FMO DATABASE

FMODB ID: 1963Z

Calculation Name: 2CBP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: copper (ii) ion

Ligand 3-letter code: CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CBP

Chain ID: A

ChEMBL ID:

UniProt ID: P00303

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-669974.218562
FMO2-HF: Nuclear repulsion	633132.285448
FMO2-HF: Total energy	-36841.933113
FMO2-MP2: Total energy	-36947.600674

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:ALA)

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

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.
27.28	30.14	16.542	-10.64	-8.763	-0.114

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / 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	3	TYR	0	-0.022	-0.004	2.736	4.177	6.802	0.686	-1.225	-2.086	-0.006
25	A	25	ARG	1	0.946	0.984	3.837	58.829	59.036	-0.001	-0.022	-0.185	0.000
28	A	28	ASP	-1	-0.842	-0.908	1.742	-130.304	-131.017	15.836	-9.162	-5.961	-0.106
29	A	29	ILE	0	-0.011	-0.011	3.197	15.241	15.982	0.021	-0.231	-0.531	-0.002
4	A	4	VAL	0	0.007	0.006	6.009	1.711	1.711	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.003	0.000	9.686	0.876	0.876	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.055	0.026	12.218	1.042	1.042	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.063	-0.024	12.090	0.947	0.947	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.008	-0.026	13.079	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.005	0.011	16.186	0.832	0.832	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.031	-0.004	15.773	0.621	0.621	0.000	0.000	0.000	0.000
11	A	11	TRP	0	-0.062	-0.053	16.494	-0.403	-0.403	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.009	-0.019	17.789	1.053	1.053	0.000	0.000	0.000	0.000
13	A	13	PHE	0	0.054	0.002	20.715	-0.405	-0.405	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.062	-0.023	22.287	-0.164	-0.164	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.006	0.007	16.513	-0.519	-0.519	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.881	-0.941	17.113	-14.900	-14.900	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.002	-0.002	17.717	-0.706	-0.706	0.000	0.000	0.000	0.000
18	A	18	TRP	0	0.033	0.019	8.375	-0.693	-0.693	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.015	0.007	11.575	-1.404	-1.404	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.986	1.001	11.972	15.019	15.019	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.011	-0.014	13.069	-0.459	-0.459	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.842	0.942	7.744	23.754	23.754	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.912	0.936	7.382	27.731	27.731	0.000	0.000	0.000	0.000
24	A	24	PHE	0	0.012	0.022	5.156	-3.571	-3.571	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.019	-0.001	5.702	-3.181	-3.181	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.022	-0.009	5.832	-2.963	-2.963	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.018	0.001	5.806	-2.370	-2.370	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.006	-0.006	8.659	2.051	2.051	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.015	-0.001	10.673	0.828	0.828	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.025	0.011	13.597	0.884	0.884	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.072	-0.055	16.585	0.841	0.841	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.099	0.071	20.296	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.028	0.001	22.915	0.182	0.182	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.039	-0.031	24.624	0.371	0.371	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.042	-0.018	26.580	0.469	0.469	0.000	0.000	0.000	0.000
39	A	39	HIS	1	0.853	0.917	22.701	13.110	13.110	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.085	0.012	22.424	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.009	0.033	16.134	-0.176	-0.176	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.008	-0.004	19.606	0.095	0.095	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.001	0.003	16.345	-0.421	-0.421	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.005	-0.011	18.780	0.977	0.977	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.039	0.017	19.629	-0.589	-0.589	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.067	0.030	21.693	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.038	0.036	22.584	0.275	0.275	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.031	0.020	25.158	0.373	0.373	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.001	-0.014	19.219	0.137	0.137	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.038	-0.040	23.043	0.092	0.092	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.032	-0.020	25.652	0.386	0.386	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.068	-0.011	23.961	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.004	0.019	27.171	0.332	0.332	0.000	0.000	0.000	0.000
54	A	54	THR	0	0.010	0.001	25.500	-0.619	-0.619	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.010	-0.005	24.403	0.375	0.375	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.049	0.022	27.104	-0.149	-0.149	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.015	0.005	26.627	-0.171	-0.171	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.031	0.001	23.034	-0.542	-0.542	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.894	0.957	19.005	16.380	16.380	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.042	0.020	20.474	-0.686	-0.686	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.050	-0.033	15.537	0.093	0.093	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.055	0.008	20.353	0.076	0.076	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.001	-0.028	17.927	0.390	0.390	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.023	0.021	19.994	0.371	0.371	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.915	0.946	14.420	18.496	18.496	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.762	-0.819	14.997	-18.710	-18.710	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.004	-0.008	9.196	-4.101	-4.101	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.012	-0.003	10.436	1.182	1.182	0.000	0.000	0.000	0.000
69	A	69	LYS	0	-0.001	0.021	6.158	-3.562	-3.562	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.004	-0.001	6.745	4.315	4.315	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.044	0.029	8.574	-2.004	-2.004	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.875	0.905	10.507	21.725	21.725	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.008	0.014	12.030	1.946	1.946	0.000	0.000	0.000	0.000
74	A	74	GLN	0	0.040	0.032	12.613	-1.207	-1.207	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.028	-0.019	12.713	-0.391	-0.391	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.017	-0.019	14.807	-0.310	-0.310	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.023	0.007	12.407	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.014	-0.002	17.738	0.291	0.291	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.015	0.043	20.909	-0.217	-0.217	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.023	-0.027	22.902	0.303	0.303	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.061	0.037	26.316	0.446	0.446	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.027	0.000	28.415	-0.148	-0.148	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.053	0.032	30.373	0.121	0.121	0.000	0.000	0.000	0.000
84	A	84	HIS	0	0.019	0.012	25.170	-0.602	-0.602	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.067	0.013	25.009	-0.383	-0.383	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.031	0.000	26.962	0.280	0.280	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.096	0.041	23.532	-0.244	-0.244	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.100	-0.027	20.459	-0.468	-0.468	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.842	0.927	19.531	13.407	13.407	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.033	-0.016	12.578	-0.361	-0.361	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.037	0.027	15.899	0.193	0.193	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.006	-0.007	10.276	-0.643	-0.643	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.004	-0.019	11.841	2.043	2.043	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.028	-0.002	8.446	-1.462	-1.462	0.000	0.000	0.000	0.000
95	A	96	LEU	-1	-0.810	-0.890	9.027	-27.840	-27.840	0.000	0.000	0.000	0.000

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