FMO DATABASE

FMODB ID: 4LN3N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1425301.482993
FMO2-HF: Nuclear repulsion	1366129.317087
FMO2-HF: Total energy	-59172.165906
FMO2-MP2: Total energy	-59344.908666

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.
-33.235	-26.592	3.599	-4.084	-6.155	0.031

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 : -0.856 / q_NPA : -0.951

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	0.047	0.028	2.764	-7.056	-4.659	0.123	-1.196	-1.324	0.003
4	B	8	LYS	1	0.945	0.970	2.321	-64.690	-61.513	3.468	-2.446	-4.198	0.029
5	B	9	LYS	1	0.923	0.975	3.128	-34.570	-33.643	0.009	-0.429	-0.506	-0.001
6	B	10	LEU	0	0.015	0.005	4.747	-4.163	-4.021	-0.001	-0.013	-0.127	0.000
7	B	11	LEU	0	-0.057	-0.021	7.060	-2.810	-2.810	0.000	0.000	0.000	0.000
8	B	12	GLU	-1	-0.849	-0.933	6.548	30.557	30.557	0.000	0.000	0.000	0.000
9	B	13	ALA	0	0.008	0.019	8.507	-2.312	-2.312	0.000	0.000	0.000	0.000
10	B	14	ALA	0	-0.019	-0.018	10.466	-1.891	-1.891	0.000	0.000	0.000	0.000
11	B	15	ARG	1	0.860	0.923	9.740	-25.672	-25.672	0.000	0.000	0.000	0.000
12	B	16	ALA	0	-0.038	-0.015	12.697	-1.248	-1.248	0.000	0.000	0.000	0.000
13	B	17	GLY	0	0.019	0.021	14.353	-0.924	-0.924	0.000	0.000	0.000	0.000
14	B	18	GLN	0	-0.043	-0.030	11.786	0.364	0.364	0.000	0.000	0.000	0.000
15	B	19	ASP	-1	-0.838	-0.947	14.222	15.325	15.325	0.000	0.000	0.000	0.000
16	B	20	ASP	-1	-0.836	-0.903	16.315	14.644	14.644	0.000	0.000	0.000	0.000
17	B	21	GLU	-1	-0.858	-0.928	10.304	22.800	22.800	0.000	0.000	0.000	0.000
18	B	22	VAL	0	-0.021	0.003	11.867	1.365	1.365	0.000	0.000	0.000	0.000
19	B	23	ARG	1	0.884	0.915	12.907	-13.716	-13.716	0.000	0.000	0.000	0.000
20	B	24	ILE	0	-0.007	0.005	11.282	0.288	0.288	0.000	0.000	0.000	0.000
21	B	25	LEU	0	-0.057	-0.036	6.397	1.146	1.146	0.000	0.000	0.000	0.000
22	B	26	MET	0	-0.044	-0.023	10.109	0.800	0.800	0.000	0.000	0.000	0.000
23	B	27	ALA	0	-0.030	0.010	12.109	-0.540	-0.540	0.000	0.000	0.000	0.000
24	B	28	ASN	0	-0.046	-0.034	9.168	-1.613	-1.613	0.000	0.000	0.000	0.000
25	B	29	GLY	0	0.024	0.027	10.544	0.191	0.191	0.000	0.000	0.000	0.000
26	B	30	ALA	0	-0.088	-0.049	6.698	2.373	2.373	0.000	0.000	0.000	0.000
27	B	31	PRO	0	-0.013	-0.001	4.977	-2.205	-2.205	0.000	0.000	0.000	0.000
28	B	32	PHE	0	0.047	0.008	7.010	2.326	2.326	0.000	0.000	0.000	0.000
29	B	33	THR	0	-0.066	-0.023	5.589	1.178	1.178	0.000	0.000	0.000	0.000
30	B	34	THR	0	0.036	-0.006	8.636	-1.785	-1.785	0.000	0.000	0.000	0.000
31	B	35	ASP	-1	-0.821	-0.901	9.249	26.236	26.236	0.000	0.000	0.000	0.000
32	B	36	TRP	0	0.007	-0.007	10.551	-1.355	-1.355	0.000	0.000	0.000	0.000
33	B	37	LEU	0	-0.014	-0.010	12.618	-1.591	-1.591	0.000	0.000	0.000	0.000
34	B	38	GLY	0	0.001	0.000	13.955	-1.341	-1.341	0.000	0.000	0.000	0.000
35	B	39	THR	0	-0.011	-0.001	13.803	-1.281	-1.281	0.000	0.000	0.000	0.000
36	B	40	SER	0	0.012	-0.036	12.289	2.148	2.148	0.000	0.000	0.000	0.000
