FMO DATABASE

FMODB ID: LNM89

Calculation Name: 2VXW-A-Xray372

Preferred Name: C-C motif chemokine 5

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2VXW

Chain ID: A

ChEMBL ID: CHEMBL1275217

UniProt ID: P13501

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-402621.288226
FMO2-HF: Nuclear repulsion	374200.094692
FMO2-HF: Total energy	-28421.193534
FMO2-MP2: Total energy	-28501.362162

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:0:PHE)

Summations of interaction energy for fragment #1(A:0:PHE)

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.
-2.863	-0.339	0.034	-1.124	-1.433	0.002

Interaction energy analysis for fragmet #1(A:0:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.003

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	2	PRO	0	0.001	-0.019	3.361	-2.230	-0.069	0.029	-1.033	-1.157	0.002
4	A	3	LEU	0	0.012	0.010	3.621	-0.905	-0.542	0.005	-0.091	-0.276	0.000
5	A	4	SER	0	-0.001	-0.002	6.184	0.187	0.187	0.000	0.000	0.000	0.000
6	A	5	SER	0	0.018	0.017	9.469	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.031	-0.007	11.290	0.114	0.114	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.012	0.010	14.623	0.010	0.010	0.000	0.000	0.000	0.000
9	A	8	SER	0	-0.019	-0.015	15.835	0.035	0.035	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.026	0.020	18.213	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	10	CYS	0	-0.054	-0.030	16.760	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	11	CYS	0	0.021	0.034	23.354	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	12	PHE	0	0.051	0.025	23.671	0.004	0.004	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.016	0.023	29.167	0.000	0.000	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.031	-0.040	28.796	0.001	0.001	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.028	-0.013	33.794	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.010	0.002	36.748	0.004	0.004	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.943	0.972	39.733	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	18	PRO	0	0.033	0.015	39.545	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	LEU	0	0.018	0.019	35.808	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.030	0.010	40.023	0.003	0.003	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.915	0.967	37.155	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.055	0.036	39.313	0.001	0.001	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.017	-0.010	39.445	0.000	0.000	0.000	0.000	0.000	0.000
25	A	24	ILE	0	-0.050	-0.017	33.806	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.794	0.888	31.601	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.805	-0.874	27.643	0.059	0.059	0.000	0.000	0.000	0.000
28	A	27	TYR	0	-0.110	-0.093	27.186	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	28	PHE	0	0.034	0.025	23.147	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	TYR	0	0.042	0.017	22.800	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.013	-0.013	22.079	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.019	0.009	15.995	0.034	0.034	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.025	0.005	17.500	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.950	0.972	11.066	-0.069	-0.069	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.017	-0.003	20.474	0.012	0.012	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.013	-0.009	22.742	0.009	0.009	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.017	0.037	24.165	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.001	-0.022	25.073	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.023	0.038	25.825	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.000	-0.004	25.938	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.003	0.004	28.508	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.010	0.005	27.987	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.023	-0.035	31.084	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.941	0.943	33.941	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.959	0.974	35.705	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.046	0.026	31.410	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.953	0.996	31.189	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.071	0.044	25.569	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.038	-0.026	30.470	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.012	0.000	30.645	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.002	-0.008	30.752	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	PRO	0	0.034	0.022	28.014	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.795	-0.866	30.476	0.093	0.093	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.886	0.953	33.570	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.881	0.917	36.112	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	57	TRP	0	0.073	0.031	36.398	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.021	0.004	32.301	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.925	0.921	29.775	-0.093	-0.093	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.775	-0.871	34.325	0.053	0.053	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.090	-0.079	35.528	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.005	0.009	29.656	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	63	ASN	0	0.044	0.032	32.722	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.009	0.016	34.454	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.066	-0.028	32.072	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.825	-0.894	29.159	0.101	0.101	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.048	-0.023	32.375	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.097	-0.046	34.433	-0.009	-0.009	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:0:PHE)