FMO DATABASE

FMODB ID: N9NNQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-952105.85705
FMO2-HF: Nuclear repulsion	905686.471094
FMO2-HF: Total energy	-46419.385956
FMO2-MP2: Total energy	-46552.154714

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.
-24.898	-12.89	10.976	-7.286	-15.696	-0.038

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 : 0.013 / 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	0.012	0.002	2.667	-3.031	-0.449	0.729	-1.441	-1.870	-0.009
4	A	323	TRP	0	0.071	0.007	5.089	-0.438	-0.215	-0.001	-0.011	-0.210	0.000
5	A	324	GLN	0	0.046	0.033	2.390	-3.628	-1.581	3.626	-2.019	-3.655	-0.019
6	A	325	PHE	0	0.016	0.008	2.801	-1.822	0.036	0.385	-0.568	-1.674	-0.003
7	A	326	LEU	0	-0.008	-0.013	3.608	0.323	0.447	0.028	0.049	-0.201	0.000
8	A	327	LEU	0	0.033	0.023	6.322	0.170	0.170	0.000	0.000	0.000	0.000
9	A	328	GLU	-1	-0.779	-0.845	3.067	-3.675	-1.955	0.334	-0.932	-1.121	-0.008
10	A	329	LEU	0	-0.011	-0.006	6.354	0.271	0.271	0.000	0.000	0.000	0.000
11	A	330	LEU	0	-0.028	0.000	8.931	0.101	0.101	0.000	0.000	0.000	0.000
12	A	331	THR	0	-0.049	-0.032	9.165	0.044	0.044	0.000	0.000	0.000	0.000
13	A	332	ASP	-1	-0.820	-0.891	10.583	-0.199	-0.199	0.000	0.000	0.000	0.000
14	A	333	LYS	1	0.831	0.879	12.269	0.235	0.235	0.000	0.000	0.000	0.000
15	A	334	ASP	-1	-0.856	-0.911	14.675	-0.088	-0.088	0.000	0.000	0.000	0.000
16	A	335	ALA	0	-0.010	-0.007	11.823	0.038	0.038	0.000	0.000	0.000	0.000
17	A	336	ARG	1	0.914	0.957	13.777	0.188	0.188	0.000	0.000	0.000	0.000
18	A	337	ASP	-1	-0.875	-0.937	16.209	-0.068	-0.068	0.000	0.000	0.000	0.000
19	A	338	CYM	-1	-0.804	-0.836	13.467	-0.043	-0.043	0.000	0.000	0.000	0.000
20	A	339	ILE	0	-0.028	-0.037	10.712	0.018	0.018	0.000	0.000	0.000	0.000
21	A	340	SER	0	0.031	0.032	14.200	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	341	TRP	0	0.025	0.003	12.464	0.014	0.014	0.000	0.000	0.000	0.000
23	A	342	VAL	0	-0.095	-0.057	17.259	0.028	0.028	0.000	0.000	0.000	0.000
24	A	343	GLY	0	0.023	0.015	20.755	0.014	0.014	0.000	0.000	0.000	0.000
25	A	344	ASP	-1	-0.810	-0.894	20.297	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	345	GLU	-1	-0.911	-0.967	20.585	-0.196	-0.196	0.000	0.000	0.000	0.000
27	A	346	GLY	0	0.047	0.012	16.896	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	347	GLU	-1	-0.805	-0.879	16.439	-0.172	-0.172	0.000	0.000	0.000	0.000
29	A	348	PHE	0	0.013	0.006	12.257	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	349	LYS	1	0.902	0.938	16.539	0.095	0.095	0.000	0.000	0.000	0.000
31	A	350	LEU	0	0.010	0.016	12.927	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	351	ASN	0	-0.036	-0.020	16.172	0.034	0.034	0.000	0.000	0.000	0.000
33	A	352	GLN	0	-0.028	-0.024	16.946	0.036	0.036	0.000	0.000	0.000	0.000
34	A	353	PRO	0	0.014	0.003	15.603	0.021	0.021	0.000	0.000	0.000	0.000
35	A	354	GLU	-1	-0.744	-0.874	14.705	0.249	0.249	0.000	0.000	0.000	0.000
