FMO DATABASE

FMODB ID: 37YQL

Calculation Name: 2BSQ-F-Xray540

Preferred Name:

Target Type:

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

Ligand 3-letter code: 5IU

Ligand of Interest (LOI):

PDB ID: 2BSQ

Chain ID: F

ChEMBL ID:

UniProt ID: Q5F881

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-268682.265637
FMO2-HF: Nuclear repulsion	244899.333202
FMO2-HF: Total energy	-23782.932434
FMO2-MP2: Total energy	-23852.63331

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.
0.884	3.456	-0.02	-1.434	-1.118	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 : 0.158 / q_NPA : 0.019

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].
4	F	3	SER	0	-0.008	0.085	4.463	0.626	0.979	-0.001	-0.153	-0.199	0.000
5	F	4	VAL	0	0.013	-0.139	3.791	-2.210	-0.035	-0.018	-1.274	-0.883	0.008
6	F	4	VAL	0	-0.017	0.138	4.588	0.081	0.125	-0.001	-0.007	-0.036	0.000
7	F	5	VAL	0	0.068	-0.103	6.765	0.229	0.229	0.000	0.000	0.000	0.000
8	F	5	VAL	0	-0.087	0.113	9.289	0.041	0.041	0.000	0.000	0.000	0.000
9	F	6	ILE	0	0.063	-0.119	10.368	0.025	0.025	0.000	0.000	0.000	0.000
10	F	6	ILE	0	-0.038	0.133	10.746	0.013	0.013	0.000	0.000	0.000	0.000
11	F	7	ARG	0	0.076	-0.087	13.240	0.063	0.063	0.000	0.000	0.000	0.000
12	F	7	ARG	1	0.867	1.048	12.579	0.823	0.823	0.000	0.000	0.000	0.000
13	F	8	ASN	0	0.069	-0.059	16.588	-0.022	-0.022	0.000	0.000	0.000	0.000
14	F	8	ASN	0	-0.105	0.068	19.791	0.019	0.019	0.000	0.000	0.000	0.000
15	F	9	LEU	0	0.177	-0.103	18.535	0.015	0.015	0.000	0.000	0.000	0.000
16	F	9	LEU	0	-0.121	0.109	16.524	-0.010	-0.010	0.000	0.000	0.000	0.000
17	F	10	SER	0	0.119	-0.025	19.584	0.028	0.028	0.000	0.000	0.000	0.000
18	F	10	SER	0	-0.051	0.039	22.965	0.007	0.007	0.000	0.000	0.000	0.000
19	F	11	GLU	0	0.156	-0.092	22.313	-0.037	-0.037	0.000	0.000	0.000	0.000
20	F	11	GLU	-1	-0.955	-0.813	23.636	-0.315	-0.315	0.000	0.000	0.000	0.000
21	F	12	ALA	0	0.117	-0.080	23.989	-0.009	-0.009	0.000	0.000	0.000	0.000
22	F	12	ALA	0	-0.063	0.117	26.471	0.004	0.004	0.000	0.000	0.000	0.000
23	F	13	THR	0	0.030	-0.062	21.974	0.013	0.013	0.000	0.000	0.000	0.000
24	F	13	THR	0	-0.016	0.073	20.088	0.002	0.002	0.000	0.000	0.000	0.000
25	F	14	HIS	0	0.075	-0.105	19.775	-0.026	-0.026	0.000	0.000	0.000	0.000
26	F	14	HIS	0	-0.067	0.107	18.251	-0.040	-0.040	0.000	0.000	0.000	0.000
