FMO DATABASE

FMODB ID: G6551

Calculation Name: 1AWC-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: BRU

PDB ID: 1AWC

Chain ID: A

ChEMBL ID:

UniProt ID: Q00420

Base Structure: X-ray

Registration Date: 2023-06-22

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	110
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-950310.386305
FMO2-HF: Nuclear repulsion	903892.093079
FMO2-HF: Total energy	-46418.293226
FMO2-MP2: Total energy	-46551.110094

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:320:ILE)

Summations of interaction energy for fragment #1(A:320:ILE)

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.
-13.218	-4.062	14.118	-6.696	-16.577	-0.035

Interaction energy analysis for fragmet #1(A:320:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.011

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	322	LEU	0	-0.001	-0.011	2.780	-3.858	-0.804	0.422	-1.489	-1.987	-0.006
4	A	323	TRP	0	0.083	0.019	5.220	-0.604	-0.352	-0.001	-0.012	-0.239	0.000
5	A	324	GLN	0	0.071	0.042	2.203	-2.823	-0.476	2.819	-1.963	-3.202	-0.017
6	A	325	PHE	0	0.009	0.016	2.076	-2.024	-1.013	2.973	-1.163	-2.821	-0.004
7	A	326	LEU	0	-0.013	-0.008	3.044	1.114	0.512	0.162	0.732	-0.292	0.000
8	A	327	LEU	0	0.037	0.022	6.282	0.181	0.181	0.000	0.000	0.000	0.000
9	A	328	GLU	-1	-0.855	-0.913	3.199	-3.889	-2.275	0.186	-0.852	-0.948	-0.007
10	A	329	LEU	0	-0.015	-0.014	6.244	0.272	0.272	0.000	0.000	0.000	0.000
11	A	330	LEU	0	-0.043	-0.018	8.508	0.118	0.118	0.000	0.000	0.000	0.000
12	A	331	THR	0	-0.080	-0.040	9.227	0.079	0.079	0.000	0.000	0.000	0.000
13	A	332	ASP	-1	-0.859	-0.924	10.170	-0.373	-0.373	0.000	0.000	0.000	0.000
14	A	333	LYS	1	0.891	0.922	12.039	0.300	0.300	0.000	0.000	0.000	0.000
15	A	334	ASP	-1	-0.895	-0.942	14.395	-0.212	-0.212	0.000	0.000	0.000	0.000
16	A	335	ALA	0	-0.027	-0.013	11.645	0.022	0.022	0.000	0.000	0.000	0.000
17	A	336	ARG	1	0.887	0.949	13.683	0.228	0.228	0.000	0.000	0.000	0.000
18	A	337	ASP	-1	-0.849	-0.922	16.263	-0.160	-0.160	0.000	0.000	0.000	0.000
19	A	338	CYM	-1	-0.854	-0.883	13.360	-0.275	-0.275	0.000	0.000	0.000	0.000
20	A	339	ILE	0	-0.031	-0.035	10.258	0.009	0.009	0.000	0.000	0.000	0.000
21	A	340	SER	0	0.027	0.044	14.210	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	341	TRP	0	0.027	0.005	12.676	0.011	0.011	0.000	0.000	0.000	0.000
23	A	342	VAL	0	-0.087	-0.045	17.078	0.018	0.018	0.000	0.000	0.000	0.000
24	A	343	GLY	0	0.017	0.005	20.499	0.009	0.009	0.000	0.000	0.000	0.000
25	A	344	ASP	-1	-0.889	-0.952	20.708	-0.168	-0.168	0.000	0.000	0.000	0.000
26	A	345	GLU	-1	-0.893	-0.961	21.486	-0.116	-0.116	0.000	0.000	0.000	0.000
27	A	346	GLY	0	0.009	0.003	17.079	0.003	0.003	0.000	0.000	0.000	0.000
28	A	347	GLU	-1	-0.869	-0.943	16.334	-0.154	-0.154	0.000	0.000	0.000	0.000
29	A	348	PHE	0	0.028	0.020	12.350	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	349	LYS	1	0.935	0.970	16.419	0.155	0.155	0.000	0.000	0.000	0.000
31	A	350	LEU	0	-0.002	0.013	12.746	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	351	ASN	0	-0.058	-0.063	15.741	0.040	0.040	0.000	0.000	0.000	0.000