36	A	355	LEU	0	0.022	0.037	14.449	0.053	0.053	0.000	0.000	0.000	0.000
37	A	356	VAL	0	0.012	0.003	10.329	0.047	0.047	0.000	0.000	0.000	0.000
38	A	357	ALA	0	-0.002	-0.001	10.282	0.078	0.078	0.000	0.000	0.000	0.000
39	A	358	GLN	0	0.011	-0.001	10.692	0.121	0.121	0.000	0.000	0.000	0.000
40	A	359	LYS	1	0.801	0.861	8.756	0.142	0.142	0.000	0.000	0.000	0.000
41	A	360	TRP	0	0.003	-0.001	2.455	-0.581	0.470	0.481	-0.391	-1.141	-0.002
42	A	361	GLY	0	0.012	-0.013	6.465	0.527	0.527	0.000	0.000	0.000	0.000
43	A	362	GLN	0	-0.015	-0.009	9.018	0.162	0.162	0.000	0.000	0.000	0.000
44	A	363	ARG	1	0.786	0.864	2.406	-1.040	-0.064	3.277	-0.892	-3.362	-0.005
45	A	364	LYS	1	0.848	0.927	2.256	-9.437	-8.010	2.117	-1.081	-2.462	0.008
46	A	365	ASN	0	0.028	0.023	5.472	-0.380	-0.380	0.000	0.000	0.000	0.000
47	A	366	LYS	1	0.824	0.894	8.654	-1.743	-1.743	0.000	0.000	0.000	0.000
48	A	367	PRO	0	0.057	0.016	11.116	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	368	THR	0	0.016	0.021	14.215	-0.059	-0.059	0.000	0.000	0.000	0.000
50	A	369	MET	0	-0.056	-0.002	8.752	-0.108	-0.108	0.000	0.000	0.000	0.000
51	A	370	ASN	0	0.038	-0.002	12.833	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	371	TYR	0	0.052	0.018	13.993	0.010	0.010	0.000	0.000	0.000	0.000
53	A	372	GLU	-1	-0.844	-0.885	15.540	0.120	0.120	0.000	0.000	0.000	0.000
54	A	373	LYS	1	0.892	0.947	13.173	-0.430	-0.430	0.000	0.000	0.000	0.000
55	A	374	LEU	0	0.016	0.011	9.580	0.029	0.029	0.000	0.000	0.000	0.000
56	A	375	SER	0	-0.012	-0.018	11.791	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	376	ARG	1	0.867	0.938	14.646	-0.160	-0.160	0.000	0.000	0.000	0.000
58	A	377	ALA	0	-0.020	-0.014	9.844	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	378	LEU	0	0.007	-0.008	10.163	-0.076	-0.076	0.000	0.000	0.000	0.000
60	A	379	ARG	1	0.843	0.892	12.312	-0.128	-0.128	0.000	0.000	0.000	0.000
61	A	380	TYR	0	-0.028	-0.020	12.968	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	381	TYR	0	0.017	0.014	7.521	-0.197	-0.197	0.000	0.000	0.000	0.000
63	A	382	TYR	0	-0.053	-0.032	13.687	0.000	0.000	0.000	0.000	0.000	0.000
64	A	383	ASP	-1	-0.948	-0.957	16.853	-0.106	-0.106	0.000	0.000	0.000	0.000
65	A	384	GLY	0	0.046	0.032	16.126	0.004	0.004	0.000	0.000	0.000	0.000
66	A	385	ASP	-1	-0.915	-0.942	16.463	-0.270	-0.270	0.000	0.000	0.000	0.000
67	A	386	MET	0	-0.055	-0.024	9.778	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	387	ILE	0	-0.003	-0.020	9.727	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	388	CYS	0	0.021	0.023	13.861	0.038	0.038	0.000	0.000	0.000	0.000
70	A	389	LYS	1	0.791	0.881	16.874	0.065	0.065	0.000	0.000	0.000	0.000
71	A	390	VAL	0	0.033	0.024	19.060	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	391	GLN	0	0.031	0.011	21.721	0.016	0.016	0.000	0.000	0.000	0.000
