FMO DATABASE

FMODB ID: 59K2Z

Calculation Name: 3B5K-A-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-743651.95978
FMO2-HF: Nuclear repulsion	701102.050126
FMO2-HF: Total energy	-42549.909654
FMO2-MP2: Total energy	-42675.774386

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:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

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.
2.279	3.105	-0.005	-0.294	-0.527	0

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.028

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].
3	A	8	SER	0	0.047	0.027	3.845	1.121	1.869	-0.005	-0.283	-0.460
4	A	9	THR	0	-0.029	-0.047	6.022	0.274	0.274	0.000	0.000	0.000
5	A	10	VAL	0	0.166	0.099	6.958	0.115	0.115	0.000	0.000	0.000
6	A	11	VAL	0	-0.010	0.034	8.997	0.123	0.123	0.000	0.000	0.000
7	A	12	LYS	1	1.002	0.993	10.903	0.311	0.311	0.000	0.000	0.000
8	A	13	GLU	-1	-0.867	-0.914	12.011	-0.491	-0.491	0.000	0.000	0.000
9	A	14	THR	0	-0.036	-0.072	11.373	0.057	0.057	0.000	0.000	0.000
10	A	15	LEU	0	-0.017	-0.015	14.136	0.055	0.055	0.000	0.000	0.000
11	A	16	THR	0	-0.005	0.014	16.674	0.054	0.054	0.000	0.000	0.000
12	A	17	GLN	0	-0.015	-0.019	14.258	0.031	0.031	0.000	0.000	0.000
13	A	18	LEU	0	0.012	0.011	18.300	0.024	0.024	0.000	0.000	0.000
14	A	19	SER	0	-0.050	-0.018	20.098	0.030	0.030	0.000	0.000	0.000
15	A	20	ALA	0	0.034	0.010	22.105	0.016	0.016	0.000	0.000	0.000
16	A	21	HIS	0	0.000	0.012	20.821	0.021	0.021	0.000	0.000	0.000
17	A	22	ARG	1	0.977	0.990	24.293	0.146	0.146	0.000	0.000	0.000
18	A	23	ALA	0	0.034	0.017	26.144	0.006	0.006	0.000	0.000	0.000
19	A	24	LEU	0	0.035	0.018	25.527	0.004	0.004	0.000	0.000	0.000
20	A	25	LEU	0	-0.007	-0.008	22.149	0.003	0.003	0.000	0.000	0.000
21	A	26	THR	0	-0.075	-0.026	26.886	0.003	0.003	0.000	0.000	0.000
22	A	27	SER	0	-0.034	-0.021	29.617	0.009	0.009	0.000	0.000	0.000
23	A	28	ASN	0	0.007	0.015	31.180	0.010	0.010	0.000	0.000	0.000
24	A	29	GLU	-1	-0.890	-0.947	32.270	-0.077	-0.077	0.000	0.000	0.000
25	A	30	THR	0	-0.023	-0.022	34.659	0.003	0.003	0.000	0.000	0.000
26	A	31	LEU	0	-0.071	-0.024	28.536	0.003	0.003	0.000	0.000	0.000
27	A	32	ARG	1	0.884	0.955	31.972	0.070	0.070	0.000	0.000	0.000
28	A	33	LEU	0	0.012	0.004	25.665	-0.002	-0.002	0.000	0.000	0.000
29	A	34	PRO	0	-0.012	0.007	25.264	0.005	0.005	0.000	0.000	0.000
30	A	35	VAL	0	0.012	-0.009	26.069	-0.011	-0.011	0.000	0.000	0.000
31	A	36	PRO	0	-0.022	-0.014	23.379	0.008	0.008	0.000	0.000	0.000
32	A	37	THR	0	0.027	0.020	26.687	-0.002	-0.002	0.000	0.000	0.000
