FMO DATABASE

FMODB ID: Z95QN

Calculation Name: 1ID2-A-Xray549

Preferred Name:

Target Type:

Ligand Name: copper (ii) ion

Ligand 3-letter code: CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ID2

Chain ID: A

ChEMBL ID:

UniProt ID: P22365

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-812773.598064
FMO2-HF: Nuclear repulsion	771071.36578
FMO2-HF: Total energy	-41702.232284
FMO2-MP2: Total energy	-41821.304473

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:GLN)

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

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.
-80.691	-78.963	-0.013	-0.856	-0.859	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.893

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	LYS	1	0.841	0.929	3.461	30.375	32.103	-0.013	-0.856	-0.859	-0.004
4	A	4	ILE	0	-0.021	-0.009	6.114	5.753	5.753	0.000	0.000	0.000	0.000
5	A	5	THR	0	0.002	0.003	5.773	-7.422	-7.422	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.039	-0.019	7.899	3.171	3.171	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.025	-0.021	9.938	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.038	-0.036	12.880	0.633	0.633	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.964	-0.967	13.277	-20.605	-20.605	0.000	0.000	0.000	0.000
10	A	10	LYS	1	1.014	1.010	14.257	13.930	13.930	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.053	-0.011	17.974	-0.281	-0.281	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.029	-0.003	19.583	0.291	0.291	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.008	-0.006	22.228	0.261	0.261	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.003	-0.021	25.040	-0.290	-0.290	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.041	-0.023	26.803	0.051	0.051	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.848	-0.919	23.677	-11.986	-11.986	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.072	-0.028	22.691	-0.598	-0.598	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.005	0.013	22.334	0.532	0.532	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.009	-0.031	25.368	-0.087	-0.087	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.921	-0.955	24.802	-12.445	-12.445	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.025	0.003	22.419	-0.389	-0.389	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.025	0.012	20.391	0.537	0.537	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.016	-0.013	21.667	-0.684	-0.684	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.022	-0.003	21.550	0.596	0.596	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.035	0.016	23.996	-0.105	-0.105	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.040	-0.026	22.517	-0.127	-0.127	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.780	-0.905	27.032	-9.243	-9.243	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.761	0.880	30.726	9.233	9.233	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.042	-0.017	29.871	0.034	0.034	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.951	0.973	28.658	9.558	9.558	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.012	-0.001	21.191	0.061	0.061	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.054	-0.041	26.338	0.279	0.279	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.003	0.002	24.880	0.316	0.316	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.031	-0.014	24.312	-0.552	-0.552	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.908	-0.954	22.883	-13.522	-13.522	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.007	0.002	19.942	0.556	0.556	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.032	-0.001	20.203	-0.765	-0.765	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.007	0.001	15.534	0.478	0.478	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.912	0.959	17.554	14.544	14.544	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.000	-0.008	12.377	-0.544	-0.544	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.035	-0.018	12.725	0.809	0.809	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.845	-0.914	13.713	-14.775	-14.775	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.021	-0.020	14.565	-1.999	-1.999	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.009	0.017	15.886	1.153	1.153	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.052	0.012	17.013	-0.747	-0.747	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.020	-0.009	15.955	0.380	0.380	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.060	0.015	21.437	-0.046	-0.046	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.060	-0.034	24.669	0.424	0.424	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.061	0.042	26.725	0.205	0.205	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.767	-0.863	29.934	-9.585	-9.585	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.002	-0.014	30.060	-0.267	-0.267	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.023	0.008	29.106	-0.107	-0.107	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.005	0.001	26.048	-0.257	-0.257	0.000	0.000	0.000	0.000
54	A	54	HIS	1	0.805	0.864	24.136	11.581	11.581	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.040	0.000	18.052	0.527	0.527	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.032	0.041	15.813	0.537	0.537	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.026	-0.004	14.982	-0.919	-0.919	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.070	0.030	12.195	0.690	0.690	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.886	0.943	13.493	16.157	16.157	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.969	0.972	11.497	19.901	19.901	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.005	0.008	10.232	2.078	2.078	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.084	-0.012	11.079	0.082	0.082	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.053	0.017	8.413	-0.070	-0.070	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.094	0.048	5.679	-7.910	-7.910	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.968	-0.967	5.702	-26.514	-26.514	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.886	-0.957	7.336	-27.927	-27.927	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.076	-0.042	9.052	0.038	0.038	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.052	0.038	8.927	-0.319	-0.319	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.843	0.886	11.042	18.597	18.597	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.104	0.071	14.306	0.138	0.138	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.853	-0.928	15.102	-14.943	-14.943	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.108	-0.045	18.149	-0.117	-0.117	0.000	0.000	0.000	0.000
73	A	73	MET	0	0.017	0.042	20.020	0.248	0.248	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.040	-0.040	23.398	0.483	0.483	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.831	0.877	26.929	9.319	9.319	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.855	-0.915	28.576	-9.827	-9.827	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.018	0.040	23.870	-0.221	-0.221	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.020	-0.004	22.447	0.089	0.089	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.034	-0.023	13.896	-0.651	-0.651	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.044	0.023	16.340	0.439	0.439	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.019	0.002	10.822	-0.944	-0.944	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.000	0.001	10.890	0.988	0.988	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.014	-0.001	10.391	-2.826	-2.826	0.000	0.000	0.000	0.000
84	A	84	ASN	0	0.000	-0.012	5.751	5.870	5.870	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.841	-0.919	5.851	-40.749	-40.749	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.046	0.028	9.938	0.737	0.737	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.022	-0.013	12.317	-1.403	-1.403	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.057	-0.034	14.396	1.753	1.753	0.000	0.000	0.000	0.000
89	A	89	TYR	0	-0.029	-0.022	10.196	-1.460	-1.460	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.866	-0.934	15.053	-15.634	-15.634	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.009	-0.004	16.422	-0.880	-0.880	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.047	-0.043	16.782	1.185	1.185	0.000	0.000	0.000	0.000
93	A	93	CYS	0	0.005	0.041	19.490	-0.632	-0.632	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.002	-0.019	18.947	0.011	0.011	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.005	-0.003	21.151	0.224	0.224	0.000	0.000	0.000	0.000
96	A	96	HIS	0	0.026	0.012	24.384	0.331	0.331	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.058	0.028	23.645	-0.072	-0.072	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.017	0.003	24.804	-0.171	-0.171	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.070	-0.009	25.058	0.168	0.168	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.859	0.906	22.718	12.316	12.316	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.052	0.026	21.685	0.698	0.698	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.835	0.926	19.072	14.219	14.219	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.004	0.007	15.849	0.736	0.736	0.000	0.000	0.000	0.000
104	A	104	ILE	0	-0.015	-0.008	16.689	-0.975	-0.975	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.039	-0.022	13.126	0.048	0.048	0.000	0.000	0.000	0.000
106	A	106	GLU	-2	-1.761	-1.877	16.112	-32.396	-32.396	0.000	0.000	0.000	0.000

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