FMO DATABASE

FMODB ID: M8Y3Z

Calculation Name: 5XTB-C-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: C

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1503876.01029
FMO2-HF: Nuclear repulsion	1439055.652463
FMO2-HF: Total energy	-64820.357827
FMO2-MP2: Total energy	-65000.985391

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:SER)

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

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.
68.473	72.278	3.045	-3.205	-3.645	-0.032

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.921

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	GLY	0	0.083	0.029	3.555	-7.020	-5.377	-0.009	-0.909	-0.725	-0.001
5	A	62	TYR	0	0.003	-0.002	2.232	-6.415	-4.613	3.050	-2.189	-2.664	-0.030
6	A	63	VAL	0	0.008	0.003	3.617	-0.054	0.306	0.004	-0.107	-0.256	-0.001
4	A	61	GLU	-1	-0.787	-0.878	6.406	-28.788	-28.788	0.000	0.000	0.000	0.000
7	A	64	VAL	0	0.030	0.023	5.410	4.491	4.491	0.000	0.000	0.000	0.000
8	A	65	ALA	0	-0.002	-0.009	7.552	2.663	2.663	0.000	0.000	0.000	0.000
9	A	66	LYS	1	0.916	0.953	6.249	39.778	39.778	0.000	0.000	0.000	0.000
10	A	67	LEU	0	0.007	0.021	8.629	2.077	2.077	0.000	0.000	0.000	0.000
11	A	68	ASP	-1	-0.763	-0.907	11.013	-17.305	-17.305	0.000	0.000	0.000	0.000
12	A	69	ASP	-1	-0.941	-0.969	10.999	-24.207	-24.207	0.000	0.000	0.000	0.000
13	A	70	LEU	0	-0.019	-0.002	12.985	1.623	1.623	0.000	0.000	0.000	0.000
14	A	71	VAL	0	0.017	0.007	14.740	1.448	1.448	0.000	0.000	0.000	0.000
15	A	72	ASN	0	-0.020	-0.020	16.461	1.985	1.985	0.000	0.000	0.000	0.000
16	A	73	TRP	0	-0.089	-0.048	17.325	0.626	0.626	0.000	0.000	0.000	0.000
17	A	74	ALA	0	0.032	0.005	18.821	0.793	0.793	0.000	0.000	0.000	0.000
18	A	75	ARG	1	0.957	0.992	20.771	14.266	14.266	0.000	0.000	0.000	0.000
19	A	76	ARG	1	0.923	0.969	18.249	15.868	15.868	0.000	0.000	0.000	0.000
20	A	77	SER	0	-0.043	-0.027	22.621	0.375	0.375	0.000	0.000	0.000	0.000
21	A	78	SER	0	0.018	0.013	24.599	0.083	0.083	0.000	0.000	0.000	0.000
22	A	79	LEU	0	-0.022	0.015	26.916	0.121	0.121	0.000	0.000	0.000	0.000
23	A	80	TRP	0	-0.031	-0.030	29.426	0.313	0.313	0.000	0.000	0.000	0.000
24	A	81	PRO	0	0.014	0.006	32.813	0.149	0.149	0.000	0.000	0.000	0.000
25	A	82	MET	0	-0.013	0.003	35.450	0.143	0.143	0.000	0.000	0.000	0.000
26	A	83	THR	0	-0.038	-0.014	38.575	0.071	0.071	0.000	0.000	0.000	0.000
27	A	84	PHE	0	0.011	-0.021	41.964	0.099	0.099	0.000	0.000	0.000	0.000
28	A	85	GLY	0	-0.010	0.000	43.758	0.037	0.037	0.000	0.000	0.000	0.000
29	A	86	LEU	0	0.002	0.005	45.862	0.141	0.141	0.000	0.000	0.000	0.000
30	A	87	ALA	0	0.008	0.004	48.678	0.163	0.163	0.000	0.000	0.000	0.000
31	A	88	CYS	0	0.010	0.004	49.319	-0.129	-0.129	0.000	0.000	0.000	0.000
32	A	89	CYS	0	0.008	0.011	45.159	-0.057	-0.057	0.000	0.000	0.000	0.000
33	A	90	ALA	0	0.022	0.010	45.515	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	91	VAL	0	0.014	0.001	46.074	-0.089	-0.089	0.000	0.000	0.000	0.000
35	A	92	GLU	-1	-0.817	-0.908	44.420	-6.952	-6.952	0.000	0.000	0.000	0.000
