FMO DATABASE

FMODB ID: 7G8ZK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-268665.45876
FMO2-HF: Nuclear repulsion	244869.476512
FMO2-HF: Total energy	-23795.982248
FMO2-MP2: Total energy	-23865.940548

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.
0.757	3.273	-0.012	-1.421	-1.082	0.005

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 : 0.076 / q_NPA : 0.044

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	0.025	0.012	3.882	-0.859	1.657	-0.012	-1.421	-1.082	0.005
4	F	5	VAL	0	0.018	0.019	6.256	-0.037	-0.037	0.000	0.000	0.000	0.000
5	F	6	ILE	0	0.034	0.019	9.916	0.164	0.164	0.000	0.000	0.000	0.000
6	F	7	ARG	1	0.898	0.930	11.558	0.320	0.320	0.000	0.000	0.000	0.000
7	F	8	ASN	0	0.004	-0.002	15.874	0.006	0.006	0.000	0.000	0.000	0.000
8	F	9	LEU	0	0.014	0.029	16.250	0.021	0.021	0.000	0.000	0.000	0.000
9	F	10	SER	0	0.040	0.019	19.083	0.006	0.006	0.000	0.000	0.000	0.000
10	F	11	GLU	-1	-0.749	-0.896	22.102	-0.253	-0.253	0.000	0.000	0.000	0.000
11	F	12	ALA	0	0.002	0.024	24.025	-0.009	-0.009	0.000	0.000	0.000	0.000
12	F	13	THR	0	0.027	0.000	19.655	0.002	0.002	0.000	0.000	0.000	0.000
13	F	14	HIS	0	-0.018	0.004	17.947	-0.033	-0.033	0.000	0.000	0.000	0.000
14	F	15	ASN	0	-0.023	-0.036	20.382	-0.023	-0.023	0.000	0.000	0.000	0.000
15	F	16	ALA	0	0.017	0.025	22.601	0.000	0.000	0.000	0.000	0.000	0.000
16	F	17	ILE	0	0.014	0.006	16.223	0.000	0.000	0.000	0.000	0.000	0.000
17	F	18	LYS	1	0.880	0.927	19.481	0.229	0.229	0.000	0.000	0.000	0.000
18	F	19	PHE	0	-0.013	-0.008	20.706	-0.003	-0.003	0.000	0.000	0.000	0.000
19	F	20	ARG	1	0.917	0.944	18.959	0.236	0.236	0.000	0.000	0.000	0.000
20	F	21	ALA	0	0.009	0.009	18.239	0.005	0.005	0.000	0.000	0.000	0.000
21	F	22	ARG	1	0.884	0.944	19.317	0.362	0.362	0.000	0.000	0.000	0.000
22	F	23	ALA	0	0.005	0.007	22.788	0.012	0.012	0.000	0.000	0.000	0.000
23	F	24	ALA	0	-0.007	0.004	20.781	0.018	0.018	0.000	0.000	0.000	0.000
24	F	25	GLY	0	-0.008	0.011	21.224	-0.006	-0.006	0.000	0.000	0.000	0.000
25	F	26	ARG	1	0.866	0.919	16.510	0.279	0.279	0.000	0.000	0.000	0.000
26	F	27	SER	0	0.027	0.007	13.845	0.021	0.021	0.000	0.000	0.000	0.000
27	F	28	THR	0	0.042	-0.007	15.713	-0.005	-0.005	0.000	0.000	0.000	0.000
28	F	29	GLU	-1	-0.831	-0.877	8.758	-1.566	-1.566	0.000	0.000	0.000	0.000
29	F	30	ALA	0	0.038	0.020	11.290	-0.095	-0.095	0.000	0.000	0.000	0.000
30	F	31	GLU	-1	-0.765	-0.861	12.345	-0.310	-0.310	0.000	0.000	0.000	0.000
