FMO DATABASE

FMODB ID: 4J3RN

Calculation Name: 4XDX-A-Xray372

Preferred Name: Interleukin-8

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4XDX

Chain ID: A

ChEMBL ID: CHEMBL2157

UniProt ID: P10145

Base Structure: X-ray

Registration Date: 2023-09-20

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-437047.170239
FMO2-HF: Nuclear repulsion	407877.846993
FMO2-HF: Total energy	-29169.323246
FMO2-MP2: Total energy	-29252.91986

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
52.792	55.707	2.968	-1.878	-4.005	-0.007

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.969 / q_NPA : 0.989

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	5	LEU	0	-0.089	-0.045	2.229	-11.952	-9.135	2.969	-1.865	-3.922	-0.007
4	A	6	ARG	1	0.997	0.999	4.800	38.005	38.103	-0.001	-0.013	-0.083	0.000
5	A	7	CYS	0	-0.071	-0.048	8.107	-1.106	-1.106	0.000	0.000	0.000	0.000
6	A	8	GLN	0	0.040	0.011	6.660	-2.496	-2.496	0.000	0.000	0.000	0.000
7	A	9	CYS	0	-0.048	0.007	10.139	0.266	0.266	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.003	-0.001	13.904	0.302	0.302	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.965	0.972	16.359	14.967	14.967	0.000	0.000	0.000	0.000
10	A	12	THR	0	0.018	0.016	18.389	-0.539	-0.539	0.000	0.000	0.000	0.000
11	A	13	TYR	0	-0.043	-0.022	20.641	0.551	0.551	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.035	0.004	23.179	0.096	0.096	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.942	0.986	26.512	10.254	10.254	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.043	0.013	27.634	-0.289	-0.289	0.000	0.000	0.000	0.000
15	A	17	PHE	0	-0.028	-0.012	22.434	0.229	0.229	0.000	0.000	0.000	0.000
16	A	18	HIS	0	0.048	0.023	28.055	-0.261	-0.261	0.000	0.000	0.000	0.000
17	A	19	PRO	0	0.099	0.036	25.526	-0.226	-0.226	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.911	0.970	25.339	8.870	8.870	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.043	-0.024	25.268	0.040	0.040	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.001	0.023	19.690	-0.373	-0.373	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.846	0.910	18.477	14.614	14.614	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.842	-0.902	12.595	-19.123	-19.123	0.000	0.000	0.000	0.000
23	A	25	LEU	0	0.014	0.006	15.969	0.179	0.179	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.920	0.953	6.421	30.166	30.166	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.016	-0.003	13.069	0.387	0.387	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.034	-0.008	8.770	-0.500	-0.500	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.920	-0.962	12.056	-15.579	-15.579	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.018	-0.010	13.059	-1.153	-1.153	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.041	0.000	13.383	0.394	0.394	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.007	-0.007	12.124	0.061	0.061	0.000	0.000	0.000	0.000
31	A	33	HIS	0	-0.007	0.025	8.714	-0.843	-0.843	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.027	0.022	12.903	0.759	0.759	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.026	-0.010	15.631	1.609	1.609	0.000	0.000	0.000	0.000
34	A	37	THR	0	0.038	0.013	14.843	-1.110	-1.110	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.791	-0.886	11.109	-23.567	-23.567	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.003	0.004	14.538	-0.193	-0.193	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.010	-0.005	10.719	0.503	0.503	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.015	-0.006	14.787	0.111	0.111	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.876	0.938	12.040	19.776	19.776	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.018	-0.004	17.246	0.808	0.808	0.000	0.000	0.000	0.000
41	A	44	SER	0	0.041	0.003	20.454	-0.370	-0.370	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.799	-0.876	22.126	-12.972	-12.972	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.048	-0.016	18.313	-0.181	-0.181	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.859	0.917	16.995	11.884	11.884	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.875	-0.943	12.320	-21.506	-21.506	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.073	-0.031	16.718	0.404	0.404	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.028	-0.022	17.407	1.003	1.003	0.000	0.000	0.000	0.000
48	A	52	ASP	-1	-0.822	-0.914	19.390	-13.593	-13.593	0.000	0.000	0.000	0.000
49	A	53	PRO	0	0.012	-0.004	19.092	0.564	0.564	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.951	0.971	21.584	13.428	13.428	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.861	-0.922	24.875	-9.921	-9.921	0.000	0.000	0.000	0.000
52	A	56	ASN	0	0.047	0.038	26.617	0.160	0.160	0.000	0.000	0.000	0.000
53	A	57	TRP	0	0.010	-0.007	24.994	-0.068	-0.068	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.030	0.020	22.129	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.008	-0.011	24.300	0.212	0.212	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.891	0.938	25.391	9.243	9.243	0.000	0.000	0.000	0.000
57	A	61	VAL	0	-0.044	-0.019	23.966	0.128	0.128	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.000	-0.006	20.496	-0.079	-0.079	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.808	-0.898	22.934	-10.941	-10.941	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.904	0.938	25.178	9.531	9.531	0.000	0.000	0.000	0.000
61	A	65	PHE	0	-0.055	-0.028	19.046	0.224	0.224	0.000	0.000	0.000	0.000
62	A	66	LEU	0	0.021	0.025	20.123	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.828	0.909	22.990	11.035	11.035	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.843	0.915	24.113	11.405	11.405	0.000	0.000	0.000	0.000
65	A	69	ALA	0	-0.039	-0.028	21.719	0.163	0.163	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.806	-0.896	22.953	-11.169	-11.169	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.066	-0.030	24.588	0.474	0.474	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.070	-0.021	24.031	0.142	0.142	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)