FMO DATABASE

FMODB ID: 2N2YR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1263753.557519
FMO2-HF: Nuclear repulsion	1208421.143447
FMO2-HF: Total energy	-55332.414072
FMO2-MP2: Total energy	-55495.205104

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.
-26.19	-15.886	14.577	-10.098	-14.782	-0.085

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 : 0.005 / q_NPA : -0.004

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	-0.013	-0.009	3.873	-0.200	1.713	-0.016	-0.962	-0.935	0.005
4	A	4	LEU	0	-0.018	-0.016	6.312	0.281	0.281	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.757	-0.838	9.832	-0.549	-0.549	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.006	-0.043	12.779	-0.047	-0.047	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.070	-0.040	15.834	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.027	0.024	12.236	0.067	0.067	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.000	0.000	13.300	0.033	0.033	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.019	-0.030	15.078	0.104	0.104	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.791	-0.875	18.088	-0.463	-0.463	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.007	-0.013	16.721	0.071	0.071	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.037	-0.003	19.655	0.055	0.055	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.809	0.895	22.385	0.483	0.483	0.000	0.000	0.000	0.000
15	A	15	PRO	0	-0.045	-0.043	24.849	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.019	-0.006	26.879	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.017	0.031	21.562	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.024	-0.008	20.703	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.821	-0.921	20.359	-0.572	-0.572	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.846	0.942	17.786	0.528	0.528	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.009	-0.003	15.305	-0.093	-0.093	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.010	-0.003	15.399	-0.106	-0.106	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.043	0.021	16.169	-0.057	-0.057	0.000	0.000	0.000	0.000
24	A	24	TRP	0	0.007	0.004	8.545	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.022	-0.008	11.035	-0.198	-0.198	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.908	-0.954	11.925	-0.851	-0.851	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.143	-0.079	11.761	0.030	0.030	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.031	-0.013	7.218	-0.219	-0.219	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.007	0.003	7.493	0.365	0.365	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.006	0.001	6.858	-0.542	-0.542	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.886	-0.966	6.855	-0.879	-0.879	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.869	-0.932	1.985	-20.158	-18.181	8.316	-5.422	-4.871	-0.067
33	A	33	VAL	0	-0.021	-0.001	2.513	-4.373	-2.634	1.683	-1.746	-1.676	-0.019
34	A	34	TYR	0	0.001	0.010	2.804	-0.802	1.144	0.548	-0.582	-1.912	-0.007
35	A	35	LEU	0	-0.021	-0.005	6.631	-0.077	-0.077	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.054	0.033	8.976	0.135	0.135	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.038	-0.006	10.998	0.006	0.006	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.026	-0.002	13.724	0.030	0.030	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.060	0.026	13.166	0.011	0.011	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.016	0.004	13.402	0.025	0.025	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.032	-0.012	16.129	0.041	0.041	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.850	-0.904	18.225	-0.436	-0.436	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.023	-0.004	15.799	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.817	0.869	18.437	0.282	0.282	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.000	0.006	22.108	0.026	0.026	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.023	0.005	23.252	0.019	0.019	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.016	-0.015	23.451	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.000	-0.008	26.029	0.022	0.022	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.003	0.000	27.283	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.041	0.007	27.934	0.009	0.009	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.038	0.018	31.243	0.013	0.013	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.011	0.004	34.253	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.090	0.040	34.847	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.965	0.980	34.315	0.140	0.140	0.000	0.000	0.000	0.000
55	A	55	LYS	1	1.011	1.002	29.442	0.252	0.252	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.830	0.922	29.890	0.166	0.166	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.038	-0.023	29.370	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.024	0.011	28.247	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.007	0.011	23.692	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.011	0.008	24.740	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.820	-0.886	24.694	-0.190	-0.190	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.813	0.871	23.051	0.237	0.237	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.024	0.028	19.819	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.782	-0.871	19.889	-0.279	-0.279	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.032	-0.014	21.100	0.021	0.021	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.075	-0.045	20.387	0.014	0.014	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.002	0.002	16.296	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.027	0.004	15.321	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.007	-0.001	14.632	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.007	0.024	13.627	0.043	0.043	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.014	0.001	9.187	-0.088	-0.088	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.010	0.009	10.697	0.046	0.046	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.033	-0.019	10.113	0.019	0.019	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.829	0.918	5.898	1.182	1.182	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.027	-0.012	7.433	-0.285	-0.285	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.023	0.017	4.362	0.035	0.164	-0.001	-0.010	-0.117	0.000