31	F	32	ILE	0	-0.023	-0.016	10.292	0.043	0.043	0.000	0.000	0.000	0.000
32	F	33	ARG	1	0.865	0.903	6.861	1.523	1.523	0.000	0.000	0.000	0.000
33	F	34	LEU	0	0.021	0.018	9.624	0.075	0.075	0.000	0.000	0.000	0.000
34	F	35	ILE	0	-0.020	-0.004	12.479	0.094	0.094	0.000	0.000	0.000	0.000
35	F	36	LEU	0	0.005	-0.007	7.514	0.066	0.066	0.000	0.000	0.000	0.000
36	F	37	ASP	-1	-0.814	-0.882	9.790	-0.080	-0.080	0.000	0.000	0.000	0.000
37	F	38	ASN	0	-0.055	-0.040	10.806	0.127	0.127	0.000	0.000	0.000	0.000
38	F	39	ILE	0	-0.022	-0.006	12.789	0.044	0.044	0.000	0.000	0.000	0.000
39	F	40	ALA	0	0.006	0.001	10.231	0.046	0.046	0.000	0.000	0.000	0.000
40	F	41	LYS	1	0.826	0.883	12.271	0.123	0.123	0.000	0.000	0.000	0.000
41	F	42	ALA	0	-0.018	-0.001	15.296	0.021	0.021	0.000	0.000	0.000	0.000
42	F	43	GLN	0	-0.045	-0.019	13.388	0.027	0.027	0.000	0.000	0.000	0.000
43	F	44	GLN	0	-0.026	0.003	14.484	0.002	0.002	0.000	0.000	0.000	0.000
44	F	45	THR	0	0.004	-0.001	17.321	-0.019	-0.019	0.000	0.000	0.000	0.000
45	F	46	VAL	0	0.013	0.000	18.404	0.020	0.020	0.000	0.000	0.000	0.000
46	F	47	ARG	1	0.945	0.969	20.832	-0.153	-0.153	0.000	0.000	0.000	0.000
47	F	48	LEU	0	0.032	0.009	23.748	0.009	0.009	0.000	0.000	0.000	0.000
48	F	49	GLY	0	0.043	0.028	24.952	0.003	0.003	0.000	0.000	0.000	0.000
49	F	50	SER	0	0.002	-0.010	24.848	0.001	0.001	0.000	0.000	0.000	0.000
50	F	51	MET	0	0.000	0.007	19.367	0.019	0.019	0.000	0.000	0.000	0.000
51	F	52	LEU	0	0.025	0.016	23.291	0.007	0.007	0.000	0.000	0.000	0.000
52	F	53	ALA	0	0.025	0.015	26.043	0.001	0.001	0.000	0.000	0.000	0.000
53	F	54	SER	0	-0.026	-0.010	22.918	0.003	0.003	0.000	0.000	0.000	0.000
54	F	55	ILE	0	0.023	0.012	20.881	0.002	0.002	0.000	0.000	0.000	0.000
55	F	56	GLY	0	0.016	0.011	24.531	-0.005	-0.005	0.000	0.000	0.000	0.000
56	F	57	GLN	0	-0.040	-0.036	27.736	-0.011	-0.011	0.000	0.000	0.000	0.000
57	F	58	GLU	-1	-0.987	-0.982	21.369	0.235	0.235	0.000	0.000	0.000	0.000
58	F	59	ILE	0	-0.065	-0.034	25.499	0.000	0.000	0.000	0.000	0.000	0.000
59	F	60	GLY	0	-0.020	-0.001	27.833	-0.009	-0.009	0.000	0.000	0.000	0.000
60	F	61	GLY	0	-0.033	-0.004	30.676	-0.007	-0.007	0.000	0.000	0.000	0.000
61	F	62	VAL	0	-0.044	-0.036	30.327	-0.002	-0.002	0.000	0.000	0.000	0.000
62	F	63	GLU	-1	-0.845	-0.897	33.311	0.047	0.047	0.000	0.000	0.000	0.000
63	F	64	LEU	0	-0.095	-0.058	30.177	0.000	0.000	0.000	0.000	0.000	0.000
64	F	65	GLU	-1	-1.028	-1.018	34.882	0.023	0.023	0.000	0.000	0.000	0.000

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