FMO DATABASE

FMODB ID: 22Z5R

Calculation Name: 2BSQ-E-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: 5IU

PDB ID: 2BSQ

Chain ID: E

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-283995.915283
FMO2-HF: Nuclear repulsion	258709.86078
FMO2-HF: Total energy	-25286.054503
FMO2-MP2: Total energy	-25360.548167

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(E:2:ALA)

Summations of interaction energy for fragment #1(E: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.
0.124	1.781	-0.031	-0.778	-0.848	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / 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

Sort

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	E	4	VAL	0	0.027	0.007	3.777	-0.582	1.075	-0.031	-0.778	-0.848	0.003
4	E	5	VAL	0	0.005	0.005	6.617	0.013	0.013	0.000	0.000	0.000	0.000
5	E	6	ILE	0	0.003	-0.002	10.129	-0.005	-0.005	0.000	0.000	0.000	0.000
6	E	7	ARG	1	0.957	0.974	13.100	0.028	0.028	0.000	0.000	0.000	0.000
7	E	8	ASN	0	-0.022	-0.011	16.515	-0.006	-0.006	0.000	0.000	0.000	0.000
8	E	9	LEU	0	0.031	0.034	16.100	-0.011	-0.011	0.000	0.000	0.000	0.000
9	E	10	SER	0	0.057	0.019	19.185	0.016	0.016	0.000	0.000	0.000	0.000
10	E	11	GLU	-1	-0.827	-0.932	22.029	-0.101	-0.101	0.000	0.000	0.000	0.000
11	E	12	ALA	0	-0.006	-0.001	24.148	-0.004	-0.004	0.000	0.000	0.000	0.000
12	E	13	THR	0	0.002	-0.006	19.481	-0.001	-0.001	0.000	0.000	0.000	0.000
13	E	14	HIS	0	0.014	0.022	18.860	-0.035	-0.035	0.000	0.000	0.000	0.000
14	E	15	ASN	0	0.047	0.015	20.888	-0.018	-0.018	0.000	0.000	0.000	0.000
15	E	16	ALA	0	0.013	0.027	22.751	-0.004	-0.004	0.000	0.000	0.000	0.000
16	E	17	ILE	0	-0.007	-0.010	16.679	-0.009	-0.009	0.000	0.000	0.000	0.000
17	E	18	LYS	1	0.912	0.947	19.859	0.128	0.128	0.000	0.000	0.000	0.000
18	E	19	PHE	0	-0.043	-0.022	21.056	0.003	0.003	0.000	0.000	0.000	0.000
19	E	20	ARG	1	0.928	0.963	19.043	0.266	0.266	0.000	0.000	0.000	0.000
20	E	21	ALA	0	-0.030	-0.016	18.485	-0.006	-0.006	0.000	0.000	0.000	0.000
21	E	22	ARG	1	0.959	0.979	20.133	0.104	0.104	0.000	0.000	0.000	0.000
22	E	23	ALA	0	-0.040	-0.003	23.096	0.010	0.010	0.000	0.000	0.000	0.000
23	E	24	ALA	0	-0.021	0.010	20.745	0.006	0.006	0.000	0.000	0.000	0.000
24	E	25	GLY	0	0.051	0.020	21.892	0.008	0.008	0.000	0.000	0.000	0.000
25	E	26	ARG	1	0.833	0.892	16.185	0.308	0.308	0.000	0.000	0.000	0.000
26	E	27	SER	0	0.048	0.040	13.897	0.005	0.005	0.000	0.000	0.000	0.000
27	E	28	THR	0	0.082	-0.002	15.905	-0.029	-0.029	0.000	0.000	0.000	0.000
28	E	29	GLU	-1	-0.895	-0.936	9.000	-0.480	-0.480	0.000	0.000	0.000	0.000
29	E	30	ALA	0	-0.044	-0.030	11.502	-0.135	-0.135	0.000	0.000	0.000	0.000
30	E	31	GLU	-1	-0.754	-0.862	12.731	-0.394	-0.394	0.000	0.000	0.000	0.000
31	E	32	ILE	0	-0.021	-0.006	10.534	0.001	0.001	0.000	0.000	0.000	0.000
