FMO DATABASE

FMODB ID: J3VM9

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-738612.455754
FMO2-HF: Nuclear repulsion	696231.424541
FMO2-HF: Total energy	-42381.031214
FMO2-MP2: Total energy	-42506.098131

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.
-5.398	1.145	3.567	-2.833	-7.276	-0.006

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 : 0.056 / 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

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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	0.037	-0.002	3.889	-2.408	-0.735	-0.003	-0.793	-0.876	-0.001
4	A	10	VAL	0	0.097	0.068	2.465	-1.220	-0.249	1.478	-0.526	-1.924	0.001
5	A	11	VAL	0	0.047	0.045	3.516	-0.127	0.267	0.008	-0.100	-0.302	0.000
6	A	12	LYS	1	0.950	0.968	4.792	0.474	0.540	-0.001	-0.006	-0.059	0.000
7	A	13	GLU	-1	-0.764	-0.836	7.411	-0.070	-0.070	0.000	0.000	0.000	0.000
8	A	14	THR	0	-0.036	-0.042	5.335	0.032	0.032	0.000	0.000	0.000	0.000
9	A	15	LEU	0	-0.004	-0.002	7.916	0.158	0.158	0.000	0.000	0.000	0.000
10	A	16	THR	0	-0.008	-0.013	10.490	0.143	0.143	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.002	-0.016	9.421	0.157	0.157	0.000	0.000	0.000	0.000
12	A	18	LEU	0	-0.002	0.007	11.763	0.048	0.048	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.045	-0.024	13.493	0.063	0.063	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.008	0.002	15.817	0.037	0.037	0.000	0.000	0.000	0.000
15	A	21	HIS	0	0.024	0.028	14.779	0.082	0.082	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.960	0.989	17.722	0.434	0.434	0.000	0.000	0.000	0.000
17	A	23	ALA	0	0.030	0.007	19.252	0.003	0.003	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.019	0.020	20.424	0.013	0.013	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.021	-0.013	15.701	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.044	-0.021	20.360	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.029	-0.017	23.096	0.021	0.021	0.000	0.000	0.000	0.000
22	A	28	ASN	0	0.028	0.038	25.028	0.034	0.034	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.873	-0.938	26.421	-0.215	-0.215	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.065	-0.047	28.625	0.001	0.001	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.018	0.007	21.807	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.811	0.889	25.341	0.254	0.254	0.000	0.000	0.000	0.000
27	A	33	LEU	0	0.010	0.005	19.114	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	34	PRO	0	0.001	0.007	19.634	0.022	0.022	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.007	-0.008	20.060	-0.050	-0.050	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.015	-0.004	18.150	0.035	0.035	0.000	0.000	0.000	0.000
31	A	37	THR	0	-0.001	0.004	21.457	0.000	0.000	0.000	0.000	0.000	0.000
32	A	38	HIS	0	0.013	-0.001	19.986	0.032	0.032	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.985	0.979	19.274	0.388	0.388	0.000	0.000	0.000	0.000
34	A	40	ASN	0	-0.004	0.022	17.752	-0.094	-0.094	0.000	0.000	0.000	0.000
35	A	41	HIS	0	0.009	-0.024	13.891	0.036	0.036	0.000	0.000	0.000	0.000
36	A	42	GLN	0	0.012	-0.002	11.234	-0.221	-0.221	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.017	0.006	14.630	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.021	0.000	16.717	0.046	0.046	0.000	0.000	0.000	0.000
39	A	45	ILE	0	-0.016	-0.009	10.962	-0.061	-0.061	0.000	0.000	0.000	0.000
40	A	46	GLY	0	0.019	0.017	13.898	-0.064	-0.064	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.778	-0.903	16.346	-0.574	-0.574	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.017	-0.001	12.544	0.007	0.007	0.000	0.000	0.000	0.000
43	A	49	PHE	0	-0.022	-0.028	7.803	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	50	GLN	0	-0.006	0.001	13.512	0.020	0.020	0.000	0.000	0.000	0.000
45	A	51	GLY	0	0.025	0.016	17.077	0.056	0.056	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.023	-0.017	11.063	0.023	0.023	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.813	-0.897	15.190	-0.612	-0.612	0.000	0.000	0.000	0.000
48	A	54	ILE	0	0.006	0.007	16.808	0.052	0.052	0.000	0.000	0.000	0.000
49	A	55	LEU	0	0.001	0.015	16.182	0.029	0.029	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.824	0.897	13.195	0.724	0.724	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.073	-0.036	17.544	0.041	0.041	0.000	0.000	0.000	0.000
