FMO DATABASE

FMODB ID: 5N93Z

Calculation Name: 1AWC-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: BRU

PDB ID: 1AWC

Chain ID: B

ChEMBL ID:

UniProt ID: Q00420

Base Structure: X-ray

Registration Date: 2023-09-26

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1426971.428333
FMO2-HF: Nuclear repulsion	1367798.349478
FMO2-HF: Total energy	-59173.078855
FMO2-MP2: Total energy	-59345.797515

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(B:5:ASP)

Summations of interaction energy for fragment #1(B:5:ASP)

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.
-91.448	-85.788	14.419	-8.617	-11.459	0.108

Interaction energy analysis for fragmet #1(B:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.866 / q_NPA : -0.940

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	B	7	GLY	0	0.057	0.041	2.174	-16.939	-14.985	4.298	-2.800	-3.452	0.032
4	B	8	LYS	1	0.882	0.929	1.918	-99.661	-97.463	10.106	-5.172	-7.131	0.074
5	B	9	LYS	1	0.873	0.945	3.358	-44.351	-43.188	0.018	-0.614	-0.567	0.002
6	B	10	LEU	0	0.021	0.013	5.125	-7.237	-7.095	-0.001	-0.010	-0.131	0.000
7	B	11	LEU	0	-0.050	-0.021	5.973	-4.739	-4.739	0.000	0.000	0.000	0.000
8	B	12	GLU	-1	-0.826	-0.902	6.166	29.324	29.324	0.000	0.000	0.000	0.000
9	B	13	ALA	0	0.011	0.016	8.799	-3.226	-3.226	0.000	0.000	0.000	0.000
10	B	14	ALA	0	-0.018	-0.021	10.809	-2.562	-2.562	0.000	0.000	0.000	0.000
11	B	15	ARG	1	0.826	0.894	9.546	-29.074	-29.074	0.000	0.000	0.000	0.000
12	B	16	ALA	0	-0.031	-0.017	12.941	-1.619	-1.619	0.000	0.000	0.000	0.000
13	B	17	GLY	0	0.016	0.018	14.649	-1.171	-1.171	0.000	0.000	0.000	0.000
14	B	18	GLN	0	-0.056	-0.033	12.520	0.302	0.302	0.000	0.000	0.000	0.000
15	B	19	ASP	-1	-0.811	-0.925	14.650	16.872	16.872	0.000	0.000	0.000	0.000
16	B	20	ASP	-1	-0.792	-0.881	16.682	16.028	16.028	0.000	0.000	0.000	0.000
17	B	21	GLU	-1	-0.861	-0.923	10.321	26.790	26.790	0.000	0.000	0.000	0.000
18	B	22	VAL	0	-0.012	0.002	11.980	1.741	1.741	0.000	0.000	0.000	0.000
19	B	23	ARG	1	0.804	0.878	12.700	-14.906	-14.906	0.000	0.000	0.000	0.000
20	B	24	ILE	0	0.001	-0.002	11.368	0.423	0.423	0.000	0.000	0.000	0.000
21	B	25	LEU	0	-0.047	-0.028	6.606	1.306	1.306	0.000	0.000	0.000	0.000
22	B	26	MET	0	-0.039	-0.020	9.978	1.197	1.197	0.000	0.000	0.000	0.000
23	B	27	ALA	0	-0.028	0.010	11.784	-0.746	-0.746	0.000	0.000	0.000	0.000
24	B	28	ASN	0	-0.061	-0.040	9.317	-1.765	-1.765	0.000	0.000	0.000	0.000
