FMO DATABASE

FMODB ID: 8599Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-950621.441222
FMO2-HF: Nuclear repulsion	904202.440925
FMO2-HF: Total energy	-46419.000297
FMO2-MP2: Total energy	-46551.821055

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.
-14.108	-1.147	10.489	-7.676	-15.773	-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 : 0.042 / q_NPA : 0.039

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	0.018	-0.002	2.822	-3.743	0.139	0.420	-2.039	-2.262	0.001
4	A	323	TRP	0	0.072	0.009	5.013	-0.313	-0.076	-0.001	-0.011	-0.225	0.000
5	A	324	GLN	0	0.070	0.037	2.290	-3.786	-1.487	3.254	-2.126	-3.427	-0.021
6	A	325	PHE	0	0.010	0.011	2.728	-2.290	-0.337	0.552	-0.674	-1.831	-0.003
7	A	326	LEU	0	-0.006	-0.006	3.328	0.525	0.503	0.052	0.193	-0.224	0.000
8	A	327	LEU	0	0.045	0.029	6.423	0.182	0.182	0.000	0.000	0.000	0.000
9	A	328	GLU	-1	-0.789	-0.852	3.030	-3.431	-1.616	0.303	-1.016	-1.102	-0.009
10	A	329	LEU	0	-0.017	-0.015	6.169	0.274	0.274	0.000	0.000	0.000	0.000
11	A	330	LEU	0	-0.044	-0.015	8.583	0.116	0.116	0.000	0.000	0.000	0.000
12	A	331	THR	0	-0.069	-0.035	9.151	0.085	0.085	0.000	0.000	0.000	0.000
13	A	332	ASP	-1	-0.797	-0.900	10.275	-0.154	-0.154	0.000	0.000	0.000	0.000
14	A	333	LYS	1	0.803	0.884	11.966	0.142	0.142	0.000	0.000	0.000	0.000
15	A	334	ASP	-1	-0.852	-0.913	14.537	-0.083	-0.083	0.000	0.000	0.000	0.000
16	A	335	ALA	0	-0.021	-0.009	11.727	0.017	0.017	0.000	0.000	0.000	0.000
17	A	336	ARG	1	0.906	0.949	13.771	0.174	0.174	0.000	0.000	0.000	0.000
18	A	337	ASP	-1	-0.869	-0.932	16.367	-0.124	-0.124	0.000	0.000	0.000	0.000
19	A	338	CYM	-1	-0.809	-0.836	13.521	-0.229	-0.229	0.000	0.000	0.000	0.000
20	A	339	ILE	0	-0.027	-0.036	10.623	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	340	SER	0	0.032	0.033	14.433	0.005	0.005	0.000	0.000	0.000	0.000
22	A	341	TRP	0	0.025	0.007	12.587	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	342	VAL	0	-0.088	-0.048	17.208	0.024	0.024	0.000	0.000	0.000	0.000
24	A	343	GLY	0	0.016	0.005	20.660	0.000	0.000	0.000	0.000	0.000	0.000
25	A	344	ASP	-1	-0.851	-0.932	20.789	-0.178	-0.178	0.000	0.000	0.000	0.000
26	A	345	GLU	-1	-0.892	-0.957	21.574	-0.161	-0.161	0.000	0.000	0.000	0.000
27	A	346	GLY	0	0.025	0.010	17.174	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	347	GLU	-1	-0.825	-0.900	16.488	-0.227	-0.227	0.000	0.000	0.000	0.000
29	A	348	PHE	0	0.026	0.018	12.363	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	349	LYS	1	0.881	0.927	16.629	0.171	0.171	0.000	0.000	0.000	0.000
31	A	350	LEU	0	0.007	0.015	12.855	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	351	ASN	0	-0.021	-0.016	16.049	0.029	0.029	0.000	0.000	0.000	0.000
33	A	352	GLN	0	-0.017	-0.013	17.120	0.031	0.031	0.000	0.000	0.000	0.000
34	A	353	PRO	0	0.006	0.001	15.721	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	354	GLU	-1	-0.744	-0.890	14.969	-0.146	-0.146	0.000	0.000	0.000	0.000
