FMO DATABASE

FMODB ID: 9G522

Calculation Name: 2BSQ-F-Xray372

Preferred Name:

Target Type:

Ligand Name: 5-iodo-2'-deoxyuridine-5'-monophosphate

ligand 3-letter code: 5IU

PDB ID: 2BSQ

Chain ID: F

ChEMBL ID:

UniProt ID: Q5F881

Base Structure: X-ray

Registration Date: 2023-06-21

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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-268835.259655
FMO2-HF: Nuclear repulsion	245040.321716
FMO2-HF: Total energy	-23794.937939
FMO2-MP2: Total energy	-23865.053113

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(F:2:ALA)

Summations of interaction energy for fragment #1(F:2:ALA)

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.
0.448	2.037	-0.008	-0.763	-0.818	0.002

Interaction energy analysis for fragmet #1(F:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.003

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	F	4	VAL	0	0.035	0.006	3.706	-0.637	0.952	-0.008	-0.763	-0.818	0.002
4	F	5	VAL	0	-0.017	0.004	6.091	0.172	0.172	0.000	0.000	0.000	0.000
5	F	6	ILE	0	0.002	0.002	9.804	0.057	0.057	0.000	0.000	0.000	0.000
6	F	7	ARG	1	0.953	0.964	12.184	0.389	0.389	0.000	0.000	0.000	0.000
7	F	8	ASN	0	-0.008	-0.008	15.851	0.009	0.009	0.000	0.000	0.000	0.000
8	F	9	LEU	0	0.014	0.024	16.087	-0.003	-0.003	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.030	0.008	19.013	0.023	0.023	0.000	0.000	0.000	0.000
10	F	11	GLU	-1	-0.803	-0.927	21.689	-0.211	-0.211	0.000	0.000	0.000	0.000
11	F	12	ALA	0	-0.003	0.010	23.634	-0.007	-0.007	0.000	0.000	0.000	0.000
12	F	13	THR	0	-0.018	-0.003	19.561	-0.008	-0.008	0.000	0.000	0.000	0.000
13	F	14	HIS	0	0.076	0.040	17.776	-0.050	-0.050	0.000	0.000	0.000	0.000
14	F	15	ASN	0	-0.012	-0.011	20.507	-0.006	-0.006	0.000	0.000	0.000	0.000
15	F	16	ALA	0	0.000	-0.003	22.521	0.003	0.003	0.000	0.000	0.000	0.000
16	F	17	ILE	0	0.027	0.018	16.282	0.001	0.001	0.000	0.000	0.000	0.000
17	F	18	LYS	1	0.903	0.953	19.320	0.182	0.182	0.000	0.000	0.000	0.000
18	F	19	PHE	0	-0.020	-0.013	20.242	0.010	0.010	0.000	0.000	0.000	0.000
19	F	20	ARG	1	0.950	0.976	19.683	0.304	0.304	0.000	0.000	0.000	0.000
20	F	21	ALA	0	0.024	0.021	17.462	0.007	0.007	0.000	0.000	0.000	0.000
21	F	22	ARG	1	0.949	0.990	19.099	0.214	0.214	0.000	0.000	0.000	0.000
22	F	23	ALA	0	-0.034	0.010	21.906	0.015	0.015	0.000	0.000	0.000	0.000
23	F	24	ALA	0	0.010	0.005	20.464	0.009	0.009	0.000	0.000	0.000	0.000
24	F	25	GLY	0	-0.041	-0.022	21.324	0.001	0.001	0.000	0.000	0.000	0.000
25	F	26	ARG	1	0.900	0.943	15.838	0.311	0.311	0.000	0.000	0.000	0.000
26	F	27	SER	0	0.008	0.004	13.654	-0.008	-0.008	0.000	0.000	0.000	0.000
27	F	28	THR	0	0.070	-0.011	14.996	-0.014	-0.014	0.000	0.000	0.000	0.000
