FMO DATABASE

FMODB ID: 8928Y

Calculation Name: 4ZK9-B-Xray372

Preferred Name: C-C motif chemokine 2

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 4ZK9

Chain ID: B

ChEMBL ID: CHEMBL1649052

UniProt ID: P13500

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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-354157.367451
FMO2-HF: Nuclear repulsion	328513.264576
FMO2-HF: Total energy	-25644.102875
FMO2-MP2: Total energy	-25715.87496

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(B:9:VAL)

Summations of interaction energy for fragment #1(B:9:VAL)

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.
-4.346	-1.627	0.019	-1.104	-1.635	0.004

Interaction energy analysis for fragmet #1(B:9:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.026

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

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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	B	11	CYS	0	-0.055	-0.038	3.786	-1.469	0.150	-0.003	-0.774	-0.842	0.003
4	B	12	CYS	0	0.023	0.036	6.371	0.177	0.177	0.000	0.000	0.000	0.000
5	B	13	TYR	0	0.060	0.025	9.385	-0.105	-0.105	0.000	0.000	0.000	0.000
6	B	14	ASN	0	0.006	0.016	12.535	-0.024	-0.024	0.000	0.000	0.000	0.000
7	B	15	PHE	0	0.013	-0.004	12.112	0.059	0.059	0.000	0.000	0.000	0.000
8	B	16	THR	0	-0.016	-0.008	16.011	-0.043	-0.043	0.000	0.000	0.000	0.000
9	B	17	ASN	0	-0.028	-0.025	18.721	-0.013	-0.013	0.000	0.000	0.000	0.000
10	B	18	ARG	1	0.962	0.996	21.468	-0.156	-0.156	0.000	0.000	0.000	0.000
11	B	19	LYS	1	0.997	0.998	21.875	-0.112	-0.112	0.000	0.000	0.000	0.000
12	B	20	ILE	0	-0.042	-0.014	20.323	-0.013	-0.013	0.000	0.000	0.000	0.000
13	B	21	SER	0	0.006	0.000	22.902	0.004	0.004	0.000	0.000	0.000	0.000
14	B	22	VAL	0	0.111	0.035	22.216	0.012	0.012	0.000	0.000	0.000	0.000
15	B	23	GLN	0	0.035	0.023	22.696	0.019	0.019	0.000	0.000	0.000	0.000
16	B	24	ARG	1	0.948	0.979	22.318	-0.187	-0.187	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.053	-0.016	17.779	0.027	0.027	0.000	0.000	0.000	0.000
18	B	26	ALA	0	0.015	0.010	17.272	-0.029	-0.029	0.000	0.000	0.000	0.000
19	B	27	SER	0	0.009	0.012	13.862	0.000	0.000	0.000	0.000	0.000	0.000
20	B	28	TYR	0	-0.074	-0.085	12.843	0.035	0.035	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.876	0.946	4.089	-4.001	-3.841	-0.001	-0.024	-0.135	0.000
22	B	30	ARG	1	0.951	0.966	9.447	-0.351	-0.351	0.000	0.000	0.000	0.000
23	B	31	ILE	0	-0.069	-0.040	3.944	0.268	0.403	0.000	-0.019	-0.115	0.000
24	B	32	THR	0	0.010	-0.020	6.715	-0.101	-0.101	0.000	0.000	0.000	0.000
25	B	33	SER	0	-0.004	0.006	4.359	-0.290	-0.201	-0.001	-0.006	-0.083	0.000
26	B	34	SER	0	0.082	0.028	6.424	0.007	0.007	0.000	0.000	0.000	0.000
27	B	35	LYS	1	0.918	0.967	3.333	1.048	1.764	0.024	-0.281	-0.460	0.001
28	B	37	PRO	0	0.033	0.020	7.950	0.066	0.066	0.000	0.000	0.000	0.000
29	B	38	LYS	1	0.806	0.888	10.358	-0.043	-0.043	0.000	0.000	0.000	0.000
30	B	39	GLU	-1	-0.788	-0.851	9.819	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	40	ALA	0	-0.066	-0.053	8.898	0.018	0.018	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.020	0.010	10.132	0.048	0.048	0.000	0.000	0.000	0.000
33	B	42	ILE	0	-0.038	-0.022	6.827	-0.015	-0.015	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.031	0.018	10.908	0.037	0.037	0.000	0.000	0.000	0.000
35	B	44	LYS	1	0.856	0.910	9.788	-0.690	-0.690	0.000	0.000	0.000	0.000
36	B	45	THR	0	-0.049	-0.038	13.812	-0.068	-0.068	0.000	0.000	0.000	0.000
37	B	46	ILE	0	0.072	0.028	16.977	0.019	0.019	0.000	0.000	0.000	0.000
38	B	47	VAL	0	-0.047	-0.014	18.060	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	48	ALA	0	0.020	0.003	15.156	0.003	0.003	0.000	0.000	0.000	0.000
40	B	49	LYS	1	0.959	0.987	13.087	-0.186	-0.186	0.000	0.000	0.000	0.000
41	B	50	GLU	-1	-0.779	-0.874	8.054	1.527	1.527	0.000	0.000	0.000	0.000
42	B	51	ILE	0	-0.032	-0.019	11.786	-0.064	-0.064	0.000	0.000	0.000	0.000
43	B	53	ALA	0	0.007	-0.003	12.577	-0.103	-0.103	0.000	0.000	0.000	0.000
44	B	54	ASP	-1	-0.752	-0.847	13.345	0.184	0.184	0.000	0.000	0.000	0.000
45	B	55	PRO	0	0.040	0.018	13.302	-0.010	-0.010	0.000	0.000	0.000	0.000
46	B	56	LYS	1	0.829	0.899	16.035	-0.128	-0.128	0.000	0.000	0.000	0.000
47	B	57	GLN	0	0.052	0.024	19.124	-0.013	-0.013	0.000	0.000	0.000	0.000
48	B	58	LYS	1	0.929	0.960	20.659	-0.115	-0.115	0.000	0.000	0.000	0.000
49	B	59	TRP	0	0.025	0.018	18.924	0.012	0.012	0.000	0.000	0.000	0.000
50	B	60	VAL	0	-0.004	0.017	16.006	0.016	0.016	0.000	0.000	0.000	0.000
51	B	61	GLN	0	0.020	-0.013	18.630	0.016	0.016	0.000	0.000	0.000	0.000
52	B	62	ASP	-1	-0.842	-0.912	20.096	0.138	0.138	0.000	0.000	0.000	0.000
53	B	63	SER	0	-0.083	-0.056	19.296	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	64	MET	0	-0.065	-0.017	15.570	0.030	0.030	0.000	0.000	0.000	0.000
55	B	65	ASP	-1	-0.802	-0.910	18.797	0.148	0.148	0.000	0.000	0.000	0.000
56	B	66	HIS	0	-0.027	-0.001	22.258	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	67	LEU	0	-0.037	-0.011	17.376	0.000	0.000	0.000	0.000	0.000	0.000
58	B	68	ASP	-1	-0.822	-0.860	18.707	0.258	0.258	0.000	0.000	0.000	0.000
59	B	69	LYS	1	0.796	0.879	21.345	-0.160	-0.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:VAL)