FMO DATABASE

FMODB ID: LNGY9

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	OptAll
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	-859973.134223
FMO2-HF: Nuclear repulsion	816468.153308
FMO2-HF: Total energy	-43504.980916
FMO2-MP2: Total energy	-43635.503296

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.
-1.793	1.302	0.234	-1.157	-2.171	0.004

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 : 0.000 / q_NPA : -0.020

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	0.021	-0.008	3.597	1.173	2.412	0.002	-0.458	-0.783	0.001
4	C	143	VAL	0	-0.026	0.004	3.338	-0.673	0.521	0.105	-0.495	-0.804	0.003
5	C	144	ILE	0	-0.006	-0.002	3.986	-0.156	0.108	0.001	-0.059	-0.205	0.000
6	C	145	GLU	-1	-0.846	-0.909	6.864	-0.391	-0.391	0.000	0.000	0.000	0.000
7	C	146	ASN	0	0.002	-0.015	8.159	0.072	0.072	0.000	0.000	0.000	0.000
8	C	147	LEU	0	-0.063	-0.024	9.165	0.006	0.006	0.000	0.000	0.000	0.000
9	C	148	GLN	0	-0.044	-0.026	10.735	0.002	0.002	0.000	0.000	0.000	0.000
10	C	149	ARG	1	0.767	0.865	10.684	0.009	0.009	0.000	0.000	0.000	0.000
11	C	150	ASN	0	-0.094	-0.042	13.999	0.024	0.024	0.000	0.000	0.000	0.000
12	C	151	GLU	-1	-0.802	-0.885	13.183	0.146	0.146	0.000	0.000	0.000	0.000
13	C	152	LEU	0	-0.028	0.000	8.777	0.089	0.089	0.000	0.000	0.000	0.000
14	C	153	THR	0	-0.028	-0.054	13.389	-0.089	-0.089	0.000	0.000	0.000	0.000
15	C	154	PRO	0	-0.026	-0.040	14.256	0.059	0.059	0.000	0.000	0.000	0.000
16	C	155	ARG	1	0.997	1.002	15.015	-0.367	-0.367	0.000	0.000	0.000	0.000
17	C	156	GLU	-1	-0.755	-0.825	11.167	0.684	0.684	0.000	0.000	0.000	0.000
18	C	157	ILE	0	-0.031	-0.017	10.016	0.203	0.203	0.000	0.000	0.000	0.000
19	C	158	ALA	0	0.002	-0.003	10.557	0.016	0.016	0.000	0.000	0.000	0.000
20	C	159	ASP	-1	-0.821	-0.920	11.193	0.698	0.698	0.000	0.000	0.000	0.000
21	C	160	PHE	0	-0.080	-0.044	2.800	-0.323	0.075	0.126	-0.145	-0.379	0.000
22	C	161	ILE	0	-0.001	-0.008	7.800	-0.066	-0.066	0.000	0.000	0.000	0.000
23	C	162	GLY	0	0.040	0.025	9.900	-0.083	-0.083	0.000	0.000	0.000	0.000
24	C	163	ARG	1	0.961	0.978	6.356	-2.141	-2.141	0.000	0.000	0.000	0.000
25	C	164	GLU	-1	-0.786	-0.819	5.353	0.551	0.551	0.000	0.000	0.000	0.000
26	C	165	LEU	0	-0.026	-0.022	8.306	-0.146	-0.146	0.000	0.000	0.000	0.000
27	C	166	ALA	0	-0.002	0.006	11.444	-0.068	-0.068	0.000	0.000	0.000	0.000
28	C	167	LYS	1	0.807	0.890	5.574	-0.872	-0.872	0.000	0.000	0.000	0.000
29	C	168	GLY	0	0.041	0.031	11.073	-0.062	-0.062	0.000	0.000	0.000	0.000
30	C	169	LYS	1	0.821	0.899	5.499	-0.192	-0.192	0.000	0.000	0.000	0.000
31	C	170	LYS	1	0.940	0.961	12.245	-0.004	-0.004	0.000	0.000	0.000	0.000
32	C	171	LYS	1	1.028	1.004	13.491	-0.159	-0.159	0.000	0.000	0.000	0.000
33	C	172	GLY	0	0.026	0.005	14.311	-0.003	-0.003	0.000	0.000	0.000	0.000
34	C	173	ASP	-1	-0.847	-0.922	12.108	-0.073	-0.073	0.000	0.000	0.000	0.000
35	C	174	ILE	0	0.025	0.004	8.479	-0.066	-0.066	0.000	0.000	0.000	0.000
