FMO DATABASE

FMODB ID: G75M1

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	60
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-262640.329401
FMO2-HF: Nuclear repulsion	239130.918616
FMO2-HF: Total energy	-23509.410785
FMO2-MP2: Total energy	-23580.479488

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.
57.963	58.502	13.455	-5.985	-8.008	-0.06

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 : 0.867 / 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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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	PRO	0	0.059	0.022	2.007	-0.619	0.783	1.976	-1.032	-2.345	-0.005
4	A	4	THR	0	-0.018	-0.004	1.859	-19.381	-20.378	11.463	-5.125	-5.341	-0.055
5	A	5	LEU	0	0.004	0.030	3.105	8.150	8.284	0.016	0.172	-0.322	0.000
6	A	6	THR	0	0.049	0.000	5.823	4.531	4.531	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.062	0.039	5.923	3.849	3.849	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.876	0.938	5.417	40.401	40.401	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.063	0.031	6.864	3.204	3.204	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.090	0.081	8.686	3.104	3.104	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.052	-0.050	9.751	2.846	2.846	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.035	-0.024	9.981	1.194	1.194	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.003	0.001	11.437	0.713	0.713	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.030	0.015	12.541	1.559	1.559	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.887	0.953	13.440	21.308	21.308	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.911	0.967	15.160	16.087	16.087	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.085	0.034	18.039	-0.277	-0.277	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.073	0.025	20.510	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.032	-0.026	16.268	0.544	0.544	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.021	0.033	16.617	-0.479	-0.479	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.022	0.012	17.816	0.105	0.105	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.008	-0.006	19.680	0.139	0.139	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.039	-0.051	15.518	-0.270	-0.270	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.039	0.031	17.970	-0.242	-0.242	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.003	0.001	20.027	0.328	0.328	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.036	-0.015	17.319	0.243	0.243	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.010	-0.004	18.732	-0.051	-0.051	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.011	-0.006	19.325	0.308	0.308	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.048	0.037	22.984	0.323	0.323	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.046	-0.020	16.913	0.177	0.177	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.023	-0.022	21.108	0.207	0.207	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.926	-0.955	22.594	-10.622	-10.622	0.000	0.000	0.000	0.000
33	A	33	ARG	1	1.002	0.996	25.622	11.311	11.311	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.022	-0.008	22.728	0.237	0.237	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.055	-0.030	24.720	0.200	0.200	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.912	-0.950	26.386	-9.642	-9.642	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.028	0.013	27.440	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.025	-0.018	26.870	0.170	0.170	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.042	-0.029	27.814	0.181	0.181	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.928	-0.961	30.735	-8.733	-8.733	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.031	0.016	29.784	0.242	0.242	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.052	-0.021	31.004	0.172	0.172	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.032	-0.027	32.717	0.395	0.395	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.936	-0.963	34.719	-8.573	-8.573	0.000	0.000	0.000	0.000
45	A	45	HIS	0	-0.050	-0.038	32.661	0.075	0.075	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.088	-0.027	36.128	0.183	0.183	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.038	-0.022	38.222	0.335	0.335	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.814	-0.887	40.661	-7.112	-7.112	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.026	-0.016	42.263	0.117	0.117	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.870	0.912	44.373	6.762	6.762	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.015	0.020	41.224	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	52	TRP	0	0.075	0.033	42.606	0.105	0.105	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.767	0.882	44.501	6.148	6.148	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.002	0.005	46.897	0.056	0.056	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.065	0.035	46.626	0.127	0.127	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.904	0.956	49.093	6.209	6.209	0.000	0.000	0.000	0.000
57	A	57	HIS	-1	-0.945	-0.978	51.308	-5.800	-5.800	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.830	0.905	52.977	5.594	5.594	0.000	0.000	0.000	0.000
59	A	59	TYR	-1	-0.933	-0.971	46.412	-6.727	-6.727	0.000	0.000	0.000	0.000
60	A	60	GLU	-2	-1.849	-1.896	51.874	-11.276	-11.276	0.000	0.000	0.000	0.000

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