FMO DATABASE

FMODB ID: Z6RJN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-470051.410389
FMO2-HF: Nuclear repulsion	439463.614661
FMO2-HF: Total energy	-30587.795727
FMO2-MP2: Total energy	-30674.386688

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.
-3.089	2.102	0.344	-2.574	-2.962	-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 : 0.070 / q_NPA : 0.021

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	0.018	-0.009	2.731	-5.135	-0.160	0.345	-2.541	-2.779	-0.002
4	A	9	ALA	0	0.100	0.055	4.248	0.493	0.709	-0.001	-0.033	-0.183	0.000
5	A	10	LEU	0	-0.006	-0.011	6.906	0.193	0.193	0.000	0.000	0.000	0.000
6	A	11	ARG	1	0.937	0.970	7.018	1.058	1.058	0.000	0.000	0.000	0.000
7	A	12	GLU	-1	-0.877	-0.939	8.564	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.003	0.000	10.514	0.103	0.103	0.000	0.000	0.000	0.000
9	A	14	ILE	0	-0.043	-0.025	11.391	0.079	0.079	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.908	-0.968	11.685	-0.368	-0.368	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.821	-0.900	14.730	-0.085	-0.085	0.000	0.000	0.000	0.000
12	A	17	LEU	0	-0.003	-0.015	16.226	0.028	0.028	0.000	0.000	0.000	0.000
13	A	18	VAL	0	-0.047	-0.030	17.317	0.019	0.019	0.000	0.000	0.000	0.000
14	A	19	ASN	0	-0.052	-0.012	18.840	0.026	0.026	0.000	0.000	0.000	0.000
15	A	20	ILE	0	-0.007	0.000	20.619	0.016	0.016	0.000	0.000	0.000	0.000
16	A	21	THR	0	-0.096	-0.049	22.400	0.009	0.009	0.000	0.000	0.000	0.000
17	A	22	GLN	0	0.003	0.018	23.325	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	43	MET	0	-0.020	-0.012	16.581	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	44	TYR	0	0.087	0.015	10.380	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	45	CYS	0	-0.108	-0.025	12.180	0.009	0.009	0.000	0.000	0.000	0.000
21	A	46	ALA	0	0.068	0.036	19.227	0.009	0.009	0.000	0.000	0.000	0.000
22	A	47	ALA	0	-0.011	-0.002	19.296	0.007	0.007	0.000	0.000	0.000	0.000
23	A	48	LEU	0	0.001	-0.001	18.245	0.006	0.006	0.000	0.000	0.000	0.000
24	A	49	GLU	-1	-0.835	-0.937	21.042	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	50	SER	0	0.003	0.015	24.199	0.009	0.009	0.000	0.000	0.000	0.000
26	A	51	LEU	0	-0.023	-0.014	21.218	0.003	0.003	0.000	0.000	0.000	0.000
27	A	52	ILE	0	-0.027	0.004	23.559	0.005	0.005	0.000	0.000	0.000	0.000
28	A	53	ASN	0	-0.077	-0.049	25.475	0.012	0.012	0.000	0.000	0.000	0.000
29	A	54	VAL	0	-0.059	-0.017	27.972	0.004	0.004	0.000	0.000	0.000	0.000
30	A	55	SER	0	0.026	0.003	28.214	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	56	GLY	0	0.008	0.010	30.399	0.003	0.003	0.000	0.000	0.000	0.000
32	A	57	CYS	0	-0.056	-0.018	28.435	0.000	0.000	0.000	0.000	0.000	0.000
33	A	58	SER	0	0.069	0.024	28.082	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	59	ALA	0	0.015	0.007	24.839	0.001	0.001	0.000	0.000	0.000	0.000
35	A	60	ILE	0	0.023	0.003	22.688	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	61	GLU	-1	-0.844	-0.902	22.179	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	62	LYS	1	0.818	0.897	16.217	0.120	0.120	0.000	0.000	0.000	0.000
38	A	63	THR	0	0.057	0.017	17.626	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	64	GLN	0	0.015	-0.002	17.649	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	65	ARG	1	0.873	0.924	17.604	0.026	0.026	0.000	0.000	0.000	0.000
41	A	66	MET	0	-0.007	0.012	12.632	0.001	0.001	0.000	0.000	0.000	0.000
42	A	67	LEU	0	0.015	0.004	13.183	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	68	SER	0	-0.054	-0.019	15.022	0.005	0.005	0.000	0.000	0.000	0.000
44	A	69	GLY	0	-0.002	0.008	11.871	0.030	0.030	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.062	-0.028	8.714	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	72	PRO	0	0.014	0.006	14.578	0.022	0.022	0.000	0.000	0.000	0.000
47	A	73	HIS	0	-0.015	0.005	16.133	0.026	0.026	0.000	0.000	0.000	0.000
48	A	74	LYS	1	0.948	0.955	17.344	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	75	VAL	0	0.032	0.019	20.606	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	76	SER	0	-0.052	-0.027	22.907	0.006	0.006	0.000	0.000	0.000	0.000
51	A	77	ALA	0	0.027	0.022	26.201	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	88	THR	0	0.007	-0.015	33.881	0.002	0.002	0.000	0.000	0.000	0.000
53	A	89	LYS	1	0.953	0.969	34.206	0.042	0.042	0.000	0.000	0.000	0.000
54	A	90	ILE	0	-0.003	0.007	30.383	0.002	0.002	0.000	0.000	0.000	0.000
55	A	91	GLU	-1	-0.890	-0.942	31.907	-0.065	-0.065	0.000	0.000	0.000	0.000
56	A	92	VAL	0	0.046	0.012	26.408	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	93	ALA	0	0.044	0.020	26.825	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	94	GLN	0	0.012	0.003	27.079	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	95	PHE	0	0.041	0.037	22.767	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	96	VAL	0	0.039	0.021	21.674	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	97	LYS	1	0.913	0.954	21.882	0.089	0.089	0.000	0.000	0.000	0.000
62	A	98	ASP	-1	-0.869	-0.935	22.772	-0.139	-0.139	0.000	0.000	0.000	0.000
63	A	99	LEU	0	-0.001	0.009	18.180	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	100	LEU	0	0.002	0.002	17.135	-0.039	-0.039	0.000	0.000	0.000	0.000
65	A	101	LEU	0	-0.009	-0.012	17.738	-0.037	-0.037	0.000	0.000	0.000	0.000
66	A	102	HIS	0	-0.066	-0.045	18.081	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	103	LEU	0	0.032	0.012	13.666	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	104	LYS	1	0.960	0.985	13.154	0.186	0.186	0.000	0.000	0.000	0.000
69	A	105	LYS	1	0.874	0.943	14.373	0.180	0.180	0.000	0.000	0.000	0.000
70	A	106	LEU	0	0.010	0.009	11.781	0.003	0.003	0.000	0.000	0.000	0.000
71	A	107	PHE	0	0.000	0.007	7.751	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	108	ARG	1	0.909	0.950	10.177	0.262	0.262	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.885	-0.936	12.717	-0.231	-0.231	0.000	0.000	0.000	0.000
74	A	110	GLY	0	0.008	0.029	8.271	0.022	0.022	0.000	0.000	0.000	0.000
75	A	111	ARG	1	0.825	0.901	8.548	0.312	0.312	0.000	0.000	0.000	0.000

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