FMO DATABASE

FMODB ID: 6NQVZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1006586.797015
FMO2-HF: Nuclear repulsion	958039.6306
FMO2-HF: Total energy	-48547.166415
FMO2-MP2: Total energy	-48686.965871

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.
-29.815	-29.316	28.821	-14.576	-14.744	-0.049

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 : 0.016 / 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	-0.072	-0.031	2.134	-10.721	-5.444	3.370	-4.523	-4.124	0.041
4	A	44	VAL	0	-0.015	-0.005	2.276	-7.817	-5.360	1.883	-1.848	-2.492	-0.016
5	A	45	ASP	-1	-0.826	-0.914	4.408	-0.405	-0.283	0.000	-0.027	-0.094	0.000
6	A	46	PRO	0	-0.008	-0.019	7.811	-0.014	-0.014	0.000	0.000	0.000	0.000
7	A	47	ILE	0	0.097	0.067	9.791	0.065	0.065	0.000	0.000	0.000	0.000
8	A	48	ALA	0	-0.007	0.004	8.840	0.109	0.109	0.000	0.000	0.000	0.000
9	A	49	VAL	0	0.008	0.000	6.030	0.101	0.101	0.000	0.000	0.000	0.000
10	A	50	CYS	0	-0.026	-0.013	9.109	0.174	0.174	0.000	0.000	0.000	0.000
11	A	51	HIS	0	-0.013	-0.013	12.407	0.186	0.186	0.000	0.000	0.000	0.000
12	A	52	GLU	-1	-0.909	-0.940	10.086	-0.326	-0.326	0.000	0.000	0.000	0.000
13	A	53	LEU	0	-0.033	-0.008	9.492	0.114	0.114	0.000	0.000	0.000	0.000
14	A	54	TYR	0	-0.015	-0.010	12.834	0.111	0.111	0.000	0.000	0.000	0.000
15	A	55	ASN	0	0.009	-0.012	15.597	0.065	0.065	0.000	0.000	0.000	0.000
16	A	56	THR	0	-0.013	-0.006	13.562	0.068	0.068	0.000	0.000	0.000	0.000
17	A	57	ILE	0	-0.050	-0.025	15.994	0.050	0.050	0.000	0.000	0.000	0.000
18	A	58	ARG	1	0.761	0.849	18.562	0.268	0.268	0.000	0.000	0.000	0.000
19	A	59	ASP	-1	-0.766	-0.866	19.435	-0.166	-0.166	0.000	0.000	0.000	0.000
20	A	60	TYR	0	-0.033	0.000	18.790	0.029	0.029	0.000	0.000	0.000	0.000
21	A	61	LYS	1	0.942	0.965	20.989	0.078	0.078	0.000	0.000	0.000	0.000
22	A	62	ASP	-1	-0.776	-0.876	23.311	-0.091	-0.091	0.000	0.000	0.000	0.000
23	A	63	GLU	-1	-0.922	-0.981	25.100	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	64	GLN	0	-0.093	-0.038	27.157	0.010	0.010	0.000	0.000	0.000	0.000
25	A	65	GLY	0	-0.011	0.003	28.065	0.003	0.003	0.000	0.000	0.000	0.000
26	A	66	ARG	1	0.837	0.900	28.517	0.084	0.084	0.000	0.000	0.000	0.000
27	A	67	LEU	0	0.043	0.024	24.279	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	68	LEU	0	-0.016	-0.014	23.335	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	69	CYS	0	-0.010	0.001	22.945	0.001	0.001	0.000	0.000	0.000	0.000
30	A	70	GLU	-1	-0.901	-0.953	24.884	-0.122	-0.122	0.000	0.000	0.000	0.000
31	A	71	LEU	0	-0.071	-0.029	28.294	0.004	0.004	0.000	0.000	0.000	0.000
32	A	72	PHE	0	-0.029	-0.021	25.336	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	73	ILE	0	0.033	0.021	26.885	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	74	ARG	1	0.911	0.944	28.288	0.135	0.135	0.000	0.000	0.000	0.000
35	A	75	ALA	0	0.018	0.028	30.348	0.005	0.005	0.000	0.000	0.000	0.000
36	A	76	PRO	0	0.024	0.017	31.889	0.009	0.009	0.000	0.000	0.000	0.000
37	A	77	LYS	1	0.942	0.984	35.445	0.105	0.105	0.000	0.000	0.000	0.000