73	A	392	GLY	0	0.036	0.029	25.008	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.890	0.929	23.285	0.125	0.125	0.000	0.000	0.000	0.000
75	A	394	ARG	1	0.985	0.988	22.712	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	395	PHE	0	-0.016	-0.020	18.667	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	396	VAL	0	0.006	0.020	18.022	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	397	TYR	0	-0.012	-0.014	15.126	0.036	0.036	0.000	0.000	0.000	0.000
79	A	398	LYS	1	0.867	0.916	16.446	0.190	0.190	0.000	0.000	0.000	0.000
80	A	399	PHE	0	0.025	0.006	8.847	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	400	VAL	0	-0.024	-0.021	14.825	0.034	0.034	0.000	0.000	0.000	0.000
82	A	401	CYS	0	-0.017	0.025	12.164	0.012	0.012	0.000	0.000	0.000	0.000
83	A	402	ASP	-1	-0.779	-0.878	15.909	-0.341	-0.341	0.000	0.000	0.000	0.000
84	A	403	LEU	0	-0.016	-0.023	11.702	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	404	LYS	1	0.798	0.884	14.798	0.256	0.256	0.000	0.000	0.000	0.000
86	A	405	THR	0	-0.022	-0.038	17.280	0.006	0.006	0.000	0.000	0.000	0.000
87	A	406	LEU	0	-0.085	-0.028	10.213	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	407	ILE	0	-0.048	-0.030	9.917	-0.078	-0.078	0.000	0.000	0.000	0.000
89	A	408	GLY	0	0.034	0.033	13.365	0.022	0.022	0.000	0.000	0.000	0.000
90	A	409	TYR	0	-0.054	-0.027	15.347	0.067	0.067	0.000	0.000	0.000	0.000
91	A	410	SER	0	0.031	-0.019	15.740	-0.036	-0.036	0.000	0.000	0.000	0.000
92	A	411	ALA	0	0.024	-0.001	15.987	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	412	ALA	0	0.049	0.041	16.982	0.003	0.003	0.000	0.000	0.000	0.000
94	A	413	GLU	-1	-0.806	-0.849	18.792	-0.268	-0.268	0.000	0.000	0.000	0.000
95	A	414	LEU	0	0.003	0.004	12.514	0.002	0.002	0.000	0.000	0.000	0.000
96	A	415	ASN	0	-0.033	-0.031	16.194	0.006	0.006	0.000	0.000	0.000	0.000
97	A	416	ARG	1	0.896	0.924	18.133	0.221	0.221	0.000	0.000	0.000	0.000
98	A	417	LEU	0	-0.021	-0.009	17.151	0.018	0.018	0.000	0.000	0.000	0.000
99	A	418	VAL	0	-0.015	-0.005	14.244	0.021	0.021	0.000	0.000	0.000	0.000
100	A	419	ILE	0	0.015	0.015	16.990	0.024	0.024	0.000	0.000	0.000	0.000
101	A	420	GLU	-1	-0.803	-0.871	20.486	-0.160	-0.160	0.000	0.000	0.000	0.000
102	A	421	CYS	0	-0.071	-0.032	17.192	0.021	0.021	0.000	0.000	0.000	0.000
103	A	422	GLU	-1	-0.787	-0.881	19.312	-0.118	-0.118	0.000	0.000	0.000	0.000
104	A	423	GLN	0	-0.013	-0.021	20.682	0.024	0.024	0.000	0.000	0.000	0.000
105	A	424	LYS	1	0.861	0.928	22.776	0.173	0.173	0.000	0.000	0.000	0.000
106	A	425	LYS	1	0.813	0.898	18.952	0.118	0.118	0.000	0.000	0.000	0.000
107	A	426	LEU	0	0.000	-0.001	23.141	0.013	0.013	0.000	0.000	0.000	0.000
108	A	427	ALA	0	-0.011	0.005	25.920	0.009	0.009	0.000	0.000	0.000	0.000
109	A	428	ARG	1	0.842	0.910	21.739	0.093	0.093	0.000	0.000	0.000	0.000
110	A	429	MET	0	-0.009	0.023	23.334	0.012	0.012	0.000	0.000	0.000	0.000

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