FMO DATABASE

FMODB ID: Q5V5Y

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-424086.937567
FMO2-HF: Nuclear repulsion	391357.266416
FMO2-HF: Total energy	-32729.671151
FMO2-MP2: Total energy	-32827.408336

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.
14.6	19.636	6.674	-5.986	-5.723	-0.082

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 : 0.826 / q_NPA : 0.906

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	ALA	0	0.004	0.003	2.907	6.640	9.024	0.038	-1.120	-1.302	-0.003
4	A	4	ALA	0	0.028	0.030	4.806	5.473	5.602	-0.001	-0.010	-0.117	0.000
8	A	8	HIS	0	0.068	0.013	2.060	-31.358	-28.835	6.637	-4.856	-4.304	-0.079
5	A	5	LYS	0	0.006	-0.002	7.239	1.910	1.910	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.000	-0.005	7.844	1.516	1.516	0.000	0.000	0.000	0.000
7	A	7	GLU	0	-0.058	-0.061	7.959	-1.556	-1.556	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.007	0.022	5.630	-1.885	-1.885	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.077	0.026	8.465	2.203	2.203	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.053	0.028	5.935	-0.313	-0.313	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.083	0.046	8.536	0.707	0.707	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.050	0.021	12.082	0.387	0.387	0.000	0.000	0.000	0.000
14	A	14	ARG	1	1.000	0.997	15.645	18.244	18.244	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.007	-0.012	11.494	0.084	0.084	0.000	0.000	0.000	0.000
16	A	16	TRP	0	0.052	0.037	13.269	-0.795	-0.795	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.984	1.010	14.513	15.036	15.036	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.032	-0.017	14.449	0.523	0.523	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.052	0.023	10.144	0.528	0.528	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.011	-0.009	14.222	0.526	0.526	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.039	-0.020	17.430	0.284	0.284	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.019	-0.006	17.078	0.604	0.604	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.015	0.000	11.743	-0.831	-0.831	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.008	-0.004	15.054	0.632	0.632	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.002	0.003	16.617	0.619	0.619	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.015	0.000	18.628	0.530	0.530	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.005	0.019	16.247	0.706	0.706	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.043	0.018	18.774	0.471	0.471	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.003	0.028	21.448	0.624	0.624	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.013	0.008	19.865	0.477	0.477	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.014	-0.015	21.103	0.341	0.341	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.057	-0.050	23.126	0.555	0.555	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.011	0.009	26.106	0.428	0.428	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.008	-0.009	23.973	0.688	0.688	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.023	-0.012	26.815	0.420	0.420	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.041	-0.018	28.514	0.380	0.380	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.017	-0.016	29.034	0.284	0.284	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.053	-0.028	28.841	0.074	0.074	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.024	0.001	31.836	0.201	0.201	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.026	0.009	34.246	0.158	0.158	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.051	-0.017	37.634	-0.225	-0.225	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.904	0.953	39.829	7.521	7.521	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.918	-0.959	41.768	-6.381	-6.381	0.000	0.000	0.000	0.000
44	A	44	ARG	0	0.006	-0.002	44.334	-0.163	-0.163	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.051	-0.033	44.695	0.075	0.075	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.912	-0.947	47.558	-5.785	-5.785	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.006	0.043	49.977	-0.101	-0.101	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.034	0.010	50.320	0.099	0.099	0.000	0.000	0.000	0.000
49	A	49	PRO	0	-0.007	0.009	51.554	-0.120	-0.120	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.013	-0.017	47.128	0.102	0.102	0.000	0.000	0.000	0.000
51	A	51	HIS	0	0.009	-0.012	50.253	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	52	HIS	0	-0.066	-0.017	43.603	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.004	0.002	43.553	-0.178	-0.178	0.000	0.000	0.000	0.000
54	A	54	ARG	0	-0.015	0.017	46.316	0.156	0.156	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.003	0.013	46.689	0.136	0.136	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.865	0.906	49.338	5.704	5.704	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.003	0.000	51.390	0.067	0.067	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.949	0.982	53.236	5.984	5.984	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.044	-0.018	52.999	-0.093	-0.093	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.029	0.012	46.169	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.063	-0.043	50.121	0.126	0.126	0.000	0.000	0.000	0.000
62	A	62	TRP	0	0.014	0.010	48.402	0.090	0.090	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.026	0.025	51.654	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.789	-0.896	53.745	-5.731	-5.731	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.007	0.016	52.481	0.070	0.070	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.027	-0.028	51.152	0.079	0.079	0.000	0.000	0.000	0.000
67	A	67	HIS	0	0.088	0.083	44.411	-0.141	-0.141	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.029	-0.023	43.386	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.053	-0.033	39.186	0.061	0.061	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.022	-0.016	37.506	0.027	0.027	0.000	0.000	0.000	0.000
71	A	71	HIS	-1	-0.875	-0.946	42.134	-6.714	-6.714	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.020	-0.020	41.194	0.074	0.074	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.102	0.046	44.263	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.934	0.993	44.495	6.921	6.921	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.076	-0.056	40.935	-0.105	-0.105	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.049	-0.025	43.772	-0.108	-0.108	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.024	0.025	45.174	0.108	0.108	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.066	0.040	48.405	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.061	-0.052	50.277	-0.056	-0.056	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.025	-0.026	52.833	0.033	0.033	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.023	-0.027	53.079	0.099	0.099	0.000	0.000	0.000	0.000
82	A	82	TYR	-1	-0.975	-1.010	49.744	-6.358	-6.358	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.964	-0.977	52.865	-5.720	-5.720	0.000	0.000	0.000	0.000
84	A	84	LYS	0	-0.008	0.007	54.823	-0.132	-0.132	0.000	0.000	0.000	0.000

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