FMO DATABASE

FMODB ID: 1932Z

Calculation Name: 3CE1-A-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: 3CE1

Chain ID: A

ChEMBL ID:

UniProt ID: A0ZPR9

Base Structure: X-ray

Registration Date: 2025-10-05

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1298505.064047
FMO2-HF: Nuclear repulsion	1243723.581987
FMO2-HF: Total energy	-54781.48206
FMO2-MP2: Total energy	-54941.926691

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-147.746	-139.079	15.696	-11.545	-12.815	-0.123

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.787 / q_NPA : 0.884

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	7	ALA	0	0.012	0.016	3.448	1.927	4.343	0.008	-1.166	-1.258	-0.004
20	A	24	THR	0	-0.005	-0.008	4.645	-3.999	-3.862	-0.001	-0.040	-0.097	0.000
21	A	25	GLN	0	0.084	0.027	2.933	7.055	8.653	0.030	-0.589	-1.039	-0.002
22	A	26	GLU	-1	-0.904	-0.933	1.771	-111.034	-111.613	13.261	-7.396	-5.285	-0.091
23	A	27	SER	0	0.000	-0.015	2.624	-8.429	-5.599	0.788	-1.613	-2.004	-0.020
24	A	28	SER	0	-0.002	-0.020	4.286	2.012	2.050	-0.001	-0.009	-0.028	0.000
106	A	110	LEU	0	0.018	0.015	2.577	0.978	2.016	1.270	-0.480	-1.827	-0.004
107	A	111	VAL	0	-0.025	-0.002	2.726	0.016	1.020	0.344	-0.240	-1.108	-0.002
108	A	112	GLY	0	0.058	0.044	5.357	1.762	1.776	-0.001	0.000	-0.012	0.000
113	A	117	ILE	0	0.015	0.001	4.359	0.605	0.678	-0.001	-0.005	-0.067	0.000
150	A	155	ILE	0	0.024	-0.008	4.289	-2.241	-2.143	-0.001	-0.007	-0.090	0.000
4	A	8	ILE	0	-0.029	-0.022	5.503	0.604	0.604	0.000	0.000	0.000	0.000
5	A	9	ALA	0	0.038	0.034	9.352	0.689	0.689	0.000	0.000	0.000	0.000
6	A	10	VAL	0	-0.020	-0.012	12.594	0.236	0.236	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.043	-0.021	15.323	0.236	0.236	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.969	0.965	18.636	13.456	13.456	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.062	0.021	22.229	-0.370	-0.370	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.954	-0.944	24.975	-9.480	-9.480	0.000	0.000	0.000	0.000
11	A	15	SER	0	-0.013	-0.025	26.811	0.244	0.244	0.000	0.000	0.000	0.000
12	A	16	PRO	0	0.012	0.007	28.178	-0.188	-0.188	0.000	0.000	0.000	0.000
13	A	17	VAL	0	-0.024	0.006	23.458	-0.263	-0.263	0.000	0.000	0.000	0.000
14	A	18	GLN	0	-0.010	-0.011	22.520	-0.596	-0.596	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.042	0.015	19.752	0.174	0.174	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.062	-0.014	14.205	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	21	ILE	0	-0.002	0.009	11.809	0.155	0.155	0.000	0.000	0.000	0.000
18	A	22	THR	0	-0.046	-0.031	9.469	-1.281	-1.281	0.000	0.000	0.000	0.000
19	A	23	PHE	0	0.043	0.006	6.305	1.885	1.885	0.000	0.000	0.000	0.000
25	A	29	GLY	0	-0.014	0.007	7.322	3.434	3.434	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.002	0.005	8.282	1.934	1.934	0.000	0.000	0.000	0.000
27	A	31	PRO	0	0.005	0.017	8.340	-1.791	-1.791	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.025	-0.008	6.082	-4.694	-4.694	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.012	-0.007	7.632	6.116	6.116	0.000	0.000	0.000	0.000