33	A	38	HIS	0	0.017	0.009	24.372	0.003	0.003	0.000	0.000	0.000
34	A	39	LYS	1	0.965	0.965	23.455	0.067	0.067	0.000	0.000	0.000
35	A	40	ASN	0	0.061	0.049	21.296	-0.009	-0.009	0.000	0.000	0.000
36	A	41	HIS	0	0.003	-0.024	18.111	0.002	0.002	0.000	0.000	0.000
37	A	42	GLN	0	0.069	0.021	14.949	-0.022	-0.022	0.000	0.000	0.000
38	A	43	LEU	0	-0.026	0.000	17.966	0.002	0.002	0.000	0.000	0.000
39	A	44	CYS	0	-0.023	0.002	20.684	0.007	0.007	0.000	0.000	0.000
40	A	45	ILE	0	0.020	0.008	14.769	-0.016	-0.016	0.000	0.000	0.000
41	A	46	GLY	0	0.011	0.012	18.410	-0.016	-0.016	0.000	0.000	0.000
42	A	47	GLU	-1	-0.849	-0.944	20.655	-0.093	-0.093	0.000	0.000	0.000
43	A	48	ILE	0	-0.053	-0.005	18.004	-0.007	-0.007	0.000	0.000	0.000
44	A	49	PHE	0	-0.022	-0.044	13.629	-0.018	-0.018	0.000	0.000	0.000
45	A	50	GLN	0	0.029	0.024	19.030	-0.004	-0.004	0.000	0.000	0.000
46	A	51	GLY	0	0.035	0.021	22.490	0.007	0.007	0.000	0.000	0.000
47	A	52	LEU	0	-0.048	-0.028	17.234	-0.005	-0.005	0.000	0.000	0.000
48	A	53	ASP	-1	-0.953	-0.988	21.021	-0.167	-0.167	0.000	0.000	0.000
49	A	54	ILE	0	0.032	0.030	22.468	0.006	0.006	0.000	0.000	0.000
50	A	55	LEU	0	-0.036	-0.015	22.963	0.002	0.002	0.000	0.000	0.000
51	A	56	LYS	1	0.953	0.956	17.718	0.249	0.249	0.000	0.000	0.000
52	A	57	ASN	0	-0.075	-0.027	23.800	-0.005	-0.005	0.000	0.000	0.000
53	A	58	GLN	0	0.040	0.017	26.633	0.007	0.007	0.000	0.000	0.000
54	A	59	THR	0	-0.035	0.005	24.498	0.003	0.003	0.000	0.000	0.000
55	A	60	VAL	0	0.017	0.001	27.038	-0.002	-0.002	0.000	0.000	0.000
56	A	61	ARG	1	0.854	0.928	21.578	0.163	0.163	0.000	0.000	0.000
57	A	62	GLY	0	0.001	-0.003	23.856	0.011	0.011	0.000	0.000	0.000
58	A	63	GLY	0	0.019	0.013	24.362	-0.001	-0.001	0.000	0.000	0.000
59	A	64	THR	0	0.032	0.000	21.711	-0.007	-0.007	0.000	0.000	0.000
60	A	65	VAL	0	-0.005	-0.007	20.314	-0.027	-0.027	0.000	0.000	0.000
61	A	66	GLU	-1	-0.817	-0.905	19.167	-0.239	-0.239	0.000	0.000	0.000
62	A	67	ARG	1	0.940	0.982	15.816	0.263	0.263	0.000	0.000	0.000
63	A	68	LEU	0	-0.010	-0.016	15.025	-0.068	-0.068	0.000	0.000	0.000
64	A	69	PHE	0	0.007	-0.004	15.201	-0.055	-0.055	0.000	0.000	0.000
65	A	70	GLN	0	0.063	0.029	11.977	0.053	0.053	0.000	0.000	0.000
66	A	71	ASN	0	-0.010	-0.001	10.814	-0.188	-0.188	0.000	0.000	0.000
67	A	72	LEU	0	-0.016	0.000	10.578	-0.140	-0.140	0.000	0.000	0.000
68	A	73	SER	0	-0.009	-0.004	12.303	0.012	0.012	0.000	0.000	0.000
69	A	74	LEU	0	0.005	-0.010	5.538	0.048	0.048	0.000	0.000	0.000
70	A	75	ILE	0	-0.007	-0.001	8.070	-0.075	-0.075	0.000	0.000	0.000