37	B	41	PRO	0	0.043	-0.001	10.329	-0.930	-0.930	0.000	0.000	0.000	0.000
38	B	42	LEU	0	0.041	0.029	12.992	-0.773	-0.773	0.000	0.000	0.000	0.000
39	B	43	HIS	0	-0.023	0.027	16.298	0.114	0.114	0.000	0.000	0.000	0.000
40	B	44	LEU	0	0.006	0.004	11.923	-0.565	-0.565	0.000	0.000	0.000	0.000
41	B	45	ALA	0	0.001	0.002	16.033	-0.626	-0.626	0.000	0.000	0.000	0.000
42	B	46	ALA	0	0.010	-0.004	17.398	-0.695	-0.695	0.000	0.000	0.000	0.000
43	B	47	GLN	0	0.009	-0.001	18.564	0.024	0.024	0.000	0.000	0.000	0.000
44	B	48	TYR	0	-0.028	-0.022	16.532	-0.050	-0.050	0.000	0.000	0.000	0.000
45	B	49	GLY	0	0.030	0.046	20.198	-0.372	-0.372	0.000	0.000	0.000	0.000
46	B	50	HIS	0	-0.020	-0.007	16.952	-0.842	-0.842	0.000	0.000	0.000	0.000
47	B	51	PHE	0	0.017	-0.005	20.370	0.481	0.481	0.000	0.000	0.000	0.000
48	B	52	SER	0	0.072	0.031	20.930	-0.033	-0.033	0.000	0.000	0.000	0.000
49	B	53	THR	0	0.027	0.015	15.264	0.122	0.122	0.000	0.000	0.000	0.000
50	B	54	THR	0	0.006	-0.013	18.069	0.599	0.599	0.000	0.000	0.000	0.000
51	B	55	GLU	-1	-0.917	-0.953	19.746	11.804	11.804	0.000	0.000	0.000	0.000
52	B	56	VAL	0	-0.032	-0.016	16.895	-0.104	-0.104	0.000	0.000	0.000	0.000
53	B	57	LEU	0	0.003	0.002	13.652	0.495	0.495	0.000	0.000	0.000	0.000
54	B	58	LEU	0	0.006	0.015	17.282	0.103	0.103	0.000	0.000	0.000	0.000
55	B	59	ARG	1	0.896	0.948	20.444	-11.875	-11.875	0.000	0.000	0.000	0.000
56	B	60	ALA	0	0.024	0.014	16.051	-0.146	-0.146	0.000	0.000	0.000	0.000
57	B	61	GLY	0	-0.055	-0.023	17.430	0.362	0.362	0.000	0.000	0.000	0.000
58	B	62	VAL	0	-0.043	-0.012	14.380	0.250	0.250	0.000	0.000	0.000	0.000
59	B	63	SER	0	-0.031	-0.017	16.802	-1.184	-1.184	0.000	0.000	0.000	0.000
60	B	64	ARG	1	0.895	0.934	18.830	-12.943	-12.943	0.000	0.000	0.000	0.000
61	B	65	ASP	-1	-0.857	-0.923	21.646	12.063	12.063	0.000	0.000	0.000	0.000
62	B	66	ALA	0	-0.030	-0.015	17.210	0.104	0.104	0.000	0.000	0.000	0.000
63	B	67	ARG	1	0.873	0.902	19.314	-12.584	-12.584	0.000	0.000	0.000	0.000
64	B	68	THR	0	0.010	0.022	17.970	0.535	0.535	0.000	0.000	0.000	0.000
65	B	69	LYS	1	0.890	0.926	15.603	-19.736	-19.736	0.000	0.000	0.000	0.000
66	B	70	VAL	0	-0.037	-0.015	20.004	-0.453	-0.453	0.000	0.000	0.000	0.000
67	B	71	ASP	-1	-0.870	-0.945	22.439	12.073	12.073	0.000	0.000	0.000	0.000
68	B	72	ARG	1	0.905	0.986	22.177	-12.747	-12.747	0.000	0.000	0.000	0.000
69	B	73	THR	0	0.068	0.030	21.508	0.754	0.754	0.000	0.000	0.000	0.000
70	B	74	PRO	0	0.004	-0.019	19.256	-0.161	-0.161	0.000	0.000	0.000	0.000
71	B	75	LEU	0	0.062	0.042	21.717	-0.141	-0.141	0.000	0.000	0.000	0.000
72	B	76	HIS	0	-0.017	0.014	24.755	0.087	0.087	0.000	0.000	0.000	0.000
73	B	77	MET	0	-0.055	-0.019	19.540	-0.412	-0.412	0.000	0.000	0.000	0.000
74	B	78	ALA	0	0.038	0.018	24.057	-0.219	-0.219	0.000	0.000	0.000	0.000
75	B	79	ALA	0	0.006	0.001	25.424	-0.305	-0.305	0.000	0.000	0.000	0.000
76	B	80	SER	0	-0.022	-0.022	26.492	-0.326	-0.326	0.000	0.000	0.000	0.000
