FMO DATABASE

FMODB ID: 3JZLL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-855898.378584
FMO2-HF: Nuclear repulsion	812393.73164
FMO2-HF: Total energy	-43504.646944
FMO2-MP2: Total energy	-43635.137956

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.
-3.162	0.405	0.538	-1.366	-2.74	0.008

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 : -0.017 / q_NPA : -0.025

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	-0.003	-0.016	3.044	1.326	3.035	0.082	-0.648	-1.143	0.002
4	C	143	VAL	0	-0.028	0.003	2.982	-1.877	-0.498	0.428	-0.608	-1.199	0.006
5	C	144	ILE	0	0.016	-0.002	4.403	-0.490	-0.285	-0.001	-0.036	-0.169	0.000
6	C	145	GLU	-1	-0.878	-0.927	7.103	-0.440	-0.440	0.000	0.000	0.000	0.000
7	C	146	ASN	0	-0.008	-0.029	7.687	-0.094	-0.094	0.000	0.000	0.000	0.000
8	C	147	LEU	0	-0.043	-0.016	9.382	-0.053	-0.053	0.000	0.000	0.000	0.000
9	C	148	GLN	0	-0.023	-0.005	10.952	-0.030	-0.030	0.000	0.000	0.000	0.000
10	C	149	ARG	1	0.770	0.866	10.476	-0.239	-0.239	0.000	0.000	0.000	0.000
11	C	150	ASN	0	-0.079	-0.035	14.380	0.017	0.017	0.000	0.000	0.000	0.000
12	C	151	GLU	-1	-0.782	-0.871	13.208	0.266	0.266	0.000	0.000	0.000	0.000
13	C	152	LEU	0	-0.068	-0.010	8.632	0.083	0.083	0.000	0.000	0.000	0.000
14	C	153	THR	0	-0.023	-0.050	13.254	-0.115	-0.115	0.000	0.000	0.000	0.000
15	C	154	PRO	0	-0.006	-0.031	14.180	0.062	0.062	0.000	0.000	0.000	0.000
16	C	155	ARG	1	1.021	1.003	14.848	-0.343	-0.343	0.000	0.000	0.000	0.000
17	C	156	GLU	-1	-0.750	-0.822	11.156	0.746	0.746	0.000	0.000	0.000	0.000
18	C	157	ILE	0	-0.052	-0.024	10.214	0.169	0.169	0.000	0.000	0.000	0.000
19	C	158	ALA	0	-0.003	-0.008	10.806	0.005	0.005	0.000	0.000	0.000	0.000
20	C	159	ASP	-1	-0.836	-0.920	11.346	0.641	0.641	0.000	0.000	0.000	0.000
21	C	160	PHE	0	-0.078	-0.046	3.138	-0.149	0.125	0.029	-0.074	-0.229	0.000
22	C	161	ILE	0	-0.017	-0.014	8.005	-0.098	-0.098	0.000	0.000	0.000	0.000
23	C	162	GLY	0	0.047	0.030	10.196	-0.082	-0.082	0.000	0.000	0.000	0.000
24	C	163	ARG	1	0.975	0.988	6.227	-1.885	-1.885	0.000	0.000	0.000	0.000
25	C	164	GLU	-1	-0.807	-0.852	5.901	0.236	0.236	0.000	0.000	0.000	0.000
26	C	165	LEU	0	-0.005	-0.016	8.707	-0.120	-0.120	0.000	0.000	0.000	0.000
27	C	166	ALA	0	-0.019	0.004	11.918	-0.055	-0.055	0.000	0.000	0.000	0.000
28	C	167	LYS	1	0.822	0.904	5.783	-0.683	-0.683	0.000	0.000	0.000	0.000
29	C	168	GLY	0	0.041	0.036	11.504	-0.052	-0.052	0.000	0.000	0.000	0.000
30	C	169	LYS	1	0.828	0.905	5.726	0.064	0.064	0.000	0.000	0.000	0.000
31	C	170	LYS	1	0.931	0.956	12.495	0.022	0.022	0.000	0.000	0.000	0.000
32	C	171	LYS	1	1.036	1.006	13.807	-0.141	-0.141	0.000	0.000	0.000	0.000
33	C	172	GLY	0	0.007	0.005	14.393	0.000	0.000	0.000	0.000	0.000	0.000
34	C	173	ASP	-1	-0.847	-0.946	12.508	-0.101	-0.101	0.000	0.000	0.000	0.000
35	C	174	ILE	0	-0.004	0.010	8.789	-0.057	-0.057	0.000	0.000	0.000	0.000
