FMO DATABASE

FMODB ID: 2RJGR

Calculation Name: 3E6Z-X-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion | copper (ii) ion

Ligand 3-letter code: ACT | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E6Z

Chain ID: X

ChEMBL ID:

UniProt ID: P77214

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-493131.520919
FMO2-HF: Nuclear repulsion	461980.756023
FMO2-HF: Total energy	-31150.764896
FMO2-MP2: Total energy	-31239.928496

3D Structure Molmil

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:9:MET)

Summations of interaction energy for fragment #1(A:9:MET)

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.
19.319	20.888	-0.017	-0.748	-0.803	-0.001

Interaction energy analysis for fragmet #1(A:9:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.881

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	A	11	ALA	0	0.006	0.002	3.730	-3.246	-1.677	-0.017	-0.748	-0.803	-0.001
4	A	12	GLN	0	-0.004	-0.013	4.813	6.334	6.334	0.000	0.000	0.000	0.000
5	A	13	PRO	0	0.008	0.001	7.386	2.379	2.379	0.000	0.000	0.000	0.000
6	A	14	GLN	0	-0.020	0.000	9.334	1.591	1.591	0.000	0.000	0.000	0.000
7	A	15	VAL	0	-0.023	-0.018	13.341	1.219	1.219	0.000	0.000	0.000	0.000
8	A	16	ILE	0	-0.028	-0.005	15.034	-0.799	-0.799	0.000	0.000	0.000	0.000
9	A	17	SER	0	0.008	-0.013	17.915	0.661	0.661	0.000	0.000	0.000	0.000
10	A	18	ALA	0	-0.058	-0.031	21.127	-0.361	-0.361	0.000	0.000	0.000	0.000
11	A	19	THR	0	-0.002	-0.025	23.737	0.231	0.231	0.000	0.000	0.000	0.000
12	A	20	GLY	0	0.049	0.025	27.244	-0.323	-0.323	0.000	0.000	0.000	0.000
13	A	21	VAL	0	-0.043	-0.005	29.962	0.297	0.297	0.000	0.000	0.000	0.000
14	A	22	VAL	0	0.010	0.011	32.817	-0.195	-0.195	0.000	0.000	0.000	0.000
15	A	23	LYS	1	0.901	0.938	33.756	8.992	8.992	0.000	0.000	0.000	0.000
16	A	24	GLY	0	0.019	0.000	34.825	0.306	0.306	0.000	0.000	0.000	0.000
17	A	25	ILE	0	0.005	0.005	34.577	-0.345	-0.345	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.790	-0.851	35.156	-8.438	-8.438	0.000	0.000	0.000	0.000
19	A	27	LEU	0	0.043	0.006	35.245	-0.307	-0.307	0.000	0.000	0.000	0.000
20	A	28	GLU	-1	-0.910	-0.926	37.384	-7.700	-7.700	0.000	0.000	0.000	0.000
21	A	29	SER	0	-0.093	-0.090	34.101	-0.291	-0.291	0.000	0.000	0.000	0.000
22	A	30	LYS	1	0.837	0.910	31.829	8.575	8.575	0.000	0.000	0.000	0.000
23	A	31	LYS	1	0.883	0.937	27.907	10.683	10.683	0.000	0.000	0.000	0.000
24	A	32	ILE	0	0.036	0.023	30.132	0.387	0.387	0.000	0.000	0.000	0.000
25	A	33	THR	0	-0.043	-0.018	29.842	-0.428	-0.428	0.000	0.000	0.000	0.000
26	A	34	ILE	0	0.004	0.002	27.961	0.402	0.402	0.000	0.000	0.000	0.000
27	A	35	HIS	0	0.043	0.025	29.085	-0.291	-0.291	0.000	0.000	0.000	0.000
28	A	36	HIS	1	0.809	0.884	23.339	13.356	13.356	0.000	0.000	0.000	0.000
29	A	37	ASP	-1	-0.763	-0.870	27.076	-10.864	-10.864	0.000	0.000	0.000	0.000
30	A	38	PRO	0	-0.006	0.006	24.266	-0.515	-0.515	0.000	0.000	0.000	0.000
31	A	39	ILE	0	-0.024	0.002	18.931	-0.073	-0.073	0.000	0.000	0.000	0.000
32	A	40	ALA	0	0.039	0.004	19.215	-0.791	-0.791	0.000	0.000	0.000	0.000
33	A	41	ALA	0	-0.018	-0.009	15.505	-0.651	-0.651	0.000	0.000	0.000	0.000
34	A	42	VAL	0	-0.021	-0.016	13.749	-1.712	-1.712	0.000	0.000	0.000	0.000
35	A	43	ASN	0	-0.060	-0.023	14.921	0.869	0.869	0.000	0.000	0.000	0.000
36	A	44	ALA	0	0.020	0.027	18.158	0.482	0.482	0.000	0.000	0.000	0.000
