FMO DATABASE

FMODB ID: 4Y4YN

Calculation Name: 5XTB-L-Other547

Preferred Name: Mitochondrial complex I (NADH dehydrogenase)

Target Type: PROTEIN COMPLEX

Ligand Name: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | flavin mononucleotide | s-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate | iron/sulfur cluster | fe2/s2 (inorganic) cluster

Ligand 3-letter code: NDP | FMN | 8Q1 | SF4 | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XTB

Chain ID: L

ChEMBL ID: CHEMBL2363065

UniProt ID: O14561

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-829022.891414
FMO2-HF: Nuclear repulsion	780952.967734
FMO2-HF: Total energy	-48069.92368
FMO2-MP2: Total energy	-48209.744765

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:58:LYS)

Summations of interaction energy for fragment #1(A:58:LYS)

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.
-200.324	-194.688	21.743	-13.83	-13.546	-0.168

Interaction energy analysis for fragmet #1(A:58:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.685 / q_NPA : 1.823

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	60	ASP	-1	-0.806	-0.907	2.239	-162.738	-153.797	4.652	-6.299	-7.293	-0.081
4	A	61	ILE	0	-0.017	-0.016	5.012	10.104	10.179	-0.001	-0.011	-0.062	0.000
82	A	139	GLU	-1	-0.856	-0.928	1.699	-177.832	-182.565	17.071	-6.965	-5.373	-0.083
83	A	140	LYS	1	0.895	0.963	3.454	40.984	42.089	0.020	-0.508	-0.616	-0.004
85	A	142	GLY	0	0.027	0.030	3.315	5.486	5.661	0.002	-0.045	-0.132	0.000
86	A	143	TRP	0	-0.043	-0.024	4.396	1.767	1.840	-0.001	-0.002	-0.070	0.000
5	A	62	THR	0	0.012	0.002	6.928	5.154	5.154	0.000	0.000	0.000	0.000
6	A	63	THR	0	0.015	0.009	9.329	2.710	2.710	0.000	0.000	0.000	0.000
7	A	64	LEU	0	-0.014	0.003	10.468	3.117	3.117	0.000	0.000	0.000	0.000
8	A	65	THR	0	-0.045	-0.021	11.486	3.117	3.117	0.000	0.000	0.000	0.000
9	A	66	GLY	0	0.024	0.013	14.028	-0.104	-0.104	0.000	0.000	0.000	0.000
10	A	67	VAL	0	-0.035	-0.018	11.864	2.275	2.275	0.000	0.000	0.000	0.000
11	A	68	PRO	0	0.018	-0.001	15.128	-0.698	-0.698	0.000	0.000	0.000	0.000
12	A	69	GLU	-1	-0.826	-0.909	13.373	-38.584	-38.584	0.000	0.000	0.000	0.000
13	A	70	GLU	-1	-0.875	-0.932	13.462	-34.410	-34.410	0.000	0.000	0.000	0.000
14	A	71	HIS	0	-0.015	-0.032	14.536	-1.510	-1.510	0.000	0.000	0.000	0.000
15	A	72	ILE	0	-0.021	0.004	6.910	-0.313	-0.313	0.000	0.000	0.000	0.000
16	A	73	LYS	1	0.858	0.921	9.763	37.968	37.968	0.000	0.000	0.000	0.000
17	A	74	THR	0	-0.036	0.002	11.900	0.631	0.631	0.000	0.000	0.000	0.000
18	A	75	ARG	1	0.754	0.848	12.663	35.635	35.635	0.000	0.000	0.000	0.000
19	A	76	LYS	1	0.857	0.934	10.698	34.444	34.444	0.000	0.000	0.000	0.000
20	A	77	VAL	0	-0.012	0.003	9.757	3.145	3.145	0.000	0.000	0.000	0.000
21	A	78	ARG	1	0.897	0.946	12.102	28.884	28.884	0.000	0.000	0.000	0.000
22	A	79	ILE	0	-0.010	-0.004	9.628	1.118	1.118	0.000	0.000	0.000	0.000
23	A	80	PHE	0	-0.001	-0.003	14.142	1.510	1.510	0.000	0.000	0.000	0.000
24	A	81	VAL	0	-0.004	-0.003	17.613	-0.077	-0.077	0.000	0.000	0.000	0.000
25	A	82	PRO	0	-0.024	0.013	20.828	0.580	0.580	0.000	0.000	0.000	0.000
26	A	83	ALA	0	0.022	-0.008	23.746	0.580	0.580	0.000	0.000	0.000	0.000
27	A	84	ARG	1	0.876	0.936	26.766	18.180	18.180	0.000	0.000	0.000	0.000
