FMO DATABASE

FMODB ID: Y1K22

Calculation Name: 1ADW-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: 1ADW

Chain ID: A

ChEMBL ID:

UniProt ID: P80401

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1015805.509801
FMO2-HF: Nuclear repulsion	968023.118117
FMO2-HF: Total energy	-47782.391684
FMO2-MP2: Total energy	-47918.384831

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.
-221.134	-220.603	17.634	-10.515	-7.65	-0.113

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 : 0.784 / q_NPA : 0.879

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	HIS	0	-0.004	0.001	3.600	8.338	10.011	-0.013	-0.756	-0.904	-0.002
29	A	29	ASP	-1	-0.804	-0.867	1.673	-142.795	-144.552	17.636	-9.583	-6.296	-0.110
30	A	30	VAL	0	-0.039	-0.022	3.323	17.000	17.615	0.011	-0.176	-0.450	-0.001
4	A	4	GLU	-1	-0.899	-0.949	6.650	-21.846	-21.846	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.001	0.004	10.285	0.711	0.711	0.000	0.000	0.000	0.000
6	A	6	HIS	0	-0.007	-0.008	13.433	1.135	1.135	0.000	0.000	0.000	0.000
7	A	7	MET	0	-0.059	-0.015	16.909	0.218	0.218	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.024	0.010	19.896	0.439	0.439	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.062	-0.053	22.834	0.295	0.295	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.878	0.925	25.619	11.355	11.355	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.079	0.057	22.351	-0.199	-0.199	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.961	-0.991	21.460	-11.894	-11.894	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.052	-0.013	21.406	0.509	0.509	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.023	-0.014	23.694	0.461	0.461	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.026	-0.019	25.590	-0.235	-0.235	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.055	-0.029	25.725	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.012	0.015	21.344	0.109	0.109	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.006	-0.001	16.896	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.816	-0.904	17.219	-14.436	-14.436	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.039	0.009	12.148	-0.207	-0.207	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.015	0.005	14.673	-0.726	-0.726	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.004	0.006	13.473	-0.291	-0.291	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.022	-0.011	8.315	-0.555	-0.555	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.817	0.911	8.970	24.996	24.996	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.029	-0.022	5.596	-2.798	-2.798	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.854	-0.944	5.085	-28.470	-28.470	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.022	-0.018	5.241	-5.804	-5.804	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.008	0.000	5.204	-1.835	-1.835	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.029	0.011	5.536	-1.215	-1.215	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.023	-0.004	8.610	5.060	5.060	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.058	0.020	11.078	0.840	0.840	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.033	0.004	14.022	0.776	0.776	0.000	0.000	0.000	0.000
35	A	35	PRO	0	-0.044	-0.012	16.727	0.529	0.529	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.018	0.013	18.593	0.345	0.345	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.818	-0.880	21.020	-11.665	-11.665	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.949	0.961	23.931	10.929	10.929	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.080	-0.052	26.493	0.279	0.279	0.000	0.000	0.000	0.000
40	A	40	HIS	0	0.091	0.015	22.862	0.159	0.159	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.000	-0.032	21.844	0.217	0.217	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.053	0.036	16.618	0.058	0.058	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.832	-0.897	19.994	-12.343	-12.343	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.073	0.047	19.007	-0.182	-0.182	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.049	-0.037	20.130	1.123	1.123	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.969	0.978	21.416	12.179	12.179	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.933	-0.969	23.039	-12.442	-12.442	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.061	-0.026	18.820	0.165	0.165	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.041	0.026	17.100	-1.002	-1.002	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.014	0.014	14.463	1.003	1.003	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.903	-0.952	17.777	-13.336	-13.336	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.001	0.000	18.581	-0.710	-0.710	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.055	-0.012	14.922	-0.532	-0.532	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.880	-0.945	17.574	-13.572	-13.572	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.049	-0.024	18.338	-0.537	-0.537	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.005	0.005	15.840	0.294	0.294	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.803	0.879	19.317	12.833	12.833	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.031	0.043	18.948	0.165	0.165	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.859	0.905	20.980	13.691	13.691	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.011	-0.015	23.081	-0.443	-0.443	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.047	-0.044	23.754	0.499	0.499	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.831	-0.882	20.560	-13.948	-13.948	0.000	0.000	0.000	0.000
