FMO DATABASE

FMODB ID: KK4Z3

Calculation Name: 1WS8-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | copper (ii) ion

Ligand 3-letter code: GOL | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WS8

Chain ID: A

ChEMBL ID:

UniProt ID: P80728

Base Structure: X-ray

Registration Date: 2025-10-03

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-786472.600231
FMO2-HF: Nuclear repulsion	745916.651864
FMO2-HF: Total energy	-40555.948367
FMO2-MP2: Total energy	-40673.579285

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:MET)

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

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.
36.489	38.448	0.026	-0.846	-1.139	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.919

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	THR	0	-0.027	-0.012	3.490	-0.957	0.924	0.027	-0.841	-1.067	-0.003
4	A	4	VAL	0	0.000	-0.002	4.984	3.737	3.815	-0.001	-0.005	-0.072	0.000
5	A	5	HIS	1	0.781	0.871	7.806	32.684	32.684	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.983	0.982	10.832	21.461	21.461	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.019	0.009	14.032	0.284	0.284	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.055	0.027	16.978	0.777	0.777	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.895	-0.945	15.395	-17.272	-17.272	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.058	-0.033	17.186	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.026	-0.006	19.979	0.766	0.766	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.015	0.016	20.175	0.467	0.467	0.000	0.000	0.000	0.000
13	A	13	TRP	0	-0.021	-0.006	21.215	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.005	-0.030	22.869	0.572	0.572	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.026	0.004	26.541	-0.102	-0.102	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.063	-0.016	29.431	0.299	0.299	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.028	0.015	28.350	0.329	0.329	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.005	-0.001	29.010	-0.311	-0.311	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.027	0.017	19.686	-0.242	-0.242	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.826	-0.909	24.495	-12.424	-12.424	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.045	-0.022	20.459	-0.499	-0.499	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.021	0.023	20.433	-0.777	-0.777	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.916	0.963	20.899	11.515	11.515	0.000	0.000	0.000	0.000
24	A	24	TRP	0	-0.019	-0.003	13.788	-0.771	-0.771	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.017	0.008	16.371	-1.210	-1.210	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.051	-0.040	16.221	-0.858	-0.858	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.085	-0.034	16.493	-0.314	-0.314	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.024	-0.002	11.780	-3.161	-3.161	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.955	0.973	9.705	24.204	24.204	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.028	-0.009	9.163	-3.067	-3.067	0.000	0.000	0.000	0.000
31	A	31	HIS	1	0.828	0.886	5.661	40.703	40.703	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.035	0.010	7.776	0.630	0.630	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.039	-0.013	6.544	-4.813	-4.813	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.768	-0.862	5.873	-51.437	-51.437	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.060	-0.040	7.916	4.302	4.302	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.003	0.018	10.505	-1.120	-1.120	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.007	-0.006	13.343	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.011	0.005	15.015	0.280	0.280	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.028	0.013	17.422	0.301	0.301	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.078	-0.061	20.414	0.545	0.545	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.054	0.025	24.254	0.076	0.076	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.004	-0.019	26.980	0.471	0.471	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.938	0.975	28.684	9.578	9.578	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.017	-0.003	30.766	0.272	0.272	0.000	0.000	0.000	0.000
45	A	45	HIS	0	-0.020	-0.013	27.202	0.030	0.030	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.072	0.011	26.662	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.010	0.021	21.025	-0.115	-0.115	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.011	0.010	24.440	0.054	0.054	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.026	-0.010	20.530	-0.817	-0.817	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.010	-0.008	24.092	0.474	0.474	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.769	-0.876	24.718	-11.313	-11.313	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.058	0.007	26.261	0.124	0.124	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.940	-0.963	27.461	-9.106	-9.106	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.024	0.016	29.393	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.005	0.004	24.814	0.147	0.147	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.878	0.934	28.432	10.950	10.950	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.020	-0.034	30.961	0.193	0.193	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.039	0.009	29.361	-0.134	-0.134	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.041	0.062	32.493	0.146	0.146	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.009	-0.010	31.503	-0.201	-0.201	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.038	-0.037	32.517	-0.094	-0.094	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.014	-0.001	33.124	0.179	0.179	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.006	0.000	28.193	-0.203	-0.203	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.017	0.018	25.163	0.110	0.110	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.038	-0.023	23.424	-0.274	-0.274	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.002	-0.004	25.511	0.196	0.196	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.035	-0.011	20.757	-0.195	-0.195	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.035	0.006	24.458	0.146	0.146	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.007	-0.039	22.190	0.338	0.338	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.012	0.008	23.945	0.310	0.310	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.004	0.000	19.328	-0.160	-0.160	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.752	-0.814	18.821	-14.332	-14.332	0.000	0.000	0.000	0.000
73	A	73	SER	0	0.008	0.002	13.378	-0.917	-0.917	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.004	0.001	14.961	0.740	0.740	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.013	0.002	12.386	-1.236	-1.236	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.019	-0.002	10.718	1.819	1.819	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.954	0.964	11.008	16.595	16.595	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.955	0.979	13.162	17.246	17.246	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.060	0.031	12.514	-0.284	-0.284	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.004	0.013	14.205	1.306	1.306	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.049	-0.027	16.456	-0.816	-0.816	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.031	-0.001	15.536	0.589	0.589	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.013	0.002	19.606	-0.142	-0.142	0.000	0.000	0.000	0.000
84	A	84	PHE	0	0.019	0.004	18.171	0.073	0.073	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.022	0.003	23.134	0.161	0.161	0.000	0.000	0.000	0.000
86	A	86	CYS	0	-0.058	0.022	26.062	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.023	-0.019	27.727	0.279	0.279	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.008	0.008	30.765	0.371	0.371	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.037	0.004	33.076	-0.105	-0.105	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.037	0.020	35.503	0.061	0.061	0.000	0.000	0.000	0.000
91	A	91	HIS	1	0.824	0.920	29.903	9.848	9.848	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.048	0.009	30.413	-0.325	-0.325	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.042	-0.011	32.050	0.066	0.066	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.030	0.021	28.983	-0.121	-0.121	0.000	0.000	0.000	0.000
95	A	96	GLN	0	0.048	0.033	25.304	-0.092	-0.092	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.782	0.858	25.073	10.873	10.873	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.016	-0.015	19.047	-0.140	-0.140	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.870	-0.928	20.774	-13.600	-13.600	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.022	-0.021	14.970	-0.491	-0.491	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.909	0.963	15.923	15.378	15.378	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.024	-0.014	10.759	-1.422	-1.422	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.805	-0.888	8.903	-32.084	-32.084	0.000	0.000	0.000	0.000
103	A	104	PRO	-1	-0.915	-0.940	11.895	-18.345	-18.345	0.000	0.000	0.000	0.000

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