27	F	15	ASN	0	0.147	-0.056	20.785	-0.013	-0.013	0.000	0.000	0.000	0.000
28	F	15	ASN	0	-0.131	0.049	25.096	0.017	0.017	0.000	0.000	0.000	0.000
29	F	16	ALA	0	0.067	-0.127	23.259	0.015	0.015	0.000	0.000	0.000	0.000
30	F	16	ALA	0	-0.094	0.111	22.900	0.001	0.001	0.000	0.000	0.000	0.000
31	F	17	ILE	0	0.085	-0.109	18.512	0.038	0.038	0.000	0.000	0.000	0.000
32	F	17	ILE	0	-0.088	0.113	16.362	-0.007	-0.007	0.000	0.000	0.000	0.000
33	F	18	LYS	0	0.193	-0.064	19.530	-0.001	-0.001	0.000	0.000	0.000	0.000
34	F	18	LYS	1	0.769	1.039	20.231	0.281	0.281	0.000	0.000	0.000	0.000
35	F	19	PHE	0	-0.013	-0.114	20.440	0.013	0.013	0.000	0.000	0.000	0.000
36	F	19	PHE	0	-0.070	0.085	24.222	0.003	0.003	0.000	0.000	0.000	0.000
37	F	20	ARG	0	0.107	-0.086	20.870	0.035	0.035	0.000	0.000	0.000	0.000
38	F	20	ARG	1	0.858	1.047	19.369	0.338	0.338	0.000	0.000	0.000	0.000
39	F	21	ALA	0	0.109	-0.065	18.375	0.029	0.029	0.000	0.000	0.000	0.000
40	F	21	ALA	0	-0.091	0.078	17.683	-0.012	-0.012	0.000	0.000	0.000	0.000
41	F	22	ARG	0	0.070	-0.056	19.259	0.021	0.021	0.000	0.000	0.000	0.000
42	F	22	ARG	1	0.848	1.044	19.305	0.276	0.276	0.000	0.000	0.000	0.000
43	F	23	ALA	0	0.065	-0.077	22.121	0.023	0.023	0.000	0.000	0.000	0.000
44	F	23	ALA	0	-0.062	0.112	24.394	0.000	0.000	0.000	0.000	0.000	0.000
45	F	24	ALA	0	0.083	-0.092	21.494	0.024	0.024	0.000	0.000	0.000	0.000
46	F	24	ALA	0	-0.097	0.086	20.593	-0.004	-0.004	0.000	0.000	0.000	0.000
47	F	25	GLY	0	-0.091	-0.153	21.466	0.010	0.010	0.000	0.000	0.000	0.000
48	F	26	ARG	0	0.035	-0.024	17.322	0.027	0.027	0.000	0.000	0.000	0.000
49	F	26	ARG	1	0.845	1.034	16.030	0.269	0.269	0.000	0.000	0.000	0.000
50	F	27	SER	0	0.040	-0.056	15.788	0.009	0.009	0.000	0.000	0.000	0.000
51	F	27	SER	0	0.011	0.073	14.029	-0.019	-0.019	0.000	0.000	0.000	0.000
52	F	28	THR	0	0.034	-0.075	15.316	-0.028	-0.028	0.000	0.000	0.000	0.000
53	F	28	THR	0	-0.026	0.048	15.790	0.028	0.028	0.000	0.000	0.000	0.000
54	F	29	GLU	0	0.115	-0.088	11.807	-0.040	-0.040	0.000	0.000	0.000	0.000
55	F	29	GLU	-1	-0.920	-0.795	8.399	-1.124	-1.124	0.000	0.000	0.000	0.000
56	F	30	ALA	0	0.112	-0.097	11.043	-0.203	-0.203	0.000	0.000	0.000	0.000
57	F	30	ALA	0	-0.088	0.099	12.796	0.031	0.031	0.000	0.000	0.000	0.000
58	F	31	GLU	0	0.092	-0.072	12.157	-0.033	-0.033	0.000	0.000	0.000	0.000
59	F	31	GLU	-1	-0.902	-0.807	15.587	-0.387	-0.387	0.000	0.000	0.000	0.000
