FMO DATABASE

FMODB ID: R9JG8

Calculation Name: 3IU5-A-Xray372

Preferred Name: Protein polybromo-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3IU5

Chain ID: A

ChEMBL ID: CHEMBL1795184

UniProt ID: Q86U86

Base Structure: X-ray

Registration Date: 2023-09-20

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1008046.449932
FMO2-HF: Nuclear repulsion	959498.310393
FMO2-HF: Total energy	-48548.139539
FMO2-MP2: Total energy	-48687.889063

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(A:41:SER)

Summations of interaction energy for fragment #1(A:41:SER)

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.
-33.697	-31.616	29.433	-14.916	-16.598	-0.065

Interaction energy analysis for fragmet #1(A:41:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.007

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	A	43	THR	0	-0.066	-0.038	2.091	-8.294	-3.866	4.344	-4.593	-4.179	0.042
4	A	44	VAL	0	0.009	0.018	1.862	-13.064	-14.953	10.164	-4.238	-4.037	-0.040
5	A	45	ASP	-1	-0.777	-0.883	4.418	-0.316	-0.194	0.000	-0.043	-0.079	0.000
6	A	46	PRO	0	-0.012	-0.013	7.976	-0.107	-0.107	0.000	0.000	0.000	0.000
7	A	47	ILE	0	0.057	0.042	9.796	0.104	0.104	0.000	0.000	0.000	0.000
8	A	48	ALA	0	0.005	0.005	9.011	0.117	0.117	0.000	0.000	0.000	0.000
9	A	49	VAL	0	-0.008	-0.003	6.071	0.112	0.112	0.000	0.000	0.000	0.000
10	A	50	CYS	0	-0.044	-0.028	9.188	0.169	0.169	0.000	0.000	0.000	0.000
11	A	51	HIS	0	-0.017	-0.017	12.612	0.220	0.220	0.000	0.000	0.000	0.000
12	A	52	GLU	-1	-0.835	-0.902	10.567	-0.368	-0.368	0.000	0.000	0.000	0.000
13	A	53	LEU	0	-0.032	0.002	9.420	0.121	0.121	0.000	0.000	0.000	0.000
14	A	54	TYR	0	-0.004	-0.009	12.842	0.126	0.126	0.000	0.000	0.000	0.000
15	A	55	ASN	0	-0.024	-0.031	15.307	0.088	0.088	0.000	0.000	0.000	0.000
16	A	56	THR	0	-0.018	-0.016	13.415	0.074	0.074	0.000	0.000	0.000	0.000
17	A	57	ILE	0	-0.067	-0.040	15.908	0.054	0.054	0.000	0.000	0.000	0.000
18	A	58	ARG	1	0.719	0.842	18.291	0.329	0.329	0.000	0.000	0.000	0.000
19	A	59	ASP	-1	-0.752	-0.848	19.530	-0.197	-0.197	0.000	0.000	0.000	0.000
20	A	60	TYR	0	-0.007	0.000	19.027	0.029	0.029	0.000	0.000	0.000	0.000
21	A	61	LYS	1	0.879	0.942	20.896	0.105	0.105	0.000	0.000	0.000	0.000
22	A	62	ASP	-1	-0.775	-0.866	23.247	-0.095	-0.095	0.000	0.000	0.000	0.000
23	A	63	GLU	-1	-0.787	-0.894	24.371	-0.081	-0.081	0.000	0.000	0.000	0.000
24	A	64	GLN	0	-0.121	-0.059	27.146	0.011	0.011	0.000	0.000	0.000	0.000
25	A	65	GLY	0	0.027	0.024	28.151	0.001	0.001	0.000	0.000	0.000	0.000
26	A	66	ARG	1	0.840	0.895	28.449	0.087	0.087	0.000	0.000	0.000	0.000
27	A	67	LEU	0	0.021	0.014	24.104	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	68	LEU	0	0.005	-0.005	23.497	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	69	CYS	0	-0.002	-0.007	22.988	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	70	GLU	-1	-0.903	-0.967	24.605	-0.135	-0.135	0.000	0.000	0.000	0.000
31	A	71	LEU	0	-0.074	-0.033	28.088	0.004	0.004	0.000	0.000	0.000	0.000
32	A	72	PHE	0	-0.013	-0.009	25.172	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	73	ILE	0	0.017	0.015	26.728	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	74	ARG	1	0.891	0.929	28.129	0.162	0.162	0.000	0.000	0.000	0.000