77	B	81	GLU	-1	-0.986	-1.000	23.692	12.060	12.060	0.000	0.000	0.000	0.000
78	B	82	GLY	0	0.027	0.033	27.161	-0.160	-0.160	0.000	0.000	0.000	0.000
79	B	83	HIS	0	-0.030	-0.011	23.456	-0.540	-0.540	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.056	0.020	27.992	0.177	0.177	0.000	0.000	0.000	0.000
81	B	85	ASN	0	0.033	0.017	26.709	-0.043	-0.043	0.000	0.000	0.000	0.000
82	B	86	ILE	0	-0.022	-0.002	22.802	0.128	0.128	0.000	0.000	0.000	0.000
83	B	87	VAL	0	0.004	-0.008	26.102	0.203	0.203	0.000	0.000	0.000	0.000
84	B	88	GLU	-1	-0.924	-0.959	28.381	9.158	9.158	0.000	0.000	0.000	0.000
85	B	89	VAL	0	-0.001	0.004	25.065	-0.074	-0.074	0.000	0.000	0.000	0.000
86	B	90	LEU	0	0.008	-0.004	22.184	0.181	0.181	0.000	0.000	0.000	0.000
87	B	91	LEU	0	0.012	0.024	26.035	0.022	0.022	0.000	0.000	0.000	0.000
88	B	92	LYS	1	0.895	0.952	29.480	-9.226	-9.226	0.000	0.000	0.000	0.000
89	B	93	HIS	0	-0.138	-0.076	24.660	0.152	0.152	0.000	0.000	0.000	0.000
90	B	94	GLY	0	-0.024	-0.024	26.348	0.339	0.339	0.000	0.000	0.000	0.000
91	B	95	ALA	0	-0.041	0.002	25.648	0.120	0.120	0.000	0.000	0.000	0.000
92	B	96	ASP	-1	-0.877	-0.942	27.110	9.661	9.661	0.000	0.000	0.000	0.000
93	B	97	VAL	0	-0.004	-0.010	29.067	0.256	0.256	0.000	0.000	0.000	0.000
94	B	98	ASN	0	-0.010	0.008	31.492	-0.086	-0.086	0.000	0.000	0.000	0.000
95	B	99	ALA	0	0.004	0.021	27.282	-0.018	-0.018	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.937	0.955	29.413	-9.395	-9.395	0.000	0.000	0.000	0.000
97	B	101	ASP	-1	-0.775	-0.868	26.592	11.204	11.204	0.000	0.000	0.000	0.000
98	B	102	MET	0	0.018	0.005	25.446	-0.418	-0.418	0.000	0.000	0.000	0.000
99	B	103	LEU	0	-0.089	-0.043	28.337	-0.362	-0.362	0.000	0.000	0.000	0.000
100	B	104	LYS	1	0.876	0.929	31.017	-9.176	-9.176	0.000	0.000	0.000	0.000
101	B	105	MET	0	0.047	0.028	31.235	-0.327	-0.327	0.000	0.000	0.000	0.000
102	B	106	THR	0	0.047	0.013	30.598	0.395	0.395	0.000	0.000	0.000	0.000
103	B	107	ALA	0	0.021	-0.004	29.233	0.011	0.011	0.000	0.000	0.000	0.000
104	B	108	LEU	0	0.050	0.037	30.802	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	109	HIS	0	-0.001	0.022	33.468	0.105	0.105	0.000	0.000	0.000	0.000
106	B	110	TRP	0	-0.032	-0.038	29.174	-0.031	-0.031	0.000	0.000	0.000	0.000
107	B	111	ALA	0	0.015	0.014	32.199	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	112	THR	0	0.002	-0.002	33.233	-0.237	-0.237	0.000	0.000	0.000	0.000
109	B	113	GLU	-1	-0.975	-0.989	33.609	8.671	8.671	0.000	0.000	0.000	0.000
110	B	114	HIS	0	-0.040	-0.025	29.878	-0.174	-0.174	0.000	0.000	0.000	0.000
111	B	115	ASN	0	-0.029	-0.010	33.974	-0.211	-0.211	0.000	0.000	0.000	0.000
112	B	116	HIS	0	0.012	0.016	30.380	-0.317	-0.317	0.000	0.000	0.000	0.000
113	B	117	GLN	0	0.045	0.018	35.137	0.096	0.096	0.000	0.000	0.000	0.000
114	B	118	GLU	-1	-0.860	-0.933	36.034	7.983	7.983	0.000	0.000	0.000	0.000
115	B	119	VAL	0	-0.093	-0.036	31.271	0.117	0.117	0.000	0.000	0.000	0.000