36	C	175	ALA	0	-0.032	-0.018	10.682	-0.029	-0.029	0.000	0.000	0.000	0.000
37	C	176	LYS	1	0.914	0.949	12.935	0.091	0.091	0.000	0.000	0.000	0.000
38	C	177	GLH	0	-0.047	-0.028	6.241	-0.070	-0.070	0.000	0.000	0.000	0.000
39	C	178	ILE	0	-0.011	-0.007	7.331	-0.127	-0.127	0.000	0.000	0.000	0.000
40	C	179	GLY	0	0.027	0.030	9.787	0.050	0.050	0.000	0.000	0.000	0.000
41	C	180	LYS	1	0.899	0.958	13.100	0.013	0.013	0.000	0.000	0.000	0.000
42	C	181	SER	0	0.069	0.031	15.147	-0.010	-0.010	0.000	0.000	0.000	0.000
43	C	182	PRO	0	0.067	0.001	16.857	0.021	0.021	0.000	0.000	0.000	0.000
44	C	183	ALA	0	0.035	0.016	18.470	0.019	0.019	0.000	0.000	0.000	0.000
45	C	184	PHE	0	0.042	0.028	12.840	0.009	0.009	0.000	0.000	0.000	0.000
46	C	185	ILE	0	0.029	0.024	12.329	0.037	0.037	0.000	0.000	0.000	0.000
47	C	186	THR	0	-0.058	-0.028	15.800	0.027	0.027	0.000	0.000	0.000	0.000
48	C	187	GLN	0	0.034	0.017	19.121	0.011	0.011	0.000	0.000	0.000	0.000
49	C	188	HIS	1	0.863	0.929	14.707	-0.271	-0.271	0.000	0.000	0.000	0.000
50	C	189	VAL	0	0.000	-0.013	15.297	0.021	0.021	0.000	0.000	0.000	0.000
51	C	190	THR	0	-0.026	-0.019	17.000	0.003	0.003	0.000	0.000	0.000	0.000
52	C	191	LEU	0	-0.023	-0.022	17.900	-0.006	-0.006	0.000	0.000	0.000	0.000
53	C	192	LEU	0	-0.094	-0.029	14.256	0.015	0.015	0.000	0.000	0.000	0.000
54	C	193	ASP	-1	-0.970	-0.966	18.269	0.167	0.167	0.000	0.000	0.000	0.000
55	C	194	LEU	0	-0.039	0.000	21.834	-0.016	-0.016	0.000	0.000	0.000	0.000
56	C	195	PRO	0	0.009	-0.003	24.387	0.000	0.000	0.000	0.000	0.000	0.000
57	C	196	GLU	-1	-0.853	-0.929	27.923	0.150	0.150	0.000	0.000	0.000	0.000
58	C	197	LYS	1	0.958	0.991	29.125	-0.089	-0.089	0.000	0.000	0.000	0.000
59	C	198	ILE	0	-0.051	-0.043	26.538	0.001	0.001	0.000	0.000	0.000	0.000
60	C	199	ALA	0	-0.012	-0.013	24.857	0.010	0.010	0.000	0.000	0.000	0.000
61	C	200	ASP	-1	-0.866	-0.912	25.752	0.155	0.155	0.000	0.000	0.000	0.000
62	C	201	ALA	0	-0.016	-0.015	28.077	0.005	0.005	0.000	0.000	0.000	0.000
63	C	202	PHE	0	-0.055	-0.028	19.598	0.010	0.010	0.000	0.000	0.000	0.000
64	C	203	ASN	0	-0.052	-0.045	22.148	0.036	0.036	0.000	0.000	0.000	0.000
65	C	204	THR	0	0.007	0.017	24.685	0.002	0.002	0.000	0.000	0.000	0.000
66	C	205	GLY	0	-0.083	-0.038	26.761	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	206	ARG	1	0.856	0.931	27.624	-0.100	-0.100	0.000	0.000	0.000	0.000
68	C	207	VAL	0	0.010	0.015	27.160	-0.008	-0.008	0.000	0.000	0.000	0.000
69	C	208	ARG	1	0.963	0.972	25.029	-0.139	-0.139	0.000	0.000	0.000	0.000
70	C	209	ASP	-1	-0.802	-0.867	23.979	0.122	0.122	0.000	0.000	0.000	0.000
71	C	210	VAL	0	0.064	0.010	19.628	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	211	THR	0	-0.032	-0.013	22.879	-0.003	-0.003	0.000	0.000	0.000	0.000
73	C	212	VAL	0	0.035	0.020	25.157	-0.006	-0.006	0.000	0.000	0.000	0.000
74	C	213	VAL	0	0.028	0.030	23.518	-0.004	-0.004	0.000	0.000	0.000	0.000
