000	0.000
48	A	47	TYR	0	0.002	-0.026	15.231	-0.252	-0.252	0.000	0.000	0.000	0.000
49	A	48	ARG	1	0.895	0.946	16.632	17.641	17.641	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.040	0.028	21.841	0.503	0.503	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.921	0.979	20.768	14.432	14.432	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.047	-0.047	21.571	-0.350	-0.350	0.000	0.000	0.000	0.000
53	A	52	MET	0	-0.027	-0.015	14.641	-0.277	-0.277	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.836	-0.899	19.904	-12.696	-12.696	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.807	-0.888	18.637	-16.160	-16.160	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.026	-0.024	18.364	0.651	0.651	0.000	0.000	0.000	0.000
57	A	56	HIS	0	0.023	0.031	16.978	-0.741	-0.741	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.059	-0.058	11.457	-1.177	-1.177	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.021	-0.004	8.177	0.944	0.944	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.015	-0.022	9.994	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.783	-0.854	11.665	-18.651	-18.651	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.079	-0.050	14.546	1.705	1.705	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.953	-0.976	14.022	-17.806	-17.806	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.054	-0.013	11.146	-0.068	-0.068	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.904	0.937	9.747	20.142	20.142	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.020	-0.015	6.116	-0.810	-0.810	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.019	-0.019	9.194	2.336	2.336	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.750	-0.828	11.465	-20.160	-20.160	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.067	-0.041	13.611	-0.166	-0.166	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.015	0.007	14.201	0.494	0.494	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.004	-0.020	16.917	0.060	0.060	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.011	0.011	19.961	-0.180	-0.180	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.011	-0.007	21.480	0.493	0.493	0.000	0.000	0.000	0.000
74	A	73	VAL	0	0.028	0.007	24.700	-0.295	-0.295	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.820	0.899	26.682	10.437	10.437	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.007	-0.008	29.456	0.062	0.062	0.000	0.000	0.000	0.000
77	A	76	SER	-1	-0.845	-0.892	31.331	-9.583	-9.583	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)