FMO DATABASE

FMODB ID: MN35Z

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	OptH
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	-1260542.331774
FMO2-HF: Nuclear repulsion	1205211.60121
FMO2-HF: Total energy	-55330.730563
FMO2-MP2: Total energy	-55493.72145

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.
-11.404	-7.059	28.654	-15.248	-17.752	-0.077

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 : 0.024 / 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	-0.021	-0.013	3.770	-1.394	1.268	-0.028	-1.357	-1.277	0.006
4	A	4	LEU	0	-0.026	-0.022	6.074	0.232	0.232	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.822	-0.911	9.486	-0.426	-0.426	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.018	-0.056	12.468	0.006	0.006	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.036	-0.034	15.658	0.017	0.017	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.042	0.027	12.957	0.046	0.046	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.001	0.000	13.145	0.041	0.041	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.036	-0.024	15.063	0.051	0.051	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.792	-0.900	18.274	-0.182	-0.182	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.021	-0.003	17.025	0.033	0.033	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.044	-0.012	19.677	0.025	0.025	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.796	0.910	22.214	0.210	0.210	0.000	0.000	0.000	0.000
15	A	15	PRO	0	-0.029	-0.031	24.657	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.030	-0.004	26.922	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.053	0.004	22.057	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.039	0.016	21.045	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.866	-0.956	20.784	-0.121	-0.121	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.927	0.978	18.398	0.110	0.110	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.069	-0.041	15.701	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.023	-0.002	15.706	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.008	0.015	16.576	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	TRP	0	0.024	0.001	8.534	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.023	-0.012	11.363	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.867	-0.925	12.029	-0.215	-0.215	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.204	-0.082	11.848	0.049	0.049	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.017	-0.019	6.946	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.039	0.024	7.569	0.053	0.053	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.031	0.013	7.021	-0.166	-0.166	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.952	-0.992	6.608	-0.536	-0.536	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.887	-0.932	1.948	-1.685	-4.496	16.312	-8.614	-4.887	-0.049
33	A	33	VAL	0	-0.017	0.000	2.333	-3.545	-2.225	2.764	-1.796	-2.288	-0.026
34	A	34	TYR	0	-0.006	0.014	2.226	-1.446	-0.143	2.140	-0.893	-2.550	-0.002
35	A	35	LEU	0	-0.015	-0.002	5.917	0.101	0.101	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.062	0.045	9.342	0.010	0.010	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.032	-0.002	11.088	0.057	0.057	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.009	0.002	14.135	0.047	0.047	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.073	0.031	12.871	0.020	0.020	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.011	-0.004	13.908	0.042	0.042	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.043	-0.015	16.180	0.044	0.044	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.825	-0.895	18.020	-0.305	-0.305	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.014	0.005	16.059	0.015	0.015	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.833	0.882	18.973	0.323	0.323	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.032	-0.010	21.858	0.025	0.025	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.027	0.000	22.950	0.019	0.019	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.037	-0.011	23.002	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.026	-0.022	25.633	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.004	-0.001	27.476	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.034	0.005	27.802	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.009	-0.008	31.044	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.042	-0.025	34.068	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.101	0.048	34.391	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.929	0.965	33.376	0.098	0.098	0.000	0.000	0.000	0.000
55	A	55	LYS	1	1.024	1.002	29.526	0.122	0.122	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.960	0.987	29.142	0.131	0.131	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.049	-0.024	28.756	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.035	0.018	27.599	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	0.014	23.180	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.019	0.009	24.041	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.820	-0.904	24.292	-0.147	-0.147	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.872	0.925	22.545	0.139	0.139	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.003	0.013	19.393	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.813	-0.904	19.305	-0.295	-0.295	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.032	-0.021	20.779	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.089	-0.043	19.655	0.013	0.013	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.004	-0.002	15.216	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.061	0.031	14.673	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.007	0.023	14.224	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.009	0.004	12.706	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.005	0.000	8.566	-0.040	-0.040	