25	B	29	GLY	0	0.030	0.028	10.274	-0.246	-0.246	0.000	0.000	0.000	0.000
26	B	30	ALA	0	-0.086	-0.045	6.391	3.034	3.034	0.000	0.000	0.000	0.000
27	B	31	PRO	0	-0.010	0.002	4.411	-3.104	-2.970	-0.001	-0.020	-0.112	0.000
28	B	32	PHE	0	0.048	0.007	6.206	5.157	5.157	0.000	0.000	0.000	0.000
29	B	33	THR	0	-0.048	-0.016	5.060	1.686	1.755	-0.001	-0.001	-0.066	0.000
30	B	34	THR	0	0.065	0.009	7.605	-3.507	-3.507	0.000	0.000	0.000	0.000
31	B	35	ASP	-1	-0.851	-0.911	8.525	29.363	29.363	0.000	0.000	0.000	0.000
32	B	36	TRP	0	0.011	-0.008	10.255	-1.617	-1.617	0.000	0.000	0.000	0.000
33	B	37	LEU	0	-0.002	0.000	12.344	-1.828	-1.828	0.000	0.000	0.000	0.000
34	B	38	GLY	0	0.004	0.001	13.520	-1.470	-1.470	0.000	0.000	0.000	0.000
35	B	39	THR	0	-0.021	-0.008	13.166	-1.231	-1.231	0.000	0.000	0.000	0.000
36	B	40	SER	0	0.020	-0.015	11.165	3.013	3.013	0.000	0.000	0.000	0.000
37	B	41	PRO	0	0.041	0.000	9.185	-1.388	-1.388	0.000	0.000	0.000	0.000
38	B	42	LEU	0	0.046	0.030	11.929	-1.233	-1.233	0.000	0.000	0.000	0.000
39	B	43	HIS	0	-0.021	0.019	15.175	0.187	0.187	0.000	0.000	0.000	0.000
40	B	44	LEU	0	0.012	0.006	11.491	-0.850	-0.850	0.000	0.000	0.000	0.000
41	B	45	ALA	0	-0.002	0.002	15.528	-0.898	-0.898	0.000	0.000	0.000	0.000
42	B	46	ALA	0	-0.002	-0.008	17.118	-0.933	-0.933	0.000	0.000	0.000	0.000
43	B	47	GLN	0	0.017	0.001	18.350	-0.005	-0.005	0.000	0.000	0.000	0.000
44	B	48	TYR	0	-0.039	-0.035	16.108	-0.136	-0.136	0.000	0.000	0.000	0.000
45	B	49	GLY	0	0.025	0.040	20.262	-0.479	-0.479	0.000	0.000	0.000	0.000
46	B	50	HIS	0	-0.003	0.008	17.277	-0.976	-0.976	0.000	0.000	0.000	0.000
47	B	51	PHE	0	-0.004	-0.013	20.309	0.581	0.581	0.000	0.000	0.000	0.000
48	B	52	SER	0	0.061	0.022	21.190	-0.022	-0.022	0.000	0.000	0.000	0.000
49	B	53	THR	0	0.039	0.016	15.472	0.086	0.086	0.000	0.000	0.000	0.000
50	B	54	THR	0	0.009	-0.007	17.539	0.815	0.815	0.000	0.000	0.000	0.000
51	B	55	GLU	-1	-0.877	-0.924	18.922	13.103	13.103	0.000	0.000	0.000	0.000
52	B	56	VAL	0	-0.016	-0.009	16.211	-0.118	-0.118	0.000	0.000	0.000	0.000
53	B	57	LEU	0	-0.005	-0.004	12.836	0.688	0.688	0.000	0.000	0.000	0.000
54	B	58	LEU	0	-0.001	0.012	16.460	0.134	0.134	0.000	0.000	0.000	0.000
55	B	59	ARG	1	0.851	0.917	19.593	-12.971	-12.971	0.000	0.000	0.000	0.000
56	B	60	ALA	0	0.025	0.015	15.428	-0.198	-0.198	0.000	0.000	0.000	0.000
57	B	61	GLY	0	-0.054	-0.023	16.804	0.454	0.454	0.000	0.000	0.000	0.000