75	C	214	ASN	0	-0.071	-0.052	21.396	-0.008	-0.008	0.000	0.000	0.000	0.000
76	C	215	GLU	-1	-0.917	-0.944	25.436	0.068	0.068	0.000	0.000	0.000	0.000
77	C	216	LEU	0	0.037	0.020	29.021	-0.006	-0.006	0.000	0.000	0.000	0.000
78	C	217	VAL	0	0.055	0.030	25.349	-0.005	-0.005	0.000	0.000	0.000	0.000
79	C	218	THR	0	-0.129	-0.074	27.945	-0.006	-0.006	0.000	0.000	0.000	0.000
80	C	219	ALA	0	0.004	0.002	29.872	-0.006	-0.006	0.000	0.000	0.000	0.000
81	C	220	PHE	0	0.050	0.025	30.836	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	221	LYS	1	0.889	0.939	25.507	-0.106	-0.106	0.000	0.000	0.000	0.000
83	C	222	LYS	1	0.881	0.940	32.199	-0.063	-0.063	0.000	0.000	0.000	0.000
84	C	223	ARG	1	0.844	0.896	35.603	-0.054	-0.054	0.000	0.000	0.000	0.000
85	C	224	PRO	0	0.013	0.008	34.791	0.000	0.000	0.000	0.000	0.000	0.000
86	C	225	GLU	-1	-0.898	-0.935	36.085	0.061	0.061	0.000	0.000	0.000	0.000
87	C	226	GLU	-1	-0.769	-0.863	39.143	0.053	0.053	0.000	0.000	0.000	0.000
88	C	227	VAL	0	-0.061	-0.033	33.337	0.001	0.001	0.000	0.000	0.000	0.000
89	C	228	GLU	-1	-0.851	-0.940	34.269	0.099	0.099	0.000	0.000	0.000	0.000
90	C	229	ALA	0	0.002	0.009	36.512	0.001	0.001	0.000	0.000	0.000	0.000
91	C	230	TRP	0	-0.023	-0.029	34.304	0.003	0.003	0.000	0.000	0.000	0.000
92	C	231	LEU	0	-0.037	-0.026	32.278	0.002	0.002	0.000	0.000	0.000	0.000
93	C	232	ASP	-1	-0.857	-0.918	36.237	0.085	0.085	0.000	0.000	0.000	0.000
94	C	233	ASP	-1	-0.858	-0.881	38.483	0.062	0.062	0.000	0.000	0.000	0.000
95	C	234	ASP	-1	-0.871	-0.959	37.156	0.091	0.091	0.000	0.000	0.000	0.000
96	C	235	THR	0	-0.159	-0.090	38.925	0.001	0.001	0.000	0.000	0.000	0.000
97	C	236	GLN	0	-0.050	-0.021	37.633	-0.004	-0.004	0.000	0.000	0.000	0.000
98	C	237	GLU	-1	-0.869	-0.930	35.550	0.087	0.087	0.000	0.000	0.000	0.000
99	C	238	ILE	0	-0.040	0.005	31.805	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	239	THR	0	0.000	-0.004	32.832	0.003	0.003	0.000	0.000	0.000	0.000
101	C	240	ARG	1	0.896	0.899	26.019	-0.092	-0.092	0.000	0.000	0.000	0.000
102	C	241	GLY	0	-0.010	0.007	33.105	-0.003	-0.003	0.000	0.000	0.000	0.000
103	C	242	THR	0	-0.008	-0.023	36.733	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	243	VAL	0	0.055	0.021	32.062	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	244	LYS	1	0.759	0.859	35.315	-0.045	-0.045	0.000	0.000	0.000	0.000
106	C	245	LEU	0	0.003	0.000	36.702	-0.002	-0.002	0.000	0.000	0.000	0.000
107	C	246	LEU	0	0.011	0.019	35.671	-0.002	-0.002	0.000	0.000	0.000	0.000
108	C	247	ARG	1	0.845	0.894	31.803	-0.067	-0.067	0.000	0.000	0.000	0.000
109	C	248	GLU	-1	-0.820	-0.893	37.816	0.040	0.040	0.000	0.000	0.000	0.000
110	C	249	PHE	0	-0.041	-0.010	40.911	-0.002	-0.002	0.000	0.000	0.000	0.000
111	C	250	LEU	0	-0.075	-0.022	38.067	0.000	0.000	0.000	0.000	0.000	0.000
112	C	251	ASP	-1	-0.986	-0.979	41.380	0.035	0.035	0.000	0.000	0.000	0.000

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