28	A	85	ASN	0	0.034	0.014	30.245	0.091	0.091	0.000	0.000	0.000	0.000
29	A	86	ASN	0	0.009	-0.007	32.651	0.267	0.267	0.000	0.000	0.000	0.000
30	A	87	MET	0	0.030	0.019	35.085	0.336	0.336	0.000	0.000	0.000	0.000
31	A	88	GLN	0	0.039	0.026	35.808	-0.101	-0.101	0.000	0.000	0.000	0.000
32	A	89	SER	0	0.019	0.015	36.338	-0.462	-0.462	0.000	0.000	0.000	0.000
33	A	90	GLY	0	0.033	0.014	34.830	-0.193	-0.193	0.000	0.000	0.000	0.000
34	A	91	VAL	0	0.023	-0.007	31.136	-0.541	-0.541	0.000	0.000	0.000	0.000
35	A	92	ASN	0	0.011	0.016	30.269	-0.827	-0.827	0.000	0.000	0.000	0.000
36	A	93	ASN	0	0.063	0.020	27.691	-0.368	-0.368	0.000	0.000	0.000	0.000
37	A	94	THR	0	-0.009	0.016	25.840	-0.697	-0.697	0.000	0.000	0.000	0.000
38	A	95	LYS	1	0.824	0.910	24.829	19.702	19.702	0.000	0.000	0.000	0.000
39	A	96	LYS	1	0.987	0.989	21.808	24.197	24.197	0.000	0.000	0.000	0.000
40	A	97	TRP	0	0.012	0.018	17.024	0.740	0.740	0.000	0.000	0.000	0.000
41	A	98	LYS	1	0.902	0.950	17.692	27.153	27.153	0.000	0.000	0.000	0.000
42	A	99	MET	0	-0.008	0.017	11.417	-1.940	-1.940	0.000	0.000	0.000	0.000
43	A	100	GLU	-1	-0.879	-0.952	15.657	-26.466	-26.466	0.000	0.000	0.000	0.000
44	A	101	PHE	0	0.019	0.006	12.450	-1.716	-1.716	0.000	0.000	0.000	0.000
45	A	102	ASP	-1	-0.826	-0.888	15.841	-32.985	-32.985	0.000	0.000	0.000	0.000
46	A	103	THR	0	-0.038	-0.024	18.126	0.536	0.536	0.000	0.000	0.000	0.000
47	A	104	ARG	1	0.890	0.950	17.532	30.016	30.016	0.000	0.000	0.000	0.000
48	A	105	GLU	-1	-0.852	-0.949	22.879	-19.737	-19.737	0.000	0.000	0.000	0.000
49	A	106	ARG	1	0.847	0.926	24.716	21.824	21.824	0.000	0.000	0.000	0.000
50	A	107	TRP	0	0.048	0.048	27.599	0.231	0.231	0.000	0.000	0.000	0.000
51	A	108	GLU	-1	-0.917	-0.958	32.168	-15.760	-15.760	0.000	0.000	0.000	0.000
52	A	109	ASN	0	-0.034	-0.018	35.490	0.104	0.104	0.000	0.000	0.000	0.000
53	A	110	PRO	0	0.004	-0.003	36.901	0.331	0.331	0.000	0.000	0.000	0.000
54	A	111	LEU	0	-0.009	0.002	39.925	0.488	0.488	0.000	0.000	0.000	0.000
55	A	112	MET	0	-0.040	-0.047	40.173	-0.185	-0.185	0.000	0.000	0.000	0.000
56	A	113	GLY	0	0.074	0.062	39.661	0.027	0.027	0.000	0.000	0.000	0.000
57	A	114	TRP	0	-0.078	-0.038	35.927	-0.314	-0.314	0.000	0.000	0.000	0.000
58	A	115	ALA	0	0.030	0.009	31.300	-0.090	-0.090	0.000	0.000	0.000	0.000
59	A	116	SER	0	-0.003	0.003	31.436	0.117	0.117	0.000	0.000	0.000	0.000
60	A	117	THR	0	-0.051	-0.037	25.084	-0.245	-0.245	0.000	0.000	0.000	0.000
61	A	118	ALA	0	0.047	0.044	24.303	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	119	ASP	-1	-0.798	-0.899	20.071	-27.673	-27.673	0.000	0.000	0.000	0.000
63	A	120	PRO	0	0.006	0.008	20.517	0.061	0.061	0.000	0.000	0.000	0.000
64	A	121	LEU	0	0.003	-0.006	15.354	0.394	0.394	0.000	0.000	0.000	0.000
65	A	122	SER	0	-0.015	-0.014	19.062	-0.493	-0.493	0.000	0.000	0.000	0.000
66	A	123	ASN	0	-0.046	-0.020	20.881	0.570	0.570	0.000	0.000	0.000	0.000
67	A	124	MET	0	-0.030	-0.001	17.321	0.740	0.740	0.000	0.000	0.000	0.000
68	A	125	VAL	0	-0.004	-0.006	18.813	-0.599	-0.599	0.000	0.000	0.000	0.000
69	A	126	LEU	0	-0.005	0.010	14.398	0.220	0.220	0.000	0.000	0.000	0.000
70	A	127	THR	0	-0.076	-0.048	17.658	0.270	0.270	0.000	0.000	0.000	0.000
71	A	128	PHE	0	0.029	0.012	13.542	-0.922	-0.922	0.000	0.000	0.000	0.000