28	F	29	GLU	-1	-0.890	-0.936	8.412	-0.760	-0.760	0.000	0.000	0.000	0.000
29	F	30	ALA	0	-0.007	-0.023	10.849	-0.147	-0.147	0.000	0.000	0.000	0.000
30	F	31	GLU	-1	-0.851	-0.925	11.960	-0.440	-0.440	0.000	0.000	0.000	0.000
31	F	32	ILE	0	0.010	0.002	10.398	-0.008	-0.008	0.000	0.000	0.000	0.000
32	F	33	ARG	1	0.932	0.974	6.595	1.014	1.014	0.000	0.000	0.000	0.000
33	F	34	LEU	0	0.019	0.026	9.478	-0.023	-0.023	0.000	0.000	0.000	0.000
34	F	35	ILE	0	-0.045	-0.027	12.423	0.027	0.027	0.000	0.000	0.000	0.000
35	F	36	LEU	0	-0.001	-0.019	7.804	0.059	0.059	0.000	0.000	0.000	0.000
36	F	37	ASP	-1	-0.878	-0.925	9.122	-1.103	-1.103	0.000	0.000	0.000	0.000
37	F	38	ASN	0	-0.107	-0.061	11.181	0.129	0.129	0.000	0.000	0.000	0.000
38	F	39	ILE	0	-0.005	0.000	13.040	0.065	0.065	0.000	0.000	0.000	0.000
39	F	40	ALA	0	0.005	0.012	10.460	0.062	0.062	0.000	0.000	0.000	0.000
40	F	41	LYS	1	0.936	0.951	12.594	0.480	0.480	0.000	0.000	0.000	0.000
41	F	42	ALA	0	-0.026	-0.004	15.346	0.047	0.047	0.000	0.000	0.000	0.000
42	F	43	GLN	0	-0.040	-0.025	13.667	0.011	0.011	0.000	0.000	0.000	0.000
43	F	44	GLN	0	-0.010	0.015	15.146	0.022	0.022	0.000	0.000	0.000	0.000
44	F	45	THR	0	0.001	0.012	17.393	0.019	0.019	0.000	0.000	0.000	0.000
45	F	46	VAL	0	0.009	-0.005	18.771	0.012	0.012	0.000	0.000	0.000	0.000
46	F	47	ARG	1	0.960	0.997	21.023	0.095	0.095	0.000	0.000	0.000	0.000
47	F	48	LEU	0	0.035	0.015	23.974	0.010	0.010	0.000	0.000	0.000	0.000
48	F	49	GLY	0	0.036	0.023	25.288	0.007	0.007	0.000	0.000	0.000	0.000
49	F	50	SER	0	0.004	-0.049	25.302	0.008	0.008	0.000	0.000	0.000	0.000
50	F	51	MET	0	-0.029	-0.010	19.886	0.007	0.007	0.000	0.000	0.000	0.000
51	F	52	LEU	0	0.055	0.032	23.263	0.008	0.008	0.000	0.000	0.000	0.000
52	F	53	ALA	0	0.042	0.017	25.577	0.009	0.009	0.000	0.000	0.000	0.000
53	F	54	SER	0	-0.031	-0.008	22.745	0.011	0.011	0.000	0.000	0.000	0.000
54	F	55	ILE	0	0.053	0.023	20.976	0.007	0.007	0.000	0.000	0.000	0.000
55	F	56	GLY	0	-0.023	0.002	24.145	0.008	0.008	0.000	0.000	0.000	0.000
56	F	57	GLN	0	-0.031	-0.021	27.482	0.004	0.004	0.000	0.000	0.000	0.000
57	F	58	GLU	-1	-0.984	-0.987	21.522	0.054	0.054	0.000	0.000	0.000	0.000
58	F	59	ILE	0	-0.075	-0.037	25.211	0.010	0.010	0.000	0.000	0.000	0.000
59	F	60	GLY	0	-0.032	-0.009	27.601	0.000	0.000	0.000	0.000	0.000	0.000
60	F	61	GLY	0	-0.032	-0.002	29.973	-0.003	-0.003	0.000	0.000	0.000	0.000
61	F	62	VAL	0	-0.033	-0.032	30.301	0.004	0.004	0.000	0.000	0.000	0.000
62	F	63	GLU	-1	-0.905	-0.967	32.983	-0.013	-0.013	0.000	0.000	0.000	0.000
63	F	64	LEU	0	-0.091	-0.034	29.779	0.002	0.002	0.000	0.000	0.000	0.000
64	F	65	GLU	-1	-0.976	-0.971	34.477	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:ALA)