52	A	58	GLN	0	0.038	0.031	20.801	0.025	0.025	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.048	-0.022	19.047	0.019	0.019	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.021	0.007	21.471	0.003	0.003	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.807	0.885	16.793	0.368	0.368	0.000	0.000	0.000	0.000
56	A	62	GLY	0	-0.008	-0.011	19.331	0.026	0.026	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.030	0.025	20.069	0.026	0.026	0.000	0.000	0.000	0.000
58	A	64	THR	0	-0.013	-0.051	16.741	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.018	0.015	14.974	-0.031	-0.031	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.765	-0.863	13.883	-0.462	-0.462	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.874	0.927	10.686	0.072	0.072	0.000	0.000	0.000	0.000
62	A	68	LEU	0	-0.030	-0.004	9.514	-0.127	-0.127	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.031	-0.010	9.420	-0.260	-0.260	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.004	-0.002	7.740	-0.116	-0.116	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.026	-0.016	5.218	-0.071	-0.071	0.000	0.000	0.000	0.000
66	A	72	LEU	0	0.014	0.008	4.565	-1.188	-1.064	-0.001	-0.006	-0.117	0.000
67	A	73	SER	0	0.004	0.012	6.574	-0.375	-0.375	0.000	0.000	0.000	0.000
68	A	74	LEU	0	0.040	0.011	2.837	-0.707	0.010	0.240	-0.207	-0.751	0.000
69	A	75	ILE	0	-0.025	-0.016	2.544	-4.418	-3.127	1.550	-0.932	-1.908	-0.005
70	A	76	LYS	1	0.802	0.896	3.285	1.980	1.802	0.030	0.277	-0.129	0.000
71	A	77	LYS	1	0.922	0.955	5.796	1.807	1.807	0.000	0.000	0.000	0.000
72	A	78	TYR	0	-0.024	0.000	2.445	-0.851	0.587	0.267	-0.526	-1.179	-0.001
73	A	79	ILE	0	0.012	-0.004	4.564	0.979	1.026	-0.001	-0.014	-0.031	0.000
74	A	80	ASP	-1	-0.800	-0.879	7.699	-0.811	-0.811	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.805	0.860	7.749	0.413	0.413	0.000	0.000	0.000	0.000
76	A	82	GLN	0	-0.001	-0.005	7.830	0.494	0.494	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.968	0.981	10.253	0.696	0.696	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.846	-0.909	12.729	-0.240	-0.240	0.000	0.000	0.000	0.000
79	A	85	LYS	1	0.910	0.933	10.258	0.223	0.223	0.000	0.000	0.000	0.000
80	A	86	CYS	0	-0.081	-0.018	14.526	0.027	0.027	0.000	0.000	0.000	0.000
81	A	87	GLY	0	0.012	0.008	16.998	0.028	0.028	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.877	-0.888	16.155	-0.049	-0.049	0.000	0.000	0.000	0.000
83	A	89	GLU	-1	-0.797	-0.863	18.504	0.052	0.052	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.857	0.920	20.999	0.100	0.100	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.828	0.885	20.466	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.977	0.988	26.616	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	93	THR	0	0.064	0.013	29.011	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.865	0.936	27.935	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	95	GLN	0	0.059	0.015	25.297	0.002	0.002	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.026	0.005	25.424	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.010	-0.008	26.704	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.783	-0.885	26.092	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	99	TYR	0	-0.002	0.009	18.038	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	100	LEU	0	-0.008	-0.005	23.900	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.021	-0.009	26.224	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.909	-0.957	21.269	-0.114	-0.114	0.000	0.000	0.000	0.000
97	A	103	PHE	0	-0.021	-0.005	21.247	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.014	-0.021	23.356	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	105	GLY	0	0.011	0.012	26.413	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	VAL	0	0.011	0.017	20.347	0.003	0.003	0.000	0.000	0.000	0.000
101	A	107	LEU	0	-0.037	-0.015	23.636	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	108	SER	0	-0.083	-0.045	24.998	0.001	0.001	0.000	0.000	0.000	0.000
103	A	109	THR	0	-0.029	-0.025	23.885	0.014	0.014	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.939	-0.953	19.152	-0.400	-0.400	0.000	0.000	0.000	0.000
105	A	111	TRP	0	-0.047	-0.022	23.201	-0.017	-0.017	0.000	0.000	0.000	0.000

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