FMO DATABASE

FMODB ID: JQYN9

Calculation Name: 1R71-C-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: BRU

PDB ID: 1R71

Chain ID: C

ChEMBL ID:

UniProt ID: P07674

Base Structure: X-ray

Registration Date: 2023-09-23

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-855863.062014
FMO2-HF: Nuclear repulsion	812359.520653
FMO2-HF: Total energy	-43503.541361
FMO2-MP2: Total energy	-43634.080568

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(C:140:ALA)

Summations of interaction energy for fragment #1(C:140:ALA)

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.
-3.157	0.227	1.198	-1.442	-3.141	0.006

Interaction energy analysis for fragmet #1(C:140:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.027

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	C	142	GLN	0	0.022	-0.010	2.926	1.044	2.951	0.148	-0.771	-1.285	0.002
4	C	143	VAL	0	-0.020	0.000	2.773	-1.156	-0.233	1.034	-0.504	-1.453	0.004
5	C	144	ILE	0	0.017	0.000	4.197	-0.559	-0.228	0.001	-0.112	-0.220	0.000
6	C	145	GLU	-1	-0.923	-0.955	7.103	-0.787	-0.787	0.000	0.000	0.000	0.000
7	C	146	ASN	0	-0.005	-0.017	7.622	-0.142	-0.142	0.000	0.000	0.000	0.000
8	C	147	LEU	0	-0.058	-0.019	9.396	-0.032	-0.032	0.000	0.000	0.000	0.000
9	C	148	GLN	0	-0.022	-0.008	10.959	-0.021	-0.021	0.000	0.000	0.000	0.000
10	C	149	ARG	1	0.849	0.927	10.735	-0.145	-0.145	0.000	0.000	0.000	0.000
11	C	150	ASN	0	-0.072	-0.032	14.444	0.011	0.011	0.000	0.000	0.000	0.000
12	C	151	GLU	-1	-0.848	-0.931	13.438	0.234	0.234	0.000	0.000	0.000	0.000
13	C	152	LEU	0	-0.063	0.000	8.734	0.079	0.079	0.000	0.000	0.000	0.000
14	C	153	THR	0	-0.025	-0.027	13.254	-0.109	-0.109	0.000	0.000	0.000	0.000
15	C	154	PRO	0	-0.009	-0.028	14.207	0.059	0.059	0.000	0.000	0.000	0.000
16	C	155	ARG	1	1.037	1.010	14.870	-0.333	-0.333	0.000	0.000	0.000	0.000
17	C	156	GLU	-1	-0.785	-0.867	11.136	0.806	0.806	0.000	0.000	0.000	0.000
18	C	157	ILE	0	-0.039	-0.015	10.235	0.160	0.160	0.000	0.000	0.000	0.000
19	C	158	ALA	0	-0.007	-0.008	10.823	0.002	0.002	0.000	0.000	0.000	0.000
20	C	159	ASP	-1	-0.849	-0.922	11.510	0.609	0.609	0.000	0.000	0.000	0.000
21	C	160	PHE	0	-0.086	-0.043	3.271	-0.093	0.130	0.015	-0.055	-0.183	0.000
22	C	161	ILE	0	-0.013	-0.012	8.015	-0.103	-0.103	0.000	0.000	0.000	0.000
23	C	162	GLY	0	0.038	0.028	10.203	-0.082	-0.082	0.000	0.000	0.000	0.000
24	C	163	ARG	1	0.964	0.975	5.709	-2.042	-2.042	0.000	0.000	0.000	0.000
25	C	164	GLU	-1	-0.864	-0.908	5.523	0.182	0.182	0.000	0.000	0.000	0.000
26	C	165	LEU	0	-0.010	-0.026	8.701	-0.125	-0.125	0.000	0.000	0.000	0.000
27	C	166	ALA	0	-0.027	0.001	11.937	-0.054	-0.054	0.000	0.000	0.000	0.000
28	C	167	LYS	1	0.889	0.955	5.310	-0.719	-0.719	0.000	0.000	0.000	0.000
29	C	168	GLY	0	0.023	0.026	11.531	-0.052	-0.052	0.000	0.000	0.000	0.000
30	C	169	LYS	1	0.863	0.949	5.939	0.281	0.281	0.000	0.000	0.000	0.000
31	C	170	LYS	1	0.983	0.982	12.473	0.041	0.041	0.000	0.000	0.000	0.000
32	C	171	LYS	1	1.028	0.999	13.788	-0.128	-0.128	0.000	0.000	0.000	0.000