58	B	62	VAL	0	-0.053	-0.016	13.583	0.290	0.290	0.000	0.000	0.000	0.000
59	B	63	SER	0	-0.022	-0.016	15.867	-1.531	-1.531	0.000	0.000	0.000	0.000
60	B	64	ARG	1	0.892	0.936	17.874	-14.420	-14.420	0.000	0.000	0.000	0.000
61	B	65	ASP	-1	-0.854	-0.924	20.637	13.341	13.341	0.000	0.000	0.000	0.000
62	B	66	ALA	0	-0.036	-0.013	16.106	0.078	0.078	0.000	0.000	0.000	0.000
63	B	67	ARG	1	0.864	0.911	18.242	-13.697	-13.697	0.000	0.000	0.000	0.000
64	B	68	THR	0	0.005	0.015	16.909	0.661	0.661	0.000	0.000	0.000	0.000
65	B	69	LYS	1	0.871	0.914	14.680	-21.497	-21.497	0.000	0.000	0.000	0.000
66	B	70	VAL	0	-0.027	-0.017	19.453	-0.596	-0.596	0.000	0.000	0.000	0.000
67	B	71	ASP	-1	-0.852	-0.932	21.590	12.877	12.877	0.000	0.000	0.000	0.000
68	B	72	ARG	1	0.898	0.969	21.484	-13.473	-13.473	0.000	0.000	0.000	0.000
69	B	73	THR	0	0.064	0.028	20.381	0.962	0.962	0.000	0.000	0.000	0.000
70	B	74	PRO	0	-0.014	-0.030	18.117	-0.181	-0.181	0.000	0.000	0.000	0.000
71	B	75	LEU	0	0.047	0.036	20.600	-0.205	-0.205	0.000	0.000	0.000	0.000
72	B	76	HIS	0	-0.010	0.013	23.713	0.084	0.084	0.000	0.000	0.000	0.000
73	B	77	MET	0	-0.054	-0.011	18.674	-0.617	-0.617	0.000	0.000	0.000	0.000
74	B	78	ALA	0	0.029	0.015	23.151	-0.285	-0.285	0.000	0.000	0.000	0.000
75	B	79	ALA	0	-0.001	-0.008	24.692	-0.370	-0.370	0.000	0.000	0.000	0.000
76	B	80	SER	0	-0.065	-0.050	25.796	-0.468	-0.468	0.000	0.000	0.000	0.000
77	B	81	GLU	-1	-0.891	-0.942	23.817	12.584	12.584	0.000	0.000	0.000	0.000
78	B	82	GLY	0	0.037	0.034	26.945	-0.192	-0.192	0.000	0.000	0.000	0.000
79	B	83	HIS	0	-0.026	-0.003	23.787	-0.567	-0.567	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.066	0.024	27.629	0.225	0.225	0.000	0.000	0.000	0.000
81	B	85	ASN	0	0.007	0.001	26.343	0.002	0.002	0.000	0.000	0.000	0.000
82	B	86	ILE	0	-0.021	-0.002	22.165	0.146	0.146	0.000	0.000	0.000	0.000
83	B	87	VAL	0	0.014	0.000	25.462	0.253	0.253	0.000	0.000	0.000	0.000
84	B	88	GLU	-1	-0.790	-0.880	27.422	9.723	9.723	0.000	0.000	0.000	0.000
85	B	89	VAL	0	-0.013	-0.004	24.124	-0.065	-0.065	0.000	0.000	0.000	0.000
86	B	90	LEU	0	0.015	0.004	21.127	0.236	0.236	0.000	0.000	0.000	0.000
87	B	91	LEU	0	0.022	0.024	25.024	0.032	0.032	0.000	0.000	0.000	0.000
88	B	92	LYS	1	0.794	0.892	28.462	-10.071	-10.071	0.000	0.000	0.000	0.000
89	B	93	HIS	0	-0.131	-0.069	24.221	0.152	0.152	0.000	0.000	0.000	0.000
