FMO DATABASE

FMODB ID: ZYMGN

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	OptAll
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	-283489.444958
FMO2-HF: Nuclear repulsion	258202.635194
FMO2-HF: Total energy	-25286.809765
FMO2-MP2: Total energy	-25361.154088

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.
0.5	3.066	-0.018	-1.497	-1.051	0.007

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 : 0.059 / q_NPA : 0.034

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	E	4	VAL	0	0.037	0.011	3.877	-0.950	1.616	-0.018	-1.497	-1.051	0.007
4	E	5	VAL	0	0.024	0.016	6.964	-0.078	-0.078	0.000	0.000	0.000	0.000
5	E	6	ILE	0	0.008	0.009	10.485	0.136	0.136	0.000	0.000	0.000	0.000
6	E	7	ARG	1	0.933	0.951	12.398	0.328	0.328	0.000	0.000	0.000	0.000
7	E	8	ASN	0	0.003	-0.006	16.778	0.002	0.002	0.000	0.000	0.000	0.000
8	E	9	LEU	0	0.025	0.031	16.731	0.016	0.016	0.000	0.000	0.000	0.000
9	E	10	SER	0	0.042	0.022	19.501	0.009	0.009	0.000	0.000	0.000	0.000
10	E	11	GLU	-1	-0.730	-0.860	22.387	-0.274	-0.274	0.000	0.000	0.000	0.000
11	E	12	ALA	0	0.026	0.020	24.206	-0.008	-0.008	0.000	0.000	0.000	0.000
12	E	13	THR	0	0.017	0.002	19.822	0.001	0.001	0.000	0.000	0.000	0.000
13	E	14	HIS	0	-0.022	-0.018	19.299	-0.055	-0.055	0.000	0.000	0.000	0.000
14	E	15	ASN	0	-0.042	-0.048	20.830	-0.028	-0.028	0.000	0.000	0.000	0.000
15	E	16	ALA	0	0.025	0.032	23.054	0.000	0.000	0.000	0.000	0.000	0.000
16	E	17	ILE	0	0.003	-0.008	16.648	0.000	0.000	0.000	0.000	0.000	0.000
17	E	18	LYS	1	0.839	0.919	19.850	0.310	0.310	0.000	0.000	0.000	0.000
18	E	19	PHE	0	-0.003	0.001	21.175	0.000	0.000	0.000	0.000	0.000	0.000
19	E	20	ARG	1	0.900	0.931	19.077	0.273	0.273	0.000	0.000	0.000	0.000
20	E	21	ALA	0	-0.016	-0.017	18.456	0.006	0.006	0.000	0.000	0.000	0.000
21	E	22	ARG	1	0.939	0.981	20.043	0.208	0.208	0.000	0.000	0.000	0.000
22	E	23	ALA	0	-0.006	0.012	23.501	0.019	0.019	0.000	0.000	0.000	0.000
23	E	24	ALA	0	-0.042	-0.007	20.733	0.015	0.015	0.000	0.000	0.000	0.000
24	E	25	GLY	0	0.042	0.020	21.761	0.007	0.007	0.000	0.000	0.000	0.000
25	E	26	ARG	1	0.846	0.900	16.186	0.321	0.321	0.000	0.000	0.000	0.000
26	E	27	SER	0	0.076	0.043	14.291	0.016	0.016	0.000	0.000	0.000	0.000
27	E	28	THR	0	0.039	-0.011	15.966	-0.018	-0.018	0.000	0.000	0.000	0.000
28	E	29	GLU	-1	-0.818	-0.879	10.250	-1.324	-1.324	0.000	0.000	0.000	0.000
29	E	30	ALA	0	-0.005	-0.006	11.278	-0.125	-0.125	0.000	0.000	0.000	0.000
30	E	31	GLU	-1	-0.785	-0.859	12.815	-0.339	-0.339	0.000	0.000	0.000	0.000
31	E	32	ILE	0	-0.015	-0.013	10.355	0.047	0.047	0.000	0.000	0.000	0.000
32	E	33	ARG	1	0.870	0.912	6.982	1.656	1.656	0.000	0.000	0.000	0.000
