FMO DATABASE

FMODB ID: N1L3Q

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	OptHSide
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	-738061.938557
FMO2-HF: Nuclear repulsion	695681.518115
FMO2-HF: Total energy	-42380.420442
FMO2-MP2: Total energy	-42505.588549

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.
-7.555	0.046999999999999	3.162	-3.4	-7.361	-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 : 0.009 / q_NPA : -0.009

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	0.010	-0.042	3.812	-2.530	-0.538	-0.032	-0.958	-1.002	-0.001
4	A	10	VAL	0	0.113	0.072	2.729	-0.976	0.024	0.725	-0.328	-1.397	0.001
5	A	11	VAL	0	0.011	0.036	4.080	-0.629	-0.400	0.000	-0.025	-0.203	0.000
6	A	12	LYS	1	1.013	0.998	5.104	0.143	0.175	-0.001	-0.001	-0.030	0.000
7	A	13	GLU	-1	-0.789	-0.842	7.436	0.663	0.663	0.000	0.000	0.000	0.000
8	A	14	THR	0	-0.017	-0.048	5.624	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	15	LEU	0	-0.024	-0.016	8.277	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	16	THR	0	-0.013	-0.002	10.674	0.042	0.042	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.010	-0.025	8.817	0.101	0.101	0.000	0.000	0.000	0.000
12	A	18	LEU	0	0.032	0.022	12.217	0.011	0.011	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.043	-0.015	13.962	0.025	0.025	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.023	0.004	16.347	0.010	0.010	0.000	0.000	0.000	0.000
15	A	21	HIS	0	-0.007	0.013	15.253	0.051	0.051	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.976	0.991	18.268	0.277	0.277	0.000	0.000	0.000	0.000
17	A	23	ALA	0	0.036	0.015	19.975	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.038	0.018	20.050	0.000	0.000	0.000	0.000	0.000	0.000
19	A	25	LEU	0	0.004	0.006	15.960	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.089	-0.029	20.669	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.025	-0.021	23.273	0.011	0.011	0.000	0.000	0.000	0.000
22	A	28	ASN	0	0.025	0.032	24.873	0.022	0.022	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.876	-0.929	25.814	-0.152	-0.152	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.074	-0.057	28.503	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.028	0.000	21.896	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.839	0.912	25.558	0.198	0.198	0.000	0.000	0.000	0.000
27	A	33	LEU	0	0.011	0.004	19.067	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	34	PRO	0	-0.003	0.003	19.488	0.015	0.015	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.009	-0.009	20.061	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.022	-0.007	18.108	0.031	0.031	0.000	0.000	0.000	0.000
31	A	37	THR	0	0.012	0.013	21.397	0.009	0.009	0.000	0.000	0.000	0.000
32	A	38	HIS	0	0.036	0.017	20.144	0.019	0.019	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.964	0.966	18.826	0.378	0.378	0.000	0.000	0.000	0.000
34	A	40	ASN	0	0.050	0.047	18.106	-0.100	-0.100	0.000	0.000	0.000	0.000
35	A	41	HIS	0	0.018	-0.022	13.758	0.048	0.048	0.000	0.000	0.000	0.000
36	A	42	GLN	0	0.021	0.000	11.179	-0.194	-0.194	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.008	0.007	14.536	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.010	0.007	16.554	0.063	0.063	0.000	0.000	0.000	0.000
39	A	45	ILE	0	0.006	0.006	10.585	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	46	GLY	0	0.012	0.011	13.860	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.818	-0.929	16.122	-0.549	-0.549	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.054	-0.007	12.333	0.023	0.023	0.000	0.000	0.000	0.000
43	A	49	PHE	0	-0.013	-0.040	7.645	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	50	GLN	0	0.005	0.011	13.389	0.019	0.019	0.000	0.000	0.000	0.000
45	A	51	GLY	0	0.040	0.028	16.993	0.061	0.061	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.037	-0.019	10.909	0.035	0.035	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.861	-0.924	15.160	-0.414	-0.414	0.000	0.000	0.000	0.000
48	A	54	ILE	0	0.034	0.020	16.630	0.051	0.051	0.000	0.000	0.000	0.000
49	A	55	LEU	0	-0.016	-0.001	16.373	0.034	0.034	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.854	0.900	13.338	0.548	0.548	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.094	-0.038	17.998	0.051	0.051	0.000	0.000	0.000	0.000
