FMO DATABASE

FMODB ID: JMZM9

Calculation Name: 2AZ2-B-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	72
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-356803.635849
FMO2-HF: Nuclear repulsion	329111.396283
FMO2-HF: Total energy	-27692.239566
FMO2-MP2: Total energy	-27771.091686

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:1:ACE )

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

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.
1.293	1.899	0.001	-0.209	-0.398	0

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.004

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].
3	B	3	SER	0	0.084	0.033	3.869	1.056	1.662	0.001	-0.209	-0.398
4	B	4	LYS	1	0.966	0.960	6.115	0.726	0.726	0.000	0.000	0.000
5	B	5	LEU	0	0.035	0.014	9.313	0.109	0.109	0.000	0.000	0.000
6	B	6	ALA	0	0.043	0.029	7.176	0.109	0.109	0.000	0.000	0.000
7	B	7	LEU	0	-0.040	-0.016	7.518	0.223	0.223	0.000	0.000	0.000
8	B	8	ILE	0	-0.011	-0.017	10.362	0.146	0.146	0.000	0.000	0.000
9	B	9	GLN	0	0.002	-0.010	12.219	-0.009	-0.009	0.000	0.000	0.000
10	B	10	GLU	-1	-0.881	-0.926	9.707	-0.918	-0.918	0.000	0.000	0.000
11	B	11	LEU	0	-0.098	-0.037	13.812	0.076	0.076	0.000	0.000	0.000
12	B	12	PRO	0	-0.013	-0.009	16.154	0.046	0.046	0.000	0.000	0.000
13	B	13	ASP	-1	-0.818	-0.903	15.931	-0.298	-0.298	0.000	0.000	0.000
14	B	14	ARG	1	0.960	0.972	11.826	0.383	0.383	0.000	0.000	0.000
15	B	15	ILE	0	-0.022	-0.004	17.044	0.037	0.037	0.000	0.000	0.000
16	B	16	GLN	0	0.015	-0.001	20.335	0.025	0.025	0.000	0.000	0.000
17	B	17	THR	0	-0.016	-0.010	18.303	0.017	0.017	0.000	0.000	0.000
18	B	18	ALA	0	-0.055	-0.034	20.173	0.018	0.018	0.000	0.000	0.000
19	B	19	VAL	0	-0.039	-0.022	21.683	0.016	0.016	0.000	0.000	0.000
20	B	20	GLU	-1	-0.959	-0.976	23.278	-0.087	-0.087	0.000	0.000	0.000
21	B	21	ALA	0	0.021	0.019	25.757	0.007	0.007	0.000	0.000	0.000
22	B	22	ALA	0	-0.003	0.001	27.720	0.005	0.005	0.000	0.000	0.000
23	B	23	MET	0	-0.035	-0.023	29.151	-0.001	-0.001	0.000	0.000	0.000
24	B	24	GLY	0	-0.039	-0.010	29.991	0.003	0.003	0.000	0.000	0.000
25	B	25	MET	0	-0.018	0.003	31.631	0.006	0.006	0.000	0.000	0.000
26	B	26	SER	0	-0.017	-0.012	34.027	-0.001	-0.001	0.000	0.000	0.000
27	B	27	TYR	0	-0.011	-0.040	36.679	0.002	0.002	0.000	0.000	0.000
28	B	28	GLN	0	-0.007	-0.005	40.535	0.001	0.001	0.000	0.000	0.000
29	B	29	ASP	-1	-0.942	-0.960	43.212	-0.024	-0.024	0.000	0.000	0.000
30	B	30	ALA	0	-0.018	0.004	42.760	0.001	0.001	0.000	0.000	0.000
31	B	31	PRO	0	0.020	0.002	44.837	0.000	0.000	0.000	0.000	0.000
32	B	32	ASN	0	0.006	-0.003	46.225	-0.002	-0.002	0.000	0.000	0.000
33	B	33	ASN	0	0.046	0.019	46.417	-0.002	-0.002	0.000	0.000	0.000