33	C	172	GLY	0	-0.007	0.001	14.378	-0.004	-0.004	0.000	0.000	0.000	0.000
34	C	173	ASP	-1	-0.873	-0.952	12.361	-0.133	-0.133	0.000	0.000	0.000	0.000
35	C	174	ILE	0	-0.016	0.001	8.833	-0.066	-0.066	0.000	0.000	0.000	0.000
36	C	175	ALA	0	-0.041	-0.023	10.665	-0.036	-0.036	0.000	0.000	0.000	0.000
37	C	176	LYS	1	0.955	0.975	12.919	0.111	0.111	0.000	0.000	0.000	0.000
38	C	177	GLH	0	-0.052	-0.049	5.936	-0.202	-0.202	0.000	0.000	0.000	0.000
39	C	178	ILE	0	-0.021	-0.005	7.346	-0.137	-0.137	0.000	0.000	0.000	0.000
40	C	179	GLY	0	0.022	0.029	9.774	0.059	0.059	0.000	0.000	0.000	0.000
41	C	180	LYS	1	0.907	0.963	13.360	0.032	0.032	0.000	0.000	0.000	0.000
42	C	181	SER	0	0.059	0.021	15.138	-0.010	-0.010	0.000	0.000	0.000	0.000
43	C	182	PRO	0	0.067	0.003	16.849	0.020	0.020	0.000	0.000	0.000	0.000
44	C	183	ALA	0	0.045	0.022	18.459	0.019	0.019	0.000	0.000	0.000	0.000
45	C	184	PHE	0	0.043	0.029	12.626	0.008	0.008	0.000	0.000	0.000	0.000
46	C	185	ILE	0	0.029	0.023	12.390	0.037	0.037	0.000	0.000	0.000	0.000
47	C	186	THR	0	-0.056	-0.028	15.799	0.028	0.028	0.000	0.000	0.000	0.000
48	C	187	GLN	0	0.026	0.014	19.121	0.003	0.003	0.000	0.000	0.000	0.000
49	C	188	HIS	1	0.863	0.919	14.743	-0.242	-0.242	0.000	0.000	0.000	0.000
50	C	189	VAL	0	0.007	0.004	15.380	0.023	0.023	0.000	0.000	0.000	0.000
51	C	190	THR	0	-0.018	-0.024	17.009	0.006	0.006	0.000	0.000	0.000	0.000
52	C	191	LEU	0	-0.025	-0.014	17.371	-0.006	-0.006	0.000	0.000	0.000	0.000
53	C	192	LEU	0	-0.067	-0.032	14.215	0.016	0.016	0.000	0.000	0.000	0.000
54	C	193	ASP	-1	-0.992	-0.974	18.287	0.160	0.160	0.000	0.000	0.000	0.000
55	C	194	LEU	0	-0.031	-0.006	21.882	-0.017	-0.017	0.000	0.000	0.000	0.000
56	C	195	PRO	0	0.010	0.003	24.405	0.001	0.001	0.000	0.000	0.000	0.000
57	C	196	GLU	-1	-0.878	-0.942	27.944	0.144	0.144	0.000	0.000	0.000	0.000
58	C	197	LYS	1	1.050	1.047	29.149	-0.090	-0.090	0.000	0.000	0.000	0.000
59	C	198	ILE	0	-0.064	-0.049	26.450	0.001	0.001	0.000	0.000	0.000	0.000
60	C	199	ALA	0	-0.021	-0.020	24.846	0.009	0.009	0.000	0.000	0.000	0.000
61	C	200	ASP	-1	-0.870	-0.919	25.779	0.153	0.153	0.000	0.000	0.000	0.000
62	C	201	ALA	0	-0.017	-0.020	28.106	0.004	0.004	0.000	0.000	0.000	0.000
63	C	202	PHE	0	-0.040	-0.023	19.820	0.009	0.009	0.000	0.000	0.000	0.000
64	C	203	ASN	0	-0.033	-0.035	22.292	0.033	0.033	0.000	0.000	0.000	0.000
65	C	204	THR	0	-0.033	0.009	24.715	0.002	0.002	0.000	0.000	0.000	0.000
66	C	205	GLY	0	-0.080	-0.040	26.791	-0.003	-0.003	0.000	0.000	0.000	0.000
67	C	206	ARG	1	0.895	0.947	27.654	-0.100	-0.100	0.000	0.000	0.000	0.000
68	C	207	VAL	0	0.013	0.014	26.898	-0.008	-0.008	0.000	0.000	0.000	0.000
69	C	208	ARG	1	0.978	0.971	25.059	-0.133	-0.133	0.000	0.000	0.000	0.000
70	C	209	ASP	-1	-0.786	-0.879	24.001	0.111	0.111	0.000	0.000	0.000	0.000
71	C	210	VAL	0	0.066	0.010	19.717	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	211	THR	0	-0.064	-0.017	22.896	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	212	VAL	0	0.043	0.025	25.169	-0.005	-0.005	0.000	0.000	0.000	0.000