60	F	32	ILE	0	0.092	-0.095	12.223	0.054	0.054	0.000	0.000	0.000	0.000
61	F	32	ILE	0	-0.079	0.082	10.669	0.006	0.006	0.000	0.000	0.000	0.000
62	F	33	ARG	0	0.118	-0.074	8.789	-0.129	-0.129	0.000	0.000	0.000	0.000
63	F	33	ARG	1	0.784	1.020	6.762	1.044	1.044	0.000	0.000	0.000	0.000
64	F	34	LEU	0	0.126	-0.075	9.496	-0.042	-0.042	0.000	0.000	0.000	0.000
65	F	34	LEU	0	-0.109	0.093	13.273	0.019	0.019	0.000	0.000	0.000	0.000
66	F	35	ILE	0	0.082	-0.062	12.365	0.055	0.055	0.000	0.000	0.000	0.000
67	F	35	ILE	0	-0.122	0.072	13.895	0.009	0.009	0.000	0.000	0.000	0.000
68	F	36	LEU	0	0.072	-0.112	10.256	0.175	0.175	0.000	0.000	0.000	0.000
69	F	36	LEU	0	-0.083	0.092	8.756	-0.056	-0.056	0.000	0.000	0.000	0.000
70	F	37	ASP	0	0.120	-0.071	10.616	-0.039	-0.039	0.000	0.000	0.000	0.000
71	F	37	ASP	-1	-0.917	-0.804	9.876	-0.318	-0.318	0.000	0.000	0.000	0.000
72	F	38	ASN	0	0.112	-0.083	11.251	0.097	0.097	0.000	0.000	0.000	0.000
73	F	38	ASN	0	-0.186	0.014	14.696	0.060	0.060	0.000	0.000	0.000	0.000
74	F	39	ILE	0	0.105	-0.060	14.333	0.098	0.098	0.000	0.000	0.000	0.000
75	F	39	ILE	0	-0.118	0.068	13.904	-0.003	-0.003	0.000	0.000	0.000	0.000
76	F	40	ALA	0	0.099	-0.081	12.028	0.069	0.069	0.000	0.000	0.000	0.000
77	F	40	ALA	0	-0.077	0.097	11.361	-0.018	-0.018	0.000	0.000	0.000	0.000
78	F	41	LYS	0	0.059	-0.116	13.475	0.065	0.065	0.000	0.000	0.000	0.000
79	F	41	LYS	1	0.719	0.973	12.483	0.227	0.227	0.000	0.000	0.000	0.000
80	F	42	ALA	0	0.115	-0.048	15.767	0.056	0.056	0.000	0.000	0.000	0.000
81	F	42	ALA	0	-0.129	0.059	18.434	-0.004	-0.004	0.000	0.000	0.000	0.000
82	F	43	GLN	0	0.053	-0.120	16.683	0.052	0.052	0.000	0.000	0.000	0.000
83	F	43	GLN	0	-0.102	0.075	14.439	-0.046	-0.046	0.000	0.000	0.000	0.000
84	F	44	GLN	0	0.107	-0.074	17.140	0.014	0.014	0.000	0.000	0.000	0.000
85	F	44	GLN	0	-0.145	0.079	15.112	-0.003	-0.003	0.000	0.000	0.000	0.000
86	F	45	THR	0	0.031	-0.082	18.230	0.007	0.007	0.000	0.000	0.000	0.000
87	F	45	THR	0	-0.030	0.089	22.078	0.004	0.004	0.000	0.000	0.000	0.000
88	F	46	VAL	0	0.046	-0.120	20.777	0.012	0.012	0.000	0.000	0.000	0.000
89	F	46	VAL	0	-0.057	0.120	18.900	0.002	0.002	0.000	0.000	0.000	0.000
90	F	47	ARG	0	0.109	-0.065	21.451	-0.011	-0.011	0.000	0.000	0.000	0.000
91	F	47	ARG	1	0.843	1.050	23.358	-0.022	-0.022	0.000	0.000	0.000	0.000
92	F	48	LEU	0	0.078	-0.119	24.369	0.021	0.021	0.000	0.000	0.000	0.000