63	A	63	SER	0	0.018	-0.005	15.939	0.223	0.223	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.049	-0.027	14.497	1.095	1.095	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.015	0.007	9.520	-0.052	-0.052	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.014	0.002	10.983	0.898	0.898	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.006	-0.004	6.314	-4.019	-4.019	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.036	-0.002	6.684	4.070	4.070	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.032	-0.016	7.466	-4.730	-4.730	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.866	-0.933	9.949	-22.444	-22.444	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.042	0.028	11.997	-1.433	-1.433	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.008	-0.006	12.944	1.807	1.807	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.040	-0.024	13.731	-1.453	-1.453	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.025	-0.012	11.840	0.926	0.926	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.001	0.006	15.500	-0.425	-0.425	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.060	-0.023	15.970	0.270	0.270	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.906	0.952	18.950	13.518	13.518	0.000	0.000	0.000	0.000
78	A	78	CYS	0	0.011	0.054	21.700	-0.162	-0.162	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.025	-0.037	23.529	0.476	0.476	0.000	0.000	0.000	0.000
80	A	80	PRO	0	-0.036	-0.022	26.388	0.447	0.447	0.000	0.000	0.000	0.000
81	A	81	HIS	1	0.832	0.903	26.318	12.008	12.008	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.078	0.052	25.196	0.159	0.159	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.017	-0.001	27.385	0.062	0.062	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.095	-0.053	29.038	0.286	0.286	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.028	0.012	26.966	0.078	0.078	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.067	0.000	22.135	-0.067	-0.067	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.052	-0.044	21.390	0.071	0.071	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.075	0.044	17.310	0.009	0.009	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.042	-0.012	15.946	0.370	0.370	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.016	0.004	9.833	-0.700	-0.700	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.028	0.005	11.960	1.603	1.603	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.033	-0.014	8.175	-2.562	-2.562	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.090	0.052	9.885	2.063	2.063	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.897	-0.950	11.563	-20.301	-20.301	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.047	-0.021	14.889	0.273	0.273	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.030	-0.009	15.560	0.348	0.348	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.878	-0.937	17.748	-14.214	-14.214	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.044	-0.022	18.081	0.442	0.442	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.050	0.024	20.257	0.339	0.339	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.829	-0.919	21.840	-11.498	-11.498	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.015	0.040	23.432	0.508	0.508	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.031	0.010	21.080	0.282	0.282	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.866	0.918	23.075	12.201	12.201	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.056	-0.038	25.762	0.465	0.465	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.010	0.023	25.459	0.426	0.426	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.958	0.993	27.476	9.943	9.943	0.000	0.000	0.000	0.000
107	A	107	MET	0	-0.028	-0.004	23.993	0.043	0.043	0.000	0.000	0.000	0.000
108	A	108	PRO	0	-0.024	-0.020	28.811	0.382	0.382	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.890	0.928	29.816	9.022	9.022	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.973	0.995	29.319	9.593	9.593	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.009	0.013	25.967	-0.297	-0.297	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.779	0.865	24.994	11.664	11.664	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.812	-0.905	26.529	-10.045	-10.045	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.772	0.889	23.112	12.332	12.332	0.000	0.000	0.000	0.000
115	A	115	MET	0	0.041	0.029	19.918	-0.472	-0.472	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.833	-0.919	22.169	-12.086	-12.086	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.045	-0.020	23.241	-0.060	-0.060	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.849	-0.950	18.278	-15.931	-15.931	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.033	-0.029	18.515	-0.659	-0.659	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.058	-0.019	20.616	-0.042	-0.042	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.071	-0.035	16.295	0.385	0.385	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.050	-0.014	16.203	-1.066	-1.066	0.000	0.000	0.000	0.000
123	A	123	ASN	-1	-0.878	-0.919	15.404	-18.084	-18.084	0.000	0.000	0.000	0.000

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