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.007	0.010	10.703	-0.069	-0.069	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.042	-0.019	11.011	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.847	0.905	5.174	0.991	0.991	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.034	-0.017	8.079	-0.066	-0.066	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.008	-0.008	4.953	0.098	0.098	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.017	0.000	9.237	0.072	0.072	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.023	0.015	11.507	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.867	-0.941	11.811	-0.378	-0.378	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.911	-0.984	14.900	-0.164	-0.164	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.036	0.024	12.605	0.013	0.013	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.005	0.005	10.532	0.024	0.024	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.023	-0.003	13.185	0.017	0.017	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.030	0.020	16.161	0.017	0.017	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.017	0.012	10.840	0.026	0.026	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.030	0.013	14.928	0.021	0.021	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.041	-0.020	16.621	0.015	0.015	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.001	0.012	15.934	0.006	0.006	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.016	0.020	13.112	0.011	0.011	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.881	0.945	17.683	0.168	0.168	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.050	-0.044	20.914	0.013	0.013	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.005	-0.001	20.305	0.012	0.012	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.069	0.030	20.878	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.937	0.985	22.683	0.104	0.104	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.092	-0.033	25.691	0.009	0.009	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.050	-0.040	24.049	0.016	0.016	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.045	-0.005	26.809	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.889	0.980	21.594	0.151	0.151	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.859	-0.931	23.962	-0.115	-0.115	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.012	-0.017	18.590	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.010	0.003	21.592	0.011	0.011	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.016	-0.013	20.246	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.039	0.031	18.941	-0.016	-0.016	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.802	-0.919	16.533	-0.309	-0.309	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.039	-0.017	15.681	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	106	TYR	0	-0.021	-0.018	15.161	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.042	0.040	11.027	-0.039	-0.039	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.001	0.007	10.953	-0.070	-0.070	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.016	-0.020	10.951	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.022	-0.031	7.805	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.006	-0.004	6.687	-0.075	-0.075	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.868	0.929	6.389	0.194	0.194	0.000	0.000	0.000	0.000
113	A	113	GLN	0	0.023	0.017	7.305	0.035	0.035	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.023	-0.002	2.377	-0.508	-0.079	0.703	-0.221	-0.911	0.001
115	A	115	SER	0	-0.074	-0.043	2.897	-1.637	-0.129	0.267	-0.779	-0.997	-0.009
116	A	116	MET	0	-0.040	-0.003	2.002	-1.171	-1.614	6.495	-1.524	-4.528	0.002
117	A	117	THR	0	-0.017	-0.008	4.049	0.132	0.509	0.001	-0.064	-0.314	0.000
118	A	118	VAL	0	-0.006	-0.001	5.872	-0.470	-0.470	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.002	0.012	8.922	0.153	0.153	0.000	0.000	0.000	0.000
120	A	120	THR	0	0.039	0.008	10.429	0.069	0.069	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.926	0.965	14.095	0.234	0.234	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.982	-0.989	17.295	-0.188	-0.188	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.065	0.010	14.560	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.033	-0.020	16.491	0.013	0.013	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.010	-0.026	18.421	0.034	0.034	0.000	0.000	0.000	0.000
126	A	126	PHE	0	0.096	0.031	13.261	0.013	0.013	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.002	0.023	15.108	0.019	0.019	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.030	-0.012	16.073	0.030	0.030	0.000	0.000	0.000	0.000
129	A	129	ALA	0	-0.035	-0.026	15.312	0.013	0.013	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.934	-0.957	15.167	-0.030	-0.030	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.038	-0.013	9.486	0.034	0.034	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.011	0.017	7.652	0.015	0.015	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.010	-0.018	9.282	-0.159	-0.159	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.007	0.002	9.682	0.078	0.078	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.057	0.023	11.434	-0.061	-0.061	0.000	0.000	0.000	0.000
136	A	136	PRO	0	0.022	0.029	13.181	0.057	0.057	0.000	0.000	0.000	0.000
137	A	137	TRP	0	-0.021	-0.020	15.040	0.042	0.042	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.059	-0.036	17.391	0.036	0.036	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.021	-0.011	17.614	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.871	-0.939	12.243	-0.082	-0.082	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.031	-0.011	16.661	0.025	0.025	0.000	0.000	0.000	0.000
142	A	142	HIS	1	0.891	0.935	14.338	-0.094	-0.094	0.000	0.000	0.000	0.000
143	A	143	HIS	0	0.062	0.050	16.014	-0.009	-0.009	0.000	0.000	0.000	0.000

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