FMO DATABASE

FMODB ID: 17L5Z

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	OptHSide
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	-561737.796669
FMO2-HF: Nuclear repulsion	529122.305191
FMO2-HF: Total energy	-32615.491478
FMO2-MP2: Total energy	-32710.446812

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.
-8.134	-3.234	2.693	-3.838	-3.754	-0.017

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 : -0.045 / q_NPA : -0.028

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	0.087	0.043	3.758	-1.211	1.789	-0.054	-1.561	-1.384	-0.002
4	A	3	ILE	0	0.004	0.006	7.115	-0.252	-0.252	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.003	0.001	10.362	-0.035	-0.035	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.045	0.023	13.837	0.022	0.022	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.917	0.950	16.237	-0.229	-0.229	0.000	0.000	0.000	0.000
8	A	7	THR	0	0.009	-0.014	19.947	0.017	0.017	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.016	-0.015	23.161	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.818	-0.882	25.453	0.135	0.135	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.020	-0.001	24.855	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.853	0.917	25.138	-0.111	-0.111	0.000	0.000	0.000	0.000
13	A	12	GLN	0	0.035	0.021	21.837	0.005	0.005	0.000	0.000	0.000	0.000
14	A	13	THR	0	-0.003	-0.013	17.436	0.017	0.017	0.000	0.000	0.000	0.000
15	A	14	HIS	1	0.877	0.945	15.588	-0.286	-0.286	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.020	0.013	9.954	0.029	0.029	0.000	0.000	0.000	0.000
17	A	16	VAL	0	0.007	0.028	9.331	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.864	-0.939	5.951	1.079	1.079	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.018	-0.022	3.387	-0.969	-0.378	0.030	-0.250	-0.371	0.002
20	A	19	LEU	0	-0.039	0.008	4.345	-1.165	-0.879	-0.001	-0.055	-0.230	0.000
21	A	20	SER	0	0.051	0.017	2.368	-0.133	0.817	2.716	-1.946	-1.719	-0.017
22	A	21	ARG	1	1.066	1.028	3.972	-3.260	-3.187	0.002	-0.026	-0.050	0.000
23	A	22	LEU	0	-0.002	-0.002	7.014	-0.658	-0.658	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.053	-0.039	6.631	-0.251	-0.251	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.861	0.938	9.020	-0.799	-0.799	0.000	0.000	0.000	0.000
26	A	25	VAL	0	0.050	0.025	12.804	0.047	0.047	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.734	-0.865	14.821	0.615	0.615	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.868	-0.938	10.894	0.846	0.846	0.000	0.000	0.000	0.000
29	A	28	LEU	0	0.001	0.006	11.217	0.017	0.017	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.790	0.856	13.083	-0.515	-0.515	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.870	0.933	14.582	-0.685	-0.685	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.938	0.994	8.777	-1.425	-1.425	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.028	-0.017	14.247	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.028	-0.020	16.622	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.915	-0.951	14.780	0.445	0.445	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.051	-0.021	13.457	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.097	-0.060	17.122	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	37	HIS	0	-0.001	0.011	21.112	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	38	VAL	0	-0.006	0.005	22.176	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.792	-0.898	22.198	0.258	0.258	0.000	0.000	0.000	0.000
41	A	40	PRO	0	0.039	0.011	20.031	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.002	0.009	22.070	0.002	0.002	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.025	-0.003	25.169	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.041	-0.025	19.147	0.021	0.021	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.810	0.899	22.775	-0.266	-0.266	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.050	0.028	16.477	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.005	-0.007	20.116	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	47	TYR	0	0.026	-0.017	15.262	0.002	0.002	0.000	0.000	0.000	0.000
49	A	48	ARG	1	0.846	0.921	16.668	-0.390	-0.390	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.008	0.010	21.565	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.933	0.976	20.795	-0.364	-0.364	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.065	-0.057	21.311	0.012	0.012	0.000	0.000	0.000	0.000
53	A	52	MET	0	-0.033	-0.018	14.336	0.009	0.009	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.852	-0.911	19.605	0.326	0.326	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.793	-0.881	18.426	0.529	0.529	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.071	-0.041	17.991	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	56	HIS	0	0.031	0.030	16.861	0.024	0.024	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.051	-0.060	11.348	0.095	0.095	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.009	-0.011	7.776	-0.112	-0.112	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.014	-0.018	10.232	-0.101	-0.101	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.794	-0.855	11.839	0.601	0.601	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.080	-0.044	14.664	-0.124	-0.124	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.917	-0.954	13.792	0.306	0.306	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.033	-0.011	10.705	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.905	0.944	9.779	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.020	-0.016	5.856	0.067	0.067	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.034	-0.020	8.803	-0.039	-0.039	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.737	-0.811	11.110	0.356	0.356	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.076	-0.060	13.207	0.027	0.027	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.027	-0.003	14.281	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.007	-0.016	16.916	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.009	0.017	19.753	0.025	0.025	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.011	-0.008	21.394	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	73	VAL	0	0.056	0.020	24.516	0.020	0.020	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.887	0.933	26.480	-0.207	-0.207	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.031	0.006	29.325	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	76	SER	0	0.028	0.030	31.333	0.004	0.004	0.000	0.000	0.000	0.000

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