FMO DATABASE

FMODB ID: 667ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-353267.48892
FMO2-HF: Nuclear repulsion	325746.224443
FMO2-HF: Total energy	-27521.264477
FMO2-MP2: Total energy	-27599.577112

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.
0.312	3.774	0.546	-1.348	-2.66	0.002

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 : 0.055 / q_NPA : 0.016

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	0.982	0.968	3.817	-0.153	1.660	-0.018	-0.872	-0.923	0.005
4	B	5	LEU	0	0.034	0.014	6.189	0.189	0.189	0.000	0.000	0.000	0.000
5	B	6	ALA	0	0.038	0.026	3.198	-0.135	0.309	0.063	-0.133	-0.374	-0.001
6	B	7	LEU	0	-0.035	-0.013	2.463	-0.581	0.407	0.503	-0.336	-1.156	-0.002
7	B	8	ILE	0	-0.012	-0.018	4.854	0.407	0.463	-0.001	-0.004	-0.050	0.000
8	B	9	GLN	0	0.002	-0.010	8.076	0.132	0.132	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.881	-0.925	5.068	0.245	0.406	-0.001	-0.003	-0.157	0.000
10	B	11	LEU	0	-0.097	-0.036	8.812	0.056	0.056	0.000	0.000	0.000	0.000
11	B	12	PRO	0	-0.012	-0.009	10.569	0.045	0.045	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.820	-0.904	11.325	0.045	0.045	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.959	0.972	7.579	0.316	0.316	0.000	0.000	0.000	0.000
14	B	15	ILE	0	-0.020	-0.003	12.231	0.016	0.016	0.000	0.000	0.000	0.000
15	B	16	GLN	0	0.013	-0.001	15.208	0.004	0.004	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.013	-0.009	14.167	0.022	0.022	0.000	0.000	0.000	0.000
17	B	18	ALA	0	-0.054	-0.034	15.563	0.006	0.006	0.000	0.000	0.000	0.000
18	B	19	VAL	0	-0.040	-0.022	17.147	0.005	0.005	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.958	-0.975	19.351	0.045	0.045	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.021	0.019	21.498	0.002	0.002	0.000	0.000	0.000	0.000
21	B	22	ALA	0	-0.003	0.001	23.443	0.002	0.002	0.000	0.000	0.000	0.000
22	B	23	MET	0	-0.034	-0.022	24.407	0.000	0.000	0.000	0.000	0.000	0.000
23	B	24	GLY	0	-0.041	-0.011	25.560	0.003	0.003	0.000	0.000	0.000	0.000
24	B	25	MET	0	-0.018	0.002	27.287	0.006	0.006	0.000	0.000	0.000	0.000
25	B	26	SER	0	-0.016	-0.011	29.742	0.000	0.000	0.000	0.000	0.000	0.000
26	B	27	TYR	0	-0.013	-0.040	32.080	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	28	GLN	0	-0.006	-0.006	36.162	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.943	-0.960	38.843	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	30	ALA	0	-0.017	0.005	38.329	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	31	PRO	0	0.021	0.003	40.403	0.000	0.000	0.000	0.000	0.000	0.000
31	B	32	ASN	0	0.005	-0.004	41.604	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	33	ASN	0	0.046	0.019	41.566	0.000	0.000	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.106	0.053	37.525	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	35	ARG	1	0.926	0.979	37.379	0.019	0.019	0.000	0.000	0.000	0.000
35	B	36	ARG	1	0.897	0.938	36.955	0.026	0.026	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.902	-0.946	35.532	-0.047	-0.047	0.000	0.000	0.000	0.000
37	B	38	LEU	0	-0.025	-0.023	32.344	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	39	ASP	-1	-0.838	-0.910	32.126	-0.028	-0.028	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.039	-0.024	32.118	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	41	LEU	0	0.007	0.019	26.878	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	42	HIS	0	0.060	0.029	27.938	-0.012	-0.012	0.000	0.000	0.000	0.000
42	B	43	ALA	0	0.011	0.012	27.556	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	44	CYS	0	-0.070	-0.031	26.839	-0.012	-0.012	0.000	0.000	0.000	0.000
44	B	45	LEU	0	0.042	0.008	23.052	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	46	ASN	0	0.007	-0.001	22.855	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.961	0.980	23.759	0.098	0.098	0.000	0.000	0.000	0.000
47	B	48	ALA	0	0.002	0.027	20.878	-0.013	-0.013	0.000	0.000	0.000	0.000
48	B	49	LYS	1	1.014	1.005	18.903	0.033	0.033	0.000	0.000	0.000	0.000
49	B	50	LEU	0	-0.028	-0.014	19.223	-0.011	-0.011	0.000	0.000	0.000	0.000
50	B	51	THR	0	-0.097	-0.073	20.921	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	52	VAL	0	0.014	0.014	14.767	-0.014	-0.014	0.000	0.000	0.000	0.000
52	B	53	SER	0	0.019	0.008	16.558	-0.019	-0.019	0.000	0.000	0.000	0.000
53	B	54	ARG	1	0.936	0.968	17.671	0.110	0.110	0.000	0.000	0.000	0.000
54	B	55	MET	0	-0.030	-0.002	16.614	0.008	0.008	0.000	0.000	0.000	0.000
55	B	56	VAL	0	0.035	0.020	12.764	-0.023	-0.023	0.000	0.000	0.000	0.000
56	B	57	THR	0	0.003	0.000	15.263	0.001	0.001	0.000	0.000	0.000	0.000
57	B	58	SER	0	-0.032	-0.026	17.809	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	59	LEU	0	-0.042	-0.038	13.916	0.002	0.002	0.000	0.000	0.000	0.000
59	B	60	LEU	0	-0.020	-0.005	12.216	-0.014	-0.014	0.000	0.000	0.000	0.000
60	B	61	GLU	-1	-0.901	-0.944	16.145	-0.099	-0.099	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.862	0.943	18.690	0.238	0.238	0.000	0.000	0.000	0.000
62	B	63	PRO	0	0.063	0.030	18.635	-0.028	-0.028	0.000	0.000	0.000	0.000
63	B	64	SER	0	-0.017	-0.018	19.064	-0.020	-0.020	0.000	0.000	0.000	0.000
64	B	65	VAL	0	0.000	-0.003	14.488	-0.025	-0.025	0.000	0.000	0.000	0.000
65	B	66	VAL	0	0.029	0.011	14.199	-0.081	-0.081	0.000	0.000	0.000	0.000
66	B	67	ALA	0	0.057	0.039	14.438	-0.020	-0.020	0.000	0.000	0.000	0.000
67	B	68	TYR	0	-0.016	-0.006	12.231	-0.099	-0.099	0.000	0.000	0.000	0.000
68	B	69	LEU	0	-0.149	-0.071	9.804	-0.110	-0.110	0.000	0.000	0.000	0.000
69	B	70	GLU	-1	-0.905	-0.960	10.429	-0.237	-0.237	0.000	0.000	0.000	0.000
70	B	71	GLY	0	-0.093	-0.022	12.545	0.074	0.074	0.000	0.000	0.000	0.000

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