30	A	34	VAL	0	-0.029	-0.016	8.901	-3.055	-3.055	0.000	0.000	0.000	0.000
31	A	35	SER	0	0.002	-0.015	11.606	2.026	2.026	0.000	0.000	0.000	0.000
32	A	36	GLY	0	0.042	0.027	13.291	-1.116	-1.116	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.888	-0.946	16.040	-13.336	-13.336	0.000	0.000	0.000	0.000
34	A	38	ILE	0	-0.007	-0.007	18.359	-0.238	-0.238	0.000	0.000	0.000	0.000
35	A	39	LYS	1	0.894	0.946	21.321	13.813	13.813	0.000	0.000	0.000	0.000
36	A	40	ASN	0	-0.026	-0.031	24.968	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	41	MET	0	-0.018	0.005	24.065	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	42	ASP	-1	-0.786	-0.871	28.186	-9.595	-9.595	0.000	0.000	0.000	0.000
39	A	43	ALA	0	0.007	0.016	29.889	-0.388	-0.388	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.088	-0.046	31.193	0.373	0.373	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.036	0.038	29.907	0.228	0.228	0.000	0.000	0.000	0.000
42	A	46	GLN	0	-0.046	-0.028	27.406	-0.756	-0.756	0.000	0.000	0.000	0.000
43	A	47	ARG	1	0.808	0.890	25.177	10.728	10.728	0.000	0.000	0.000	0.000
44	A	48	GLY	0	0.053	0.032	23.899	-0.537	-0.537	0.000	0.000	0.000	0.000
45	A	49	PHE	0	-0.033	-0.030	15.530	-0.200	-0.200	0.000	0.000	0.000	0.000
46	A	50	HIS	1	0.842	0.900	18.305	13.254	13.254	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.005	0.005	12.650	-0.133	-0.133	0.000	0.000	0.000	0.000
48	A	52	HIS	0	-0.052	-0.037	15.706	0.685	0.685	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.004	-0.006	16.020	-0.658	-0.658	0.000	0.000	0.000	0.000
50	A	54	PHE	0	0.032	0.007	16.444	-0.727	-0.727	0.000	0.000	0.000	0.000
51	A	55	GLY	0	0.022	0.039	15.524	-0.085	-0.085	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.837	-0.903	16.239	-12.204	-12.204	0.000	0.000	0.000	0.000
53	A	57	ASN	0	-0.002	0.002	19.777	0.260	0.260	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.043	-0.030	21.640	0.511	0.511	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.014	-0.011	24.920	0.530	0.530	0.000	0.000	0.000	0.000
56	A	60	GLY	0	0.050	0.027	24.258	0.112	0.112	0.000	0.000	0.000	0.000
57	A	61	CYS	0	-0.005	-0.027	19.003	-0.511	-0.511	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.012	0.008	23.198	-0.217	-0.217	0.000	0.000	0.000	0.000
59	A	63	SER	0	-0.017	-0.026	22.701	0.141	0.141	0.000	0.000	0.000	0.000
60	A	64	ALA	0	0.028	0.029	19.195	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.020	0.022	20.062	-0.439	-0.439	0.000	0.000	0.000	0.000
62	A	66	PRO	0	0.013	0.019	22.033	0.114	0.114	0.000	0.000	0.000	0.000
63	A	67	HIS	0	0.033	0.014	19.683	-0.343	-0.343	0.000	0.000	0.000	0.000
64	A	68	PHE	0	-0.036	-0.024	12.526	0.513	0.513	0.000	0.000	0.000	0.000
65	A	69	ASN	0	0.013	-0.008	17.427	-0.711	-0.711	0.000	0.000	0.000	0.000
66	A	70	PRO	0	-0.003	0.007	15.015	0.697	0.697	0.000	0.000	0.000	0.000
67	A	71	THR	0	-0.004	-0.013	18.161	0.149	0.149	0.000	0.000	0.000	0.000
68	A	72	GLY	0	-0.017	0.011	20.536	0.495	0.495	0.000	0.000	0.000	0.000
69	A	73	THR	0	0.015	0.014	22.454	0.740	0.740	0.000	0.000	0.000	0.000