33	A	352	GLN	0	-0.020	-0.005	16.696	0.030	0.030	0.000	0.000	0.000	0.000
34	A	353	PRO	0	-0.003	-0.008	15.086	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	354	GLU	-1	-0.787	-0.919	14.324	-0.097	-0.097	0.000	0.000	0.000	0.000
36	A	355	LEU	0	0.025	0.046	13.947	0.005	0.005	0.000	0.000	0.000	0.000
37	A	356	VAL	0	0.048	0.019	9.764	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	357	ALA	0	-0.013	-0.007	9.686	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	358	GLN	0	-0.016	-0.011	10.501	0.025	0.025	0.000	0.000	0.000	0.000
40	A	359	LYS	1	0.822	0.873	8.579	0.311	0.311	0.000	0.000	0.000	0.000
41	A	360	TRP	0	-0.005	-0.003	2.238	-1.171	-0.333	1.988	-0.555	-2.271	0.000
42	A	361	GLY	0	-0.017	-0.023	6.276	0.146	0.146	0.000	0.000	0.000	0.000
43	A	362	GLN	0	-0.004	0.003	8.562	0.008	0.008	0.000	0.000	0.000	0.000
44	A	363	ARG	1	0.867	0.953	2.090	0.105	-0.107	5.403	-1.200	-3.992	-0.002
45	A	364	LYS	1	0.923	0.960	2.985	-0.768	0.041	0.167	-0.194	-0.781	0.001
46	A	365	ASN	0	0.059	0.041	5.254	-0.109	-0.064	-0.001	0.000	-0.044	0.000
47	A	366	LYS	1	0.760	0.869	8.426	-0.074	-0.074	0.000	0.000	0.000	0.000
48	A	367	PRO	0	0.064	0.010	10.592	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	368	THR	0	0.012	0.012	13.829	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	369	MET	0	-0.049	0.004	8.996	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	370	ASN	0	0.069	0.022	12.691	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	371	TYR	0	0.089	0.048	13.746	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	372	GLU	-1	-0.904	-0.929	15.362	-0.041	-0.041	0.000	0.000	0.000	0.000
54	A	373	LYS	1	0.908	0.939	13.225	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	374	LEU	0	-0.007	0.003	9.607	0.009	0.009	0.000	0.000	0.000	0.000
56	A	375	SER	0	-0.006	-0.016	11.910	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	376	ARG	1	0.908	0.973	14.723	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	377	ALA	0	-0.004	-0.018	9.742	0.020	0.020	0.000	0.000	0.000	0.000
59	A	378	LEU	0	0.027	0.004	10.823	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	379	ARG	1	0.907	0.949	12.868	0.055	0.055	0.000	0.000	0.000	0.000
61	A	380	TYR	0	-0.056	-0.022	13.217	0.013	0.013	0.000	0.000	0.000	0.000
62	A	381	TYR	0	0.029	0.022	7.313	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	382	TYR	0	-0.063	-0.047	13.924	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	383	ASP	-1	-0.933	-0.951	16.542	0.079	0.079	0.000	0.000	0.000	0.000
65	A	384	GLY	0	0.003	0.019	15.477	0.012	0.012	0.000	0.000	0.000	0.000
66	A	385	ASP	-1	-0.898	-0.935	15.819	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	386	MET	0	-0.030	-0.010	9.925	-0.066	-0.066	0.000	0.000	0.000	0.000
68	A	387	ILE	0	-0.032	-0.024	9.538	-0.048	-0.048	0.000	0.000	0.000	0.000
69	A	388	CYS	0	0.037	0.021	13.960	0.037	0.037	0.000	0.000	0.000	0.000
70	A	389	LYS	1	0.834	0.939	17.171	0.086	0.086	0.000	0.000	0.000	0.000