71	A	76	LYS	1	0.835	0.940	9.189	0.314	0.314	0.000	0.000	0.000
72	A	77	LYS	1	0.984	0.977	8.342	0.470	0.470	0.000	0.000	0.000
73	A	78	TYR	0	-0.032	0.006	4.398	0.007	0.085	0.000	-0.011	-0.067
74	A	79	ILE	0	0.007	-0.011	7.252	0.203	0.203	0.000	0.000	0.000
75	A	80	ASP	-1	-0.855	-0.923	10.585	-0.137	-0.137	0.000	0.000	0.000
76	A	81	ARG	1	0.824	0.901	8.221	-0.168	-0.168	0.000	0.000	0.000
77	A	82	GLN	0	-0.036	-0.031	8.932	0.140	0.140	0.000	0.000	0.000
78	A	83	LYS	1	0.956	0.976	11.041	0.049	0.049	0.000	0.000	0.000
79	A	84	GLU	-1	-0.911	-0.965	13.279	0.082	0.082	0.000	0.000	0.000
80	A	85	LYS	1	0.922	0.955	8.350	-0.451	-0.451	0.000	0.000	0.000
81	A	86	CYS	0	-0.068	-0.008	14.317	-0.004	-0.004	0.000	0.000	0.000
82	A	87	GLY	0	-0.010	-0.005	17.425	0.000	0.000	0.000	0.000	0.000
83	A	88	GLU	-1	-0.854	-0.892	14.644	0.191	0.191	0.000	0.000	0.000
84	A	89	GLU	-1	-0.938	-0.961	16.560	0.200	0.200	0.000	0.000	0.000
85	A	90	ARG	1	0.944	0.971	20.097	-0.068	-0.068	0.000	0.000	0.000
86	A	91	ARG	1	0.969	0.975	21.048	-0.121	-0.121	0.000	0.000	0.000
87	A	92	ARG	1	0.944	0.971	25.334	-0.077	-0.077	0.000	0.000	0.000
88	A	93	THR	0	0.089	0.020	27.997	0.004	0.004	0.000	0.000	0.000
89	A	94	ARG	1	0.964	0.997	28.699	-0.074	-0.074	0.000	0.000	0.000
90	A	95	GLN	0	0.022	-0.005	24.595	0.004	0.004	0.000	0.000	0.000
91	A	96	PHE	0	0.000	0.021	24.974	0.004	0.004	0.000	0.000	0.000
92	A	97	LEU	0	0.007	-0.005	26.378	-0.003	-0.003	0.000	0.000	0.000
93	A	98	ASP	-1	-0.880	-0.937	25.861	0.063	0.063	0.000	0.000	0.000
94	A	99	TYR	0	0.022	0.012	18.274	-0.007	-0.007	0.000	0.000	0.000
95	A	100	LEU	0	-0.021	-0.003	24.192	-0.006	-0.006	0.000	0.000	0.000
96	A	101	GLN	0	-0.032	-0.031	26.783	-0.002	-0.002	0.000	0.000	0.000
97	A	102	GLU	-1	-0.953	-0.983	21.447	0.067	0.067	0.000	0.000	0.000
98	A	103	PHE	0	-0.008	0.012	23.469	-0.005	-0.005	0.000	0.000	0.000
99	A	104	LEU	0	-0.024	-0.037	24.583	-0.007	-0.007	0.000	0.000	0.000
100	A	105	GLY	0	-0.032	-0.007	27.402	-0.004	-0.004	0.000	0.000	0.000
101	A	106	VAL	0	0.001	0.006	22.492	-0.001	-0.001	0.000	0.000	0.000
102	A	107	LEU	0	-0.013	0.001	25.699	-0.007	-0.007	0.000	0.000	0.000
103	A	108	SER	0	-0.051	-0.026	27.316	-0.005	-0.005	0.000	0.000	0.000
104	A	109	THR	0	-0.009	-0.011	26.113	0.000	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.945	-0.954	22.509	-0.026	-0.026	0.000	0.000	0.000
106	A	111	TRP	0	-0.107	-0.061	26.567	-0.005	-0.005	0.000	0.000	0.000
107	A	112	NME	0	0.001	0.018	29.643	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )