FMO DATABASE

FMODB ID: 8QVVY

Calculation Name: 4DP0-X-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol | copper (ii) ion

Ligand 3-letter code: SO4 | GOL | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DP0

Chain ID: X

ChEMBL ID:

UniProt ID: P11970

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-676924.448967
FMO2-HF: Nuclear repulsion	640030.050136
FMO2-HF: Total energy	-36894.398831
FMO2-MP2: Total energy	-37001.679555

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:VAL)

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

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.
-259.888	-248.852	22.043	-16.57	-16.506	-0.189

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.728 / q_NPA : 0.859

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	VAL	0	-0.004	-0.002	2.645	-2.557	0.947	0.719	-1.822	-2.400	-0.016
4	A	4	LEU	0	-0.025	-0.009	5.229	2.491	2.531	-0.001	-0.003	-0.035	0.000
16	A	16	PRO	0	-0.003	-0.015	4.498	-1.693	-1.593	-0.001	-0.008	-0.091	0.000
19	A	19	PHE	0	0.011	0.004	2.619	-3.987	-2.956	0.843	-0.471	-1.402	-0.005
21	A	21	VAL	0	-0.020	-0.011	2.620	-6.091	-5.581	0.754	-0.240	-1.024	-0.001
25	A	25	GLU	-1	-0.910	-0.943	1.814	-116.914	-113.605	10.645	-8.041	-5.912	-0.105
26	A	26	LYS	1	0.907	0.965	3.198	47.529	48.351	0.022	-0.362	-0.482	-0.001
27	A	27	ILE	0	0.018	0.004	1.868	-46.460	-45.557	9.055	-5.340	-4.619	-0.061
28	A	28	VAL	0	-0.044	-0.024	3.535	12.409	13.226	0.007	-0.283	-0.541	0.000
5	A	5	LEU	0	0.000	0.007	8.672	0.617	0.617	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.062	0.035	11.966	1.152	1.152	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.008	0.001	12.904	-1.268	-1.268	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.889	-0.949	14.217	-18.121	-18.121	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.890	-0.924	16.452	-14.367	-14.367	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.031	-0.013	18.115	0.750	0.750	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.063	-0.047	16.940	0.381	0.381	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.037	-0.022	16.298	-0.962	-0.962	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.031	0.011	13.441	0.183	0.183	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.033	0.022	9.078	-0.530	-0.530	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.029	0.012	8.412	1.069	1.069	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.004	-0.021	7.317	-0.390	-0.390	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.942	-0.973	9.134	-24.095	-24.095	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.036	0.014	6.098	2.391	2.391	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.017	0.026	5.531	5.161	5.161	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.010	-0.022	7.475	-3.348	-3.348	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.045	-0.016	9.344	0.730	0.730	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.056	0.030	5.560	-1.084	-1.084	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.869	0.911	7.450	36.760	36.760	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.009	0.002	9.981	0.316	0.316	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.073	-0.053	12.117	0.583	0.583	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.009	0.003	14.177	1.217	1.217	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.040	0.021	16.793	-0.455	-0.455	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.048	-0.001	16.623	0.120	0.120	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.020	-0.007	20.047	0.621	0.621	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.005	-0.041	14.954	0.169	0.169	0.000	0.000	0.000	0.000
38	A	38	ASN	0	0.044	-0.012	15.178	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.001	-0.019	9.747	-0.310	-0.310	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.010	0.018	13.113	0.053	0.053	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.000	-0.018	8.722	-1.229	-1.229	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.869	-0.946	14.619	-14.223	-14.223	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.949	-0.984	17.511	-13.330	-13.330	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.941	-0.953	20.077	-12.262	-12.262	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.098	-0.048	17.521	0.151	0.151	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.007	-0.003	14.145	-1.643	-1.643	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.021	-0.002	14.270	1.104	1.104	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.021	-0.018	17.308	0.248	0.248	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.019	-0.014	20.123	0.117	0.117	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.008	0.003	14.686	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.800	-0.849	17.597	-14.872	-14.872	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.079	0.028	16.145	-0.998	-0.998	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.045	-0.028	16.576	-0.715	-0.715	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.817	0.882	16.003	15.931	15.931	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.042	-0.013	11.917	-1.086	-1.086	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.002	-0.013	12.763	-1.614	-1.614	0.000	0.000	0.000	0.000
57	A	57	MET	0	-0.046	0.013	14.282	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.043	0.011	16.722	0.261	0.261	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.873	-0.952	19.825	-14.247	-14.247	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-1.007	-1.006	21.456	-11.395	-11.395	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.971	-0.969	18.646	-16.146	-16.146	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.021	-0.019	19.065	-0.469	-0.469	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.013	0.024	13.734	0.294	0.294	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.052	-0.065	17.962	0.705	0.705	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.051	-0.018	19.073	0.684	0.684	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.906	0.957	14.902	17.214	17.214	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.044	-0.026	14.055	0.646	0.646	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.786	-0.877	14.171	-17.864	-17.864	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.061	-0.045	10.201	-0.737	-0.737	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.042	0.030	10.318	1.713	1.713	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.943	-0.979	6.394	-42.142	-42.142	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.018	0.025	7.234	3.634	3.634	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.006	-0.001	6.491	-6.842	-6.842	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.002	0.014	7.494	3.460	3.460	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.013	-0.011	9.492	-1.446	-1.446	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.877	-0.927	12.574	-18.213	-18.213	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.817	0.890	12.576	20.051	20.051	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.001	0.003	13.016	1.469	1.469	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.902	-0.940	12.016	-19.512	-19.512	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.000	-0.027	10.367	0.945	0.945	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.028	-0.007	11.481	-1.097	-1.097	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.001	0.003	7.918	-0.147	-0.147	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.007	-0.003	12.640	0.167	0.167	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.002	0.037	14.591	-0.193	-0.193	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.027	0.022	15.970	1.013	1.013	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.006	-0.002	18.786	0.661	0.661	0.000	0.000	0.000	0.000
87	A	87	HIS	1	0.826	0.894	18.022	15.396	15.396	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.024	0.032	18.972	0.083	0.083	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.005	-0.007	19.936	0.102	0.102	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.077	-0.040	21.205	0.482	0.482	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.003	0.005	19.638	-0.115	-0.115	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.065	-0.005	13.452	-0.289	-0.289	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.003	-0.020	14.530	-0.174	-0.174	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.021	-0.009	10.877	-0.149	-0.149	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.847	0.919	10.380	19.480	19.480	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.006	0.001	5.186	-2.033	-2.033	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.022	0.002	7.924	2.368	2.368	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.002	0.010	7.833	-3.077	-3.077	0.000	0.000	0.000	0.000
99	A	99	ASN	-1	-0.794	-0.890	9.206	-21.889	-21.889	0.000	0.000	0.000	0.000

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