71	A	390	VAL	0	0.041	0.030	19.163	0.010	0.010	0.000	0.000	0.000	0.000
72	A	391	GLN	0	-0.002	-0.029	21.881	0.001	0.001	0.000	0.000	0.000	0.000
73	A	392	GLY	0	0.033	0.021	25.048	0.000	0.000	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.882	0.958	23.037	0.107	0.107	0.000	0.000	0.000	0.000
75	A	394	ARG	1	0.977	0.979	22.546	0.082	0.082	0.000	0.000	0.000	0.000
76	A	395	PHE	0	-0.022	-0.032	18.209	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	396	VAL	0	0.019	0.027	17.810	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	397	TYR	0	-0.039	-0.051	15.011	0.029	0.029	0.000	0.000	0.000	0.000
79	A	398	LYS	1	0.983	0.984	16.641	0.121	0.121	0.000	0.000	0.000	0.000
80	A	399	PHE	0	-0.011	0.001	8.838	0.008	0.008	0.000	0.000	0.000	0.000
81	A	400	VAL	0	-0.040	-0.038	14.870	0.012	0.012	0.000	0.000	0.000	0.000
82	A	401	CYS	0	-0.013	0.021	12.511	0.004	0.004	0.000	0.000	0.000	0.000
83	A	402	ASP	-1	-0.829	-0.912	16.160	-0.139	-0.139	0.000	0.000	0.000	0.000
84	A	403	LEU	0	-0.003	-0.019	12.461	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	404	LYS	1	0.946	0.987	15.718	0.109	0.109	0.000	0.000	0.000	0.000
86	A	405	THR	0	-0.031	-0.024	18.101	0.005	0.005	0.000	0.000	0.000	0.000
87	A	406	LEU	0	-0.077	-0.023	10.438	0.002	0.002	0.000	0.000	0.000	0.000
88	A	407	ILE	0	-0.047	-0.037	10.835	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	408	GLY	0	0.020	0.022	13.803	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	409	TYR	0	-0.047	-0.025	16.151	0.029	0.029	0.000	0.000	0.000	0.000
91	A	410	SER	0	0.015	0.001	16.479	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	411	ALA	0	0.048	0.015	16.273	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	412	ALA	0	0.049	0.034	17.302	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	413	GLU	-1	-0.860	-0.925	19.427	-0.160	-0.160	0.000	0.000	0.000	0.000
95	A	414	LEU	0	-0.006	-0.013	12.969	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	415	ASN	0	0.015	-0.002	16.811	-0.024	-0.024	0.000	0.000	0.000	0.000
97	A	416	ARG	1	0.996	1.006	18.327	0.168	0.168	0.000	0.000	0.000	0.000
98	A	417	LEU	0	-0.031	-0.018	17.969	0.009	0.009	0.000	0.000	0.000	0.000
99	A	418	VAL	0	-0.008	0.003	14.563	0.008	0.008	0.000	0.000	0.000	0.000
100	A	419	ILE	0	-0.006	0.000	17.440	0.010	0.010	0.000	0.000	0.000	0.000
101	A	420	GLU	-1	-0.942	-0.968	20.721	-0.144	-0.144	0.000	0.000	0.000	0.000
102	A	421	CYS	0	-0.066	-0.026	17.458	0.014	0.014	0.000	0.000	0.000	0.000
103	A	422	GLU	-1	-0.807	-0.922	19.456	-0.172	-0.172	0.000	0.000	0.000	0.000
104	A	423	GLN	0	0.000	0.013	20.923	0.021	0.021	0.000	0.000	0.000	0.000
105	A	424	LYS	1	0.958	0.983	23.363	0.161	0.161	0.000	0.000	0.000	0.000
106	A	425	LYS	1	0.821	0.906	18.721	0.205	0.205	0.000	0.000	0.000	0.000
107	A	426	LEU	0	-0.011	-0.019	23.539	0.008	0.008	0.000	0.000	0.000	0.000
108	A	427	ALA	0	-0.015	0.001	25.955	0.008	0.008	0.000	0.000	0.000	0.000
109	A	428	ARG	1	0.907	0.968	22.187	0.152	0.152	0.000	0.000	0.000	0.000
110	A	429	MET	0	-0.039	-0.005	23.504	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:320:ILE)