FMO DATABASE

FMODB ID: 66JRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-283628.761936
FMO2-HF: Nuclear repulsion	258342.264316
FMO2-HF: Total energy	-25286.497619
FMO2-MP2: Total energy	-25360.905159

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.
0.414	3.08	-0.035	-1.424	-1.208	0.008

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 : 0.041 / q_NPA : 0.029

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	0.030	0.005	3.777	-1.076	1.590	-0.035	-1.424	-1.208	0.008
4	E	5	VAL	0	0.004	0.005	6.738	-0.016	-0.016	0.000	0.000	0.000	0.000
5	E	6	ILE	0	0.011	-0.001	10.164	0.091	0.091	0.000	0.000	0.000	0.000
6	E	7	ARG	1	0.956	0.977	13.114	0.324	0.324	0.000	0.000	0.000	0.000
7	E	8	ASN	0	-0.015	-0.007	16.638	0.008	0.008	0.000	0.000	0.000	0.000
8	E	9	LEU	0	0.030	0.035	16.405	0.009	0.009	0.000	0.000	0.000	0.000
9	E	10	SER	0	0.056	0.018	19.316	0.011	0.011	0.000	0.000	0.000	0.000
10	E	11	GLU	-1	-0.764	-0.889	22.164	-0.283	-0.283	0.000	0.000	0.000	0.000
11	E	12	ALA	0	0.014	0.008	24.285	-0.006	-0.006	0.000	0.000	0.000	0.000
12	E	13	THR	0	0.008	-0.003	19.664	0.002	0.002	0.000	0.000	0.000	0.000
13	E	14	HIS	0	-0.025	-0.009	19.248	-0.056	-0.056	0.000	0.000	0.000	0.000
14	E	15	ASN	0	0.000	-0.010	21.025	-0.023	-0.023	0.000	0.000	0.000	0.000
15	E	16	ALA	0	0.037	0.038	22.958	-0.003	-0.003	0.000	0.000	0.000	0.000
16	E	17	ILE	0	-0.003	-0.010	16.674	-0.001	-0.001	0.000	0.000	0.000	0.000
17	E	18	LYS	1	0.873	0.932	19.935	0.320	0.320	0.000	0.000	0.000	0.000
18	E	19	PHE	0	-0.031	-0.020	21.134	0.003	0.003	0.000	0.000	0.000	0.000
19	E	20	ARG	1	0.906	0.939	19.254	0.304	0.304	0.000	0.000	0.000	0.000
20	E	21	ALA	0	-0.028	-0.017	18.553	0.002	0.002	0.000	0.000	0.000	0.000
21	E	22	ARG	1	0.959	0.981	20.203	0.216	0.216	0.000	0.000	0.000	0.000
22	E	23	ALA	0	-0.039	-0.005	23.223	0.017	0.017	0.000	0.000	0.000	0.000
23	E	24	ALA	0	-0.022	0.010	20.803	0.017	0.017	0.000	0.000	0.000	0.000
24	E	25	GLY	0	0.054	0.021	21.985	-0.001	-0.001	0.000	0.000	0.000	0.000
25	E	26	ARG	1	0.833	0.898	16.273	0.342	0.342	0.000	0.000	0.000	0.000
26	E	27	SER	0	0.059	0.035	14.262	0.008	0.008	0.000	0.000	0.000	0.000
27	E	28	THR	0	0.061	-0.004	16.037	-0.013	-0.013	0.000	0.000	0.000	0.000
28	E	29	GLU	-1	-0.818	-0.879	9.561	-1.427	-1.427	0.000	0.000	0.000	0.000
29	E	30	ALA	0	-0.019	-0.010	11.619	-0.112	-0.112	0.000	0.000	0.000	0.000
30	E	31	GLU	-1	-0.760	-0.853	12.835	-0.390	-0.390	0.000	0.000	0.000	0.000
31	E	32	ILE	0	-0.013	0.001	10.199	0.047	0.047	0.000	0.000	0.000	0.000
32	E	33	ARG	1	0.895	0.905	6.837	1.768	1.768	0.000	0.000	0.000	0.000
33	E	34	LEU	0	0.020	0.030	9.883	0.082	0.082	0.000	0.000	0.000	0.000
