FMO DATABASE

FMODB ID: G5NL1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-352712.643314
FMO2-HF: Nuclear repulsion	327068.730565
FMO2-HF: Total energy	-25643.912749
FMO2-MP2: Total energy	-25715.67934

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.
-2.929	0.027	0.006	-1.29	-1.672	0.006

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 : 0.058 / q_NPA : 0.023

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	-0.065	-0.041	3.790	-0.897	1.015	-0.015	-0.942	-0.955	0.004
4	B	12	CYS	0	0.004	0.025	6.682	0.122	0.122	0.000	0.000	0.000	0.000
5	B	13	TYR	0	0.032	-0.002	9.780	-0.091	-0.091	0.000	0.000	0.000	0.000
6	B	14	ASN	0	-0.030	-0.021	12.915	-0.024	-0.024	0.000	0.000	0.000	0.000
7	B	15	PHE	0	0.027	0.023	12.736	0.042	0.042	0.000	0.000	0.000	0.000
8	B	16	THR	0	0.009	0.010	16.530	-0.046	-0.046	0.000	0.000	0.000	0.000
9	B	17	ASN	0	-0.046	-0.027	18.547	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	18	ARG	1	0.985	0.996	21.922	-0.136	-0.136	0.000	0.000	0.000	0.000
11	B	19	LYS	1	0.998	0.999	22.171	-0.118	-0.118	0.000	0.000	0.000	0.000
12	B	20	ILE	0	-0.057	-0.024	20.408	-0.018	-0.018	0.000	0.000	0.000	0.000
13	B	21	SER	0	0.014	0.002	22.942	0.006	0.006	0.000	0.000	0.000	0.000
14	B	22	VAL	0	0.105	0.030	22.762	0.012	0.012	0.000	0.000	0.000	0.000
15	B	23	GLN	0	0.033	0.019	22.755	0.017	0.017	0.000	0.000	0.000	0.000
16	B	24	ARG	1	0.948	0.976	21.972	-0.166	-0.166	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.041	-0.001	17.802	0.019	0.019	0.000	0.000	0.000	0.000
18	B	26	ALA	0	0.037	0.024	17.135	-0.026	-0.026	0.000	0.000	0.000	0.000
19	B	27	SER	0	0.012	0.015	13.766	0.003	0.003	0.000	0.000	0.000	0.000
20	B	28	TYR	0	-0.060	-0.070	13.201	0.052	0.052	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.904	0.964	4.452	-3.301	-3.197	-0.001	-0.006	-0.098	0.000
22	B	30	ARG	1	0.955	0.973	10.005	-0.362	-0.362	0.000	0.000	0.000	0.000
23	B	31	ILE	0	-0.057	-0.036	4.208	0.490	0.608	-0.001	-0.014	-0.103	0.000
24	B	32	THR	0	0.002	-0.026	7.034	-0.188	-0.188	0.000	0.000	0.000	0.000
25	B	33	SER	0	-0.043	-0.006	4.328	-0.337	-0.255	-0.001	-0.006	-0.075	0.000
26	B	34	SER	0	0.082	0.030	6.409	0.025	0.025	0.000	0.000	0.000	0.000
27	B	35	LYS	1	0.902	0.954	3.315	1.139	1.879	0.024	-0.322	-0.441	0.002
28	B	37	PRO	0	0.054	0.037	7.775	0.045	0.045	0.000	0.000	0.000	0.000
29	B	38	LYS	1	0.872	0.945	11.328	-0.138	-0.138	0.000	0.000	0.000	0.000
30	B	39	GLU	-1	-0.775	-0.859	10.427	0.260	0.260	0.000	0.000	0.000	0.000
31	B	40	ALA	0	-0.065	-0.049	9.390	-0.018	-0.018	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.012	-0.003	10.368	0.101	0.101	0.000	0.000	0.000	0.000
33	B	42	ILE	0	-0.040	-0.026	6.823	-0.057	-0.057	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.022	0.016	10.911	0.020	0.020	0.000	0.000	0.000	0.000
35	B	44	LYS	1	0.846	0.905	9.540	-0.577	-0.577	0.000	0.000	0.000	0.000
36	B	45	THR	0	-0.055	-0.042	13.670	-0.058	-0.058	0.000	0.000	0.000	0.000
37	B	46	ILE	0	0.075	0.038	16.776	0.012	0.012	0.000	0.000	0.000	0.000
38	B	47	VAL	0	-0.050	-0.026	17.901	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	48	ALA	0	0.007	0.006	14.755	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	49	LYS	1	0.948	0.977	12.982	-0.161	-0.161	0.000	0.000	0.000	0.000
41	B	50	GLU	-1	-0.778	-0.877	7.850	1.271	1.271	0.000	0.000	0.000	0.000
42	B	51	ILE	0	-0.023	-0.015	11.462	-0.072	-0.072	0.000	0.000	0.000	0.000
43	B	53	ALA	0	0.026	0.002	12.809	-0.099	-0.099	0.000	0.000	0.000	0.000
44	B	54	ASP	-1	-0.777	-0.864	14.187	0.258	0.258	0.000	0.000	0.000	0.000
45	B	55	PRO	0	0.045	0.019	14.096	-0.015	-0.015	0.000	0.000	0.000	0.000
46	B	56	LYS	1	0.838	0.907	16.697	-0.202	-0.202	0.000	0.000	0.000	0.000
47	B	57	GLN	0	0.050	-0.010	19.736	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	58	LYS	1	0.921	0.964	21.414	-0.132	-0.132	0.000	0.000	0.000	0.000
49	B	59	TRP	0	0.019	0.015	19.291	0.011	0.011	0.000	0.000	0.000	0.000
50	B	60	VAL	0	0.016	0.028	16.866	0.011	0.011	0.000	0.000	0.000	0.000
51	B	61	GLN	0	0.026	-0.017	19.031	0.004	0.004	0.000	0.000	0.000	0.000
52	B	62	ASP	-1	-0.835	-0.900	20.853	0.146	0.146	0.000	0.000	0.000	0.000
53	B	63	SER	0	-0.084	-0.059	20.326	-0.008	-0.008	0.000	0.000	0.000	0.000
54	B	64	MET	0	-0.070	-0.024	16.415	0.030	0.030	0.000	0.000	0.000	0.000
55	B	65	ASP	-1	-0.802	-0.889	19.687	0.171	0.171	0.000	0.000	0.000	0.000
56	B	66	HIS	0	-0.051	-0.026	23.034	-0.011	-0.011	0.000	0.000	0.000	0.000
57	B	67	LEU	0	-0.046	-0.018	17.564	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	68	ASP	-1	-0.835	-0.871	19.303	0.261	0.261	0.000	0.000	0.000	0.000
59	B	69	LYS	1	0.804	0.903	21.619	-0.166	-0.166	0.000	0.000	0.000	0.000

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