FMO DATABASE

FMODB ID: M3K2Z

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	OptHSide
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	-268694.954562
FMO2-HF: Nuclear repulsion	244899.333202
FMO2-HF: Total energy	-23795.621359
FMO2-MP2: Total energy	-23865.642702

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.
0.721	3.382	-0.016	-1.423	-1.221	0.008

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 : 0.049 / q_NPA : 0.030

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	0.033	0.002	3.791	-1.194	1.467	-0.016	-1.423	-1.221	0.008
4	F	5	VAL	0	-0.013	0.001	6.182	0.056	0.056	0.000	0.000	0.000	0.000
5	F	6	ILE	0	0.018	0.008	9.896	0.138	0.138	0.000	0.000	0.000	0.000
6	F	7	ARG	1	0.932	0.960	11.722	0.482	0.482	0.000	0.000	0.000	0.000
7	F	8	ASN	0	-0.004	-0.005	15.940	0.010	0.010	0.000	0.000	0.000	0.000
8	F	9	LEU	0	0.015	0.028	15.981	0.017	0.017	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.033	0.008	19.089	0.014	0.014	0.000	0.000	0.000	0.000
10	F	11	GLU	-1	-0.754	-0.905	21.736	-0.299	-0.299	0.000	0.000	0.000	0.000
11	F	12	ALA	0	0.007	0.024	23.678	-0.013	-0.013	0.000	0.000	0.000	0.000
12	F	13	THR	0	0.011	0.001	19.428	0.000	0.000	0.000	0.000	0.000	0.000
13	F	14	HIS	0	0.015	0.018	18.251	-0.047	-0.047	0.000	0.000	0.000	0.000
14	F	15	ASN	0	-0.048	-0.037	20.549	-0.014	-0.014	0.000	0.000	0.000	0.000
15	F	16	ALA	0	0.018	0.007	22.619	-0.001	-0.001	0.000	0.000	0.000	0.000
16	F	17	ILE	0	0.020	0.011	16.356	0.001	0.001	0.000	0.000	0.000	0.000
17	F	18	LYS	1	0.900	0.947	19.530	0.275	0.275	0.000	0.000	0.000	0.000
18	F	19	PHE	0	-0.014	-0.013	20.440	0.003	0.003	0.000	0.000	0.000	0.000
19	F	20	ARG	1	0.947	0.976	19.369	0.294	0.294	0.000	0.000	0.000	0.000
20	F	21	ALA	0	0.012	0.011	17.683	0.008	0.008	0.000	0.000	0.000	0.000
21	F	22	ARG	1	0.946	0.995	19.259	0.378	0.378	0.000	0.000	0.000	0.000
22	F	23	ALA	0	-0.029	0.012	22.121	0.016	0.016	0.000	0.000	0.000	0.000
23	F	24	ALA	0	0.009	0.002	20.593	0.020	0.020	0.000	0.000	0.000	0.000
24	F	25	GLY	0	-0.048	-0.024	21.466	0.000	0.000	0.000	0.000	0.000	0.000
25	F	26	ARG	1	0.875	0.918	16.030	0.314	0.314	0.000	0.000	0.000	0.000
26	F	27	SER	0	0.015	0.002	14.029	0.006	0.006	0.000	0.000	0.000	0.000
27	F	28	THR	0	0.048	-0.015	15.316	-0.014	-0.014	0.000	0.000	0.000	0.000
28	F	29	GLU	-1	-0.855	-0.909	8.399	-1.757	-1.757	0.000	0.000	0.000	0.000
29	F	30	ALA	0	0.002	-0.001	11.043	-0.131	-0.131	0.000	0.000	0.000	0.000
30	F	31	GLU	-1	-0.788	-0.883	12.157	-0.391	-0.391	0.000	0.000	0.000	0.000