36	A	93	MET	0	-0.050	-0.029	40.830	-0.196	-0.196	0.000	0.000	0.000	0.000
37	A	94	MET	0	-0.012	-0.005	42.099	-0.096	-0.096	0.000	0.000	0.000	0.000
38	A	95	HIS	0	0.018	0.009	44.003	-0.144	-0.144	0.000	0.000	0.000	0.000
39	A	96	MET	0	-0.048	-0.021	37.427	-0.147	-0.147	0.000	0.000	0.000	0.000
40	A	97	ALA	0	0.006	-0.004	39.462	-0.209	-0.209	0.000	0.000	0.000	0.000
41	A	98	ALA	0	0.019	0.034	41.015	0.055	0.055	0.000	0.000	0.000	0.000
42	A	99	PRO	0	0.024	-0.005	41.743	-0.143	-0.143	0.000	0.000	0.000	0.000
43	A	100	ARG	1	0.919	0.971	41.839	6.861	6.861	0.000	0.000	0.000	0.000
44	A	101	TYR	0	-0.077	-0.028	39.535	0.013	0.013	0.000	0.000	0.000	0.000
45	A	102	ASP	-1	-0.862	-0.928	37.638	-8.832	-8.832	0.000	0.000	0.000	0.000
46	A	103	MET	0	-0.014	-0.007	35.338	-0.157	-0.157	0.000	0.000	0.000	0.000
47	A	104	ASP	-1	-0.882	-0.933	33.750	-9.470	-9.470	0.000	0.000	0.000	0.000
48	A	105	ARG	1	0.867	0.930	32.587	8.823	8.823	0.000	0.000	0.000	0.000
49	A	106	PHE	0	-0.097	-0.052	29.425	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	107	GLY	0	0.040	0.027	28.783	-0.388	-0.388	0.000	0.000	0.000	0.000
51	A	108	VAL	0	-0.085	-0.034	29.926	0.006	0.006	0.000	0.000	0.000	0.000
52	A	109	VAL	0	0.040	0.014	32.124	0.284	0.284	0.000	0.000	0.000	0.000
53	A	110	PHE	0	-0.005	-0.014	35.214	-0.039	-0.039	0.000	0.000	0.000	0.000
54	A	111	ARG	1	0.927	0.978	35.283	8.635	8.635	0.000	0.000	0.000	0.000
55	A	112	ALA	0	0.029	0.009	38.339	0.143	0.143	0.000	0.000	0.000	0.000
56	A	113	SER	0	-0.027	-0.046	38.939	-0.203	-0.203	0.000	0.000	0.000	0.000
57	A	114	PRO	0	0.037	0.028	38.981	-0.114	-0.114	0.000	0.000	0.000	0.000
58	A	115	ARG	1	0.937	0.956	36.389	8.206	8.206	0.000	0.000	0.000	0.000
59	A	116	GLN	0	0.041	0.030	34.174	-0.090	-0.090	0.000	0.000	0.000	0.000
60	A	117	SER	0	-0.021	0.006	33.383	-0.256	-0.256	0.000	0.000	0.000	0.000
61	A	118	ASP	-1	-0.784	-0.876	28.971	-10.540	-10.540	0.000	0.000	0.000	0.000
62	A	119	VAL	0	-0.027	-0.018	31.387	0.097	0.097	0.000	0.000	0.000	0.000
63	A	120	MET	0	-0.006	-0.009	33.153	0.218	0.218	0.000	0.000	0.000	0.000
64	A	121	ILE	0	0.005	-0.003	35.955	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	122	VAL	0	0.019	0.012	38.400	0.228	0.228	0.000	0.000	0.000	0.000
66	A	123	ALA	0	0.037	0.002	41.449	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	124	GLY	0	-0.019	-0.007	44.042	0.130	0.130	0.000	0.000	0.000	0.000
68	A	125	THR	0	0.002	-0.042	47.278	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	126	LEU	0	0.048	0.041	45.268	0.035	0.035	0.000	0.000	0.000	0.000
70	A	127	THR	0	0.008	-0.002	49.294	0.048	0.048	0.000	0.000	0.000	0.000
71	A	128	ASN	0	0.013	-0.028	51.543	-0.172	-0.172	0.000	0.000	0.000	0.000
72	A	129	LYS	1	0.947	0.973	52.737	5.486	5.486	0.000	0.000	0.000	0.000
73	A	130	MET	0	0.021	0.024	47.230	0.018	0.018	0.000	0.000	0.000	0.000
74	A	131	ALA	0	0.054	0.033	47.629	-0.135	-0.135	0.000	0.000	0.000	0.000
75	A	132	PRO	0	0.015	0.002	46.769	-0.168	-0.168	0.000	0.000	0.000	0.000
76	A	133	ALA	0	-0.010	-0.002	46.873	-0.113	-0.113	0.000	0.000	0.000	0.000