38	A	78	ARG	1	0.975	0.980	34.671	0.154	0.154	0.000	0.000	0.000	0.000
39	A	79	ARG	1	0.910	0.953	39.003	0.111	0.111	0.000	0.000	0.000	0.000
40	A	80	ASN	0	-0.024	-0.012	40.837	0.006	0.006	0.000	0.000	0.000	0.000
41	A	81	GLN	0	0.020	0.008	38.350	0.004	0.004	0.000	0.000	0.000	0.000
42	A	82	PRO	0	0.064	0.024	39.851	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	83	ASP	-1	-0.796	-0.882	41.172	-0.095	-0.095	0.000	0.000	0.000	0.000
44	A	84	TYR	0	-0.061	-0.046	30.919	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	85	TYR	0	-0.117	-0.108	34.155	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	86	GLU	-1	-0.937	-0.940	37.829	-0.099	-0.099	0.000	0.000	0.000	0.000
47	A	87	VAL	0	-0.047	-0.020	34.899	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	88	VAL	0	-0.035	0.003	31.358	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	89	SER	0	0.022	0.001	32.715	0.003	0.003	0.000	0.000	0.000	0.000
50	A	90	GLN	0	-0.013	-0.011	28.630	0.014	0.014	0.000	0.000	0.000	0.000
51	A	91	PRO	0	-0.019	0.007	29.189	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	92	ILE	0	0.001	-0.001	23.478	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	93	ASP	-1	-0.777	-0.898	26.437	-0.195	-0.195	0.000	0.000	0.000	0.000
54	A	94	LEU	0	0.053	0.013	21.745	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	95	MET	0	-0.071	-0.019	24.485	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	96	LYS	1	0.847	0.929	25.535	0.255	0.255	0.000	0.000	0.000	0.000
57	A	97	ILE	0	0.063	0.027	19.830	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	98	GLN	0	0.007	0.006	21.603	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	99	GLN	0	-0.012	-0.003	22.936	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	100	LYS	1	0.835	0.906	21.575	0.384	0.384	0.000	0.000	0.000	0.000
61	A	101	LEU	0	0.007	0.013	16.496	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	102	LYS	1	0.905	0.943	20.040	0.218	0.218	0.000	0.000	0.000	0.000
63	A	103	MET	0	-0.112	-0.036	22.572	0.018	0.018	0.000	0.000	0.000	0.000
64	A	104	GLU	-1	-0.931	-0.963	19.172	-0.331	-0.331	0.000	0.000	0.000	0.000
65	A	105	GLU	-1	-0.912	-0.963	19.283	-0.342	-0.342	0.000	0.000	0.000	0.000
66	A	106	TYR	0	-0.126	-0.099	15.407	0.001	0.001	0.000	0.000	0.000	0.000
67	A	107	ASP	-1	-0.877	-0.944	14.171	-0.661	-0.661	0.000	0.000	0.000	0.000
68	A	108	ASP	-1	-0.794	-0.898	12.816	-0.963	-0.963	0.000	0.000	0.000	0.000
69	A	109	VAL	0	0.024	-0.007	8.197	0.079	0.079	0.000	0.000	0.000	0.000
70	A	110	ASN	0	-0.082	-0.052	11.624	0.086	0.086	0.000	0.000	0.000	0.000
71	A	111	LEU	0	0.031	0.027	14.202	0.098	0.098	0.000	0.000	0.000	0.000
72	A	112	LEU	0	0.015	0.025	13.411	0.071	0.071	0.000	0.000	0.000	0.000
73	A	113	THR	0	-0.046	-0.024	13.043	0.046	0.046	0.000	0.000	0.000	0.000
74	A	114	ALA	0	-0.001	0.009	15.598	0.067	0.067	0.000	0.000	0.000	0.000
75	A	115	ASP	-1	-0.734	-0.832	18.958	-0.344	-0.344	0.000	0.000	0.000	0.000
76	A	116	PHE	0	0.013	-0.008	16.425	0.060	0.060	0.000	0.000	0.000	0.000