31	F	32	ILE	0	-0.008	-0.007	10.462	0.038	0.038	0.000	0.000	0.000	0.000
32	F	33	ARG	1	0.897	0.939	6.762	1.674	1.674	0.000	0.000	0.000	0.000
33	F	34	LEU	0	0.013	0.017	9.496	0.073	0.073	0.000	0.000	0.000	0.000
34	F	35	ILE	0	-0.021	-0.003	12.365	0.084	0.084	0.000	0.000	0.000	0.000
35	F	36	LEU	0	0.007	-0.013	7.773	0.071	0.071	0.000	0.000	0.000	0.000
36	F	37	ASP	-1	-0.816	-0.880	9.876	-0.162	-0.162	0.000	0.000	0.000	0.000
37	F	38	ASN	0	-0.065	-0.050	11.174	0.154	0.154	0.000	0.000	0.000	0.000
38	F	39	ILE	0	-0.017	-0.004	12.965	0.056	0.056	0.000	0.000	0.000	0.000
39	F	40	ALA	0	0.002	0.010	10.432	0.056	0.056	0.000	0.000	0.000	0.000
40	F	41	LYS	1	0.827	0.879	12.483	0.197	0.197	0.000	0.000	0.000	0.000
41	F	42	ALA	0	-0.033	-0.005	15.328	0.029	0.029	0.000	0.000	0.000	0.000
42	F	43	GLN	0	-0.048	-0.030	13.548	0.031	0.031	0.000	0.000	0.000	0.000
43	F	44	GLN	0	-0.023	0.015	14.677	0.007	0.007	0.000	0.000	0.000	0.000
44	F	45	THR	0	0.006	0.007	17.372	-0.017	-0.017	0.000	0.000	0.000	0.000
45	F	46	VAL	0	0.011	-0.002	18.589	0.021	0.021	0.000	0.000	0.000	0.000
46	F	47	ARG	1	0.943	0.959	20.989	-0.128	-0.128	0.000	0.000	0.000	0.000
47	F	48	LEU	0	0.032	0.015	23.937	0.010	0.010	0.000	0.000	0.000	0.000
48	F	49	GLY	0	0.045	0.028	25.499	0.004	0.004	0.000	0.000	0.000	0.000
49	F	50	SER	0	0.007	-0.020	25.257	0.001	0.001	0.000	0.000	0.000	0.000
50	F	51	MET	0	-0.009	-0.002	19.846	0.019	0.019	0.000	0.000	0.000	0.000
51	F	52	LEU	0	0.051	0.031	23.639	0.013	0.013	0.000	0.000	0.000	0.000
52	F	53	ALA	0	0.033	0.013	26.071	0.006	0.006	0.000	0.000	0.000	0.000
53	F	54	SER	0	-0.014	0.004	23.268	0.003	0.003	0.000	0.000	0.000	0.000
54	F	55	ILE	0	0.032	0.012	21.196	0.001	0.001	0.000	0.000	0.000	0.000
55	F	56	GLY	0	-0.013	0.004	24.802	-0.003	-0.003	0.000	0.000	0.000	0.000
56	F	57	GLN	0	-0.028	-0.021	27.988	-0.010	-0.010	0.000	0.000	0.000	0.000
57	F	58	GLU	-1	-0.997	-0.989	21.996	0.256	0.256	0.000	0.000	0.000	0.000
58	F	59	ILE	0	-0.065	-0.034	25.816	0.003	0.003	0.000	0.000	0.000	0.000
59	F	60	GLY	0	-0.025	-0.008	28.358	-0.010	-0.010	0.000	0.000	0.000	0.000
60	F	61	GLY	0	-0.034	-0.002	30.701	-0.009	-0.009	0.000	0.000	0.000	0.000
61	F	62	VAL	0	-0.038	-0.033	30.794	-0.001	-0.001	0.000	0.000	0.000	0.000
62	F	63	GLU	-1	-0.873	-0.948	33.547	0.054	0.054	0.000	0.000	0.000	0.000
63	F	64	LEU	0	-0.097	-0.039	30.071	-0.001	-0.001	0.000	0.000	0.000	0.000
64	F	65	GLU	-1	-1.000	-0.985	34.808	0.030	0.030	0.000	0.000	0.000	0.000

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