FMO DATABASE

FMODB ID: R5MQ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-353453.668841
FMO2-HF: Nuclear repulsion	325931.680534
FMO2-HF: Total energy	-27521.988308
FMO2-MP2: Total energy	-27600.151531

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.
-1.352	0.743	2.182	-1.309	-2.968	0.003

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 : 0.026 / q_NPA : -0.009

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	0.965	0.958	3.869	-1.049	0.385	-0.013	-0.671	-0.750	0.004
4	B	5	LEU	0	0.030	0.025	6.538	0.056	0.056	0.000	0.000	0.000	0.000
5	B	6	ALA	0	0.027	0.027	3.170	-0.252	0.102	0.056	-0.105	-0.304	0.000
6	B	7	LEU	0	0.015	0.000	2.279	-0.336	-0.307	2.141	-0.499	-1.672	-0.001
7	B	8	ILE	0	-0.011	-0.012	5.082	0.178	0.222	-0.001	-0.002	-0.040	0.000
8	B	9	GLN	0	0.005	-0.014	8.238	0.136	0.136	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.831	-0.896	4.281	-1.166	-0.932	-0.001	-0.032	-0.202	0.000
10	B	11	LEU	0	-0.051	-0.016	8.486	0.033	0.033	0.000	0.000	0.000	0.000
11	B	12	PRO	0	-0.018	-0.004	10.672	0.022	0.022	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.837	-0.915	11.437	-0.105	-0.105	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.864	0.929	5.107	0.853	0.853	0.000	0.000	0.000	0.000
14	B	15	ILE	0	-0.028	-0.015	12.008	0.017	0.017	0.000	0.000	0.000	0.000
15	B	16	GLN	0	0.007	-0.017	15.096	0.019	0.019	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.006	-0.014	13.996	0.016	0.016	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.056	-0.022	15.406	0.010	0.010	0.000	0.000	0.000	0.000
18	B	19	VAL	0	-0.037	-0.020	17.164	0.012	0.012	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.894	-0.945	18.872	-0.082	-0.082	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.008	0.004	21.362	0.011	0.011	0.000	0.000	0.000	0.000
21	B	22	ALA	0	-0.014	-0.002	23.238	0.007	0.007	0.000	0.000	0.000	0.000
22	B	23	MET	0	-0.060	-0.022	24.196	0.007	0.007	0.000	0.000	0.000	0.000
23	B	24	GLY	0	0.011	0.018	25.814	0.007	0.007	0.000	0.000	0.000	0.000
24	B	25	MET	0	-0.045	-0.008	27.508	0.005	0.005	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.002	-0.002	29.821	0.002	0.002	0.000	0.000	0.000	0.000
26	B	27	TYR	0	-0.018	-0.049	31.823	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	28	GLN	0	-0.020	-0.009	36.036	0.000	0.000	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.925	-0.955	38.716	-0.037	-0.037	0.000	0.000	0.000	0.000
29	B	30	ALA	0	-0.007	0.006	38.272	0.000	0.000	0.000	0.000	0.000	0.000
30	B	31	PRO	0	0.015	-0.004	40.412	0.001	0.001	0.000	0.000	0.000	0.000
31	B	32	ASN	0	-0.008	0.000	41.648	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	33	ASN	0	0.019	0.001	41.296	0.001	0.001	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.085	0.047	37.629	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	35	ARG	1	0.931	0.966	37.079	0.038	0.038	0.000	0.000	0.000	0.000
35	B	36	ARG	1	0.902	0.955	36.539	0.039	0.039	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.896	-0.954	35.888	-0.060	-0.060	0.000	0.000	0.000	0.000
37	B	38	LEU	0	-0.005	-0.006	32.061	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	39	ASP	-1	-0.790	-0.874	31.843	-0.054	-0.054	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.056	-0.027	32.093	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.004	0.006	27.245	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	42	HIS	0	0.029	0.004	27.637	-0.012	-0.012	0.000	0.000	0.000	0.000
42	B	43	ALA	0	0.010	0.003	27.297	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	44	CYS	0	-0.067	-0.028	27.332	-0.008	-0.008	0.000	0.000	0.000	0.000
44	B	45	LEU	0	0.057	0.025	22.544	-0.010	-0.010	0.000	0.000	0.000	0.000
45	B	46	ASN	0	0.026	0.007	22.740	-0.013	-0.013	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.951	0.977	23.644	0.095	0.095	0.000	0.000	0.000	0.000
47	B	48	ALA	0	-0.002	0.013	21.027	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	49	LYS	1	0.947	0.973	18.426	0.093	0.093	0.000	0.000	0.000	0.000
49	B	50	LEU	0	0.038	0.028	19.036	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.097	-0.058	21.041	0.007	0.007	0.000	0.000	0.000	0.000
51	B	52	VAL	0	0.030	0.025	14.751	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	53	SER	0	0.017	-0.001	16.718	-0.009	-0.009	0.000	0.000	0.000	0.000
53	B	54	ARG	1	0.876	0.930	17.775	0.107	0.107	0.000	0.000	0.000	0.000
54	B	55	MET	0	-0.013	0.004	16.916	0.014	0.014	0.000	0.000	0.000	0.000
55	B	56	VAL	0	0.015	0.005	12.764	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	57	THR	0	-0.001	-0.014	15.168	0.012	0.012	0.000	0.000	0.000	0.000
57	B	58	SER	0	-0.002	-0.027	17.637	0.008	0.008	0.000	0.000	0.000	0.000
58	B	59	LEU	0	-0.063	-0.038	14.093	0.008	0.008	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.000	0.001	12.281	0.006	0.006	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.867	-0.903	16.348	-0.048	-0.048	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.828	0.915	18.948	0.124	0.124	0.000	0.000	0.000	0.000
62	B	63	PRO	0	0.053	0.026	18.673	-0.013	-0.013	0.000	0.000	0.000	0.000
63	B	64	SER	0	0.000	0.000	18.830	0.003	0.003	0.000	0.000	0.000	0.000
64	B	65	VAL	0	-0.009	-0.004	14.933	-0.011	-0.011	0.000	0.000	0.000	0.000
65	B	66	VAL	0	0.023	0.014	14.216	-0.039	-0.039	0.000	0.000	0.000	0.000
66	B	67	ALA	0	0.069	0.033	13.965	0.002	0.002	0.000	0.000	0.000	0.000
67	B	68	TYR	0	-0.035	-0.016	12.328	-0.035	-0.035	0.000	0.000	0.000	0.000
68	B	69	LEU	0	-0.097	-0.055	9.877	-0.064	-0.064	0.000	0.000	0.000	0.000
69	B	70	GLU	-1	-0.937	-0.959	9.765	0.078	0.078	0.000	0.000	0.000	0.000
70	B	71	GLY	0	-0.098	-0.035	11.967	0.070	0.070	0.000	0.000	0.000	0.000

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