32	E	33	ARG	1	0.985	0.977	7.009	1.037	1.037	0.000	0.000	0.000	0.000
33	E	34	LEU	0	0.014	0.029	9.819	-0.014	-0.014	0.000	0.000	0.000	0.000
34	E	35	ILE	0	-0.074	-0.037	12.785	0.044	0.044	0.000	0.000	0.000	0.000
35	E	36	LEU	0	0.000	-0.005	8.219	0.047	0.047	0.000	0.000	0.000	0.000
36	E	37	ASP	-1	-0.896	-0.961	8.465	-1.126	-1.126	0.000	0.000	0.000	0.000
37	E	38	ASN	0	-0.081	-0.043	10.771	0.083	0.083	0.000	0.000	0.000	0.000
38	E	39	ILE	0	0.001	-0.002	12.987	0.050	0.050	0.000	0.000	0.000	0.000
39	E	40	ALA	0	-0.005	0.011	10.557	0.044	0.044	0.000	0.000	0.000	0.000
40	E	41	LYS	1	0.929	0.951	12.552	0.451	0.451	0.000	0.000	0.000	0.000
41	E	42	ALA	0	-0.005	0.000	14.707	0.041	0.041	0.000	0.000	0.000	0.000
42	E	43	GLN	0	-0.013	-0.001	14.565	0.039	0.039	0.000	0.000	0.000	0.000
43	E	44	GLN	0	-0.072	-0.021	13.948	0.032	0.032	0.000	0.000	0.000	0.000
44	E	45	THR	0	0.018	0.017	16.583	0.017	0.017	0.000	0.000	0.000	0.000
45	E	46	VAL	0	0.014	-0.003	19.272	0.015	0.015	0.000	0.000	0.000	0.000
46	E	47	ARG	1	0.928	0.966	15.427	0.261	0.261	0.000	0.000	0.000	0.000
47	E	48	LEU	0	0.058	0.023	18.348	0.013	0.013	0.000	0.000	0.000	0.000
48	E	49	GLY	0	0.045	0.026	17.949	0.015	0.015	0.000	0.000	0.000	0.000
49	E	50	SER	0	0.015	-0.014	19.144	0.005	0.005	0.000	0.000	0.000	0.000
50	E	51	MET	0	-0.019	0.008	21.176	0.013	0.013	0.000	0.000	0.000	0.000
51	E	52	LEU	0	0.049	0.012	21.719	0.010	0.010	0.000	0.000	0.000	0.000
52	E	53	ALA	0	0.011	0.012	22.803	0.009	0.009	0.000	0.000	0.000	0.000
53	E	54	SER	0	-0.027	-0.021	24.735	0.009	0.009	0.000	0.000	0.000	0.000
54	E	55	ILE	0	0.036	0.019	27.304	0.006	0.006	0.000	0.000	0.000	0.000
55	E	56	GLY	0	0.029	0.019	27.803	0.007	0.007	0.000	0.000	0.000	0.000
56	E	57	GLN	0	-0.048	-0.022	26.830	0.004	0.004	0.000	0.000	0.000	0.000
57	E	58	GLU	-1	-1.025	-1.006	30.438	-0.060	-0.060	0.000	0.000	0.000	0.000
58	E	59	ILE	0	-0.043	-0.025	32.235	0.004	0.004	0.000	0.000	0.000	0.000
59	E	60	GLY	0	-0.039	-0.007	33.509	0.004	0.004	0.000	0.000	0.000	0.000
60	E	61	GLY	0	-0.048	-0.018	30.989	0.003	0.003	0.000	0.000	0.000	0.000
61	E	62	VAL	0	-0.032	-0.018	30.932	0.003	0.003	0.000	0.000	0.000	0.000
62	E	63	GLU	-1	-0.916	-0.970	31.174	-0.018	-0.018	0.000	0.000	0.000	0.000
63	E	64	LEU	0	-0.094	-0.039	30.301	0.001	0.001	0.000	0.000	0.000	0.000
64	E	65	GLU	-1	-0.918	-0.956	33.073	-0.004	-0.004	0.000	0.000	0.000	0.000
65	E	66	ASP	-1	-0.959	-0.981	31.858	0.004	0.004	0.000	0.000	0.000	0.000
66	E	67	VAL	0	-0.028	-0.010	32.988	-0.002	-0.002	0.000	0.000	0.000	0.000
67	E	68	ARG	1	0.985	0.966	27.132	-0.002	-0.002	0.000	0.000	0.000	0.000
68	E	69	GLY	0	-0.029	0.013	33.810	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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