FMO DATABASE

FMODB ID: VZQ21

Calculation Name: 5J4Z-A-Other547

Preferred Name: Cytochrome c oxidase subunit 1

Target Type: SINGLE PROTEIN

Ligand 3-letter code: HEA | HEM | SF4 | FES | CUA | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5J4Z

Chain ID: A

ChEMBL ID: CHEMBL6011

UniProt ID: O78749

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-242670.559754
FMO2-HF: Nuclear repulsion	219860.701061
FMO2-HF: Total energy	-22809.858692
FMO2-MP2: Total energy	-22876.351605

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:PHE)

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

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.
60.763	64.373	5.62	-2.496	-6.736	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.908

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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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	ASN	0	0.047	0.019	3.175	0.473	2.769	2.508	-1.368	-3.437	-0.005
4	A	4	ARG	1	0.872	0.908	2.239	30.885	31.996	3.110	-1.149	-3.072	0.005
5	A	5	VAL	0	0.006	0.006	3.980	2.651	2.854	0.002	0.021	-0.227	0.000
6	A	6	ALA	0	0.030	0.023	6.442	2.427	2.427	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.785	-0.875	6.736	-23.925	-23.925	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.951	0.970	5.585	24.616	24.616	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.007	0.004	7.546	1.911	1.911	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.886	0.933	10.482	17.347	17.347	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.023	0.005	10.460	0.857	0.857	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.020	-0.020	11.329	0.934	0.934	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.009	-0.003	13.035	0.248	0.248	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.889	-0.923	15.048	-14.112	-14.112	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.868	-0.932	16.962	-11.396	-11.396	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.050	-0.028	19.611	0.368	0.368	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.041	0.025	21.606	0.237	0.237	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.050	-0.008	18.515	0.209	0.209	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.030	0.001	20.040	-0.421	-0.421	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.026	0.002	16.174	-0.262	-0.262	0.000	0.000	0.000	0.000
21	A	21	HIS	1	0.797	0.912	16.810	11.571	11.571	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.053	0.028	17.681	-0.316	-0.316	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.788	0.892	15.160	13.645	13.645	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.004	0.010	12.901	-0.624	-0.624	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.038	0.021	13.691	-0.520	-0.520	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.005	-0.016	16.499	0.280	0.280	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.014	-0.004	14.080	0.586	0.586	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.805	-0.902	16.822	-12.607	-12.607	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.008	0.004	18.319	0.626	0.626	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.017	0.013	19.850	0.371	0.371	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.048	0.028	17.942	0.328	0.328	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.024	0.020	21.107	0.350	0.350	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.991	1.001	23.226	9.712	9.712	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.009	0.026	23.457	0.365	0.365	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.011	-0.028	23.047	0.323	0.323	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.014	0.009	25.981	0.294	0.294	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.063	-0.062	28.581	0.326	0.326	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.018	0.018	27.987	0.274	0.274	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.023	-0.004	29.643	0.296	0.296	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.026	0.023	31.484	0.242	0.242	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.024	0.012	33.738	0.240	0.240	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.018	0.010	34.063	0.191	0.191	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.041	-0.045	34.918	0.227	0.227	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.002	0.008	37.208	0.203	0.203	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.009	-0.004	37.838	0.229	0.229	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.025	0.001	38.666	0.122	0.122	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.026	-0.003	40.584	0.139	0.139	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.020	-0.009	42.987	0.196	0.196	0.000	0.000	0.000	0.000
49	A	49	CYS	0	0.006	-0.015	42.940	0.123	0.123	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.018	0.002	44.627	0.112	0.112	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.011	-0.021	46.350	0.140	0.140	0.000	0.000	0.000	0.000
52	A	52	TRP	0	-0.029	0.000	47.721	0.085	0.085	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.010	0.004	47.546	0.073	0.073	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.063	-0.033	48.958	0.124	0.124	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.039	-0.013	50.722	0.141	0.141	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.023	-0.022	52.468	-0.058	-0.058	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.023	-0.006	52.163	0.046	0.046	0.000	0.000	0.000	0.000
58	A	58	LYS	0	0.006	0.020	54.195	-0.139	-0.139	0.000	0.000	0.000	0.000

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