35	A	75	ALA	0	0.033	0.036	30.255	0.005	0.005	0.000	0.000	0.000	0.000
36	A	76	PRO	0	0.020	0.013	31.720	0.010	0.010	0.000	0.000	0.000	0.000
37	A	77	LYS	1	0.958	0.994	35.419	0.116	0.116	0.000	0.000	0.000	0.000
38	A	78	ARG	1	0.934	0.950	34.334	0.178	0.178	0.000	0.000	0.000	0.000
39	A	79	ARG	1	0.920	0.971	38.967	0.122	0.122	0.000	0.000	0.000	0.000
40	A	80	ASN	0	-0.078	-0.059	41.104	0.002	0.002	0.000	0.000	0.000	0.000
41	A	81	GLN	0	0.010	0.005	38.583	0.000	0.000	0.000	0.000	0.000	0.000
42	A	82	PRO	0	0.036	0.031	39.837	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	83	ASP	-1	-0.722	-0.847	40.700	-0.114	-0.114	0.000	0.000	0.000	0.000
44	A	84	TYR	0	0.001	-0.019	30.789	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	85	TYR	0	-0.084	-0.090	33.787	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	86	GLU	-1	-0.957	-0.954	37.535	-0.110	-0.110	0.000	0.000	0.000	0.000
47	A	87	VAL	0	-0.052	-0.018	35.017	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	88	VAL	0	-0.021	0.005	31.249	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	89	SER	0	0.026	0.021	31.964	0.003	0.003	0.000	0.000	0.000	0.000
50	A	90	GLN	0	0.013	-0.008	29.008	0.021	0.021	0.000	0.000	0.000	0.000
51	A	91	PRO	0	-0.006	0.015	29.377	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	92	ILE	0	-0.007	-0.003	23.223	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	93	ASP	-1	-0.808	-0.897	26.249	-0.221	-0.221	0.000	0.000	0.000	0.000
54	A	94	LEU	0	0.068	0.024	21.631	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	95	MET	0	-0.063	-0.014	24.265	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	96	LYS	1	0.840	0.931	25.398	0.302	0.302	0.000	0.000	0.000	0.000
57	A	97	ILE	0	0.049	0.028	19.618	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	98	GLN	0	0.035	0.017	21.502	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	99	GLN	0	-0.060	-0.038	23.112	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	100	LYS	1	0.816	0.886	20.956	0.459	0.459	0.000	0.000	0.000	0.000
61	A	101	LEU	0	0.000	0.010	16.364	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	102	LYS	1	0.865	0.931	19.977	0.268	0.268	0.000	0.000	0.000	0.000
63	A	103	MET	0	-0.099	-0.031	22.618	0.030	0.030	0.000	0.000	0.000	0.000
64	A	104	GLU	-1	-0.910	-0.947	19.028	-0.419	-0.419	0.000	0.000	0.000	0.000
65	A	105	GLU	-1	-0.849	-0.934	18.836	-0.398	-0.398	0.000	0.000	0.000	0.000
66	A	106	TYR	0	-0.108	-0.114	15.380	0.009	0.009	0.000	0.000	0.000	0.000
67	A	107	ASP	-1	-0.844	-0.917	14.208	-0.774	-0.774	0.000	0.000	0.000	0.000
68	A	108	ASP	-1	-0.776	-0.886	12.572	-1.209	-1.209	0.000	0.000	0.000	0.000
69	A	109	VAL	0	0.049	0.019	8.339	0.108	0.108	0.000	0.000	0.000	0.000
70	A	110	ASN	0	-0.104	-0.056	11.695	0.093	0.093	0.000	0.000	0.000	0.000
71	A	111	LEU	0	0.006	0.014	14.195	0.110	0.110	0.000	0.000	0.000	0.000
72	A	112	LEU	0	0.016	0.022	13.355	0.077	0.077	0.000	0.000	0.000	0.000
73	A	113	THR	0	-0.055	-0.040	12.969	0.039	0.039	0.000	0.000	0.000	0.000
74	A	114	ALA	0	-0.007	0.001	15.446	0.072	0.072	0.000	0.000	0.000	0.000
