FMO DATABASE

FMODB ID: V5GV1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-560894.269732
FMO2-HF: Nuclear repulsion	528279.244921
FMO2-HF: Total energy	-32615.024811
FMO2-MP2: Total energy	-32709.993005

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.
-8.232	-3.172	2.808	-3.968	-3.902	-0.018

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 : -0.043 / q_NPA : -0.031

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	0.082	0.043	3.758	-1.154	1.927	-0.057	-1.597	-1.428	-0.003
4	A	3	ILE	0	-0.011	-0.001	7.045	-0.269	-0.269	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.017	-0.006	10.342	-0.027	-0.027	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.053	0.028	13.802	0.026	0.026	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.947	0.978	16.218	-0.196	-0.196	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.011	-0.042	19.927	0.018	0.018	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.021	-0.018	23.142	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.841	-0.876	25.434	0.130	0.130	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.023	-0.008	24.838	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.903	0.948	25.066	-0.101	-0.101	0.000	0.000	0.000	0.000
13	A	12	GLN	0	0.041	0.025	21.500	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.003	-0.018	17.307	0.017	0.017	0.000	0.000	0.000	0.000
15	A	14	HIS	1	0.877	0.946	15.465	-0.259	-0.259	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.029	0.020	9.973	0.035	0.035	0.000	0.000	0.000	0.000
17	A	16	VAL	0	-0.005	0.021	9.369	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.878	-0.955	5.796	0.765	0.765	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.027	-0.016	3.288	-1.215	-0.544	0.046	-0.287	-0.430	0.002
20	A	19	LEU	0	-0.019	0.017	4.316	-1.073	-0.769	-0.001	-0.058	-0.245	0.000
21	A	20	SER	0	0.037	0.006	2.356	0.132	1.058	2.818	-1.998	-1.746	-0.017
22	A	21	ARG	1	1.041	1.010	3.969	-3.342	-3.264	0.002	-0.028	-0.053	0.000
23	A	22	LEU	0	-0.005	-0.001	7.008	-0.682	-0.682	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.031	-0.010	6.724	-0.278	-0.278	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.977	0.992	9.015	-0.894	-0.894	0.000	0.000	0.000	0.000
26	A	25	VAL	0	0.060	0.031	12.798	0.049	0.049	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.806	-0.894	14.812	0.625	0.625	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.904	-0.968	10.650	0.932	0.932	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.001	0.001	11.425	0.012	0.012	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.798	0.875	13.071	-0.538	-0.538	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.923	0.974	14.973	-0.700	-0.700	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.932	0.988	8.842	-1.397	-1.397	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.016	-0.014	14.236	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.002	0.002	16.608	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.941	-0.962	14.662	0.431	0.431	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.056	-0.021	13.423	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.096	-0.061	16.979	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	37	HIS	0	0.002	0.007	21.010	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.005	0.015	22.162	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.854	-0.941	22.186	0.251	0.251	0.000	0.000	0.000	0.000
41	A	40	PRO	0	0.040	0.004	20.227	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	41	GLY	0	-0.011	0.007	22.059	0.002	0.002	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.024	-0.010	25.163	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.026	-0.018	19.046	0.021	0.021	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.828	0.914	22.807	-0.266	-0.266	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.044	0.026	16.383	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.006	-0.005	20.107	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	47	TYR	0	0.013	-0.032	15.142	0.006	0.006	0.000	0.000	0.000	0.000
49	A	48	ARG	1	0.941	0.969	17.038	-0.338	-0.338	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.005	0.009	21.548	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.953	0.986	20.968	-0.359	-0.359	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.071	-0.054	21.296	0.008	0.008	0.000	0.000	0.000	0.000
53	A	52	MET	0	-0.053	-0.022	14.098	0.005	0.005	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.859	-0.926	19.624	0.333	0.333	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.783	-0.892	18.427	0.552	0.552	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.082	-0.050	18.046	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	56	HIS	0	0.020	0.033	16.855	0.025	0.025	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.045	-0.036	11.349	0.103	0.103	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.007	-0.012	7.771	-0.124	-0.124	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.009	-0.018	10.317	-0.099	-0.099	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.791	-0.875	11.839	0.610	0.610	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.087	-0.046	14.657	-0.135	-0.135	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.995	-1.001	13.749	0.365	0.365	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.047	-0.016	10.489	-0.074	-0.074	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.914	0.947	9.646	0.019	0.019	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.014	-0.015	5.755	0.067	0.067	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.022	-0.024	8.698	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.753	-0.813	11.110	0.307	0.307	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.083	-0.063	13.187	0.029	0.029	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.027	0.000	14.299	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	70	GLN	0	0.004	-0.013	16.897	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.009	0.019	19.784	0.027	0.027	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.015	-0.015	21.376	-0.034	-0.034	0.000	0.000	0.000	0.000
74	A	73	VAL	0	0.054	0.021	24.500	0.021	0.021	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.872	0.930	26.465	-0.210	-0.210	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.042	0.010	29.310	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	76	SER	0	0.024	0.028	31.118	0.005	0.005	0.000	0.000	0.000	0.000

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