FMO DATABASE

FMODB ID: RL268

Calculation Name: 4L05-A-Xray547

Preferred Name:

Target Type:

Ligand Name: copper (ii) ion | copper (i) ion

Ligand 3-letter code: CU | CU1

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4L05

Chain ID: A

ChEMBL ID:

UniProt ID: P15453

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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1361572.624849
FMO2-HF: Nuclear repulsion	1304604.087601
FMO2-HF: Total energy	-56968.537248
FMO2-MP2: Total energy	-57133.223282

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:1:GLU)

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

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.
-110.242	-109.201	37.19	-19.927	-18.303	0.041

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / 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

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	3	THR	0	0.050	0.029	3.551	4.744	7.252	-0.004	-1.284	-1.220	-0.004
25	A	25	SER	0	-0.023	-0.029	5.137	-1.780	-1.740	-0.001	-0.024	-0.015	0.000
26	A	26	GLU	-1	-0.796	-0.898	2.063	-56.619	-55.840	12.098	-6.970	-5.907	-0.078
27	A	27	ALA	0	0.023	0.013	4.708	-0.284	-0.240	-0.001	-0.007	-0.036	0.000
116	A	116	LYS	1	0.819	0.890	3.858	15.778	16.094	0.000	-0.056	-0.259	0.000
117	A	117	LEU	0	0.043	0.018	2.278	-0.432	2.117	3.259	-2.342	-3.466	0.014
118	A	118	ALA	0	-0.002	-0.010	3.223	-0.014	1.605	0.105	-0.623	-1.101	0.004
119	A	119	GLU	-1	-0.820	-0.897	4.382	-3.234	-3.160	0.003	-0.044	-0.033	0.000
121	A	121	LYS	1	0.873	0.928	1.723	-84.498	-91.386	21.731	-8.577	-6.266	0.105
4	A	4	THR	0	-0.007	-0.002	5.968	-2.310	-2.310	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.018	0.027	9.818	0.879	0.879	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.860	0.908	12.069	-1.629	-1.629	0.000	0.000	0.000	0.000
7	A	7	MET	0	-0.034	-0.002	15.691	0.346	0.346	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.028	0.002	18.176	-0.198	-0.198	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.834	-0.907	21.801	0.328	0.328	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.024	-0.009	24.403	0.118	0.118	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.026	0.021	26.059	-0.092	-0.092	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.014	-0.024	29.165	0.080	0.080	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.012	0.001	30.527	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.011	0.001	26.897	0.072	0.072	0.000	0.000	0.000	0.000
15	A	15	PRO	0	-0.033	-0.020	22.780	-0.093	-0.093	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.022	0.018	24.906	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.823	0.901	25.466	-0.185	-0.185	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.809	-0.893	19.080	0.673	0.673	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.035	-0.025	21.422	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.011	0.005	19.789	-0.183	-0.183	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.038	-0.022	14.279	0.127	0.127	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.031	0.009	11.572	-0.289	-0.289	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.025	0.001	8.817	0.506	0.506	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.016	0.022	6.286	-0.711	-0.711	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.030	-0.031	7.676	0.781	0.781	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.002	0.010	10.642	0.749	0.749	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.058	0.041	9.812	0.922	0.922	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.052	-0.022	5.731	-1.709	-1.709	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.042	-0.020	8.411	2.043	2.043	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.032	0.000	9.350	-0.792	-0.792	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.942	0.967	11.692	3.109	3.109	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.001	0.010	13.761	0.323	0.323	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.025	-0.015	16.375	-0.354	-0.354	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.006	0.008	18.891	0.199	0.199	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.842	-0.914	21.393	-0.266	-0.266	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.832	0.897	25.139	0.203	0.203	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.008	0.033	23.337	0.060	0.060	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.016	0.003	27.637	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.001	0.002	29.145	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.010	0.018	29.756	0.049	0.049	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.025	-0.031	25.975	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	HIS	1	0.795	0.893	24.137	0.289	0.289	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.012	0.016	23.228	-0.114	-0.114	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.040	-0.032	14.365	0.128	0.128	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.849	0.909	17.585	-0.267	-0.267	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.038	0.024	12.280	0.129	0.129	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.081	-0.048	15.196	-0.390	-0.390	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.840	-0.911	15.421	2.113	2.113	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.017	0.023	15.598	0.629	0.629	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.025	0.036	13.639	-0.307	-0.307	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.008	-0.019	15.525	-0.210	-0.210	0.000	0.000	0.000	0.000
55	A	55	CYS	0	0.011	0.002	18.988	-0.073	-0.073	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.002	0.010	21.235	-0.195	-0.195	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.014	-0.015	24.459	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.002	0.005	27.313	0.111	0.111	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.937	-0.962	29.175	0.690	0.690	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.877	0.906	31.004	-0.582	-0.582	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.882	-0.924	33.392	0.521	0.521	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.019	0.011	36.998	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.912	0.966	35.486	-0.439	-0.439	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.059	0.032	32.144	0.043	0.043	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.035	-0.018	28.589	-0.067	-0.067	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.025	0.001	27.958	0.098	0.098	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.050	0.016	22.805	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.009	0.013	23.472	0.064	0.064	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.001	0.002	22.995	0.048	0.048	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.029	0.022	19.364	0.173	0.173	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.014	0.018	19.320	0.151	0.151	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.013	-0.020	21.887	-0.195	-0.195	0.000	0.000	0.000	0.000
