FMO DATABASE

FMODB ID: 82QJY

Calculation Name: 3B5K-A-Xray372

Preferred Name: Interleukin-5

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5K

Chain ID: A

ChEMBL ID: CHEMBL1163111

UniProt ID: P04401

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737985.13914
FMO2-HF: Nuclear repulsion	695606.149802
FMO2-HF: Total energy	-42378.989338
FMO2-MP2: Total energy	-42504.315478

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:7:THR)

Summations of interaction energy for fragment #1(A:7:THR)

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.
-2.141	0.182	9.877	-3.651	-8.547	0.004

Interaction energy analysis for fragmet #1(A:7:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.006

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	9	THR	0	-0.025	-0.045	3.812	-0.618	1.521	-0.028	-1.026	-1.086	-0.001
4	A	10	VAL	0	0.161	0.096	1.997	2.355	-1.296	7.062	-0.912	-2.498	0.001
5	A	11	VAL	0	-0.008	0.033	4.101	0.076	0.327	0.000	-0.039	-0.212	0.000
6	A	12	LYS	1	1.000	0.993	5.044	0.922	0.957	-0.001	-0.001	-0.032	0.000
7	A	13	GLU	-1	-0.867	-0.913	7.469	0.417	0.417	0.000	0.000	0.000	0.000
8	A	14	THR	0	-0.035	-0.071	5.452	0.207	0.207	0.000	0.000	0.000	0.000
9	A	15	LEU	0	-0.020	-0.017	8.193	0.041	0.041	0.000	0.000	0.000	0.000
10	A	16	THR	0	-0.002	0.015	10.640	0.028	0.028	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.019	-0.021	8.846	0.036	0.036	0.000	0.000	0.000	0.000
12	A	18	LEU	0	0.014	0.011	12.093	0.012	0.012	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.046	-0.017	13.935	0.007	0.007	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.031	0.008	16.265	0.007	0.007	0.000	0.000	0.000	0.000
15	A	21	HIS	0	-0.002	0.012	15.161	0.012	0.012	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.978	0.991	18.334	0.044	0.044	0.000	0.000	0.000	0.000
17	A	23	ALA	0	0.034	0.017	19.965	0.002	0.002	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.035	0.019	19.772	0.002	0.002	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.006	-0.008	15.948	0.005	0.005	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.075	-0.027	20.722	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.031	-0.020	23.277	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	28	ASN	0	0.007	0.015	24.922	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.892	-0.947	25.825	0.030	0.030	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.022	-0.022	28.312	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.071	-0.024	22.205	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.884	0.955	25.518	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	33	LEU	0	0.011	0.004	19.200	0.009	0.009	0.000	0.000	0.000	0.000
28	A	34	PRO	0	-0.011	0.008	19.316	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.011	-0.010	19.939	0.001	0.001	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.021	-0.013	17.902	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	37	THR	0	0.027	0.019	21.183	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	38	HIS	0	0.018	0.010	19.959	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.965	0.965	18.731	0.116	0.116	0.000	0.000	0.000	0.000
34	A	40	ASN	0	0.058	0.048	17.914	-0.041	-0.041	0.000	0.000	0.000	0.000
35	A	41	HIS	0	0.006	-0.024	13.427	0.042	0.042	0.000	0.000	0.000	0.000
36	A	42	GLN	0	0.068	0.020	11.042	0.073	0.073	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.027	-0.001	14.252	0.032	0.032	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.022	0.003	16.316	0.015	0.015	0.000	0.000	0.000	0.000
39	A	45	ILE	0	0.014	0.007	10.194	0.019	0.019	0.000	0.000	0.000	0.000
40	A	46	GLY	0	0.014	0.013	13.693	0.039	0.039	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.848	-0.944	16.028	0.082	0.082	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.054	-0.006	12.061	0.005	0.005	0.000	0.000	0.000	0.000
43	A	49	PHE	0	-0.023	-0.045	7.581	0.045	0.045	0.000	0.000	0.000	0.000
44	A	50	GLN	0	0.031	0.025	13.364	0.040	0.040	0.000	0.000	0.000	0.000
45	A	51	GLY	0	0.036	0.021	17.001	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.050	-0.028	11.030	0.008	0.008	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.949	-0.987	15.184	0.314	0.314	0.000	0.000	0.000	0.000