70	A	74	ASN	0	-0.009	-0.012	25.002	-0.067	-0.067	0.000	0.000	0.000	0.000
71	A	75	HIS	1	0.759	0.875	22.927	12.222	12.222	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.033	0.011	23.771	0.540	0.540	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.819	-0.907	23.479	-13.753	-13.753	0.000	0.000	0.000	0.000
74	A	78	ARG	1	0.899	0.969	16.976	16.086	16.086	0.000	0.000	0.000	0.000
75	A	79	THR	0	-0.090	-0.067	19.754	-0.481	-0.481	0.000	0.000	0.000	0.000
76	A	80	ALA	0	-0.031	-0.002	22.198	0.407	0.407	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.933	-0.965	22.480	-11.822	-11.822	0.000	0.000	0.000	0.000
78	A	82	VAL	0	-0.066	-0.033	23.408	-0.286	-0.286	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.747	0.844	15.425	17.526	17.526	0.000	0.000	0.000	0.000
80	A	84	HIS	0	-0.036	-0.019	19.853	-0.469	-0.469	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.029	0.017	13.847	-0.367	-0.367	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.025	-0.015	15.241	-0.985	-0.985	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.730	-0.854	16.291	-13.826	-13.826	0.000	0.000	0.000	0.000
84	A	88	LEU	0	-0.013	-0.022	13.775	-0.635	-0.635	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.038	0.031	18.139	0.088	0.088	0.000	0.000	0.000	0.000
86	A	90	ASN	0	0.003	0.007	21.950	0.045	0.045	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.022	-0.002	19.525	-0.417	-0.417	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.951	0.966	22.702	12.464	12.464	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.020	-0.032	24.707	-0.474	-0.474	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.822	-0.917	27.108	-11.282	-11.282	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.017	-0.014	29.244	0.126	0.126	0.000	0.000	0.000	0.000
92	A	96	SER	0	-0.057	-0.021	29.744	0.351	0.351	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.026	0.028	29.380	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	98	VAL	0	-0.056	-0.034	23.933	-0.346	-0.346	0.000	0.000	0.000	0.000
95	A	99	ALA	0	0.022	0.025	22.277	0.154	0.154	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.879	0.936	20.933	12.259	12.259	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.027	-0.004	16.135	0.177	0.177	0.000	0.000	0.000	0.000
98	A	102	GLN	0	0.036	0.026	12.901	-0.772	-0.772	0.000	0.000	0.000	0.000
99	A	103	ILE	0	-0.024	-0.012	14.520	1.135	1.135	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.001	0.005	11.344	-1.766	-1.766	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.763	-0.872	11.795	-18.316	-18.316	0.000	0.000	0.000	0.000
102	A	106	SER	0	0.003	-0.012	11.167	-2.355	-2.355	0.000	0.000	0.000	0.000
103	A	107	GLN	0	-0.003	0.015	12.874	0.184	0.184	0.000	0.000	0.000	0.000
104	A	108	LEU	0	-0.038	-0.012	9.637	-0.279	-0.279	0.000	0.000	0.000	0.000
105	A	109	SER	0	0.033	-0.007	7.072	-3.020	-3.020	0.000	0.000	0.000	0.000
109	A	113	PRO	0	0.005	-0.013	9.129	-0.165	-0.165	0.000	0.000	0.000	0.000
110	A	114	HIS	0	0.044	0.015	11.280	0.506	0.506	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.059	-0.018	6.060	-0.396	-0.396	0.000	0.000	0.000	0.000
