FMO DATABASE

FMODB ID: 3J3YL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-403123.500392
FMO2-HF: Nuclear repulsion	374702.484355
FMO2-HF: Total energy	-28421.016037
FMO2-MP2: Total energy	-28501.188043

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.
-2.6	0.052	0.164	-1.182	-1.634	-0.001

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 : 0.005 / q_NPA : -0.007

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	0.019	-0.016	3.038	-2.126	0.261	0.163	-1.117	-1.433	-0.001
4	A	3	LEU	0	0.018	0.010	3.692	-1.010	-0.745	0.001	-0.065	-0.201	0.000
5	A	4	SER	0	-0.009	-0.003	5.959	0.246	0.246	0.000	0.000	0.000	0.000
6	A	5	SER	0	0.033	0.023	9.184	-0.079	-0.079	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.049	-0.018	11.248	0.131	0.131	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.043	0.025	14.473	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	8	SER	0	-0.058	-0.038	16.084	0.025	0.025	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.007	0.014	18.480	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	10	CYS	0	-0.058	-0.026	16.792	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	11	CYS	0	0.041	0.042	23.357	0.004	0.004	0.000	0.000	0.000	0.000
13	A	12	PHE	0	0.046	0.020	23.820	0.002	0.002	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.019	0.028	29.157	0.003	0.003	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.059	-0.050	28.601	0.000	0.000	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.026	-0.018	33.794	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.020	0.006	36.546	0.003	0.003	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.943	0.978	39.733	0.000	0.000	0.000	0.000	0.000	0.000
19	A	18	PRO	0	0.025	0.010	39.338	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	19	LEU	0	0.016	0.017	35.574	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.023	0.009	39.677	0.003	0.003	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.980	0.994	36.921	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.036	0.022	39.027	0.001	0.001	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.035	-0.022	38.909	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	24	ILE	0	-0.047	-0.016	33.499	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.828	0.904	31.057	0.012	0.012	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.827	-0.893	27.462	0.041	0.041	0.000	0.000	0.000	0.000
28	A	27	TYR	0	-0.091	-0.088	27.154	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	28	PHE	0	0.026	0.023	22.715	0.002	0.002	0.000	0.000	0.000	0.000
30	A	29	TYR	0	0.052	0.027	22.825	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.021	-0.016	21.849	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.028	0.005	15.854	0.027	0.027	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.039	0.019	17.605	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.942	0.965	11.143	0.116	0.116	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.058	0.023	20.326	0.010	0.010	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.057	-0.027	22.752	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.037	0.040	24.135	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.013	-0.024	25.073	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.021	0.032	25.743	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.004	-0.003	25.848	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.001	0.001	28.270	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.011	0.001	27.756	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.009	-0.018	30.915	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.957	0.967	33.701	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.928	0.967	35.956	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.001	-0.006	30.925	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.971	1.005	31.121	0.016	0.016	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.067	0.026	24.887	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.044	-0.025	29.978	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.017	0.004	30.431	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.016	0.004	30.539	0.005	0.005	0.000	0.000	0.000	0.000
52	A	53	PRO	0	0.036	0.023	27.824	0.001	0.001	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.797	-0.885	30.441	0.059	0.059	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.883	0.959	33.211	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.958	0.982	35.779	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	57	TRP	0	0.064	0.022	36.045	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.018	0.007	32.146	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.937	0.940	29.369	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.834	-0.925	34.298	0.037	0.037	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.100	-0.079	35.412	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.012	0.012	29.593	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	ASN	0	0.027	0.016	32.779	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.014	0.013	34.605	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.071	-0.043	31.901	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.844	-0.897	28.765	0.082	0.082	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.066	-0.010	32.385	0.004	0.004	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.085	-0.042	34.158	-0.007	-0.007	0.000	0.000	0.000	0.000

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