FMO DATABASE

FMODB ID: 1N42Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-352734.890169
FMO2-HF: Nuclear repulsion	327091.116039
FMO2-HF: Total energy	-25643.774131
FMO2-MP2: Total energy	-25715.564535

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.
-2.856	0.197	0.01	-1.354	-1.709	0.005

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 : 0.056 / q_NPA : 0.025

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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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	B	11	CYS	0	-0.064	-0.034	3.841	-0.895	1.085	-0.015	-1.002	-0.963	0.004
4	B	12	CYS	0	0.002	0.018	6.759	0.094	0.094	0.000	0.000	0.000	0.000
5	B	13	TYR	0	0.034	0.003	9.554	-0.099	-0.099	0.000	0.000	0.000	0.000
6	B	14	ASN	0	-0.035	-0.026	12.992	-0.035	-0.035	0.000	0.000	0.000	0.000
7	B	15	PHE	0	0.008	0.020	13.112	0.043	0.043	0.000	0.000	0.000	0.000
8	B	16	THR	0	-0.004	0.008	16.572	-0.050	-0.050	0.000	0.000	0.000	0.000
9	B	17	ASN	0	-0.032	-0.020	18.581	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	18	ARG	1	0.973	0.992	21.936	-0.149	-0.149	0.000	0.000	0.000	0.000
11	B	19	LYS	1	1.001	1.005	22.150	-0.125	-0.125	0.000	0.000	0.000	0.000
12	B	20	ILE	0	-0.054	-0.028	20.617	-0.021	-0.021	0.000	0.000	0.000	0.000
13	B	21	SER	0	0.009	-0.002	22.895	0.006	0.006	0.000	0.000	0.000	0.000
14	B	22	VAL	0	0.101	0.032	22.635	0.012	0.012	0.000	0.000	0.000	0.000
15	B	23	GLN	0	0.037	0.020	22.631	0.017	0.017	0.000	0.000	0.000	0.000
16	B	24	ARG	1	0.948	0.976	21.983	-0.172	-0.172	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.039	-0.003	17.600	0.019	0.019	0.000	0.000	0.000	0.000
18	B	26	ALA	0	0.037	0.027	16.930	-0.027	-0.027	0.000	0.000	0.000	0.000
19	B	27	SER	0	0.011	0.013	13.848	0.005	0.005	0.000	0.000	0.000	0.000
20	B	28	TYR	0	-0.063	-0.071	13.190	0.061	0.061	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.902	0.961	4.456	-3.353	-3.251	-0.001	-0.004	-0.096	0.000
22	B	30	ARG	1	0.958	0.976	10.057	-0.377	-0.377	0.000	0.000	0.000	0.000
23	B	31	ILE	0	-0.066	-0.041	4.059	0.546	0.686	0.000	-0.021	-0.119	0.000
24	B	32	THR	0	0.009	-0.014	7.068	-0.198	-0.198	0.000	0.000	0.000	0.000
25	B	33	SER	0	-0.046	-0.009	4.345	-0.366	-0.283	-0.001	-0.006	-0.076	0.000
26	B	34	SER	0	0.084	0.032	6.403	0.029	0.029	0.000	0.000	0.000	0.000
27	B	35	LYS	1	0.906	0.958	3.312	1.200	1.948	0.027	-0.321	-0.455	0.001
28	B	37	PRO	0	0.053	0.036	7.809	0.033	0.033	0.000	0.000	0.000	0.000
29	B	38	LYS	1	0.870	0.939	11.361	-0.178	-0.178	0.000	0.000	0.000	0.000
30	B	39	GLU	-1	-0.774	-0.857	10.485	0.340	0.340	0.000	0.000	0.000	0.000
31	B	40	ALA	0	-0.066	-0.056	9.567	-0.024	-0.024	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.009	-0.001	10.434	0.107	0.107	0.000	0.000	0.000	0.000
33	B	42	ILE	0	-0.033	-0.019	6.718	-0.041	-0.041	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.013	0.007	10.784	0.011	0.011	0.000	0.000	0.000	0.000
35	B	44	LYS	1	0.897	0.953	9.354	-0.604	-0.604	0.000	0.000	0.000	0.000
36	B	45	THR	0	-0.049	-0.039	13.589	-0.060	-0.060	0.000	0.000	0.000	0.000
37	B	46	ILE	0	0.065	0.033	16.740	0.010	0.010	0.000	0.000	0.000	0.000
38	B	47	VAL	0	-0.048	-0.023	17.852	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	48	ALA	0	0.017	0.009	14.785	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	49	LYS	1	0.943	0.977	13.077	-0.167	-0.167	0.000	0.000	0.000	0.000
41	B	50	GLU	-1	-0.830	-0.929	7.516	1.405	1.405	0.000	0.000	0.000	0.000
42	B	51	ILE	0	-0.013	-0.007	11.488	-0.069	-0.069	0.000	0.000	0.000	0.000
43	B	53	ALA	0	0.034	-0.002	12.803	-0.107	-0.107	0.000	0.000	0.000	0.000
44	B	54	ASP	-1	-0.781	-0.869	14.267	0.294	0.294	0.000	0.000	0.000	0.000
45	B	55	PRO	0	0.026	0.013	14.236	-0.018	-0.018	0.000	0.000	0.000	0.000
46	B	56	LYS	1	0.863	0.920	17.035	-0.233	-0.233	0.000	0.000	0.000	0.000
47	B	57	GLN	0	0.039	-0.018	19.799	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	58	LYS	1	0.895	0.953	21.484	-0.139	-0.139	0.000	0.000	0.000	0.000
49	B	59	TRP	0	0.045	0.020	19.304	0.009	0.009	0.000	0.000	0.000	0.000
50	B	60	VAL	0	0.015	0.029	16.895	0.009	0.009	0.000	0.000	0.000	0.000
51	B	61	GLN	0	0.021	-0.019	18.679	0.000	0.000	0.000	0.000	0.000	0.000
52	B	62	ASP	-1	-0.799	-0.884	20.915	0.155	0.155	0.000	0.000	0.000	0.000
53	B	63	SER	0	-0.090	-0.056	20.139	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	64	MET	0	-0.069	-0.030	16.498	0.030	0.030	0.000	0.000	0.000	0.000
55	B	65	ASP	-1	-0.787	-0.875	19.749	0.182	0.182	0.000	0.000	0.000	0.000
56	B	66	HIS	0	-0.067	-0.039	23.086	-0.015	-0.015	0.000	0.000	0.000	0.000
57	B	67	LEU	0	-0.056	-0.025	17.521	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	68	ASP	-1	-0.822	-0.863	19.472	0.266	0.266	0.000	0.000	0.000	0.000
59	B	69	LYS	1	0.800	0.907	21.685	-0.174	-0.174	0.000	0.000	0.000	0.000

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