FMO DATABASE

FMODB ID: JQ6J9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-403324.257725
FMO2-HF: Nuclear repulsion	374903.471083
FMO2-HF: Total energy	-28420.786642
FMO2-MP2: Total energy	-28500.988152

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.
-2.417	0.305	0.252	-1.256	-1.718	-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 : 0.013 / q_NPA : -0.004

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	0.023	-0.018	2.928	-2.316	0.160	0.251	-1.196	-1.531	-0.002
4	A	3	LEU	0	0.028	0.016	3.650	-0.958	-0.712	0.001	-0.060	-0.187	0.000
5	A	4	SER	0	-0.015	-0.003	5.862	0.306	0.306	0.000	0.000	0.000	0.000
6	A	5	SER	0	0.003	0.012	9.121	-0.055	-0.055	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.016	-0.006	11.195	0.157	0.157	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.007	0.007	14.424	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	8	SER	0	-0.015	-0.019	16.040	0.020	0.020	0.000	0.000	0.000	0.000
10	A	9	ALA	0	-0.002	0.013	18.390	0.002	0.002	0.000	0.000	0.000	0.000
11	A	10	CYS	0	-0.043	-0.019	16.766	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	11	CYS	0	0.024	0.026	23.339	0.005	0.005	0.000	0.000	0.000	0.000
13	A	12	PHE	0	0.042	0.016	23.784	0.002	0.002	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.026	0.028	29.037	0.004	0.004	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.061	-0.044	28.626	0.000	0.000	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.030	-0.020	33.794	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.022	0.006	36.546	0.004	0.004	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.943	0.976	39.733	0.012	0.012	0.000	0.000	0.000	0.000
19	A	18	PRO	0	0.015	0.004	39.271	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	19	LEU	0	0.013	0.015	35.313	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.026	0.014	39.556	0.003	0.003	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.995	0.995	37.016	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.032	0.023	38.902	0.000	0.000	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.048	-0.028	38.741	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	24	ILE	0	-0.043	-0.013	33.353	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.859	0.926	30.776	0.035	0.035	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.842	-0.899	27.364	0.013	0.013	0.000	0.000	0.000	0.000
28	A	27	TYR	0	-0.099	-0.091	26.822	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	28	PHE	0	0.035	0.023	22.618	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	TYR	0	0.045	0.026	22.755	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.064	-0.038	21.784	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.063	0.026	15.902	0.029	0.029	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.047	0.023	17.588	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.932	0.956	11.126	0.258	0.258	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.050	0.017	20.224	0.011	0.011	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.055	-0.018	22.661	0.017	0.017	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.047	0.045	24.114	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.006	-0.031	25.077	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.031	0.034	25.743	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.001	0.003	25.704	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.009	-0.003	28.150	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.013	0.000	27.679	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.025	-0.026	30.804	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.961	0.967	33.599	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.937	0.972	35.861	0.029	0.029	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.013	-0.019	30.936	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.974	1.005	31.032	0.034	0.034	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.074	0.028	24.513	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.035	-0.018	29.877	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.009	0.001	30.437	0.002	0.002	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.032	0.012	30.539	0.003	0.003	0.000	0.000	0.000	0.000
52	A	53	PRO	0	0.027	0.014	27.765	0.002	0.002	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.882	-0.939	30.347	0.039	0.039	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.874	0.954	33.198	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.980	0.985	35.770	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	57	TRP	0	0.063	0.023	36.044	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.005	0.013	32.133	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	ARG	1	1.036	1.007	29.280	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.872	-0.937	34.260	0.025	0.025	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.087	-0.072	35.169	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.007	0.014	29.246	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	63	ASN	0	0.021	0.013	32.638	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.016	0.014	34.460	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.072	-0.044	31.749	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.846	-0.896	28.347	0.061	0.061	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.072	-0.012	32.244	0.004	0.004	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.078	-0.040	34.253	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:PHE)