77	A	117	GLN	0	-0.025	-0.007	19.236	0.044	0.044	0.000	0.000	0.000	0.000
78	A	118	LEU	0	-0.008	0.006	20.682	0.040	0.040	0.000	0.000	0.000	0.000
79	A	119	LEU	0	-0.032	-0.003	22.248	0.031	0.031	0.000	0.000	0.000	0.000
80	A	120	PHE	0	0.019	-0.010	19.184	0.031	0.031	0.000	0.000	0.000	0.000
81	A	121	ASN	0	-0.010	-0.010	24.219	0.023	0.023	0.000	0.000	0.000	0.000
82	A	122	ASN	0	-0.017	-0.009	26.015	0.023	0.023	0.000	0.000	0.000	0.000
83	A	123	ALA	0	-0.027	-0.004	27.491	0.017	0.017	0.000	0.000	0.000	0.000
84	A	124	LYS	1	0.897	0.934	24.601	0.239	0.239	0.000	0.000	0.000	0.000
85	A	125	SER	0	-0.014	0.003	29.519	0.009	0.009	0.000	0.000	0.000	0.000
86	A	126	TYR	0	-0.018	0.009	31.953	0.010	0.010	0.000	0.000	0.000	0.000
87	A	127	TYR	0	-0.023	-0.003	31.847	0.013	0.013	0.000	0.000	0.000	0.000
88	A	128	LYS	1	1.007	0.990	33.012	0.104	0.104	0.000	0.000	0.000	0.000
89	A	129	PRO	0	0.038	-0.001	31.992	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	130	ASP	-1	-0.887	-0.941	32.485	-0.089	-0.089	0.000	0.000	0.000	0.000
91	A	131	SER	0	-0.087	-0.042	33.110	0.002	0.002	0.000	0.000	0.000	0.000
92	A	132	PRO	0	0.040	0.001	31.749	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	133	GLU	-1	-0.823	-0.917	29.733	-0.135	-0.135	0.000	0.000	0.000	0.000
94	A	134	TYR	0	0.009	0.018	28.286	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	135	LYS	1	0.936	0.968	27.385	0.083	0.083	0.000	0.000	0.000	0.000
96	A	136	ALA	0	0.002	0.007	25.732	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	137	ALA	0	0.028	0.012	23.912	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	138	CYS	0	-0.097	-0.045	22.581	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	139	LYS	1	0.949	0.988	21.502	0.106	0.106	0.000	0.000	0.000	0.000
100	A	140	LEU	0	0.026	0.008	19.740	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	141	TRP	0	0.013	0.015	17.183	-0.054	-0.054	0.000	0.000	0.000	0.000
102	A	142	ASP	-1	-0.841	-0.915	16.757	-0.334	-0.334	0.000	0.000	0.000	0.000
103	A	143	LEU	0	-0.032	-0.010	15.393	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	144	TYR	0	0.018	-0.014	13.052	-0.057	-0.057	0.000	0.000	0.000	0.000
105	A	145	LEU	0	-0.014	-0.002	12.161	-0.143	-0.143	0.000	0.000	0.000	0.000
106	A	146	ARG	1	0.832	0.903	10.960	0.063	0.063	0.000	0.000	0.000	0.000
107	A	147	THR	0	0.003	0.003	9.928	0.026	0.026	0.000	0.000	0.000	0.000
108	A	148	ARG	1	0.918	0.947	8.058	1.140	1.140	0.000	0.000	0.000	0.000
109	A	149	ASN	0	-0.025	-0.021	6.355	-0.836	-0.836	0.000	0.000	0.000	0.000
110	A	150	GLU	-1	-0.879	-0.923	5.301	0.023	0.023	0.000	0.000	0.000	0.000
111	A	151	PHE	0	0.022	0.001	3.937	1.032	1.721	0.006	-0.277	-0.418	-0.001
112	A	152	VAL	0	-0.043	-0.020	1.944	-7.093	-9.270	8.567	-3.461	-2.929	-0.031
113	A	153	GLN	0	-0.090	-0.009	2.622	-1.409	-0.139	0.691	-0.528	-1.433	-0.001
114	A	154	LYS	1	0.990	0.994	1.795	-3.158	-10.297	14.304	-3.912	-3.254	-0.041

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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