36	A	355	LEU	0	0.026	0.049	14.234	0.010	0.010	0.000	0.000	0.000	0.000
37	A	356	VAL	0	0.044	0.014	10.296	0.007	0.007	0.000	0.000	0.000	0.000
38	A	357	ALA	0	-0.020	-0.002	10.224	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	358	GLN	0	0.004	-0.003	10.639	0.015	0.015	0.000	0.000	0.000	0.000
40	A	359	LYS	1	0.783	0.838	8.688	0.240	0.240	0.000	0.000	0.000	0.000
41	A	360	TRP	0	0.008	0.003	2.601	-1.182	0.054	0.345	-0.411	-1.169	-0.001
42	A	361	GLY	0	-0.007	-0.021	6.247	0.177	0.177	0.000	0.000	0.000	0.000
43	A	362	GLN	0	0.005	0.008	8.640	0.063	0.063	0.000	0.000	0.000	0.000
44	A	363	ARG	1	0.788	0.876	2.234	-1.134	-0.723	4.595	-1.052	-3.954	-0.005
45	A	364	LYS	1	0.856	0.931	2.388	0.894	2.044	0.969	-0.540	-1.579	0.003
46	A	365	ASN	0	0.045	0.035	5.504	-0.171	-0.171	0.000	0.000	0.000	0.000
47	A	366	LYS	1	0.788	0.877	8.724	-0.221	-0.221	0.000	0.000	0.000	0.000
48	A	367	PRO	0	0.070	0.019	10.722	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	368	THR	0	0.009	0.010	13.813	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	369	MET	0	-0.055	0.007	8.846	-0.038	-0.038	0.000	0.000	0.000	0.000
51	A	370	ASN	0	0.047	0.001	12.788	0.008	0.008	0.000	0.000	0.000	0.000
52	A	371	TYR	0	0.056	0.018	14.045	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	372	GLU	-1	-0.873	-0.924	15.739	-0.196	-0.196	0.000	0.000	0.000	0.000
54	A	373	LYS	1	0.901	0.942	13.417	0.070	0.070	0.000	0.000	0.000	0.000
55	A	374	LEU	0	-0.006	-0.001	9.960	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	375	SER	0	0.000	0.000	12.328	-0.053	-0.053	0.000	0.000	0.000	0.000
57	A	376	ARG	1	0.892	0.961	15.152	0.244	0.244	0.000	0.000	0.000	0.000
58	A	377	ALA	0	-0.010	-0.013	10.240	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	378	LEU	0	0.011	-0.002	10.571	-0.057	-0.057	0.000	0.000	0.000	0.000
60	A	379	ARG	1	0.871	0.914	12.817	0.225	0.225	0.000	0.000	0.000	0.000
61	A	380	TYR	0	-0.013	-0.009	13.442	0.036	0.036	0.000	0.000	0.000	0.000
62	A	381	TYR	0	0.023	0.016	7.499	-0.124	-0.124	0.000	0.000	0.000	0.000
63	A	382	TYR	0	-0.083	-0.049	13.974	0.032	0.032	0.000	0.000	0.000	0.000
64	A	383	ASP	-1	-0.951	-0.958	16.937	-0.294	-0.294	0.000	0.000	0.000	0.000
65	A	384	GLY	0	0.011	0.023	15.706	0.015	0.015	0.000	0.000	0.000	0.000
66	A	385	ASP	-1	-0.899	-0.939	16.026	-0.243	-0.243	0.000	0.000	0.000	0.000
67	A	386	MET	0	-0.032	-0.011	9.888	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	387	ILE	0	-0.029	-0.021	9.889	0.005	0.005	0.000	0.000	0.000	0.000
69	A	388	CYS	0	0.031	0.026	14.056	0.020	0.020	0.000	0.000	0.000	0.000
70	A	389	LYS	1	0.778	0.889	17.142	0.203	0.203	0.000	0.000	0.000	0.000
71	A	390	VAL	0	0.033	0.020	19.079	0.011	0.011	0.000	0.000	0.000	0.000
72	A	391	GLN	0	0.003	-0.019	21.799	0.010	0.010	0.000	0.000	0.000	0.000
