FMO DATABASE

FMODB ID: 76G9K

Calculation Name: 2BSQ-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: 5IU

PDB ID: 2BSQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F881

Base Structure: X-ray

Registration Date: 2023-09-21

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1260235.888485
FMO2-HF: Nuclear repulsion	1204904.064893
FMO2-HF: Total energy	-55331.823592
FMO2-MP2: Total energy	-55494.684081

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-16.891	-4.553	11.454	-9.103	-14.691	-0.056

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.021

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].
3	A	3	LEU	0	-0.009	-0.007	3.770	-1.537	1.415	-0.027	-1.563	-1.362	0.008
4	A	4	LEU	0	-0.011	-0.013	6.410	0.326	0.326	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.775	-0.863	9.460	-0.637	-0.637	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.007	-0.046	12.702	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.057	-0.036	15.708	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.027	0.026	12.540	0.067	0.067	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.003	-0.005	12.845	0.066	0.066	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.035	-0.031	14.903	0.092	0.092	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.782	-0.878	18.115	-0.361	-0.361	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.030	0.002	16.982	0.056	0.056	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.049	-0.013	19.228	0.048	0.048	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.788	0.888	22.118	0.400	0.400	0.000	0.000	0.000	0.000
15	A	15	PRO	0	-0.033	-0.035	24.535	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.017	-0.002	27.176	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.054	0.013	21.716	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.026	-0.010	20.776	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.864	-0.951	20.535	-0.367	-0.367	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.908	0.959	18.116	0.358	0.358	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.033	-0.019	15.440	-0.052	-0.052	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.008	-0.011	15.458	-0.075	-0.075	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.011	0.017	16.330	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	24	TRP	0	0.024	0.003	8.398	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.024	-0.011	11.126	-0.117	-0.117	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.872	-0.926	11.784	-0.534	-0.534	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.191	-0.081	11.871	0.051	0.051	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.016	-0.016	6.784	-0.129	-0.129	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.029	0.014	7.447	0.220	0.220	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.028	0.014	6.846	-0.310	-0.310	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.922	-0.973	6.783	-0.711	-0.711	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.909	-0.958	2.429	-8.747	-5.410	3.582	-3.590	-3.329	-0.037
33	A	33	VAL	0	-0.048	-0.019	2.427	-4.618	-2.882	2.030	-1.628	-2.139	-0.023
34	A	34	TYR	0	0.008	0.009	2.611	-1.191	0.752	1.218	-0.740	-2.422	-0.005
35	A	35	LEU	0	-0.016	-0.001	5.703	0.015	0.015	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.059	0.042	9.238	0.104	0.104	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.029	-0.004	11.174	0.058	0.058	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.016	-0.004	14.162	0.046	0.046	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.072	0.033	13.042	0.014	0.014	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.007	0.001	13.579	0.049	0.049	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.041	-0.011	16.082	0.052	0.052	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.835	-0.896	18.202	-0.476	-0.476	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.026	0.001	15.379	0.014	0.014	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.829	0.860	18.883	0.359	0.359	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.039	-0.015	21.636	0.034	0.034	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.022	0.002	22.862	0.023	0.023	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.036	-0.015	22.768	0.021	0.021	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.005	-0.006	25.425	0.023	0.023	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.002	0.001	27.164	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.030	0.009	27.260	0.012	0.012	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.029	0.010	30.831	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.004	-0.005	33.887	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.097	0.044	34.234	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.968	0.983	33.567	0.131	0.131	0.000	0.000	0.000	0.000
55	A	55	LYS	1	1.000	0.993	29.140	0.210	0.210	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.857	0.932	29.014	0.171	0.171	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.030	-0.016	28.621	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.024	0.013	27.524	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.006	0.015	22.842	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.024	0.012	23.937	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.792	-0.863	24.187	-0.178	-0.178	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.813	0.867	22.500	0.198	0.198	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.007	0.022	19.077	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.789	-0.876	19.216	-0.336	-0.336	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.057	-0.031	20.728	0.014	0.014	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.071	-0.043	19.660	0.018	0.018	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.017	-0.001	15.147	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.056	0.033	14.585	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.016	