116	B	120	VAL	0	0.024	0.013	34.253	0.085	0.085	0.000	0.000	0.000	0.000
117	B	121	GLU	-1	-0.853	-0.940	36.932	7.535	7.535	0.000	0.000	0.000	0.000
118	B	122	LEU	0	-0.079	-0.039	32.278	-0.074	-0.074	0.000	0.000	0.000	0.000
119	B	123	LEU	0	-0.040	-0.030	31.598	0.083	0.083	0.000	0.000	0.000	0.000
120	B	124	ILE	0	0.019	0.016	35.473	-0.022	-0.022	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.915	0.962	38.540	-8.063	-8.063	0.000	0.000	0.000	0.000
122	B	126	TYR	0	-0.117	-0.057	33.632	-0.027	-0.027	0.000	0.000	0.000	0.000
123	B	127	GLY	0	0.000	-0.013	35.925	0.184	0.184	0.000	0.000	0.000	0.000
124	B	128	ALA	0	-0.028	0.000	35.413	0.025	0.025	0.000	0.000	0.000	0.000
125	B	129	ASP	-1	-0.953	-0.989	36.831	7.651	7.651	0.000	0.000	0.000	0.000
126	B	130	VAL	0	0.042	-0.001	38.389	0.166	0.166	0.000	0.000	0.000	0.000
127	B	131	HIS	0	-0.041	-0.003	40.792	0.018	0.018	0.000	0.000	0.000	0.000
128	B	132	THR	0	-0.037	-0.007	36.942	0.032	0.032	0.000	0.000	0.000	0.000
129	B	133	GLN	0	0.014	-0.005	39.276	0.048	0.048	0.000	0.000	0.000	0.000
130	B	134	SER	0	0.043	0.024	35.346	0.111	0.111	0.000	0.000	0.000	0.000
131	B	135	LYS	1	0.838	0.904	32.127	-9.918	-9.918	0.000	0.000	0.000	0.000
132	B	136	PHE	0	-0.027	-0.020	34.318	-0.076	-0.076	0.000	0.000	0.000	0.000
133	B	137	CYS	0	-0.079	-0.045	38.944	-0.206	-0.206	0.000	0.000	0.000	0.000
134	B	138	LYS	1	0.871	0.955	38.995	-7.812	-7.812	0.000	0.000	0.000	0.000
135	B	139	THR	0	0.023	0.031	39.256	0.231	0.231	0.000	0.000	0.000	0.000
136	B	140	ALA	0	0.022	-0.009	38.238	0.023	0.023	0.000	0.000	0.000	0.000
137	B	141	PHE	0	0.045	0.027	39.701	0.006	0.006	0.000	0.000	0.000	0.000
138	B	142	ASP	-1	-0.803	-0.909	42.211	7.160	7.160	0.000	0.000	0.000	0.000
139	B	143	ILE	0	-0.043	0.006	36.346	-0.009	-0.009	0.000	0.000	0.000	0.000
140	B	144	SER	0	-0.007	-0.008	40.518	-0.052	-0.052	0.000	0.000	0.000	0.000
141	B	145	ILE	0	0.014	0.015	42.253	-0.092	-0.092	0.000	0.000	0.000	0.000
142	B	146	ASP	-1	-0.895	-0.940	41.774	7.367	7.367	0.000	0.000	0.000	0.000
143	B	147	ASN	0	-0.093	-0.050	37.900	-0.036	-0.036	0.000	0.000	0.000	0.000
144	B	148	GLY	0	-0.049	-0.014	42.298	-0.018	-0.018	0.000	0.000	0.000	0.000
145	B	149	ASN	0	-0.056	-0.030	40.905	-0.222	-0.222	0.000	0.000	0.000	0.000
146	B	150	GLU	-1	-0.859	-0.968	44.404	6.574	6.574	0.000	0.000	0.000	0.000
147	B	151	ASP	-1	-0.891	-0.927	44.749	6.672	6.672	0.000	0.000	0.000	0.000
148	B	152	LEU	0	-0.057	-0.036	39.025	0.070	0.070	0.000	0.000	0.000	0.000
149	B	153	ALA	0	0.046	0.014	43.429	0.017	0.017	0.000	0.000	0.000	0.000
150	B	154	GLU	-1	-0.963	-0.983	45.766	6.262	6.262	0.000	0.000	0.000	0.000
151	B	155	ILE	0	-0.105	-0.046	41.412	-0.038	-0.038	0.000	0.000	0.000	0.000
152	B	156	LEU	0	-0.052	-0.030	40.225	0.112	0.112	0.000	0.000	0.000	0.000
153	B	157	GLN	0	-0.073	-0.010	44.195	0.033	0.033	0.000	0.000	0.000	0.000

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