74	C	213	VAL	0	0.011	0.018	23.588	-0.003	-0.003	0.000	0.000	0.000	0.000
75	C	214	ASN	0	-0.078	-0.054	21.370	-0.008	-0.008	0.000	0.000	0.000	0.000
76	C	215	GLU	-1	-0.961	-0.984	25.448	0.065	0.065	0.000	0.000	0.000	0.000
77	C	216	LEU	0	0.031	0.018	29.042	-0.005	-0.005	0.000	0.000	0.000	0.000
78	C	217	VAL	0	0.069	0.037	25.431	-0.005	-0.005	0.000	0.000	0.000	0.000
79	C	218	THR	0	-0.137	-0.073	27.978	-0.006	-0.006	0.000	0.000	0.000	0.000
80	C	219	ALA	0	-0.008	-0.005	29.879	-0.006	-0.006	0.000	0.000	0.000	0.000
81	C	220	PHE	0	0.066	0.032	30.890	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	221	LYS	1	0.900	0.943	26.225	-0.092	-0.092	0.000	0.000	0.000	0.000
83	C	222	LYS	1	0.871	0.936	32.208	-0.059	-0.059	0.000	0.000	0.000	0.000
84	C	223	ARG	1	0.950	0.981	35.610	-0.050	-0.050	0.000	0.000	0.000	0.000
85	C	224	PRO	0	0.008	0.007	34.825	0.000	0.000	0.000	0.000	0.000	0.000
86	C	225	GLU	-1	-0.888	-0.932	36.099	0.059	0.059	0.000	0.000	0.000	0.000
87	C	226	GLU	-1	-0.882	-0.945	39.159	0.052	0.052	0.000	0.000	0.000	0.000
88	C	227	VAL	0	-0.071	-0.040	33.279	0.001	0.001	0.000	0.000	0.000	0.000
89	C	228	GLU	-1	-0.908	-0.965	34.621	0.095	0.095	0.000	0.000	0.000	0.000
90	C	229	ALA	0	0.027	0.028	36.531	0.001	0.001	0.000	0.000	0.000	0.000
91	C	230	TRP	0	-0.036	-0.032	34.306	0.002	0.002	0.000	0.000	0.000	0.000
92	C	231	LEU	0	-0.043	-0.030	32.364	0.002	0.002	0.000	0.000	0.000	0.000
93	C	232	ASP	-1	-0.859	-0.926	36.259	0.083	0.083	0.000	0.000	0.000	0.000
94	C	233	ASP	-1	-0.841	-0.852	38.507	0.059	0.059	0.000	0.000	0.000	0.000
95	C	234	ASP	-1	-0.929	-0.981	37.982	0.084	0.084	0.000	0.000	0.000	0.000
96	C	235	THR	0	-0.164	-0.119	38.953	0.000	0.000	0.000	0.000	0.000	0.000
97	C	236	GLN	0	-0.059	-0.021	37.682	-0.004	-0.004	0.000	0.000	0.000	0.000
98	C	237	GLU	-1	-0.869	-0.940	35.847	0.082	0.082	0.000	0.000	0.000	0.000
99	C	238	ILE	0	-0.045	0.006	31.793	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	239	THR	0	-0.007	-0.006	32.863	0.002	0.002	0.000	0.000	0.000	0.000
101	C	240	ARG	1	0.904	0.915	26.284	-0.080	-0.080	0.000	0.000	0.000	0.000
102	C	241	GLY	0	-0.011	0.007	33.119	-0.003	-0.003	0.000	0.000	0.000	0.000
103	C	242	THR	0	-0.017	-0.022	36.619	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	243	VAL	0	0.078	0.029	32.138	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	244	LYS	1	0.829	0.910	35.329	-0.039	-0.039	0.000	0.000	0.000	0.000
106	C	245	LEU	0	0.009	0.007	36.713	-0.002	-0.002	0.000	0.000	0.000	0.000
107	C	246	LEU	0	0.005	0.018	35.719	-0.002	-0.002	0.000	0.000	0.000	0.000
108	C	247	ARG	1	0.906	0.934	31.812	-0.060	-0.060	0.000	0.000	0.000	0.000
109	C	248	GLU	-1	-0.861	-0.933	37.826	0.035	0.035	0.000	0.000	0.000	0.000
110	C	249	PHE	0	-0.051	-0.014	40.919	-0.002	-0.002	0.000	0.000	0.000	0.000
111	C	250	LEU	0	-0.100	-0.043	38.138	0.000	0.000	0.000	0.000	0.000	0.000
112	C	251	ASP	-1	-0.970	-0.968	41.387	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:140:ALA)