73	A	73	HIS	1	0.794	0.893	19.459	-0.314	-0.314	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.025	-0.004	11.820	0.128	0.128	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.724	-0.840	16.904	0.478	0.478	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.009	0.006	14.712	0.021	0.021	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.001	0.002	17.240	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.073	-0.042	20.450	0.014	0.014	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.009	-0.010	22.017	-0.102	-0.102	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.113	-0.074	24.152	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.027	0.000	25.260	-0.052	-0.052	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.046	-0.042	22.485	0.091	0.091	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.020	-0.019	23.431	-0.057	-0.057	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.024	-0.019	21.623	-0.119	-0.119	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.030	-0.015	17.795	0.030	0.030	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.922	-0.977	18.217	-1.921	-1.921	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.034	0.002	20.854	0.018	0.018	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.918	-0.959	21.097	-0.633	-0.633	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.012	-0.007	22.119	0.106	0.106	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.079	-0.048	20.034	0.035	0.035	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.022	0.014	14.953	-0.059	-0.059	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.007	-0.004	14.690	-0.199	-0.199	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.745	-0.866	15.735	0.088	0.088	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.057	-0.018	13.341	-0.279	-0.279	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.005	-0.007	16.626	0.143	0.143	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.793	0.893	19.387	0.756	0.756	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.017	0.021	17.880	-0.138	-0.138	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.034	-0.036	21.915	0.166	0.166	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.017	0.007	25.006	-0.064	-0.064	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.012	-0.018	26.567	0.067	0.067	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.043	0.002	29.179	0.061	0.061	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.916	-0.944	30.294	-0.455	-0.455	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.018	0.007	29.226	0.035	0.035	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.856	0.930	25.456	0.506	0.506	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.033	0.024	20.167	-0.031	-0.031	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.007	-0.025	20.372	0.021	0.021	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.829	-0.896	18.744	-1.365	-1.365	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.061	-0.046	13.090	-0.342	-0.342	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.033	0.041	15.248	0.005	0.005	0.000	0.000	0.000	0.000
110	A	110	VAL	0	-0.007	-0.015	12.260	-0.435	-0.435	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.050	0.025	12.324	0.599	0.599	0.000	0.000	0.000	0.000
112	A	112	PRO	0	0.002	0.010	12.457	-0.486	-0.486	0.000	0.000	0.000	0.000
113	A	113	HIS	1	0.833	0.912	14.345	1.182	1.182	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.022	0.033	10.037	0.487	0.487	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.939	0.958	8.045	3.227	3.227	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.066	-0.042	7.030	-1.377	-1.377	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.035	-0.028	7.546	-2.588	-2.588	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.831	0.937	10.752	-5.487	-5.487	0.000	0.000	0.000	0.000
124	A	124	SER	0	0.032	-0.003	12.753	0.016	0.016	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.023	-0.005	11.913	-0.262	-0.262	0.000	0.000	0.000	0.000
126	A	126	MET	0	0.001	0.012	15.414	0.040	0.040	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.027	0.010	18.867	-0.216	-0.216	0.000	0.000	0.000	0.000
128	A	128	HIS	0	-0.036	-0.003	21.165	0.173	0.173	0.000	0.000	0.000	0.000
129	A	129	VAL	0	-0.008	-0.007	24.714	-0.091	-0.091	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.026	0.027	28.276	-0.065	-0.065	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.029	0.012	26.858	-0.026	-0.026	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.706	-0.862	23.207	-0.175	-0.175	0.000	0.000	0.000	0.000
133	A	133	ASN	0	-0.047	-0.020	26.196	-0.099	-0.099	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.015	-0.005	22.449	-0.077	-0.077	0.000	0.000	0.000	0.000
135	A	135	SER	0	0.040	0.023	26.048	0.005	0.005	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.740	-0.859	28.503	0.232	0.232	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.925	0.981	30.428	0.105	0.105	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.035	-0.035	32.979	-0.051	-0.051	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.928	-0.963	32.341	0.035	0.035	0.000	0.000	0.000	0.000
140	A	140	PRO	0	0.022	0.002	30.459	-0.021	-0.021	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.046	-0.031	24.819	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.020	0.029	25.880	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	143	GLY	0	0.054	0.024	27.323	-0.070	-0.070	0.000	0.000	0.000	0.000
144	A	144	GLY	0	-0.017	0.001	26.239	-0.022	-0.022	0.000	0.000	0.000	0.000
145	A	145	GLY	0	0.001	-0.008	27.256	0.019	0.019	0.000	0.000	0.000	0.000
146	A	146	ALA	0	-0.006	-0.007	27.775	0.068	0.068	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.835	0.917	23.042	-1.080	-1.080	0.000	0.000	0.000	0.000
148	A	148	PHE	0	0.008	-0.001	23.952	0.011	0.011	0.000	0.000	0.000	0.000
149	A	149	ALA	0	0.004	-0.005	21.687	0.016	0.016	0.000	0.000	0.000	0.000
150	A	151	GLY	0	0.060	0.024	16.081	-0.116	-0.116	0.000	0.000	0.000	0.000
151	A	152	VAL	0	-0.020	-0.007	13.118	-0.139	-0.139	0.000	0.000	0.000	0.000
152	A	153	ILE	0	-0.067	-0.033	8.240	-0.311	-0.311	0.000	0.000	0.000	0.000
153	A	154	GLU	-2	-1.745	-1.873	7.371	21.630	21.630	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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