FMO DATABASE

FMODB ID: KG373

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

Total energy (hartree)

FMO2-HF: Electronic energy	-437094.422773
FMO2-HF: Nuclear repulsion	407925.591553
FMO2-HF: Total energy	-29168.831221
FMO2-MP2: Total energy	-29252.426727

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.
55.205	57.063	3.299	-1.399	-3.758	-0.011

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 : 0.946 / q_NPA : 0.959

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	-0.096	-0.039	2.214	-11.383	-9.632	3.300	-1.384	-3.667	-0.011
4	A	6	ARG	1	0.998	0.999	4.770	39.217	39.324	-0.001	-0.015	-0.091	0.000
5	A	7	CYS	0	-0.082	-0.057	8.076	-1.350	-1.350	0.000	0.000	0.000	0.000
6	A	8	GLN	0	-0.007	-0.031	6.982	-2.684	-2.684	0.000	0.000	0.000	0.000
7	A	9	CYS	0	-0.047	0.007	10.107	0.205	0.205	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.006	0.010	13.872	0.303	0.303	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.966	0.962	16.316	15.238	15.238	0.000	0.000	0.000	0.000
10	A	12	THR	0	0.011	0.012	18.357	-0.552	-0.552	0.000	0.000	0.000	0.000
11	A	13	TYR	0	-0.044	-0.023	20.606	0.615	0.615	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.030	0.005	23.145	0.116	0.116	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.947	0.985	26.477	10.204	10.204	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.041	0.007	27.599	-0.296	-0.296	0.000	0.000	0.000	0.000
15	A	17	PHE	0	-0.025	-0.005	22.528	0.223	0.223	0.000	0.000	0.000	0.000
16	A	18	HIS	0	0.057	0.036	28.036	-0.279	-0.279	0.000	0.000	0.000	0.000
17	A	19	PRO	0	0.109	0.040	25.498	-0.243	-0.243	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.900	0.957	25.321	8.965	8.965	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.042	-0.024	25.209	0.036	0.036	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.005	0.022	19.679	-0.380	-0.380	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.868	0.927	18.667	14.682	14.682	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.887	-0.942	12.564	-19.136	-19.136	0.000	0.000	0.000	0.000
23	A	25	LEU	0	0.015	0.006	15.940	0.198	0.198	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.959	0.996	5.546	32.062	32.062	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.017	-0.005	13.046	0.390	0.390	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.029	-0.003	8.599	-0.413	-0.413	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.922	-0.962	11.901	-15.479	-15.479	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.039	-0.022	12.781	-1.067	-1.067	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.048	0.007	13.312	0.422	0.422	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.003	-0.007	12.269	-0.077	-0.077	0.000	0.000	0.000	0.000
31	A	33	HIS	0	0.010	0.033	8.647	-0.874	-0.874	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.032	0.026	12.867	0.749	0.749	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.013	-0.003	15.590	1.705	1.705	0.000	0.000	0.000	0.000
34	A	37	THR	0	0.036	0.010	14.800	-1.118	-1.118	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.794	-0.890	11.295	-23.047	-23.047	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.002	0.004	14.492	-0.182	-0.182	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.002	-0.007	10.801	0.491	0.491	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.004	0.000	14.768	0.114	0.114	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.944	0.985	12.698	19.310	19.310	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.005	-0.012	17.233	0.827	0.827	0.000	0.000	0.000	0.000
41	A	44	SER	0	0.029	0.002	20.444	-0.400	-0.400	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.850	-0.928	22.090	-13.198	-13.198	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.043	-0.010	18.274	-0.206	-0.206	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.900	0.947	16.952	11.944	11.944	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.895	-0.949	12.398	-21.818	-21.818	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.072	-0.025	16.665	0.427	0.427	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.041	-0.031	17.371	1.006	1.006	0.000	0.000	0.000	0.000
48	A	52	ASP	-1	-0.808	-0.911	19.349	-13.454	-13.454	0.000	0.000	0.000	0.000
49	A	53	PRO	0	-0.001	-0.005	19.045	0.567	0.567	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.954	0.971	21.539	13.232	13.232	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.886	-0.920	24.835	-10.131	-10.131	0.000	0.000	0.000	0.000
52	A	56	ASN	0	0.052	0.027	26.573	0.040	0.040	0.000	0.000	0.000	0.000
53	A	57	TRP	0	0.030	0.003	25.013	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.032	0.021	22.137	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.020	-0.019	24.276	0.141	0.141	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.901	0.943	25.366	9.221	9.221	0.000	0.000	0.000	0.000
57	A	61	VAL	0	-0.042	-0.018	23.842	0.131	0.131	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.001	-0.005	20.522	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.827	-0.903	22.911	-10.917	-10.917	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.880	0.928	25.175	9.609	9.609	0.000	0.000	0.000	0.000
61	A	65	PHE	0	-0.052	-0.027	19.008	0.238	0.238	0.000	0.000	0.000	0.000
62	A	66	LEU	0	0.030	0.032	20.346	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.928	0.977	23.047	10.619	10.619	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.842	0.924	24.188	11.486	11.486	0.000	0.000	0.000	0.000
65	A	69	ALA	0	-0.038	-0.025	21.786	0.156	0.156	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.876	-0.955	22.712	-11.472	-11.472	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.082	-0.049	24.684	0.428	0.428	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.057	-0.011	24.205	0.220	0.220	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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