36	C	175	ALA	0	-0.025	-0.013	10.309	-0.032	-0.032	0.000	0.000	0.000	0.000
37	C	176	LYS	1	0.872	0.927	12.420	0.063	0.063	0.000	0.000	0.000	0.000
38	C	177	GLH	0	-0.049	-0.037	5.559	-0.053	-0.053	0.000	0.000	0.000	0.000
39	C	178	ILE	0	0.035	0.029	7.249	-0.166	-0.166	0.000	0.000	0.000	0.000
40	C	179	GLY	0	0.037	0.034	9.652	0.042	0.042	0.000	0.000	0.000	0.000
41	C	180	LYS	1	0.845	0.922	12.965	0.112	0.112	0.000	0.000	0.000	0.000
42	C	181	SER	0	0.074	0.033	15.093	-0.004	-0.004	0.000	0.000	0.000	0.000
43	C	182	PRO	0	0.073	0.007	16.716	0.024	0.024	0.000	0.000	0.000	0.000
44	C	183	ALA	0	0.031	0.031	18.030	0.021	0.021	0.000	0.000	0.000	0.000
45	C	184	PHE	0	0.062	0.039	12.771	0.011	0.011	0.000	0.000	0.000	0.000
46	C	185	ILE	0	0.007	0.016	11.919	0.036	0.036	0.000	0.000	0.000	0.000
47	C	186	THR	0	-0.052	-0.041	15.276	0.033	0.033	0.000	0.000	0.000	0.000
48	C	187	GLN	0	0.013	0.008	18.575	0.012	0.012	0.000	0.000	0.000	0.000
49	C	188	HIS	1	0.871	0.936	14.354	-0.268	-0.268	0.000	0.000	0.000	0.000
50	C	189	VAL	0	-0.023	-0.024	15.155	0.024	0.024	0.000	0.000	0.000	0.000
51	C	190	THR	0	-0.019	-0.022	16.852	0.006	0.006	0.000	0.000	0.000	0.000
52	C	191	LEU	0	-0.020	-0.015	17.428	-0.004	-0.004	0.000	0.000	0.000	0.000
53	C	192	LEU	0	-0.095	-0.033	14.158	0.025	0.025	0.000	0.000	0.000	0.000
54	C	193	ASP	-1	-0.948	-0.962	18.192	0.183	0.183	0.000	0.000	0.000	0.000
55	C	194	LEU	0	-0.059	-0.016	21.480	-0.018	-0.018	0.000	0.000	0.000	0.000
56	C	195	PRO	0	0.027	0.015	24.408	0.001	0.001	0.000	0.000	0.000	0.000
57	C	196	GLU	-1	-0.853	-0.922	27.872	0.164	0.164	0.000	0.000	0.000	0.000
58	C	197	LYS	1	0.946	0.982	28.965	-0.092	-0.092	0.000	0.000	0.000	0.000
59	C	198	ILE	0	-0.039	-0.034	26.035	0.000	0.000	0.000	0.000	0.000	0.000
60	C	199	ALA	0	-0.014	-0.011	24.894	0.010	0.010	0.000	0.000	0.000	0.000
61	C	200	ASP	-1	-0.845	-0.911	25.740	0.154	0.154	0.000	0.000	0.000	0.000
62	C	201	ALA	0	-0.006	-0.001	28.092	0.004	0.004	0.000	0.000	0.000	0.000
63	C	202	PHE	0	-0.050	-0.032	19.432	0.005	0.005	0.000	0.000	0.000	0.000
64	C	203	ASN	0	-0.069	-0.050	21.830	0.033	0.033	0.000	0.000	0.000	0.000
65	C	204	THR	0	-0.001	0.013	24.524	0.003	0.003	0.000	0.000	0.000	0.000
66	C	205	GLY	0	-0.058	-0.022	26.694	-0.008	-0.008	0.000	0.000	0.000	0.000
67	C	206	ARG	1	0.836	0.919	27.436	-0.102	-0.102	0.000	0.000	0.000	0.000
68	C	207	VAL	0	0.014	0.008	26.725	-0.008	-0.008	0.000	0.000	0.000	0.000
69	C	208	ARG	1	0.902	0.932	24.587	-0.128	-0.128	0.000	0.000	0.000	0.000
70	C	209	ASP	-1	-0.799	-0.868	23.531	0.111	0.111	0.000	0.000	0.000	0.000
71	C	210	VAL	0	0.077	0.019	19.179	0.001	0.001	0.000	0.000	0.000	0.000
72	C	211	THR	0	-0.040	-0.020	22.491	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	212	VAL	0	0.030	0.023	24.789	-0.003	-0.003	0.000	0.000	0.000	0.000
74	C	213	VAL	0	0.048	0.033	23.095	-0.003	-0.003	0.000	0.000	0.000	0.000