77	A	77	PRO	0	-0.019	-0.014	8.680	-0.059	-0.059	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.014	0.001	11.236	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.813	-0.907	11.440	0.232	0.232	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.909	-0.967	14.624	0.193	0.193	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.045	0.015	12.811	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.027	-0.003	10.563	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.022	-0.013	13.292	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.011	0.003	16.773	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.007	0.009	11.422	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.000	-0.012	15.334	-0.049	-0.049	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.028	-0.004	16.737	-0.024	-0.024	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.034	0.038	16.276	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.006	0.017	13.340	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.821	0.901	17.987	0.126	0.126	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.050	-0.038	20.911	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.047	-0.014	19.873	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.068	0.031	20.453	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.806	0.900	22.478	0.095	0.095	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.085	-0.055	25.718	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.003	0.005	23.562	0.021	0.021	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.021	0.010	26.293	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.817	0.907	21.588	0.282	0.282	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.796	-0.900	23.329	-0.126	-0.126	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.002	0.026	17.885	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.001	0.007	21.373	0.041	0.041	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.013	-0.009	20.274	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.057	0.025	18.485	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.724	-0.848	16.177	-0.367	-0.367	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.034	0.013	15.427	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	106	TYR	0	-0.014	-0.010	14.966	0.027	0.027	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.001	0.020	10.825	0.015	0.015	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.008	0.004	10.536	-0.082	-0.082	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.006	-0.002	10.932	0.043	0.043	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.023	-0.036	7.481	0.117	0.117	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.017	0.003	6.255	0.075	0.075	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.793	0.895	6.417	0.264	0.264	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.057	-0.022	7.888	0.239	0.239	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.011	-0.002	2.794	-0.497	0.192	0.254	-0.173	-0.770	0.000
115	A	115	SER	0	-0.082	-0.038	3.917	1.301	1.741	0.005	-0.098	-0.347	0.000
116	A	116	MET	0	-0.021	0.012	2.366	-1.645	-0.658	3.788	-0.978	-3.797	0.003
117	A	117	THR	0	-0.023	-0.012	4.102	0.507	0.991	0.000	-0.127	-0.357	0.000
118	A	118	VAL	0	-0.006	-0.004	6.037	-0.630	-0.630	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.012	0.004	8.910	0.154	0.154	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.032	-0.066	10.383	0.178	0.178	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.947	0.971	14.105	0.545	0.545	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.889	-0.945	17.450	-0.394	-0.394	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.032	0.006	13.988	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.014	0.005	16.439	0.035	0.035	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.029	-0.042	18.316	0.075	0.075	0.000	0.000	0.000	0.000
126	A	126	PHE	0	0.026	-0.003	13.445	0.021	0.021	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.016	-0.001	15.095	0.030	0.030	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.035	-0.004	16.264	0.054	0.054	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.009	0.001	14.711	0.046	0.046	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.863	-0.933	15.022	0.011	0.011	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.020	-0.009	9.231	0.105	0.105	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.025	0.028	7.423	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.011	-0.014	9.268	-0.208	-0.208	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.005	0.001	9.435	0.021	0.021	0.000	0.000	0.000	0.000
135	A	135	ASN	0	-0.006	-0.019	11.226	0.015	0.015	0.000	0.000	0.000	0.000
136	A	136	PRO	0	0.001	0.014	13.015	0.100	0.100	0.000	0.000	0.000	0.000
137	A	137	TRP	0	-0.010	-0.016	14.917	0.068	0.068	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.039	-0.016	17.213	0.089	0.089	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.019	-0.009	17.655	-0.045	-0.045	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.800	-0.912	12.527	-0.911	-0.911	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.059	-0.032	16.113	0.098	0.098	0.000	0.000	0.000	0.000
142	A	142	HIS	1	0.848	0.932	13.078	0.685	0.685	0.000	0.000	0.000	0.000
143	A	143	HIS	0	0.037	0.033	15.657	0.024	0.024	0.000	0.000	0.000	0.000

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