72	A	129	SER	0	-0.049	-0.048	17.316	1.919	1.919	0.000	0.000	0.000	0.000
73	A	130	THR	0	-0.040	-0.033	15.899	0.723	0.723	0.000	0.000	0.000	0.000
74	A	131	LYS	1	0.909	0.951	13.707	37.065	37.065	0.000	0.000	0.000	0.000
75	A	132	GLU	-1	-0.779	-0.897	11.606	-41.490	-41.490	0.000	0.000	0.000	0.000
76	A	133	ASP	-1	-0.830	-0.879	10.785	-44.755	-44.755	0.000	0.000	0.000	0.000
77	A	134	ALA	0	0.046	0.032	11.247	-3.274	-3.274	0.000	0.000	0.000	0.000
78	A	135	VAL	0	0.013	0.001	7.141	-2.611	-2.611	0.000	0.000	0.000	0.000
79	A	136	SER	0	-0.048	-0.034	6.808	-8.543	-8.543	0.000	0.000	0.000	0.000
80	A	137	PHE	0	-0.003	-0.012	7.385	-6.116	-6.116	0.000	0.000	0.000	0.000
81	A	138	ALA	0	0.053	0.033	7.022	-2.444	-2.444	0.000	0.000	0.000	0.000
84	A	141	ASN	0	-0.057	-0.049	5.858	4.333	4.333	0.000	0.000	0.000	0.000
87	A	144	SER	0	0.038	0.018	5.825	-6.171	-6.171	0.000	0.000	0.000	0.000
88	A	145	TYR	0	-0.055	-0.041	5.025	11.916	11.916	0.000	0.000	0.000	0.000
89	A	146	ASP	-1	-0.833	-0.917	9.636	-38.454	-38.454	0.000	0.000	0.000	0.000
90	A	147	ILE	0	-0.020	-0.006	10.286	0.778	0.778	0.000	0.000	0.000	0.000
91	A	148	GLU	-1	-0.851	-0.913	13.817	-28.539	-28.539	0.000	0.000	0.000	0.000
92	A	149	GLU	-1	-0.932	-0.976	17.534	-26.948	-26.948	0.000	0.000	0.000	0.000
93	A	150	ARG	1	0.866	0.922	20.067	27.017	27.017	0.000	0.000	0.000	0.000
94	A	151	LYS	1	0.986	1.000	22.698	23.911	23.911	0.000	0.000	0.000	0.000
95	A	152	VAL	0	0.011	0.010	26.063	0.574	0.574	0.000	0.000	0.000	0.000
96	A	153	PRO	0	-0.025	-0.023	28.645	0.281	0.281	0.000	0.000	0.000	0.000
97	A	154	LYS	1	1.007	1.014	32.118	18.548	18.548	0.000	0.000	0.000	0.000
98	A	155	PRO	0	0.046	0.022	33.735	0.430	0.430	0.000	0.000	0.000	0.000
99	A	156	LYS	1	0.910	0.940	36.357	16.837	16.837	0.000	0.000	0.000	0.000
100	A	157	SER	0	0.050	0.041	40.394	0.065	0.065	0.000	0.000	0.000	0.000
101	A	158	LYS	1	0.928	0.951	43.423	13.998	13.998	0.000	0.000	0.000	0.000
102	A	159	SER	0	0.068	0.028	46.296	0.056	0.056	0.000	0.000	0.000	0.000
103	A	160	TYR	0	0.076	0.045	49.857	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	161	GLY	0	0.085	0.038	52.614	0.100	0.100	0.000	0.000	0.000	0.000
105	A	162	ALA	0	-0.049	-0.028	50.256	0.112	0.112	0.000	0.000	0.000	0.000
106	A	163	ASN	0	-0.012	0.001	51.228	-0.147	-0.147	0.000	0.000	0.000	0.000
107	A	164	PHE	0	0.017	0.020	53.442	0.147	0.147	0.000	0.000	0.000	0.000
108	A	165	SER	0	-0.009	-0.009	56.335	-0.206	-0.206	0.000	0.000	0.000	0.000
109	A	166	TRP	0	0.069	0.030	58.601	-0.160	-0.160	0.000	0.000	0.000	0.000
110	A	167	ASN	0	0.040	0.017	58.709	-0.115	-0.115	0.000	0.000	0.000	0.000
111	A	168	LYS	1	0.863	0.929	53.022	11.536	11.536	0.000	0.000	0.000	0.000
112	A	169	ARG	1	0.954	0.989	52.354	11.490	11.490	0.000	0.000	0.000	0.000
113	A	170	THR	0	-0.008	-0.006	51.331	-0.070	-0.070	0.000	0.000	0.000	0.000
114	A	171	ARG	1	0.934	0.984	53.867	10.382	10.382	0.000	0.000	0.000	0.000
115	A	172	VAL	0	0.012	-0.016	53.460	0.102	0.102	0.000	0.000	0.000	0.000
116	A	173	SER	0	-0.006	-0.017	56.113	0.152	0.152	0.000	0.000	0.000	0.000
117	A	174	THR	0	-0.018	0.010	59.516	0.082	0.082	0.000	0.000	0.000	0.000
118	A	175	LYS	0	0.019	0.020	56.752	0.019	0.019	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:58:LYS)