FMO DATABASE

FMODB ID: G6281

Calculation Name: 2FAZ-A-Xray372

Preferred Name: E3 ubiquitin-protein ligase UHRF1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2FAZ

Chain ID: A

ChEMBL ID: CHEMBL2424510

UniProt ID: Q96T88

Base Structure: X-ray

Registration Date: 2023-09-19

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-562728.900217
FMO2-HF: Nuclear repulsion	530113.175232
FMO2-HF: Total energy	-32615.724985
FMO2-MP2: Total energy	-32710.654576

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: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.
-6.239	-2.561	2.43	-3.077	-3.031	-0.013

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 : 0 / q_Mulliken : -0.034 / q_NPA : -0.022

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	2	TRP	0	0.044	0.020	3.863	-0.295	1.784	-0.025	-1.119	-0.935	0.001
4	A	3	ILE	0	0.006	0.005	7.182	-0.279	-0.279	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.007	0.001	10.587	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.032	0.023	14.064	0.021	0.021	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.881	0.922	16.502	-0.247	-0.247	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.022	-0.010	20.249	0.016	0.016	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.024	-0.019	23.482	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.808	-0.869	25.851	0.143	0.143	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.028	-0.014	24.877	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.863	0.920	25.220	-0.115	-0.115	0.000	0.000	0.000	0.000
13	A	12	GLN	0	0.035	0.018	22.546	0.011	0.011	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.012	0.002	18.204	0.012	0.012	0.000	0.000	0.000	0.000
15	A	14	HIS	1	0.870	0.944	15.923	-0.315	-0.315	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.016	0.013	10.407	0.007	0.007	0.000	0.000	0.000	0.000
17	A	16	VAL	0	0.015	0.014	9.550	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.825	-0.915	6.203	1.350	1.350	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.010	-0.017	4.353	-0.273	-0.131	-0.001	-0.017	-0.124	0.000
20	A	19	LEU	0	-0.027	0.006	4.066	-1.150	-0.961	-0.001	-0.041	-0.147	0.000
21	A	20	SER	0	0.036	0.011	2.387	-0.217	0.970	2.456	-1.866	-1.777	-0.014
22	A	21	ARG	1	1.028	1.015	4.240	-3.130	-3.049	0.001	-0.034	-0.048	0.000
23	A	22	LEU	0	-0.002	-0.001	7.158	-0.599	-0.599	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.046	-0.035	6.806	-0.192	-0.192	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.869	0.937	9.202	-0.786	-0.786	0.000	0.000	0.000	0.000
26	A	25	VAL	0	0.019	0.016	12.844	0.057	0.057	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.722	-0.867	15.205	0.603	0.603	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.878	-0.931	10.719	0.878	0.878	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.008	0.001	11.666	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.809	0.861	13.365	-0.493	-0.493	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.867	0.939	14.326	-0.703	-0.703	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.911	0.971	8.226	-1.557	-1.557	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.033	-0.016	14.142	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.042	-0.038	16.845	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.908	-0.960	14.821	0.509	0.509	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.055	-0.019	13.922	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.084	-0.058	17.017	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	37	HIS	0	-0.021	0.011	21.399	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.019	0.012	22.594	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.800	-0.886	22.480	0.272	0.272	0.000	0.000	0.000	0.000
41	A	40	PRO	0	0.018	0.000	20.123	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.020	0.018	22.368	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.039	-0.012	25.696	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.023	-0.026	19.343	0.018	0.018	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.787	0.891	23.114	-0.262	-0.262	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.054	0.034	16.624	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.007	-0.013	20.195	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	47	TYR	0	0.015	-0.020	15.646	0.014	0.014	0.000	0.000	0.000	0.000
49	A	48	ARG	1	0.822	0.897	16.961	-0.333	-0.333	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.034	0.027	21.998	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.872	0.948	20.950	-0.362	-0.362	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.046	-0.044	21.836	0.012	0.012	0.000	0.000	0.000	0.000
53	A	52	MET	0	-0.010	-0.010	14.808	0.006	0.006	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.843	-0.899	20.035	0.312	0.312	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.799	-0.883	18.637	0.519	0.519	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.052	-0.029	18.218	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	56	HIS	0	0.031	0.028	17.122	0.028	0.028	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.055	-0.061	11.574	0.099	0.099	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.028	0.003	8.216	-0.118	-0.118	0.000	0.000	0.000	0.000
60	A	59	PHE	0	0.005	-0.011	10.352	-0.112	-0.112	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.816	-0.870	12.071	0.586	0.586	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.059	-0.037	14.839	-0.121	-0.121	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.888	-0.925	14.137	0.260	0.260	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.023	-0.003	11.467	-0.058	-0.058	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.899	0.941	10.045	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.003	-0.004	6.118	0.091	0.091	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.031	-0.021	9.076	-0.059	-0.059	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.741	-0.832	11.567	0.325	0.325	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.054	-0.036	13.765	0.030	0.030	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.009	0.014	14.350	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.035	-0.035	17.072	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.013	0.010	19.976	0.026	0.026	0.000	0.000	0.000	0.000
73	A	72	LEU	0	0.002	0.001	21.682	-0.031	-0.031	0.000	0.000	0.000	0.000
74	A	73	VAL	0	0.040	0.012	24.664	0.019	0.019	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.903	0.949	26.812	-0.204	-0.204	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.043	0.013	29.580	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	76	SER	0	0.015	0.024	31.091	0.000	0.000	0.000	0.000	0.000	0.000

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