93	F	48	LEU	0	-0.052	0.131	24.942	-0.003	-0.003	0.000	0.000	0.000	0.000
94	F	49	GLY	0	0.050	-0.097	25.586	0.011	0.011	0.000	0.000	0.000	0.000
95	F	50	SER	0	0.065	0.040	26.566	0.010	0.010	0.000	0.000	0.000	0.000
96	F	50	SER	0	-0.010	0.049	25.810	-0.007	-0.007	0.000	0.000	0.000	0.000
97	F	51	MET	0	0.074	-0.077	23.062	0.016	0.016	0.000	0.000	0.000	0.000
98	F	51	MET	0	-0.138	0.074	19.846	0.002	0.002	0.000	0.000	0.000	0.000
99	F	52	LEU	0	0.126	-0.054	23.779	0.028	0.028	0.000	0.000	0.000	0.000
100	F	52	LEU	0	-0.059	0.092	24.696	-0.002	-0.002	0.000	0.000	0.000	0.000
101	F	53	ALA	0	0.170	-0.074	26.071	0.016	0.016	0.000	0.000	0.000	0.000
102	F	53	ALA	0	-0.087	0.101	28.820	-0.003	-0.003	0.000	0.000	0.000	0.000
103	F	54	SER	0	0.026	-0.063	24.657	-0.003	-0.003	0.000	0.000	0.000	0.000
104	F	54	SER	0	-0.043	0.055	23.715	-0.001	-0.001	0.000	0.000	0.000	0.000
105	F	55	ILE	0	0.102	-0.084	24.153	0.010	0.010	0.000	0.000	0.000	0.000
106	F	55	ILE	0	-0.101	0.099	21.196	-0.002	-0.002	0.000	0.000	0.000	0.000
107	F	56	GLY	0	-0.034	-0.124	24.802	0.006	0.006	0.000	0.000	0.000	0.000
108	F	57	GLN	0	0.147	0.028	28.321	0.000	0.000	0.000	0.000	0.000	0.000
109	F	57	GLN	0	-0.137	0.072	28.435	-0.006	-0.006	0.000	0.000	0.000	0.000
110	F	58	GLU	0	0.062	-0.116	25.235	-0.007	-0.007	0.000	0.000	0.000	0.000
111	F	58	GLU	-1	-1.060	-0.871	22.075	0.315	0.315	0.000	0.000	0.000	0.000
112	F	59	ILE	0	-0.039	-0.123	26.712	0.011	0.011	0.000	0.000	0.000	0.000
113	F	59	ILE	0	-0.116	0.083	25.816	0.001	0.001	0.000	0.000	0.000	0.000
114	F	60	GLY	0	0.003	-0.117	28.358	-0.009	-0.009	0.000	0.000	0.000	0.000
115	F	61	GLY	0	-0.020	-0.004	30.701	-0.012	-0.012	0.000	0.000	0.000	0.000
116	F	62	VAL	0	0.002	0.007	32.317	0.003	0.003	0.000	0.000	0.000	0.000
117	F	62	VAL	0	-0.079	0.055	30.794	0.000	0.000	0.000	0.000	0.000	0.000
118	F	63	GLU	0	0.128	-0.116	33.547	-0.002	-0.002	0.000	0.000	0.000	0.000
119	F	63	GLU	-1	-0.965	-0.814	37.288	0.069	0.069	0.000	0.000	0.000	0.000
120	F	64	LEU	0	-0.038	-0.105	33.462	0.000	0.000	0.000	0.000	0.000	0.000
121	F	64	LEU	0	-0.101	0.052	30.071	0.001	0.001	0.000	0.000	0.000	0.000
122	F	65	GLU	0	-0.057	-0.135	34.808	-0.008	-0.008	0.000	0.000	0.000	0.000
123	F	65	GLU	-1	-0.905	-0.945	38.244	0.058	0.058	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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