FMO DATABASE

FMODB ID: 6NLMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-469155.311504
FMO2-HF: Nuclear repulsion	438567.945006
FMO2-HF: Total energy	-30587.366499
FMO2-MP2: Total energy	-30673.925563

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.
-1.194	2.767	0.287	-1.83	-2.417	-0.002

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 : 0.061 / 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

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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	0.019	-0.006	2.825	-2.929	0.835	0.288	-1.805	-2.247	-0.002
4	A	9	ALA	0	0.092	0.053	4.361	0.160	0.357	-0.001	-0.025	-0.170	0.000
5	A	10	LEU	0	-0.012	-0.005	6.909	0.078	0.078	0.000	0.000	0.000	0.000
6	A	11	ARG	1	0.935	0.968	6.613	1.035	1.035	0.000	0.000	0.000	0.000
7	A	12	GLU	-1	-0.893	-0.948	8.584	0.309	0.309	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.001	0.006	10.614	0.057	0.057	0.000	0.000	0.000	0.000
9	A	14	ILE	0	-0.047	-0.028	11.574	0.047	0.047	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.930	-0.975	11.792	-0.211	-0.211	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.874	-0.949	14.758	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	17	LEU	0	-0.005	-0.012	16.585	0.013	0.013	0.000	0.000	0.000	0.000
13	A	18	VAL	0	-0.053	-0.027	17.174	0.008	0.008	0.000	0.000	0.000	0.000
14	A	19	ASN	0	-0.042	-0.006	18.885	0.018	0.018	0.000	0.000	0.000	0.000
15	A	20	ILE	0	-0.010	0.000	20.669	0.008	0.008	0.000	0.000	0.000	0.000
16	A	21	THR	0	-0.102	-0.056	22.324	0.003	0.003	0.000	0.000	0.000	0.000
17	A	22	GLN	0	-0.006	0.012	23.486	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	43	MET	0	-0.023	-0.007	16.568	0.001	0.001	0.000	0.000	0.000	0.000
19	A	44	TYR	0	0.085	0.008	10.970	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	45	CYS	0	-0.104	-0.026	12.195	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	46	ALA	0	0.081	0.037	19.231	0.009	0.009	0.000	0.000	0.000	0.000
22	A	47	ALA	0	-0.005	-0.002	19.358	0.005	0.005	0.000	0.000	0.000	0.000
23	A	48	LEU	0	-0.001	-0.003	18.338	0.006	0.006	0.000	0.000	0.000	0.000
24	A	49	GLU	-1	-0.892	-0.960	21.075	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	50	SER	0	-0.047	-0.008	24.223	0.007	0.007	0.000	0.000	0.000	0.000
26	A	51	LEU	0	0.005	-0.006	21.429	0.002	0.002	0.000	0.000	0.000	0.000
27	A	52	ILE	0	-0.025	0.007	23.659	0.006	0.006	0.000	0.000	0.000	0.000
28	A	53	ASN	0	-0.043	-0.023	25.523	0.008	0.008	0.000	0.000	0.000	0.000
29	A	54	VAL	0	-0.069	-0.026	28.081	0.002	0.002	0.000	0.000	0.000	0.000
30	A	55	SER	0	0.020	0.000	28.278	0.001	0.001	0.000	0.000	0.000	0.000
31	A	56	GLY	0	0.004	0.008	30.469	0.003	0.003	0.000	0.000	0.000	0.000
32	A	57	CYS	0	-0.051	-0.024	28.632	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	58	SER	0	0.068	0.029	28.244	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	59	ALA	0	0.007	0.009	24.900	0.004	0.004	0.000	0.000	0.000	0.000
35	A	60	ILE	0	0.029	0.009	22.831	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	61	GLU	-1	-0.907	-0.952	22.340	0.017	0.017	0.000	0.000	0.000	0.000
37	A	62	LYS	1	0.892	0.948	16.258	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	63	THR	0	0.046	0.012	17.765	0.001	0.001	0.000	0.000	0.000	0.000
39	A	64	GLN	0	0.017	0.003	17.715	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	65	ARG	1	0.956	0.972	17.469	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	66	MET	0	-0.018	0.005	13.260	0.009	0.009	0.000	0.000	0.000	0.000
42	A	67	LEU	0	0.014	0.007	13.243	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	68	SER	0	-0.046	-0.018	15.056	0.000	0.000	0.000	0.000	0.000	0.000
44	A	69	GLY	0	-0.006	0.009	11.922	0.021	0.021	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.054	-0.028	8.255	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	72	PRO	0	0.020	0.010	14.737	0.023	0.023	0.000	0.000	0.000	0.000
47	A	73	HIS	0	0.003	0.014	16.125	0.024	0.024	0.000	0.000	0.000	0.000
48	A	74	LYS	1	0.960	0.964	18.119	-0.084	-0.084	0.000	0.000	0.000	0.000
49	A	75	VAL	0	0.036	0.020	20.925	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	76	SER	0	-0.063	-0.034	22.933	0.008	0.008	0.000	0.000	0.000	0.000
51	A	77	ALA	0	0.035	0.028	26.237	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	88	THR	0	0.023	0.007	33.880	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	89	LYS	1	0.931	0.946	34.206	0.025	0.025	0.000	0.000	0.000	0.000
54	A	90	ILE	0	0.001	0.007	30.765	0.003	0.003	0.000	0.000	0.000	0.000
55	A	91	GLU	-1	-0.895	-0.945	32.072	-0.040	-0.040	0.000	0.000	0.000	0.000
56	A	92	VAL	0	0.056	0.019	26.516	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	93	ALA	0	0.043	0.019	26.875	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	94	GLN	0	0.000	-0.019	27.093	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	95	PHE	0	0.050	0.043	22.642	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	96	VAL	0	0.044	0.022	21.561	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	97	LYS	1	0.949	0.979	21.883	0.069	0.069	0.000	0.000	0.000	0.000
62	A	98	ASP	-1	-0.882	-0.934	22.719	-0.113	-0.113	0.000	0.000	0.000	0.000
63	A	99	LEU	0	-0.025	0.002	18.046	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	100	LEU	0	0.007	0.005	17.060	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	101	LEU	0	-0.013	-0.016	17.666	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	102	HIS	0	-0.073	-0.051	18.099	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	103	LEU	0	0.031	0.014	13.697	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	104	LYS	1	0.982	0.990	13.117	0.141	0.141	0.000	0.000	0.000	0.000
69	A	105	LYS	1	0.864	0.935	14.287	0.158	0.158	0.000	0.000	0.000	0.000
70	A	106	LEU	0	0.037	0.026	11.705	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	107	PHE	0	-0.015	-0.003	7.588	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	108	ARG	1	0.903	0.943	10.096	0.233	0.233	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.957	-0.973	12.700	-0.243	-0.243	0.000	0.000	0.000	0.000
74	A	110	GLY	0	0.002	0.023	8.282	0.015	0.015	0.000	0.000	0.000	0.000
75	A	111	ARG	1	0.913	0.949	8.692	0.299	0.299	0.000	0.000	0.000	0.000

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