34	B	34	VAL	0	0.107	0.052	42.069	-0.001	-0.001	0.000	0.000	0.000
35	B	35	ARG	1	0.927	0.980	42.129	0.032	0.032	0.000	0.000	0.000
36	B	36	ARG	1	0.899	0.939	41.823	0.029	0.029	0.000	0.000	0.000
37	B	37	ASP	-1	-0.902	-0.946	40.461	-0.037	-0.037	0.000	0.000	0.000
38	B	38	LEU	0	-0.025	-0.023	36.931	-0.003	-0.003	0.000	0.000	0.000
39	B	39	ASP	-1	-0.839	-0.910	37.014	-0.047	-0.047	0.000	0.000	0.000
40	B	40	ASN	0	-0.038	-0.024	37.271	-0.008	-0.008	0.000	0.000	0.000
41	B	41	LEU	0	0.006	0.019	31.815	-0.005	-0.005	0.000	0.000	0.000
42	B	42	HIS	0	0.061	0.030	33.057	-0.008	-0.008	0.000	0.000	0.000
43	B	43	ALA	0	0.011	0.012	32.773	-0.007	-0.007	0.000	0.000	0.000
44	B	44	CYS	0	-0.070	-0.031	32.334	-0.008	-0.008	0.000	0.000	0.000
45	B	45	LEU	0	0.041	0.007	28.155	-0.008	-0.008	0.000	0.000	0.000
46	B	46	ASN	0	0.007	-0.002	28.252	-0.009	-0.009	0.000	0.000	0.000
47	B	47	LYS	1	0.963	0.981	29.261	0.074	0.074	0.000	0.000	0.000
48	B	48	ALA	0	0.006	0.028	26.526	-0.008	-0.008	0.000	0.000	0.000
49	B	49	LYS	1	1.009	1.003	24.195	0.105	0.105	0.000	0.000	0.000
50	B	50	LEU	0	-0.027	-0.014	24.796	-0.014	-0.014	0.000	0.000	0.000
51	B	51	THR	0	-0.098	-0.073	26.588	-0.004	-0.004	0.000	0.000	0.000
52	B	52	VAL	0	0.013	0.013	20.519	-0.006	-0.006	0.000	0.000	0.000
53	B	53	SER	0	0.021	0.009	22.052	-0.021	-0.021	0.000	0.000	0.000
54	B	54	ARG	1	0.934	0.967	23.029	0.107	0.107	0.000	0.000	0.000
55	B	55	MET	0	-0.029	-0.001	21.997	-0.001	-0.001	0.000	0.000	0.000
56	B	56	VAL	0	0.036	0.020	17.944	-0.007	-0.007	0.000	0.000	0.000
57	B	57	THR	0	0.002	0.000	20.473	-0.012	-0.012	0.000	0.000	0.000
58	B	58	SER	0	-0.032	-0.025	22.609	-0.001	-0.001	0.000	0.000	0.000
59	B	59	LEU	0	-0.044	-0.038	18.826	0.008	0.008	0.000	0.000	0.000
60	B	60	LEU	0	-0.018	-0.004	16.436	-0.008	-0.008	0.000	0.000	0.000
61	B	61	GLU	-1	-0.901	-0.944	20.176	-0.154	-0.154	0.000	0.000	0.000
62	B	62	LYS	1	0.861	0.942	22.561	0.174	0.174	0.000	0.000	0.000
63	B	63	PRO	0	0.062	0.030	21.978	-0.017	-0.017	0.000	0.000	0.000
64	B	64	SER	0	-0.017	-0.018	21.625	-0.016	-0.016	0.000	0.000	0.000
65	B	65	VAL	0	0.001	-0.002	18.181	-0.004	-0.004	0.000	0.000	0.000
66	B	66	VAL	0	0.030	0.012	17.068	-0.033	-0.033	0.000	0.000	0.000
67	B	67	ALA	0	0.053	0.037	16.745	-0.027	-0.027	0.000	0.000	0.000
68	B	68	TYR	0	-0.010	-0.002	14.705	-0.027	-0.027	0.000	0.000	0.000
69	B	69	LEU	0	-0.149	-0.070	13.065	-0.027	-0.027	0.000	0.000	0.000
70	B	70	GLU	-1	-0.897	-0.963	12.507	-0.430	-0.430	0.000	0.000	0.000
71	B	71	GLY	0	-0.082	-0.017	13.683	0.010	0.010	0.000	0.000	0.000
72	B	72	NME	0	-0.026	-0.008	14.618	0.042	0.042	0.000	0.000	0.000

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