90	B	94	GLY	0	-0.021	-0.023	25.417	0.414	0.414	0.000	0.000	0.000	0.000
91	B	95	ALA	0	-0.042	0.002	24.546	0.131	0.131	0.000	0.000	0.000	0.000
92	B	96	ASP	-1	-0.865	-0.942	26.076	10.385	10.385	0.000	0.000	0.000	0.000
93	B	97	VAL	0	-0.005	-0.018	27.976	0.307	0.307	0.000	0.000	0.000	0.000
94	B	98	ASN	0	-0.039	-0.010	30.401	-0.117	-0.117	0.000	0.000	0.000	0.000
95	B	99	ALA	0	0.007	0.025	26.167	-0.035	-0.035	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.908	0.947	28.308	-9.899	-9.899	0.000	0.000	0.000	0.000
97	B	101	ASP	-1	-0.769	-0.876	25.622	11.978	11.978	0.000	0.000	0.000	0.000
98	B	102	MET	0	0.010	0.002	24.755	-0.512	-0.512	0.000	0.000	0.000	0.000
99	B	103	LEU	0	-0.088	-0.044	27.615	-0.438	-0.438	0.000	0.000	0.000	0.000
100	B	104	LYS	1	0.884	0.938	30.156	-9.570	-9.570	0.000	0.000	0.000	0.000
101	B	105	MET	0	0.035	0.033	30.256	-0.384	-0.384	0.000	0.000	0.000	0.000
102	B	106	THR	0	0.062	0.018	29.468	0.491	0.491	0.000	0.000	0.000	0.000
103	B	107	ALA	0	0.023	0.000	28.151	-0.006	-0.006	0.000	0.000	0.000	0.000
104	B	108	LEU	0	0.062	0.039	29.670	-0.015	-0.015	0.000	0.000	0.000	0.000
105	B	109	HIS	0	0.007	0.026	32.476	0.108	0.108	0.000	0.000	0.000	0.000
106	B	110	TRP	0	-0.033	-0.038	28.235	-0.019	-0.019	0.000	0.000	0.000	0.000
107	B	111	ALA	0	0.009	0.014	31.211	-0.012	-0.012	0.000	0.000	0.000	0.000
108	B	112	THR	0	0.005	-0.009	32.442	-0.262	-0.262	0.000	0.000	0.000	0.000
109	B	113	GLU	-1	-0.950	-0.969	32.852	9.042	9.042	0.000	0.000	0.000	0.000
110	B	114	HIS	0	-0.065	-0.026	28.944	-0.273	-0.273	0.000	0.000	0.000	0.000
111	B	115	ASN	0	-0.024	-0.003	33.614	-0.231	-0.231	0.000	0.000	0.000	0.000
112	B	116	HIS	0	0.025	0.026	30.246	-0.340	-0.340	0.000	0.000	0.000	0.000
113	B	117	GLN	0	0.039	0.004	34.760	0.099	0.099	0.000	0.000	0.000	0.000
114	B	118	GLU	-1	-0.864	-0.937	35.529	8.535	8.535	0.000	0.000	0.000	0.000
115	B	119	VAL	0	-0.072	-0.032	30.690	0.136	0.136	0.000	0.000	0.000	0.000
116	B	120	VAL	0	0.020	0.010	33.538	0.105	0.105	0.000	0.000	0.000	0.000
117	B	121	GLU	-1	-0.858	-0.925	36.006	7.851	7.851	0.000	0.000	0.000	0.000
118	B	122	LEU	0	-0.100	-0.053	31.349	-0.077	-0.077	0.000	0.000	0.000	0.000
119	B	123	LEU	0	-0.014	-0.021	30.413	0.104	0.104	0.000	0.000	0.000	0.000
120	B	124	ILE	0	0.017	0.016	34.382	-0.015	-0.015	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.898	0.961	37.310	-8.661	-8.661	0.000	0.000	0.000	0.000