33	E	34	LEU	0	0.031	0.031	9.872	0.105	0.105	0.000	0.000	0.000	0.000
34	E	35	ILE	0	-0.026	-0.020	12.846	0.086	0.086	0.000	0.000	0.000	0.000
35	E	36	LEU	0	0.015	0.009	8.172	0.070	0.070	0.000	0.000	0.000	0.000
36	E	37	ASP	-1	-0.859	-0.934	8.698	-0.560	-0.560	0.000	0.000	0.000	0.000
37	E	38	ASN	0	-0.114	-0.054	10.950	0.127	0.127	0.000	0.000	0.000	0.000
38	E	39	ILE	0	0.031	0.019	13.125	0.044	0.044	0.000	0.000	0.000	0.000
39	E	40	ALA	0	0.012	0.005	10.446	0.047	0.047	0.000	0.000	0.000	0.000
40	E	41	LYS	1	0.842	0.900	12.383	0.226	0.226	0.000	0.000	0.000	0.000
41	E	42	ALA	0	0.000	0.002	14.533	0.025	0.025	0.000	0.000	0.000	0.000
42	E	43	GLN	0	0.003	0.008	14.447	0.028	0.028	0.000	0.000	0.000	0.000
43	E	44	GLN	0	-0.073	-0.013	13.497	0.057	0.057	0.000	0.000	0.000	0.000
44	E	45	THR	0	0.000	-0.011	16.407	-0.008	-0.008	0.000	0.000	0.000	0.000
45	E	46	VAL	0	0.022	0.010	19.216	-0.004	-0.004	0.000	0.000	0.000	0.000
46	E	47	ARG	1	0.911	0.953	15.493	-0.137	-0.137	0.000	0.000	0.000	0.000
47	E	48	LEU	0	0.053	0.027	18.349	0.000	0.000	0.000	0.000	0.000	0.000
48	E	49	GLY	0	0.057	0.032	17.919	-0.007	-0.007	0.000	0.000	0.000	0.000
49	E	50	SER	0	0.014	-0.004	19.020	-0.011	-0.011	0.000	0.000	0.000	0.000
50	E	51	MET	0	-0.009	0.026	20.805	-0.017	-0.017	0.000	0.000	0.000	0.000
51	E	52	LEU	0	0.048	0.007	21.538	-0.009	-0.009	0.000	0.000	0.000	0.000
52	E	53	ALA	0	0.013	0.010	22.372	-0.007	-0.007	0.000	0.000	0.000	0.000
53	E	54	SER	0	-0.072	-0.041	24.308	-0.013	-0.013	0.000	0.000	0.000	0.000
54	E	55	ILE	0	0.039	0.016	26.763	-0.006	-0.006	0.000	0.000	0.000	0.000
55	E	56	GLY	0	0.016	0.012	27.515	-0.004	-0.004	0.000	0.000	0.000	0.000
56	E	57	GLN	0	-0.033	-0.032	27.109	-0.001	-0.001	0.000	0.000	0.000	0.000
57	E	58	GLU	-1	-0.990	-0.987	29.988	0.071	0.071	0.000	0.000	0.000	0.000
58	E	59	ILE	0	-0.055	-0.028	31.751	-0.006	-0.006	0.000	0.000	0.000	0.000
59	E	60	GLY	0	-0.023	-0.001	33.307	-0.002	-0.002	0.000	0.000	0.000	0.000
60	E	61	GLY	0	-0.035	-0.006	30.764	0.003	0.003	0.000	0.000	0.000	0.000
61	E	62	VAL	0	-0.043	-0.038	31.003	-0.008	-0.008	0.000	0.000	0.000	0.000
62	E	63	GLU	-1	-0.916	-0.951	30.524	0.161	0.161	0.000	0.000	0.000	0.000
63	E	64	LEU	0	-0.071	-0.034	30.035	-0.009	-0.009	0.000	0.000	0.000	0.000
64	E	65	GLU	-1	-0.928	-0.966	32.924	0.103	0.103	0.000	0.000	0.000	0.000
65	E	66	ASP	-1	-0.903	-0.968	31.342	0.153	0.153	0.000	0.000	0.000	0.000
66	E	67	VAL	0	-0.059	-0.026	32.490	0.004	0.004	0.000	0.000	0.000	0.000
67	E	68	ARG	1	0.939	0.978	27.938	-0.167	-0.167	0.000	0.000	0.000	0.000
68	E	69	GLY	0	-0.024	-0.001	33.719	-0.005	-0.005	0.000	0.000	0.000	0.000

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