FMO DATABASE

FMODB ID: JYG39

Calculation Name: 5XTC-k-Other547

Preferred Name: Mitochondrial complex I (NADH dehydrogenase)

Target Type: PROTEIN COMPLEX

Ligand Name: cardiolipin | (9r,11s)-9-({[(1s)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | s-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

Ligand 3-letter code: CDL | PLX | PEE | 8Q1

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XTC

Chain ID: k

ChEMBL ID: CHEMBL2363065

UniProt ID: O14561

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-598516.817637
FMO2-HF: Nuclear repulsion	558709.128888
FMO2-HF: Total energy	-39807.68875
FMO2-MP2: Total energy	-39914.27717

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.
-69.453	-70.766	27.561	-11.732	-14.514	-0.084

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 : 0.836 / q_NPA : 0.937

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	LEU	0	0.050	0.031	3.859	4.480	6.477	-0.014	-0.842	-1.141	-0.002
4	A	4	ILE	0	0.012	0.007	2.254	4.346	4.474	4.625	-1.185	-3.568	-0.007
5	A	5	TYR	-1	-0.827	-0.917	2.933	-70.019	-64.607	0.671	-2.727	-3.356	-0.034
6	A	6	MET	0	0.015	-0.001	5.166	5.914	6.060	-0.001	-0.010	-0.135	0.000
46	A	46	LEU	0	-0.029	-0.011	2.628	-2.594	-1.813	0.426	-0.214	-0.993	-0.001
47	A	47	MET	0	0.005	0.010	3.424	-3.935	-3.281	0.026	-0.294	-0.385	-0.002
49	A	49	LEU	0	-0.031	-0.008	4.651	2.400	2.467	-0.001	-0.003	-0.062	0.000
50	A	50	ASN	0	-0.064	-0.049	1.949	2.788	-7.776	21.830	-6.449	-4.817	-0.038
51	A	51	THR	0	-0.050	-0.028	4.916	2.305	2.371	-0.001	-0.008	-0.057	0.000
7	A	7	ASN	0	-0.019	0.001	7.321	5.391	5.391	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.010	0.011	6.567	2.772	2.772	0.000	0.000	0.000	0.000
9	A	9	MET	0	0.021	0.000	9.222	1.818	1.818	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.016	0.010	11.241	2.213	2.213	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.020	0.009	12.493	1.800	1.800	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.046	0.031	13.482	1.396	1.396	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.036	-0.027	15.182	1.430	1.430	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.000	0.000	16.509	1.133	1.133	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.039	-0.027	17.892	0.806	0.806	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.051	0.012	18.843	0.763	0.763	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.041	-0.016	21.039	0.791	0.791	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.014	-0.010	22.781	0.618	0.618	0.000	0.000	0.000	0.000
19	A	19	MET	0	-0.022	-0.018	23.956	0.395	0.395	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.028	-0.018	25.335	0.497	0.497	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.053	-0.015	27.413	0.447	0.447	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.007	0.006	29.080	0.471	0.471	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.990	0.994	30.980	9.465	9.465	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.064	-0.039	33.042	0.023	0.023	0.000	0.000	0.000	0.000
25	A	25	HIS	0	0.093	0.044	32.953	-0.061	-0.061	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.067	0.033	32.102	-0.257	-0.257	0.000	0.000	0.000	0.000
27	A	27	MET	0	0.047	0.036	30.565	-0.289	-0.289	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.017	0.003	28.409	-0.456	-0.456	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.004	-0.017	26.735	-0.426	-0.426	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.035	0.019	25.964	-0.373	-0.373	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.040	0.009	24.537	-0.413	-0.413	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.084	-0.034	22.237	-0.683	-0.683	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.033	0.016	21.117	-0.705	-0.705	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.901	-0.953	20.381	-12.678	-12.678	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.019	-0.010	18.398	-0.747	-0.747	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.034	-0.009	16.577	-1.165	-1.165	0.000	0.000	0.000	0.000
37	A	37	MET	0	0.024	0.036	15.589	-1.384	-1.384	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.008	0.007	13.802	-1.036	-1.036	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.051	-0.041	12.007	-1.579	-1.579	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.036	0.003	10.697	-2.351	-2.351	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.001	0.007	11.279	-1.210	-1.210	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.001	0.000	7.177	-1.396	-1.396	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.034	-0.017	6.828	-4.156	-4.156	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.008	0.008	6.796	-2.623	-2.623	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.001	-0.016	8.160	-1.443	-1.443	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.060	-0.037	5.544	1.140	1.140	0.000	0.000	0.000	0.000
52	A	52	HIS	0	0.036	0.031	8.478	2.642	2.642	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.021	-0.017	10.780	1.642	1.642	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.034	0.000	13.005	-0.238	-0.238	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.013	-0.001	15.015	0.117	0.117	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.025	0.020	12.098	0.424	0.424	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.033	0.009	11.558	-1.113	-1.113	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.002	0.007	13.412	0.388	0.388	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.006	0.002	13.962	0.626	0.626	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.031	0.006	11.263	0.589	0.589	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.002	0.005	14.077	0.557	0.557	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.002	-0.011	17.241	0.591	0.591	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.019	-0.011	13.870	0.730	0.730	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.012	-0.003	16.536	0.497	0.497	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.008	0.006	19.372	0.552	0.552	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.027	0.012	21.902	0.552	0.552	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.090	0.044	20.544	0.406	0.406	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.013	0.003	22.492	0.353	0.353	0.000	0.000	0.000	0.000
69	A	69	CYS	0	-0.072	-0.039	24.566	0.583	0.583	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.930	-0.964	23.520	-12.038	-12.038	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.023	0.015	25.110	0.359	0.359	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.023	-0.011	27.103	0.385	0.385	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.005	-0.008	30.071	0.390	0.390	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.018	0.006	30.099	0.281	0.281	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.016	-0.024	29.752	0.294	0.294	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.011	-0.006	32.796	0.299	0.299	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.008	-0.003	33.369	0.300	0.300	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.019	0.028	33.116	0.240	0.240	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.023	0.014	37.123	0.228	0.228	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.078	-0.028	39.522	0.260	0.260	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.062	0.022	37.623	0.202	0.202	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.064	-0.046	41.828	0.179	0.179	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.062	-0.029	43.392	0.238	0.238	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.019	-0.017	45.173	0.083	0.083	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.006	-0.011	43.491	0.159	0.159	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.054	0.044	44.736	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.106	-0.053	38.539	-0.129	-0.129	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.911	-0.937	39.617	-7.412	-7.412	0.000	0.000	0.000	0.000
89	A	89	TYR	0	-0.112	-0.076	38.464	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.022	0.012	35.494	-0.095	-0.095	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.033	-0.012	38.936	-0.074	-0.074	0.000	0.000	0.000	0.000
92	A	92	ASN	0	0.016	0.009	40.807	0.069	0.069	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.002	0.011	42.513	0.125	0.125	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.022	-0.012	43.847	0.289	0.289	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.021	-0.020	45.282	-0.070	-0.070	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.065	-0.038	46.749	0.023	0.023	0.000	0.000	0.000	0.000
97	A	97	GLN	-1	-0.908	-0.931	41.163	-7.532	-7.532	0.000	0.000	0.000	0.000

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