48	A	54	ILE	0	0.028	0.029	16.721	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	55	LEU	0	-0.038	-0.016	16.813	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.955	0.957	12.829	-0.466	-0.466	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.073	-0.027	18.142	0.012	0.012	0.000	0.000	0.000	0.000
52	A	58	GLN	0	0.039	0.016	21.365	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.033	0.006	18.727	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.014	0.000	21.636	0.015	0.015	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.853	0.927	17.272	-0.285	-0.285	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.001	-0.002	19.127	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.020	0.013	19.966	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	64	THR	0	0.031	0.000	16.837	0.019	0.019	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.006	-0.007	15.179	0.018	0.018	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.814	-0.905	13.971	0.384	0.384	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.940	0.983	11.186	-0.101	-0.101	0.000	0.000	0.000	0.000
62	A	68	LEU	0	-0.008	-0.017	9.828	0.099	0.099	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.007	-0.004	9.424	0.095	0.095	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.061	0.029	7.889	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.010	-0.002	5.536	0.744	0.744	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.018	0.000	4.795	0.278	0.381	-0.001	-0.002	-0.099	0.000
67	A	73	SER	0	-0.005	-0.002	6.503	0.034	0.034	0.000	0.000	0.000	0.000
68	A	74	LEU	0	0.003	-0.011	2.694	-2.098	-0.586	0.800	-0.692	-1.621	0.005
69	A	75	ILE	0	-0.010	-0.003	2.342	0.176	0.553	1.925	-0.601	-1.701	-0.001
70	A	76	LYS	1	0.836	0.941	3.349	-0.590	-0.741	0.020	0.240	-0.109	0.000
71	A	77	LYS	1	0.987	0.978	6.303	-1.452	-1.452	0.000	0.000	0.000	0.000
72	A	78	TYR	0	-0.035	0.004	3.257	-2.614	-0.925	0.101	-0.616	-1.173	0.000
73	A	79	ILE	0	0.008	-0.010	5.172	-0.514	-0.495	-0.001	-0.002	-0.016	0.000
74	A	80	ASP	-1	-0.855	-0.923	8.015	0.467	0.467	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.825	0.901	7.494	-0.347	-0.347	0.000	0.000	0.000	0.000
76	A	82	GLN	0	-0.033	-0.030	7.521	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.955	0.976	10.193	-0.139	-0.139	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.909	-0.965	12.799	0.273	0.273	0.000	0.000	0.000	0.000
79	A	85	LYS	1	0.924	0.956	9.427	-0.079	-0.079	0.000	0.000	0.000	0.000
80	A	86	CYS	0	-0.071	-0.010	14.449	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	87	GLY	0	-0.010	-0.005	17.053	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.853	-0.892	15.456	0.127	0.127	0.000	0.000	0.000	0.000
83	A	89	GLU	-1	-0.938	-0.960	17.987	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.944	0.971	20.925	-0.048	-0.048	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.968	0.975	22.202	0.026	0.026	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.946	0.972	26.388	0.018	0.018	0.000	0.000	0.000	0.000
87	A	93	THR	0	0.088	0.019	28.840	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.965	0.997	30.246	0.036	0.036	0.000	0.000	0.000	0.000
89	A	95	GLN	0	0.022	-0.005	25.543	0.002	0.002	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.003	0.020	25.451	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.009	-0.004	26.386	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.881	-0.937	26.213	-0.056	-0.056	0.000	0.000	0.000	0.000
93	A	99	TYR	0	0.022	0.011	17.525	0.000	0.000	0.000	0.000	0.000	0.000
94	A	100	LEU	0	-0.022	-0.003	23.665	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.031	-0.031	26.046	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.951	-0.982	21.035	-0.114	-0.114	0.000	0.000	0.000	0.000
97	A	103	PHE	0	-0.004	0.013	21.912	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.030	-0.039	23.275	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	105	GLY	0	-0.034	-0.008	26.119	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	VAL	0	0.004	0.008	20.706	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	107	LEU	0	-0.013	0.001	23.596	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	108	SER	0	-0.049	-0.025	25.088	0.002	0.002	0.000	0.000	0.000	0.000
103	A	109	THR	0	-0.010	-0.011	23.627	0.002	0.002	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.946	-0.953	19.848	-0.155	-0.155	0.000	0.000	0.000	0.000
105	A	111	TRP	0	-0.104	-0.044	23.674	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:THR)