37	A	45	PRO	0	0.038	0.018	20.605	0.213	0.213	0.000	0.000	0.000	0.000
38	A	46	GLU	-1	-0.866	-0.952	24.424	-11.551	-11.551	0.000	0.000	0.000	0.000
39	A	47	MET	0	-0.041	-0.023	22.799	-0.254	-0.254	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.041	-0.009	27.311	0.139	0.139	0.000	0.000	0.000	0.000
41	A	49	MET	0	-0.020	0.001	21.560	-0.252	-0.252	0.000	0.000	0.000	0.000
42	A	50	ARG	1	0.944	0.972	27.050	10.525	10.525	0.000	0.000	0.000	0.000
43	A	51	PHE	0	0.051	0.029	22.622	-0.391	-0.391	0.000	0.000	0.000	0.000
44	A	52	THR	0	-0.020	-0.007	25.727	0.633	0.633	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.005	0.005	26.697	-0.368	-0.368	0.000	0.000	0.000	0.000
46	A	54	THR	0	0.006	-0.010	25.333	0.019	0.019	0.000	0.000	0.000	0.000
47	A	55	PRO	0	0.015	-0.009	28.691	0.138	0.138	0.000	0.000	0.000	0.000
48	A	56	GLN	0	0.030	0.013	25.178	0.218	0.218	0.000	0.000	0.000	0.000
49	A	57	THR	0	-0.049	-0.022	26.712	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	58	LYS	1	0.873	0.931	27.854	11.446	11.446	0.000	0.000	0.000	0.000
51	A	59	MET	0	0.017	0.009	29.820	-0.269	-0.269	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.011	0.004	32.357	0.174	0.174	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.964	-0.982	35.015	-7.772	-7.772	0.000	0.000	0.000	0.000
54	A	62	ILE	0	-0.019	-0.012	33.127	-0.152	-0.152	0.000	0.000	0.000	0.000
55	A	63	LYS	1	0.884	0.926	37.259	8.015	8.015	0.000	0.000	0.000	0.000
56	A	64	THR	0	-0.007	-0.015	37.804	-0.181	-0.181	0.000	0.000	0.000	0.000
57	A	65	GLY	0	-0.028	-0.014	37.845	0.212	0.212	0.000	0.000	0.000	0.000
58	A	66	ASP	-1	-0.808	-0.875	36.495	-8.276	-8.276	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.904	0.949	34.047	8.731	8.731	0.000	0.000	0.000	0.000
60	A	68	VAL	0	-0.025	-0.020	30.145	0.137	0.137	0.000	0.000	0.000	0.000
61	A	69	ALA	0	0.016	0.013	28.052	-0.266	-0.266	0.000	0.000	0.000	0.000
62	A	70	PHE	0	-0.027	-0.019	24.351	0.274	0.274	0.000	0.000	0.000	0.000
63	A	71	ASN	0	0.015	0.012	21.620	-1.126	-1.126	0.000	0.000	0.000	0.000
64	A	72	PHE	0	-0.007	-0.008	18.988	0.555	0.555	0.000	0.000	0.000	0.000
65	A	73	VAL	0	0.064	0.040	17.105	-0.840	-0.840	0.000	0.000	0.000	0.000
66	A	74	GLN	0	0.021	0.022	15.511	1.217	1.217	0.000	0.000	0.000	0.000
67	A	75	GLN	0	0.002	-0.005	16.132	-0.479	-0.479	0.000	0.000	0.000	0.000
68	A	76	GLY	0	0.036	0.014	16.987	0.912	0.912	0.000	0.000	0.000	0.000
69	A	77	ASN	0	0.000	-0.006	18.375	-0.450	-0.450	0.000	0.000	0.000	0.000
70	A	78	LEU	0	-0.043	-0.012	21.153	0.729	0.729	0.000	0.000	0.000	0.000
71	A	79	SER	0	0.013	0.004	20.569	-0.609	-0.609	0.000	0.000	0.000	0.000
72	A	80	LEU	0	-0.039	-0.025	21.146	0.927	0.927	0.000	0.000	0.000	0.000
73	A	81	LEU	0	0.026	0.014	22.147	-0.564	-0.564	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.001	0.016	20.734	0.242	0.242	0.000	0.000	0.000	0.000
75	A	83	ASP	-1	-0.867	-0.923	24.002	-12.214	-12.214	0.000	0.000	0.000	0.000
76	A	84	ILE	0	0.024	-0.002	26.689	-0.273	-0.273	0.000	0.000	0.000	0.000
77	A	85	LYS	1	0.903	0.955	29.420	10.405	10.405	0.000	0.000	0.000	0.000
78	A	86	VAL	0	0.080	0.043	32.026	-0.213	-0.213	0.000	0.000	0.000	0.000
79	A	87	SER	0	-0.096	-0.048	31.733	-0.223	-0.223	0.000	0.000	0.000	0.000
80	A	88	GLN	-1	-0.820	-0.899	33.849	-9.217	-9.217	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:MET)