52	A	58	GLN	0	0.042	0.021	21.202	0.013	0.013	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.030	-0.001	19.073	0.017	0.017	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.001	-0.010	21.603	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.830	0.907	16.826	0.184	0.184	0.000	0.000	0.000	0.000
56	A	62	GLY	0	-0.003	-0.013	19.240	0.014	0.014	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.010	0.007	20.001	0.024	0.024	0.000	0.000	0.000	0.000
58	A	64	THR	0	0.016	-0.014	16.792	0.020	0.020	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.009	-0.009	15.122	0.011	0.011	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.769	-0.856	14.021	-0.167	-0.167	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.885	0.935	11.041	-0.332	-0.332	0.000	0.000	0.000	0.000
62	A	68	LEU	0	-0.018	-0.010	9.820	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.018	-0.006	9.497	-0.161	-0.161	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.006	-0.006	8.179	-0.214	-0.214	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.014	-0.001	5.641	0.106	0.106	0.000	0.000	0.000	0.000
66	A	72	LEU	0	0.007	0.012	4.796	-0.768	-0.660	-0.001	-0.002	-0.104	0.000
67	A	73	SER	0	-0.001	0.003	6.378	-0.604	-0.604	0.000	0.000	0.000	0.000
68	A	74	LEU	0	0.041	0.009	2.996	-1.509	-0.161	0.209	-0.515	-1.042	0.003
69	A	75	ILE	0	-0.026	-0.015	2.475	-4.568	-3.619	1.887	-0.953	-1.883	-0.003
70	A	76	LYS	1	0.786	0.896	3.311	1.472	1.310	0.025	0.266	-0.128	0.000
71	A	77	LYS	1	0.957	0.960	5.542	1.293	1.293	0.000	0.000	0.000	0.000
72	A	78	TYR	0	-0.034	-0.001	2.390	-1.674	0.378	0.351	-0.865	-1.538	-0.004
73	A	79	ILE	0	0.017	-0.006	4.482	1.008	1.062	-0.001	-0.019	-0.034	0.000
74	A	80	ASP	-1	-0.822	-0.886	7.782	-0.876	-0.876	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.807	0.858	7.501	0.825	0.825	0.000	0.000	0.000	0.000
76	A	82	GLN	0	-0.012	-0.018	7.516	0.475	0.475	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.964	0.987	10.203	0.941	0.941	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.856	-0.918	12.690	-0.463	-0.463	0.000	0.000	0.000	0.000
79	A	85	LYS	1	0.874	0.925	9.505	1.022	1.022	0.000	0.000	0.000	0.000
80	A	86	CYS	0	-0.059	-0.002	14.611	0.028	0.028	0.000	0.000	0.000	0.000
81	A	87	GLY	0	-0.001	-0.003	17.068	0.057	0.057	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.853	-0.881	15.996	-0.324	-0.324	0.000	0.000	0.000	0.000
83	A	89	GLU	-1	-0.812	-0.882	18.115	-0.157	-0.157	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.898	0.956	21.103	0.213	0.213	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.845	0.895	20.712	0.188	0.188	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.961	0.977	26.227	0.087	0.087	0.000	0.000	0.000	0.000
87	A	93	THR	0	0.070	0.011	28.626	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.883	0.950	27.635	0.108	0.108	0.000	0.000	0.000	0.000
89	A	95	GLN	0	0.039	0.010	25.137	0.002	0.002	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.034	0.006	25.319	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.029	0.000	26.419	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.789	-0.893	26.101	-0.158	-0.158	0.000	0.000	0.000	0.000
93	A	99	TYR	0	0.019	0.015	17.803	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	100	LEU	0	-0.021	-0.004	23.702	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.034	-0.034	26.080	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.916	-0.965	21.205	-0.305	-0.305	0.000	0.000	0.000	0.000
97	A	103	PHE	0	-0.021	0.006	21.497	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.023	-0.033	23.312	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	105	GLY	0	-0.026	-0.004	26.141	0.010	0.010	0.000	0.000	0.000	0.000
100	A	106	VAL	0	-0.005	0.000	20.666	0.011	0.011	0.000	0.000	0.000	0.000
101	A	107	LEU	0	-0.014	0.002	23.634	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	108	SER	0	-0.062	-0.031	25.122	0.000	0.000	0.000	0.000	0.000	0.000
103	A	109	THR	0	0.005	0.002	23.788	0.023	0.023	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.979	-0.977	19.626	-0.492	-0.492	0.000	0.000	0.000	0.000
105	A	111	TRP	0	-0.068	-0.028	23.731	-0.012	-0.012	0.000	0.000	0.000	0.000

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