75	A	115	ASP	-1	-0.755	-0.832	18.976	-0.405	-0.405	0.000	0.000	0.000	0.000
76	A	116	PHE	0	0.024	-0.004	16.194	0.067	0.067	0.000	0.000	0.000	0.000
77	A	117	GLN	0	-0.037	-0.003	19.153	0.048	0.048	0.000	0.000	0.000	0.000
78	A	118	LEU	0	0.010	0.007	20.633	0.043	0.043	0.000	0.000	0.000	0.000
79	A	119	LEU	0	-0.037	-0.013	22.094	0.034	0.034	0.000	0.000	0.000	0.000
80	A	120	PHE	0	0.037	0.002	19.001	0.035	0.035	0.000	0.000	0.000	0.000
81	A	121	ASN	0	0.001	0.004	24.185	0.024	0.024	0.000	0.000	0.000	0.000
82	A	122	ASN	0	-0.005	-0.006	26.023	0.028	0.028	0.000	0.000	0.000	0.000
83	A	123	ALA	0	-0.010	0.000	27.354	0.019	0.019	0.000	0.000	0.000	0.000
84	A	124	LYS	1	0.828	0.888	25.647	0.232	0.232	0.000	0.000	0.000	0.000
85	A	125	SER	0	-0.010	0.011	29.456	0.011	0.011	0.000	0.000	0.000	0.000
86	A	126	TYR	0	-0.032	-0.019	31.934	0.010	0.010	0.000	0.000	0.000	0.000
87	A	127	TYR	0	-0.045	-0.020	31.752	0.010	0.010	0.000	0.000	0.000	0.000
88	A	128	LYS	1	0.849	0.903	33.498	0.134	0.134	0.000	0.000	0.000	0.000
89	A	129	PRO	0	0.017	0.000	31.970	0.000	0.000	0.000	0.000	0.000	0.000
90	A	130	ASP	-1	-0.788	-0.891	32.256	-0.092	-0.092	0.000	0.000	0.000	0.000
91	A	131	SER	0	-0.035	-0.008	33.112	0.001	0.001	0.000	0.000	0.000	0.000
92	A	132	PRO	0	0.029	-0.001	31.433	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	133	GLU	-1	-0.763	-0.874	29.361	-0.143	-0.143	0.000	0.000	0.000	0.000
94	A	134	TYR	0	0.037	0.022	28.065	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	135	LYS	1	0.815	0.900	27.255	0.089	0.089	0.000	0.000	0.000	0.000
96	A	136	ALA	0	0.003	0.005	25.357	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	137	ALA	0	0.016	0.012	23.646	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	138	CYS	0	-0.075	-0.026	22.557	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	139	LYS	1	0.854	0.915	21.261	0.100	0.100	0.000	0.000	0.000	0.000
100	A	140	LEU	0	0.023	0.012	19.497	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	141	TRP	0	0.021	0.013	16.784	-0.059	-0.059	0.000	0.000	0.000	0.000
102	A	142	ASP	-1	-0.819	-0.885	16.611	-0.323	-0.323	0.000	0.000	0.000	0.000
103	A	143	LEU	0	-0.006	0.006	15.092	-0.040	-0.040	0.000	0.000	0.000	0.000
104	A	144	TYR	0	0.014	0.007	12.990	-0.063	-0.063	0.000	0.000	0.000	0.000
105	A	145	LEU	0	-0.004	-0.003	12.067	-0.151	-0.151	0.000	0.000	0.000	0.000
106	A	146	ARG	1	0.794	0.871	10.880	0.087	0.087	0.000	0.000	0.000	0.000
107	A	147	THR	0	0.014	-0.006	9.686	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	148	ARG	1	0.910	0.946	7.906	1.112	1.112	0.000	0.000	0.000	0.000
109	A	149	ASN	0	-0.028	-0.021	6.385	-0.811	-0.811	0.000	0.000	0.000	0.000
110	A	150	GLU	-1	-0.883	-0.923	5.178	-0.290	-0.252	-0.001	-0.004	-0.033	0.000
111	A	151	PHE	0	0.030	0.007	3.861	0.809	1.613	0.004	-0.334	-0.474	-0.001
112	A	152	VAL	0	-0.053	-0.014	2.030	-8.593	-8.630	6.680	-3.471	-3.172	-0.030
113	A	153	GLN	0	-0.087	-0.029	2.586	-0.084	0.330	1.354	-0.013	-1.755	-0.002
114	A	154	LYS	1	0.971	0.981	2.012	-3.284	-5.083	6.888	-2.220	-2.869	-0.034

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Interactive mode: IFIE and PIEDA for fragment #1(A:41:SER)