73	A	392	GLY	0	0.046	0.026	24.939	0.005	0.005	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.892	0.957	23.278	0.172	0.172	0.000	0.000	0.000	0.000
75	A	394	ARG	1	0.998	0.993	22.634	0.105	0.105	0.000	0.000	0.000	0.000
76	A	395	PHE	0	-0.016	-0.022	18.648	0.004	0.004	0.000	0.000	0.000	0.000
77	A	396	VAL	0	0.018	0.027	18.132	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	397	TYR	0	-0.014	-0.018	15.120	0.012	0.012	0.000	0.000	0.000	0.000
79	A	398	LYS	1	0.894	0.928	16.601	0.226	0.226	0.000	0.000	0.000	0.000
80	A	399	PHE	0	0.007	0.001	8.914	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	400	VAL	0	-0.025	-0.028	15.008	0.032	0.032	0.000	0.000	0.000	0.000
82	A	401	CYS	0	-0.026	0.019	12.567	0.015	0.015	0.000	0.000	0.000	0.000
83	A	402	ASP	-1	-0.800	-0.893	16.303	-0.206	-0.206	0.000	0.000	0.000	0.000
84	A	403	LEU	0	-0.013	-0.023	12.487	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	404	LYS	1	0.858	0.925	15.639	0.147	0.147	0.000	0.000	0.000	0.000
86	A	405	THR	0	-0.013	-0.018	17.750	0.023	0.023	0.000	0.000	0.000	0.000
87	A	406	LEU	0	-0.088	-0.030	10.370	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	407	ILE	0	-0.044	-0.040	10.294	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	408	GLY	0	0.033	0.035	13.656	0.024	0.024	0.000	0.000	0.000	0.000
90	A	409	TYR	0	-0.073	-0.041	15.812	0.032	0.032	0.000	0.000	0.000	0.000
91	A	410	SER	0	0.037	-0.010	16.362	-0.034	-0.034	0.000	0.000	0.000	0.000
92	A	411	ALA	0	0.046	0.015	16.268	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	412	ALA	0	0.044	0.037	17.298	0.000	0.000	0.000	0.000	0.000	0.000
94	A	413	GLU	-1	-0.805	-0.868	19.327	-0.154	-0.154	0.000	0.000	0.000	0.000
95	A	414	LEU	0	-0.006	-0.009	13.182	0.005	0.005	0.000	0.000	0.000	0.000
96	A	415	ASN	0	-0.021	-0.022	16.719	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	416	ARG	1	0.925	0.951	18.306	0.130	0.130	0.000	0.000	0.000	0.000
98	A	417	LEU	0	-0.034	-0.015	17.795	0.014	0.014	0.000	0.000	0.000	0.000
99	A	418	VAL	0	-0.019	-0.006	14.508	0.018	0.018	0.000	0.000	0.000	0.000
100	A	419	ILE	0	0.008	0.008	17.357	0.014	0.014	0.000	0.000	0.000	0.000
101	A	420	GLU	-1	-0.808	-0.880	20.679	-0.083	-0.083	0.000	0.000	0.000	0.000
102	A	421	CYS	0	-0.068	-0.035	17.285	0.019	0.019	0.000	0.000	0.000	0.000
103	A	422	GLU	-1	-0.801	-0.899	19.411	-0.116	-0.116	0.000	0.000	0.000	0.000
104	A	423	GLN	0	-0.008	-0.001	20.861	0.019	0.019	0.000	0.000	0.000	0.000
105	A	424	LYS	1	0.877	0.936	23.140	0.090	0.090	0.000	0.000	0.000	0.000
106	A	425	LYS	1	0.829	0.909	18.608	0.116	0.116	0.000	0.000	0.000	0.000
107	A	426	LEU	0	0.007	-0.003	23.436	0.009	0.009	0.000	0.000	0.000	0.000
108	A	427	ALA	0	-0.016	0.003	25.902	0.006	0.006	0.000	0.000	0.000	0.000
109	A	428	ARG	1	0.899	0.962	22.093	0.049	0.049	0.000	0.000	0.000	0.000
110	A	429	MET	0	-0.066	-0.024	23.175	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:320:ILE)