FMO DATABASE

FMODB ID: R9NZ8

Calculation Name: 4PS4-A-Xray372

Preferred Name: Interleukin-13

Target Type: SINGLE PROTEIN

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 4PS4

Chain ID: A

ChEMBL ID: CHEMBL3580486

UniProt ID: P35225

Base Structure: X-ray

Registration Date: 2023-06-21

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-473951.269082
FMO2-HF: Nuclear repulsion	443363.08369
FMO2-HF: Total energy	-30588.185392
FMO2-MP2: Total energy	-30674.822389

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:PRO)

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

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.
-2.774	2.057	0.753	-2.515	-3.069	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.023

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	8	THR	0	0.010	-0.002	2.441	-4.776	-0.189	0.753	-2.463	-2.877	-0.004
4	A	9	ALA	0	0.128	0.071	4.191	0.452	0.696	0.000	-0.052	-0.192	0.000
5	A	10	LEU	0	-0.007	-0.004	6.806	0.277	0.277	0.000	0.000	0.000	0.000
6	A	11	ARG	1	0.839	0.912	7.056	0.880	0.880	0.000	0.000	0.000	0.000
7	A	12	GLU	-1	-0.884	-0.948	7.933	-0.108	-0.108	0.000	0.000	0.000	0.000
8	A	13	LEU	0	0.015	0.010	10.289	0.114	0.114	0.000	0.000	0.000	0.000
9	A	14	ILE	0	-0.043	-0.026	11.236	0.092	0.092	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.850	-0.927	11.653	-0.371	-0.371	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.804	-0.894	14.228	-0.102	-0.102	0.000	0.000	0.000	0.000
12	A	17	LEU	0	-0.013	-0.006	16.013	0.032	0.032	0.000	0.000	0.000	0.000
13	A	18	VAL	0	-0.023	-0.015	17.364	0.023	0.023	0.000	0.000	0.000	0.000
14	A	19	ASN	0	-0.041	-0.003	18.548	0.028	0.028	0.000	0.000	0.000	0.000
15	A	20	ILE	0	-0.009	-0.005	20.414	0.018	0.018	0.000	0.000	0.000	0.000
16	A	21	THR	0	-0.103	-0.057	21.879	0.007	0.007	0.000	0.000	0.000	0.000
17	A	22	GLN	0	-0.006	0.012	22.713	0.001	0.001	0.000	0.000	0.000	0.000
18	A	43	MET	0	-0.008	-0.009	16.105	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	44	TYR	0	0.069	0.006	10.682	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	45	CYS	0	-0.069	-0.003	12.236	0.013	0.013	0.000	0.000	0.000	0.000
21	A	46	ALA	0	0.091	0.051	18.964	0.011	0.011	0.000	0.000	0.000	0.000
22	A	47	ALA	0	-0.029	-0.013	18.751	0.010	0.010	0.000	0.000	0.000	0.000
23	A	48	LEU	0	-0.003	0.003	18.261	0.011	0.011	0.000	0.000	0.000	0.000
24	A	49	GLU	-1	-0.830	-0.930	20.855	-0.090	-0.090	0.000	0.000	0.000	0.000
25	A	50	SER	0	-0.001	0.018	23.904	0.013	0.013	0.000	0.000	0.000	0.000
26	A	51	LEU	0	-0.039	-0.023	20.941	0.008	0.008	0.000	0.000	0.000	0.000
27	A	52	ILE	0	-0.035	-0.017	23.309	0.007	0.007	0.000	0.000	0.000	0.000
28	A	53	ASN	0	-0.038	-0.003	25.102	0.015	0.015	0.000	0.000	0.000	0.000
29	A	54	VAL	0	-0.049	-0.017	27.555	0.006	0.006	0.000	0.000	0.000	0.000
30	A	55	SER	0	0.030	0.005	27.559	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	56	GLY	0	-0.004	0.005	29.788	0.003	0.003	0.000	0.000	0.000	0.000
32	A	57	CYS	0	-0.036	-0.023	28.346	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	58	SER	0	0.057	0.027	27.217	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	59	ALA	0	0.001	0.009	24.195	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	60	ILE	0	0.036	0.003	22.199	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	61	GLU	-1	-0.805	-0.873	21.824	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	62	LYS	1	0.855	0.917	16.207	0.135	0.135	0.000	0.000	0.000	0.000
38	A	63	THR	0	0.033	-0.007	17.307	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	64	GLN	0	-0.013	-0.013	17.360	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	65	ARG	1	0.839	0.905	17.732	0.040	0.040	0.000	0.000	0.000	0.000
41	A	66	MET	0	-0.003	0.016	12.035	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	67	LEU	0	0.008	-0.005	13.299	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	68	SER	0	-0.064	-0.030	14.942	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	69	GLY	0	0.015	0.010	11.886	0.034	0.034	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.066	-0.033	9.281	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	72	PRO	0	0.031	0.014	14.852	0.026	0.026	0.000	0.000	0.000	0.000
47	A	73	HIS	0	-0.006	-0.003	16.355	0.024	0.024	0.000	0.000	0.000	0.000
48	A	74	LYS	1	0.844	0.907	16.727	0.042	0.042	0.000	0.000	0.000	0.000
49	A	75	VAL	0	0.038	0.033	20.507	0.003	0.003	0.000	0.000	0.000	0.000
50	A	76	SER	0	-0.057	-0.045	22.932	0.010	0.010	0.000	0.000	0.000	0.000
51	A	77	ALA	0	0.012	0.007	26.136	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	88	THR	0	0.032	-0.001	33.653	0.003	0.003	0.000	0.000	0.000	0.000
53	A	89	LYS	1	0.933	0.974	33.446	0.049	0.049	0.000	0.000	0.000	0.000
54	A	90	ILE	0	0.015	0.004	29.850	0.003	0.003	0.000	0.000	0.000	0.000
55	A	91	GLU	-1	-0.890	-0.943	31.477	-0.074	-0.074	0.000	0.000	0.000	0.000
56	A	92	VAL	0	0.029	0.000	26.307	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	93	ALA	0	0.050	0.029	26.706	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	94	GLN	0	-0.036	-0.007	27.327	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	95	PHE	0	0.033	0.021	22.479	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	96	VAL	0	0.043	0.015	21.560	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	97	LYS	1	0.917	0.955	21.547	0.096	0.096	0.000	0.000	0.000	0.000
62	A	98	ASP	-1	-0.832	-0.918	22.358	-0.154	-0.154	0.000	0.000	0.000	0.000
63	A	99	LEU	0	-0.002	0.009	18.115	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	100	LEU	0	0.009	0.009	16.772	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	101	LEU	0	-0.010	-0.013	17.770	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	102	HIS	0	-0.058	-0.036	18.139	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	103	LEU	0	0.024	0.008	13.640	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	104	LYS	1	0.944	0.985	13.228	0.198	0.198	0.000	0.000	0.000	0.000
69	A	105	LYS	1	0.864	0.950	14.466	0.202	0.202	0.000	0.000	0.000	0.000
70	A	106	LEU	0	-0.013	-0.014	11.853	0.001	0.001	0.000	0.000	0.000	0.000
71	A	107	PHE	0	0.011	0.006	7.184	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	108	ARG	1	0.871	0.931	10.267	0.270	0.270	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.837	-0.914	12.523	-0.244	-0.244	0.000	0.000	0.000	0.000
74	A	110	GLY	0	0.018	0.024	8.283	0.040	0.040	0.000	0.000	0.000	0.000
75	A	111	ARG	1	0.848	0.921	8.423	0.351	0.351	0.000	0.000	0.000	0.000

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