75	C	214	ASN	0	-0.051	-0.035	21.142	-0.003	-0.003	0.000	0.000	0.000	0.000
76	C	215	GLU	-1	-0.902	-0.921	25.231	0.067	0.067	0.000	0.000	0.000	0.000
77	C	216	LEU	0	0.049	0.032	28.679	-0.005	-0.005	0.000	0.000	0.000	0.000
78	C	217	VAL	0	0.037	0.017	24.957	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	218	THR	0	-0.132	-0.084	27.587	-0.005	-0.005	0.000	0.000	0.000	0.000
80	C	219	ALA	0	0.015	0.011	29.559	-0.006	-0.006	0.000	0.000	0.000	0.000
81	C	220	PHE	0	0.072	0.034	30.485	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	221	LYS	1	0.892	0.937	24.730	-0.123	-0.123	0.000	0.000	0.000	0.000
83	C	222	LYS	1	0.843	0.920	31.711	-0.070	-0.070	0.000	0.000	0.000	0.000
84	C	223	ARG	1	0.834	0.893	35.346	-0.056	-0.056	0.000	0.000	0.000	0.000
85	C	224	PRO	0	0.019	0.015	34.626	0.001	0.001	0.000	0.000	0.000	0.000
86	C	225	GLU	-1	-0.891	-0.944	35.792	0.066	0.066	0.000	0.000	0.000	0.000
87	C	226	GLU	-1	-0.780	-0.855	38.674	0.056	0.056	0.000	0.000	0.000	0.000
88	C	227	VAL	0	-0.051	-0.030	33.037	0.000	0.000	0.000	0.000	0.000	0.000
89	C	228	GLU	-1	-0.869	-0.946	33.597	0.107	0.107	0.000	0.000	0.000	0.000
90	C	229	ALA	0	0.021	0.006	36.030	0.001	0.001	0.000	0.000	0.000	0.000
91	C	230	TRP	0	-0.037	-0.024	34.082	0.001	0.001	0.000	0.000	0.000	0.000
92	C	231	LEU	0	-0.033	-0.030	31.768	0.001	0.001	0.000	0.000	0.000	0.000
93	C	232	ASP	-1	-0.876	-0.933	35.673	0.089	0.089	0.000	0.000	0.000	0.000
94	C	233	ASP	-1	-0.833	-0.866	37.966	0.063	0.063	0.000	0.000	0.000	0.000
95	C	234	ASP	-1	-0.887	-0.957	36.277	0.095	0.095	0.000	0.000	0.000	0.000
96	C	235	THR	0	-0.148	-0.091	38.544	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	236	GLN	0	-0.043	-0.021	37.423	-0.005	-0.005	0.000	0.000	0.000	0.000
98	C	237	GLU	-1	-0.866	-0.923	34.940	0.085	0.085	0.000	0.000	0.000	0.000
99	C	238	ILE	0	-0.035	0.002	31.525	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	239	THR	0	-0.003	-0.006	32.224	0.002	0.002	0.000	0.000	0.000	0.000
101	C	240	ARG	1	0.881	0.894	25.586	-0.083	-0.083	0.000	0.000	0.000	0.000
102	C	241	GLY	0	-0.016	0.010	32.645	-0.003	-0.003	0.000	0.000	0.000	0.000
103	C	242	THR	0	0.000	-0.022	36.251	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	243	VAL	0	0.042	0.021	31.670	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	244	LYS	1	0.777	0.868	34.864	-0.043	-0.043	0.000	0.000	0.000	0.000
106	C	245	LEU	0	0.002	-0.002	36.163	-0.002	-0.002	0.000	0.000	0.000	0.000
107	C	246	LEU	0	0.011	0.022	35.420	-0.002	-0.002	0.000	0.000	0.000	0.000
108	C	247	ARG	1	0.837	0.881	31.646	-0.068	-0.068	0.000	0.000	0.000	0.000
109	C	248	GLU	-1	-0.828	-0.894	37.287	0.039	0.039	0.000	0.000	0.000	0.000
110	C	249	PHE	0	-0.034	-0.014	40.546	-0.002	-0.002	0.000	0.000	0.000	0.000
111	C	250	LEU	0	-0.053	-0.014	37.780	0.000	0.000	0.000	0.000	0.000	0.000
112	C	251	ASP	-1	-1.004	-0.985	41.546	0.037	0.037	0.000	0.000	0.000	0.000

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