122	B	126	TYR	0	-0.131	-0.074	32.476	-0.026	-0.026	0.000	0.000	0.000	0.000
123	B	127	GLY	0	0.004	-0.010	34.863	0.214	0.214	0.000	0.000	0.000	0.000
124	B	128	ALA	0	-0.031	0.004	34.262	0.023	0.023	0.000	0.000	0.000	0.000
125	B	129	ASP	-1	-0.939	-0.981	35.731	8.077	8.077	0.000	0.000	0.000	0.000
126	B	130	VAL	0	0.018	-0.008	37.265	0.182	0.182	0.000	0.000	0.000	0.000
127	B	131	HIS	0	-0.052	-0.013	39.666	-0.030	-0.030	0.000	0.000	0.000	0.000
128	B	132	THR	0	-0.018	0.002	35.717	0.035	0.035	0.000	0.000	0.000	0.000
129	B	133	GLN	0	0.000	-0.010	38.146	0.048	0.048	0.000	0.000	0.000	0.000
130	B	134	SER	0	0.034	0.021	34.499	0.123	0.123	0.000	0.000	0.000	0.000
131	B	135	LYS	1	0.834	0.896	31.279	-10.539	-10.539	0.000	0.000	0.000	0.000
132	B	136	PHE	0	-0.015	-0.015	33.581	-0.090	-0.090	0.000	0.000	0.000	0.000
133	B	137	CYS	0	-0.082	-0.043	38.337	-0.224	-0.224	0.000	0.000	0.000	0.000
134	B	138	LYS	1	0.848	0.927	38.349	-8.029	-8.029	0.000	0.000	0.000	0.000
135	B	139	THR	0	0.001	-0.013	38.252	0.250	0.250	0.000	0.000	0.000	0.000
136	B	140	ALA	0	0.017	-0.007	37.077	0.012	0.012	0.000	0.000	0.000	0.000
137	B	141	PHE	0	0.062	0.037	38.564	-0.011	-0.011	0.000	0.000	0.000	0.000
138	B	142	ASP	-1	-0.811	-0.884	41.307	7.486	7.486	0.000	0.000	0.000	0.000
139	B	143	ILE	0	-0.002	0.023	35.513	-0.036	-0.036	0.000	0.000	0.000	0.000
140	B	144	SER	0	0.026	0.006	39.678	-0.003	-0.003	0.000	0.000	0.000	0.000
141	B	145	ILE	0	-0.006	0.007	41.464	-0.110	-0.110	0.000	0.000	0.000	0.000
142	B	146	ASP	-1	-0.904	-0.932	41.055	7.704	7.704	0.000	0.000	0.000	0.000
143	B	147	ASN	0	-0.115	-0.079	37.768	0.051	0.051	0.000	0.000	0.000	0.000
144	B	148	GLY	0	-0.041	-0.004	41.823	-0.023	-0.023	0.000	0.000	0.000	0.000
145	B	149	ASN	0	-0.051	-0.034	40.495	-0.235	-0.235	0.000	0.000	0.000	0.000
146	B	150	GLU	-1	-0.853	-0.971	43.974	6.843	6.843	0.000	0.000	0.000	0.000
147	B	151	ASP	-1	-0.923	-0.940	44.274	6.965	6.965	0.000	0.000	0.000	0.000
148	B	152	LEU	0	-0.033	-0.025	38.492	0.074	0.074	0.000	0.000	0.000	0.000
149	B	153	ALA	0	0.012	0.003	42.713	0.022	0.022	0.000	0.000	0.000	0.000
150	B	154	GLU	-1	-0.949	-0.979	44.877	6.449	6.449	0.000	0.000	0.000	0.000
151	B	155	ILE	0	-0.071	-0.034	40.596	-0.049	-0.049	0.000	0.000	0.000	0.000
152	B	156	LEU	0	-0.034	-0.016	38.987	0.121	0.121	0.000	0.000	0.000	0.000
153	B	157	GLN	0	-0.077	-0.013	43.066	-0.031	-0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:5:ASP)