77	A	134	LEU	0	0.012	0.006	42.385	-0.135	-0.135	0.000	0.000	0.000	0.000
78	A	135	ARG	1	0.829	0.880	38.625	7.723	7.723	0.000	0.000	0.000	0.000
79	A	136	LYS	1	0.921	0.961	41.771	6.812	6.812	0.000	0.000	0.000	0.000
80	A	137	VAL	0	0.003	-0.008	40.587	-0.129	-0.129	0.000	0.000	0.000	0.000
81	A	138	TYR	0	0.051	0.019	33.880	-0.167	-0.167	0.000	0.000	0.000	0.000
82	A	139	ASP	-1	-0.828	-0.900	37.154	-8.179	-8.179	0.000	0.000	0.000	0.000
83	A	140	GLN	0	-0.086	-0.037	37.968	-0.114	-0.114	0.000	0.000	0.000	0.000
84	A	141	MET	0	-0.031	0.006	34.684	-0.128	-0.128	0.000	0.000	0.000	0.000
85	A	142	PRO	0	-0.013	-0.006	30.865	-0.041	-0.041	0.000	0.000	0.000	0.000
86	A	143	GLU	-1	-0.824	-0.894	28.068	-10.247	-10.247	0.000	0.000	0.000	0.000
87	A	144	PRO	0	-0.148	-0.067	24.660	-0.332	-0.332	0.000	0.000	0.000	0.000
88	A	145	ARG	1	0.880	0.931	27.759	9.380	9.380	0.000	0.000	0.000	0.000
89	A	146	TYR	0	-0.039	-0.035	24.641	-0.262	-0.262	0.000	0.000	0.000	0.000
90	A	147	VAL	0	-0.015	-0.010	31.537	0.292	0.292	0.000	0.000	0.000	0.000
91	A	148	VAL	0	-0.023	-0.011	33.773	-0.117	-0.117	0.000	0.000	0.000	0.000
92	A	149	SER	0	0.012	-0.002	36.147	0.265	0.265	0.000	0.000	0.000	0.000
93	A	150	MET	0	-0.016	-0.006	39.342	-0.110	-0.110	0.000	0.000	0.000	0.000
94	A	151	GLY	0	0.044	0.009	41.549	0.178	0.178	0.000	0.000	0.000	0.000
95	A	152	SER	0	-0.034	-0.023	44.832	-0.058	-0.058	0.000	0.000	0.000	0.000
96	A	153	CYS	-1	-0.835	-0.903	47.132	-6.390	-6.390	0.000	0.000	0.000	0.000
97	A	154	ALA	0	0.009	0.027	43.377	0.014	0.014	0.000	0.000	0.000	0.000
98	A	155	ASN	0	-0.023	-0.021	41.783	-0.234	-0.234	0.000	0.000	0.000	0.000
99	A	156	GLY	0	0.029	0.002	43.794	-0.078	-0.078	0.000	0.000	0.000	0.000
100	A	157	GLY	0	-0.022	-0.002	46.860	0.142	0.142	0.000	0.000	0.000	0.000
101	A	158	GLY	0	-0.018	-0.003	49.266	0.119	0.119	0.000	0.000	0.000	0.000
102	A	159	TYR	0	0.003	-0.009	50.580	0.050	0.050	0.000	0.000	0.000	0.000
103	A	160	TYR	0	0.027	0.013	53.372	0.160	0.160	0.000	0.000	0.000	0.000
104	A	161	HIS	0	-0.027	0.014	50.778	-0.040	-0.040	0.000	0.000	0.000	0.000
105	A	162	TYR	0	-0.002	-0.006	53.544	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	163	SER	0	0.035	0.007	56.007	0.098	0.098	0.000	0.000	0.000	0.000
107	A	164	TYR	0	0.040	0.021	57.180	-0.109	-0.109	0.000	0.000	0.000	0.000
108	A	165	SER	0	-0.001	0.009	56.868	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	166	VAL	0	0.006	0.013	51.774	-0.068	-0.068	0.000	0.000	0.000	0.000
110	A	167	VAL	0	-0.019	-0.003	48.909	0.049	0.049	0.000	0.000	0.000	0.000
111	A	168	ARG	1	0.791	0.872	48.465	5.791	5.791	0.000	0.000	0.000	0.000
112	A	169	GLY	0	0.063	0.051	45.102	-0.027	-0.027	0.000	0.000	0.000	0.000
113	A	170	CYS	0	0.027	-0.002	41.625	0.025	0.025	0.000	0.000	0.000	0.000
114	A	171	ASP	-1	-0.796	-0.886	38.874	-8.229	-8.229	0.000	0.000	0.000	0.000
115	A	172	ARG	1	0.868	0.948	41.340	6.554	6.554	0.000	0.000	0.000	0.000
116	A	173	ILE	0	-0.072	-0.016	43.216	0.096	0.096	0.000	0.000	0.000	0.000
