FMO DATABASE

FMODB ID: ZYL7N

Calculation Name: 2AZ2-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 5-bromo-uridine-5'-monophosphate

ligand 3-letter code: 5BU

PDB ID: 2AZ2

Chain ID: B

ChEMBL ID:

UniProt ID: P68831

Base Structure: X-ray

Registration Date: 2023-03-13

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-352983.069351
FMO2-HF: Nuclear repulsion	325461.350441
FMO2-HF: Total energy	-27521.71891
FMO2-MP2: Total energy	-27599.967511

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(B:2:PRO)

Summations of interaction energy for fragment #1(B:2:PRO)

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.
-0.726	2.094	1.417	-1.376	-2.86	0

Interaction energy analysis for fragmet #1(B:2:PRO)

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 : 0.001

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	B	4	LYS	1	0.979	0.974	3.817	-0.657	0.919	-0.020	-0.732	-0.825	0.004
4	B	5	LEU	0	0.028	0.019	6.232	0.096	0.096	0.000	0.000	0.000	0.000
5	B	6	ALA	0	0.026	0.014	3.222	-0.178	0.224	0.060	-0.121	-0.341	-0.001
6	B	7	LEU	0	-0.020	-0.015	2.330	-0.731	-0.157	1.379	-0.504	-1.448	-0.003
7	B	8	ILE	0	-0.006	-0.016	4.994	0.264	0.319	-0.001	-0.003	-0.051	0.000
8	B	9	GLN	0	-0.006	-0.011	8.270	0.152	0.152	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.830	-0.890	4.492	-0.617	-0.404	-0.001	-0.016	-0.195	0.000
10	B	11	LEU	0	-0.082	-0.032	8.728	0.025	0.025	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.002	-0.002	10.707	0.028	0.028	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.853	-0.917	11.029	-0.063	-0.063	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.894	0.935	5.563	0.780	0.780	0.000	0.000	0.000	0.000
14	B	15	ILE	0	-0.028	-0.010	12.042	0.021	0.021	0.000	0.000	0.000	0.000
15	B	16	GLN	0	0.030	0.016	15.192	0.017	0.017	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.013	-0.010	14.045	0.017	0.017	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.061	-0.036	15.409	0.011	0.011	0.000	0.000	0.000	0.000
18	B	19	VAL	0	-0.034	-0.022	17.042	0.013	0.013	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.929	-0.966	18.888	-0.055	-0.055	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.011	0.013	21.391	0.009	0.009	0.000	0.000	0.000	0.000
21	B	22	ALA	0	0.007	0.004	23.345	0.007	0.007	0.000	0.000	0.000	0.000
22	B	23	MET	0	-0.030	-0.011	24.310	0.005	0.005	0.000	0.000	0.000	0.000
23	B	24	GLY	0	-0.043	-0.009	25.411	0.007	0.007	0.000	0.000	0.000	0.000
24	B	25	MET	0	-0.029	-0.001	27.142	0.006	0.006	0.000	0.000	0.000	0.000
25	B	26	SER	0	-0.007	-0.008	29.628	0.002	0.002	0.000	0.000	0.000	0.000
26	B	27	TYR	0	-0.018	-0.054	31.885	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	28	GLN	0	-0.005	0.000	36.043	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.939	-0.956	38.705	-0.032	-0.032	0.000	0.000	0.000	0.000
29	B	30	ALA	0	-0.016	-0.002	38.194	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	31	PRO	0	0.017	0.000	40.290	0.001	0.001	0.000	0.000	0.000	0.000
31	B	32	ASN	0	0.006	0.000	41.475	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	33	ASN	0	0.047	0.011	41.515	0.000	0.000	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.091	0.047	37.534	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	35	ARG	1	0.914	0.970	37.317	0.038	0.038	0.000	0.000	0.000	0.000
35	B	36	ARG	1	0.888	0.935	36.882	0.041	0.041	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.903	-0.946	35.617	-0.066	-0.066	0.000	0.000	0.000	0.000
37	B	38	LEU	0	-0.019	-0.023	32.274	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	39	ASP	-1	-0.807	-0.879	32.060	-0.053	-0.053	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.037	-0.019	32.157	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	41	LEU	0	0.000	0.012	27.122	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	42	HIS	0	0.061	0.023	27.915	-0.013	-0.013	0.000	0.000	0.000	0.000
42	B	43	ALA	0	-0.010	-0.001	27.605	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	44	CYS	0	-0.069	-0.032	27.052	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	45	LEU	0	0.052	0.015	22.762	-0.012	-0.012	0.000	0.000	0.000	0.000
45	B	46	ASN	0	0.020	0.009	22.962	-0.012	-0.012	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.959	0.979	23.887	0.109	0.109	0.000	0.000	0.000	0.000
47	B	48	ALA	0	-0.002	0.017	21.021	-0.009	-0.009	0.000	0.000	0.000	0.000
48	B	49	LYS	1	0.978	0.984	18.715	0.085	0.085	0.000	0.000	0.000	0.000
49	B	50	LEU	0	0.002	0.008	19.360	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.089	-0.066	21.190	0.005	0.005	0.000	0.000	0.000	0.000
51	B	52	VAL	0	0.022	0.024	14.801	-0.007	-0.007	0.000	0.000	0.000	0.000
52	B	53	SER	0	0.021	0.001	16.693	-0.014	-0.014	0.000	0.000	0.000	0.000
53	B	54	ARG	1	0.910	0.958	17.827	0.120	0.120	0.000	0.000	0.000	0.000
54	B	55	MET	0	-0.022	-0.002	16.870	0.015	0.015	0.000	0.000	0.000	0.000
55	B	56	VAL	0	0.035	0.019	12.971	-0.012	-0.012	0.000	0.000	0.000	0.000
56	B	57	THR	0	-0.006	-0.010	15.413	0.011	0.011	0.000	0.000	0.000	0.000
57	B	58	SER	0	0.015	0.001	17.981	0.003	0.003	0.000	0.000	0.000	0.000
58	B	59	LEU	0	-0.056	-0.036	14.191	0.010	0.010	0.000	0.000	0.000	0.000
59	B	60	LEU	0	-0.004	0.004	12.271	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.892	-0.936	16.307	-0.066	-0.066	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.800	0.895	18.924	0.176	0.176	0.000	0.000	0.000	0.000
62	B	63	PRO	0	0.061	0.032	18.762	-0.016	-0.016	0.000	0.000	0.000	0.000
63	B	64	SER	0	-0.007	-0.014	19.086	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	65	VAL	0	-0.010	-0.008	14.629	-0.015	-0.015	0.000	0.000	0.000	0.000
65	B	66	VAL	0	0.033	0.013	14.337	-0.055	-0.055	0.000	0.000	0.000	0.000
66	B	67	ALA	0	0.051	0.036	14.452	0.004	0.004	0.000	0.000	0.000	0.000
67	B	68	TYR	0	0.004	0.007	12.387	-0.063	-0.063	0.000	0.000	0.000	0.000
68	B	69	LEU	0	-0.142	-0.070	9.684	-0.073	-0.073	0.000	0.000	0.000	0.000
69	B	70	GLU	-1	-0.896	-0.955	10.439	0.010	0.010	0.000	0.000	0.000	0.000
70	B	71	GLY	0	-0.107	-0.030	12.545	0.064	0.064	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:PRO)