FMO DATABASE

FMODB ID: 5J3ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-436422.835735
FMO2-HF: Nuclear repulsion	407253.351724
FMO2-HF: Total energy	-29169.48401
FMO2-MP2: Total energy	-29253.068136

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.
18.317	19.881	12.546	-6.782	-7.328	-0.074

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 : 0.936 / q_NPA : 0.966

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	LEU	0	-0.074	-0.045	1.779	-49.428	-48.037	12.547	-6.732	-7.206	-0.074
4	A	6	ARG	1	1.000	1.003	4.236	41.027	41.200	-0.001	-0.050	-0.122	0.000
5	A	7	CYS	0	-0.074	-0.050	7.587	-0.977	-0.977	0.000	0.000	0.000	0.000
6	A	8	GLN	0	0.038	0.015	6.898	-2.649	-2.649	0.000	0.000	0.000	0.000
7	A	9	CYS	0	-0.062	-0.008	10.472	0.768	0.768	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.009	0.006	13.525	0.685	0.685	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.954	0.975	16.177	15.381	15.381	0.000	0.000	0.000	0.000
10	A	12	THR	0	0.020	0.015	18.438	-0.537	-0.537	0.000	0.000	0.000	0.000
11	A	13	TYR	0	-0.032	-0.017	20.638	0.597	0.597	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.009	-0.001	23.188	0.126	0.126	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.944	0.975	26.495	10.655	10.655	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.055	0.022	27.400	-0.311	-0.311	0.000	0.000	0.000	0.000
15	A	17	PHE	0	-0.028	-0.010	22.529	0.239	0.239	0.000	0.000	0.000	0.000
16	A	18	HIS	0	0.047	0.020	28.193	-0.276	-0.276	0.000	0.000	0.000	0.000
17	A	19	PRO	0	0.081	0.030	25.658	-0.176	-0.176	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.919	0.972	25.529	8.951	8.951	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.043	-0.019	25.737	0.059	0.059	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.005	0.020	19.973	-0.350	-0.350	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.812	0.885	18.646	14.466	14.466	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.849	-0.912	12.624	-19.574	-19.574	0.000	0.000	0.000	0.000
23	A	25	LEU	0	0.002	-0.001	15.773	0.290	0.290	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.920	0.955	6.623	31.908	31.908	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.009	-0.004	12.321	0.589	0.589	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.035	-0.011	8.948	-0.905	-0.905	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.901	-0.952	11.747	-16.433	-16.433	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.018	-0.002	13.102	-1.309	-1.309	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.021	-0.010	13.350	0.599	0.599	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.012	-0.010	11.050	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	33	HIS	0	-0.005	0.028	8.200	-1.711	-1.711	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.057	0.038	12.628	0.879	0.879	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.023	-0.011	15.691	1.819	1.819	0.000	0.000	0.000	0.000
34	A	37	THR	0	0.034	0.015	15.320	-1.331	-1.331	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.787	-0.890	11.367	-25.204	-25.204	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.005	0.005	14.758	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.005	-0.007	10.866	0.345	0.345	0.000	0.000	0.000	0.000
38	A	41	VAL	0	0.001	0.005	15.059	0.282	0.282	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.843	0.925	12.168	20.158	20.158	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.014	-0.002	17.540	0.785	0.785	0.000	0.000	0.000	0.000
41	A	44	SER	0	0.036	-0.001	20.723	-0.322	-0.322	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.754	-0.825	22.148	-13.190	-13.190	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.010	-0.020	18.687	-0.076	-0.076	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.849	0.911	17.255	12.043	12.043	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.863	-0.932	12.116	-22.459	-22.459	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.054	-0.029	16.478	0.467	0.467	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.046	-0.033	17.257	1.135	1.135	0.000	0.000	0.000	0.000
48	A	52	ASP	-1	-0.809	-0.910	19.210	-14.401	-14.401	0.000	0.000	0.000	0.000
49	A	53	PRO	0	0.010	-0.004	19.380	0.610	0.610	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.949	0.975	21.728	14.129	14.129	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.831	-0.919	24.948	-10.212	-10.212	0.000	0.000	0.000	0.000
52	A	56	ASN	0	0.032	0.026	26.390	0.199	0.199	0.000	0.000	0.000	0.000
53	A	57	TRP	0	-0.018	-0.015	25.012	0.065	0.065	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.018	0.016	22.151	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	59	GLN	0	0.013	0.004	24.085	0.309	0.309	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.880	0.936	25.127	9.490	9.490	0.000	0.000	0.000	0.000
57	A	61	VAL	0	-0.039	-0.019	24.235	0.187	0.187	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.007	-0.001	20.064	-0.054	-0.054	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.781	-0.890	22.556	-11.376	-11.376	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.923	0.949	24.497	9.729	9.729	0.000	0.000	0.000	0.000
61	A	65	PHE	0	-0.052	-0.021	18.754	0.265	0.265	0.000	0.000	0.000	0.000
62	A	66	LEU	0	0.008	0.018	19.488	0.021	0.021	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.813	0.912	22.390	11.360	11.360	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.839	0.916	24.282	11.566	11.566	0.000	0.000	0.000	0.000
65	A	69	ALA	0	-0.015	-0.009	20.876	0.155	0.155	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.838	-0.938	22.651	-11.266	-11.266	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.080	-0.035	24.179	0.528	0.528	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.064	-0.019	23.796	0.085	0.085	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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