0.025	14.174	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.005	0.007	12.917	0.023	0.023	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.001	-0.014	8.413	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.006	0.010	10.641	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.038	-0.018	10.513	0.029	0.029	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.839	0.923	5.394	1.159	1.159	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.038	-0.019	7.898	-0.223	-0.223	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.020	0.000	4.825	0.149	0.149	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.014	0.000	9.404	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.008	0.004	11.758	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.869	-0.942	12.183	-0.131	-0.131	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.909	-0.979	15.171	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.021	0.013	12.805	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.001	0.008	10.664	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.019	0.000	13.395	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.029	0.017	16.603	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.017	0.010	11.317	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.012	-0.003	15.396	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.044	-0.021	16.780	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.026	0.022	16.625	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.003	0.007	13.336	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.852	0.922	17.967	0.229	0.229	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.044	-0.030	20.984	0.012	0.012	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.041	-0.023	20.138	0.023	0.023	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.068	0.033	20.777	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.889	0.946	22.736	0.166	0.166	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.081	-0.033	26.118	0.011	0.011	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.031	-0.030	23.803	0.016	0.016	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.050	-0.006	26.637	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.827	0.919	21.692	0.323	0.323	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.797	-0.884	23.812	-0.187	-0.187	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.023	-0.016	18.436	-0.016	-0.016	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.016	0.014	21.710	0.033	0.033	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.013	-0.001	20.265	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.045	0.027	18.823	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.714	-0.885	16.696	-0.449	-0.449	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.020	-0.006	15.756	-0.050	-0.050	0.000	0.000	0.000	0.000
106	A	106	TYR	0	-0.019	-0.011	15.067	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.024	0.036	11.160	-0.035	-0.035	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.004	0.011	10.793	-0.127	-0.127	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.015	-0.001	10.798	-0.045	-0.045	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.024	-0.044	7.868	0.054	0.054	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.008	-0.005	6.490	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.824	0.914	6.464	0.271	0.271	0.000	0.000	0.000	0.000
113	A	113	GLN	0	0.019	0.026	7.920	0.127	0.127	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.028	-0.012	2.650	-0.287	0.259	0.225	-0.121	-0.649	0.000
115	A	115	SER	0	-0.074	-0.041	3.688	0.272	0.698	0.013	-0.147	-0.292	-0.001
116	A	116	MET	0	-0.058	-0.003	2.324	-1.594	-0.596	4.414	-1.238	-4.175	0.002
117	A	117	THR	0	-0.015	-0.008	4.140	1.091	1.491	-0.001	-0.076	-0.323	0.000
118	A	118	VAL	0	-0.014	-0.005	6.144	-0.571	-0.571	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.012	0.006	8.949	0.212	0.212	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.005	-0.045	10.429	0.143	0.143	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.931	0.974	14.095	0.464	0.464	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.950	-0.971	17.377	-0.382	-0.382	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.058	0.005	14.539	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.039	-0.021	16.865	0.018	0.018	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.009	0.001	18.438	0.061	0.061	0.000	0.000	0.000	0.000
126	A	126	PHE	0	0.079	0.020	13.355	0.017	0.017	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.006	0.032	15.278	0.024	0.024	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.026	-0.012	16.250	0.046	0.046	0.000	0.000	0.000	0.000
129	A	129	ALA	0	-0.031	-0.022	15.099	0.038	0.038	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.892	-0.946	15.009	-0.185	-0.185	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.028	-0.011	9.417	0.035	0.035	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.011	0.018	7.922	0.045	0.045	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.009	-0.015	9.522	-0.222	-0.222	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.011	0.001	9.870	0.093	0.093	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.025	0.003	11.661	-0.054	-0.054	0.000	0.000	0.000	0.000
136	A	136	PRO	0	0.018	0.027	13.016	0.088	0.088	0.000	0.000	0.000	0.000
137	A	137	TRP	0	0.001	-0.006	14.905	0.075	0.075	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.063	-0.026	17.547	0.079	0.079	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.021	-0.006	17.641	-0.027	-0.027	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.843	-0.936	12.461	-0.590	-0.590	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.047	-0.015	16.592	0.069	0.069	0.000	0.000	0.000	0.000
142	A	142	HIS	1	0.868	0.928	13.583	0.337	0.337	0.000	0.000	0.000	0.000
143	A	143	HIS	0	0.061	0.051	15.943	0.011	0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)