112	A	116	ILE	0	0.009	-0.003	7.793	2.647	2.647	0.000	0.000	0.000	0.000
114	A	118	GLY	0	-0.012	0.000	8.324	1.463	1.463	0.000	0.000	0.000	0.000
115	A	119	ARG	1	0.819	0.919	11.409	20.946	20.946	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.011	-0.019	13.119	-0.529	-0.529	0.000	0.000	0.000	0.000
117	A	121	ILE	0	-0.034	-0.003	13.340	0.084	0.084	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.005	-0.014	15.228	0.530	0.530	0.000	0.000	0.000	0.000
119	A	123	ILE	0	-0.031	-0.010	19.021	-0.313	-0.313	0.000	0.000	0.000	0.000
120	A	124	HIS	0	-0.020	-0.016	21.473	-0.114	-0.114	0.000	0.000	0.000	0.000
121	A	125	ALA	0	0.002	-0.004	25.053	-0.040	-0.040	0.000	0.000	0.000	0.000
122	A	126	GLY	0	0.008	0.015	28.496	0.307	0.307	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.910	-0.963	27.648	-10.729	-10.729	0.000	0.000	0.000	0.000
124	A	128	ASP	-1	-0.775	-0.877	24.213	-12.241	-12.241	0.000	0.000	0.000	0.000
125	A	129	ASP	-1	-0.745	-0.851	27.297	-10.016	-10.016	0.000	0.000	0.000	0.000
126	A	130	LEU	0	-0.035	-0.033	25.749	0.184	0.184	0.000	0.000	0.000	0.000
127	A	131	GLY	0	-0.006	0.011	27.835	-0.144	-0.144	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.819	0.913	29.500	10.456	10.456	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.022	-0.030	32.761	0.333	0.333	0.000	0.000	0.000	0.000
130	A	134	ASP	-1	-0.899	-0.949	35.101	-8.057	-8.057	0.000	0.000	0.000	0.000
131	A	135	HIS	0	0.046	0.035	34.370	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	136	PRO	0	0.011	-0.002	34.324	-0.254	-0.254	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.857	-0.946	29.661	-10.224	-10.224	0.000	0.000	0.000	0.000
134	A	138	SER	0	-0.056	-0.017	29.569	-0.441	-0.441	0.000	0.000	0.000	0.000
135	A	139	LEU	0	0.030	-0.011	28.826	-0.434	-0.434	0.000	0.000	0.000	0.000
136	A	140	LYS	1	0.851	0.943	27.323	9.325	9.325	0.000	0.000	0.000	0.000
137	A	141	THR	0	-0.033	-0.053	25.069	-0.434	-0.434	0.000	0.000	0.000	0.000
138	A	142	GLY	0	0.034	0.028	25.850	-0.287	-0.287	0.000	0.000	0.000	0.000
139	A	143	ASN	0	-0.040	-0.021	27.697	0.132	0.132	0.000	0.000	0.000	0.000
140	A	144	ALA	0	0.043	0.033	26.170	0.175	0.175	0.000	0.000	0.000	0.000
141	A	145	GLY	0	0.022	0.014	28.242	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	146	ALA	0	0.009	0.004	28.043	-0.316	-0.316	0.000	0.000	0.000	0.000
143	A	147	ARG	1	0.857	0.919	23.088	11.929	11.929	0.000	0.000	0.000	0.000
144	A	148	SER	0	0.033	0.021	25.124	0.135	0.135	0.000	0.000	0.000	0.000
145	A	149	ALA	0	0.004	0.018	21.801	0.136	0.136	0.000	0.000	0.000	0.000
146	A	151	GLY	0	0.066	0.032	16.026	0.363	0.363	0.000	0.000	0.000	0.000
147	A	152	VAL	0	-0.033	-0.004	13.194	-0.674	-0.674	0.000	0.000	0.000	0.000
148	A	153	ILE	0	-0.037	-0.016	7.924	-0.494	-0.494	0.000	0.000	0.000	0.000
149	A	154	GLY	0	0.018	0.017	9.326	0.085	0.085	0.000	0.000	0.000	0.000
151	A	156	ALA	0	-0.064	-0.029	5.257	3.749	3.749	0.000	0.000	0.000	0.000
152	A	157	ALA	-1	-0.837	-0.901	5.476	-45.783	-45.783	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)