34	E	35	ILE	0	-0.053	-0.031	12.838	0.084	0.084	0.000	0.000	0.000	0.000
35	E	36	LEU	0	-0.009	-0.005	8.359	0.063	0.063	0.000	0.000	0.000	0.000
36	E	37	ASP	-1	-0.880	-0.948	8.808	-0.678	-0.678	0.000	0.000	0.000	0.000
37	E	38	ASN	0	-0.106	-0.057	10.807	0.147	0.147	0.000	0.000	0.000	0.000
38	E	39	ILE	0	0.027	0.018	13.272	0.054	0.054	0.000	0.000	0.000	0.000
39	E	40	ALA	0	0.008	0.014	10.593	0.054	0.054	0.000	0.000	0.000	0.000
40	E	41	LYS	1	0.884	0.925	12.571	0.277	0.277	0.000	0.000	0.000	0.000
41	E	42	ALA	0	-0.003	0.003	14.715	0.030	0.030	0.000	0.000	0.000	0.000
42	E	43	GLN	0	-0.015	-0.003	14.568	0.037	0.037	0.000	0.000	0.000	0.000
43	E	44	GLN	0	-0.068	-0.023	13.912	0.056	0.056	0.000	0.000	0.000	0.000
44	E	45	THR	0	0.013	0.013	16.573	-0.004	-0.004	0.000	0.000	0.000	0.000
45	E	46	VAL	0	0.027	0.004	19.259	0.000	0.000	0.000	0.000	0.000	0.000
46	E	47	ARG	1	0.905	0.953	15.532	-0.093	-0.093	0.000	0.000	0.000	0.000
47	E	48	LEU	0	0.053	0.021	18.297	0.002	0.002	0.000	0.000	0.000	0.000
48	E	49	GLY	0	0.047	0.028	17.951	-0.002	-0.002	0.000	0.000	0.000	0.000
49	E	50	SER	0	0.028	-0.004	19.134	-0.010	-0.010	0.000	0.000	0.000	0.000
50	E	51	MET	0	-0.027	0.014	21.165	-0.014	-0.014	0.000	0.000	0.000	0.000
51	E	52	LEU	0	0.068	0.016	21.844	-0.008	-0.008	0.000	0.000	0.000	0.000
52	E	53	ALA	0	0.011	0.010	22.742	-0.004	-0.004	0.000	0.000	0.000	0.000
53	E	54	SER	0	-0.044	-0.017	24.711	-0.010	-0.010	0.000	0.000	0.000	0.000
54	E	55	ILE	0	0.041	0.019	27.289	-0.004	-0.004	0.000	0.000	0.000	0.000
55	E	56	GLY	0	0.031	0.022	27.784	-0.003	-0.003	0.000	0.000	0.000	0.000
56	E	57	GLN	0	-0.054	-0.039	27.390	0.002	0.002	0.000	0.000	0.000	0.000
57	E	58	GLU	-1	-1.017	-1.003	30.406	0.055	0.055	0.000	0.000	0.000	0.000
58	E	59	ILE	0	-0.042	-0.026	32.236	-0.005	-0.005	0.000	0.000	0.000	0.000
59	E	60	GLY	0	-0.036	-0.003	33.467	-0.001	-0.001	0.000	0.000	0.000	0.000
60	E	61	GLY	0	-0.049	-0.017	30.949	0.004	0.004	0.000	0.000	0.000	0.000
61	E	62	VAL	0	-0.035	-0.025	31.087	-0.006	-0.006	0.000	0.000	0.000	0.000
62	E	63	GLU	-1	-0.906	-0.960	30.896	0.145	0.145	0.000	0.000	0.000	0.000
63	E	64	LEU	0	-0.098	-0.041	30.400	-0.007	-0.007	0.000	0.000	0.000	0.000
64	E	65	GLU	-1	-0.928	-0.963	33.030	0.093	0.093	0.000	0.000	0.000	0.000
65	E	66	ASP	-1	-0.951	-0.980	31.679	0.141	0.141	0.000	0.000	0.000	0.000
66	E	67	VAL	0	-0.037	-0.012	32.956	0.001	0.001	0.000	0.000	0.000	0.000
67	E	68	ARG	1	0.997	0.972	27.621	-0.148	-0.148	0.000	0.000	0.000	0.000
68	E	69	GLY	0	-0.032	0.012	33.720	0.002	0.002	0.000	0.000	0.000	0.000

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