117	A	174	VAL	0	-0.006	-0.016	38.404	-0.063	-0.063	0.000	0.000	0.000	0.000
118	A	175	PRO	0	0.024	0.031	35.082	0.085	0.085	0.000	0.000	0.000	0.000
119	A	176	VAL	0	-0.003	-0.005	35.313	-0.210	-0.210	0.000	0.000	0.000	0.000
120	A	177	ASP	-1	-0.861	-0.918	30.979	-10.097	-10.097	0.000	0.000	0.000	0.000
121	A	178	ILE	0	-0.109	-0.070	31.599	-0.250	-0.250	0.000	0.000	0.000	0.000
122	A	179	TYR	0	-0.017	-0.013	34.414	0.242	0.242	0.000	0.000	0.000	0.000
123	A	180	ILE	0	-0.004	0.011	36.153	-0.097	-0.097	0.000	0.000	0.000	0.000
124	A	181	PRO	0	-0.003	0.008	39.438	0.217	0.217	0.000	0.000	0.000	0.000
125	A	182	GLY	0	0.061	0.010	42.726	-0.060	-0.060	0.000	0.000	0.000	0.000
126	A	183	CYS	0	-0.073	-0.035	45.650	0.024	0.024	0.000	0.000	0.000	0.000
127	A	184	PRO	0	0.076	0.054	46.581	0.131	0.131	0.000	0.000	0.000	0.000
128	A	185	PRO	0	-0.035	-0.027	42.152	0.048	0.048	0.000	0.000	0.000	0.000
129	A	186	THR	0	0.053	0.023	43.255	0.018	0.018	0.000	0.000	0.000	0.000
130	A	187	ALA	0	0.049	0.019	41.884	-0.216	-0.216	0.000	0.000	0.000	0.000
131	A	188	GLU	-1	-0.896	-0.950	38.864	-8.144	-8.144	0.000	0.000	0.000	0.000
132	A	189	ALA	0	-0.014	-0.006	37.842	-0.268	-0.268	0.000	0.000	0.000	0.000
133	A	190	LEU	0	-0.009	-0.019	37.572	-0.208	-0.208	0.000	0.000	0.000	0.000
134	A	191	LEU	0	0.041	0.021	34.008	-0.275	-0.275	0.000	0.000	0.000	0.000
135	A	192	TYR	0	0.014	-0.001	32.376	-0.523	-0.523	0.000	0.000	0.000	0.000
136	A	193	GLY	0	0.029	0.010	32.619	-0.331	-0.331	0.000	0.000	0.000	0.000
137	A	194	ILE	0	0.036	0.013	31.009	-0.319	-0.319	0.000	0.000	0.000	0.000
138	A	195	LEU	0	0.040	0.017	29.058	-0.472	-0.472	0.000	0.000	0.000	0.000
139	A	196	GLN	0	-0.074	-0.033	27.976	-0.406	-0.406	0.000	0.000	0.000	0.000
140	A	197	LEU	0	0.008	0.010	28.021	-0.400	-0.400	0.000	0.000	0.000	0.000
141	A	198	GLN	0	0.016	0.004	25.292	-0.491	-0.491	0.000	0.000	0.000	0.000
142	A	199	ARG	1	0.876	0.936	23.762	10.250	10.250	0.000	0.000	0.000	0.000
143	A	200	LYS	1	0.887	0.957	23.547	10.407	10.407	0.000	0.000	0.000	0.000
144	A	201	ILE	0	0.054	0.027	21.813	-0.503	-0.503	0.000	0.000	0.000	0.000
145	A	202	LYS	1	0.915	0.957	18.239	15.316	15.316	0.000	0.000	0.000	0.000
146	A	203	ARG	1	0.900	0.951	18.609	12.024	12.024	0.000	0.000	0.000	0.000
147	A	204	GLU	-1	-0.856	-0.897	19.968	-13.206	-13.206	0.000	0.000	0.000	0.000
148	A	205	ARG	1	0.946	0.975	15.499	16.300	16.300	0.000	0.000	0.000	0.000
149	A	206	ARG	1	0.919	0.938	17.091	13.837	13.837	0.000	0.000	0.000	0.000
150	A	207	LEU	0	-0.019	0.009	12.370	0.336	0.336	0.000	0.000	0.000	0.000
151	A	208	GLN	0	0.002	-0.020	11.557	-0.118	-0.118	0.000	0.000	0.000	0.000
152	A	209	ILE	0	-0.032	-0.015	13.817	-0.050	-0.050	0.000	0.000	0.000	0.000
153	A	210	TRP	0	-0.036	-0.011	13.180	0.039	0.039	0.000	0.000	0.000	0.000
154	A	211	TYR	0	0.004	-0.011	10.694	-0.816	-0.816	0.000	0.000	0.000	0.000
155	A	212	ARG	1	0.827	0.909	12.853	20.461	20.461	0.000	0.000	0.000	0.000
156	A	213	ARG	0	0.081	0.074	16.523	0.419	0.419	0.000	0.000	0.000	0.000

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