FMO DATABASE

FMODB ID: G7181

Calculation Name: 1S3A-A-Other549

Preferred Name: Mitochondrial complex I (NADH dehydrogenase)

Target Type: PROTEIN COMPLEX

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1S3A

Chain ID: A

ChEMBL ID: CHEMBL2363065

UniProt ID: O43678

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-594975.786257
FMO2-HF: Nuclear repulsion	561335.838308
FMO2-HF: Total energy	-33639.947949
FMO2-MP2: Total energy	-33739.066447

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:15:GLY)

Summations of interaction energy for fragment #1(A:15:GLY)

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.
-87.924	-82.923	14.156	-10.761	-8.395	-0.126

Interaction energy analysis for fragmet #1(A:15:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.793 / q_NPA : 0.901

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	17	ARG	1	0.991	0.995	3.843	29.812	30.910	-0.021	-0.603	-0.475	-0.001
36	A	50	ASP	-1	-0.891	-0.939	2.518	-56.536	-55.288	0.835	-1.039	-1.043	-0.009
37	A	51	LEU	0	-0.045	-0.035	1.852	-43.218	-43.494	8.454	-4.834	-3.344	-0.070
38	A	52	PRO	0	0.001	0.012	4.117	9.781	9.927	-0.001	-0.049	-0.096	0.000
55	A	70	ALA	0	-0.030	-0.019	4.992	3.876	3.953	-0.001	-0.011	-0.064	0.000
80	A	95	LEU	0	-0.024	-0.024	1.787	-2.201	-3.641	4.424	-1.460	-1.524	-0.014
81	A	96	SER	0	-0.042	-0.042	2.695	-36.632	-32.657	0.461	-2.748	-1.688	-0.032
82	A	97	GLY	0	-0.003	0.003	3.660	4.213	4.386	0.005	-0.017	-0.161	0.000
4	A	18	GLU	-1	-0.778	-0.851	7.166	-22.073	-22.073	0.000	0.000	0.000	0.000
5	A	19	ILE	0	0.027	0.031	6.344	-0.553	-0.553	0.000	0.000	0.000	0.000
6	A	20	ARG	1	0.739	0.842	8.746	25.385	25.385	0.000	0.000	0.000	0.000
7	A	21	ILE	0	0.039	0.019	12.504	0.176	0.176	0.000	0.000	0.000	0.000
8	A	22	HIS	0	0.017	0.008	14.534	0.744	0.744	0.000	0.000	0.000	0.000
9	A	23	LEU	0	-0.014	0.003	18.066	0.093	0.093	0.000	0.000	0.000	0.000
10	A	24	CYS	0	-0.025	-0.002	20.560	0.326	0.326	0.000	0.000	0.000	0.000
11	A	25	GLN	0	-0.017	-0.016	24.273	-0.322	-0.322	0.000	0.000	0.000	0.000
12	A	26	ARG	1	0.937	0.956	27.173	11.438	11.438	0.000	0.000	0.000	0.000
13	A	27	SER	0	-0.059	-0.031	27.093	0.396	0.396	0.000	0.000	0.000	0.000
14	A	28	PRO	0	0.021	0.008	26.631	-0.253	-0.253	0.000	0.000	0.000	0.000
15	A	29	GLY	0	0.043	0.017	23.726	-0.564	-0.564	0.000	0.000	0.000	0.000
16	A	30	SER	0	0.015	0.025	21.958	0.506	0.506	0.000	0.000	0.000	0.000
17	A	31	GLN	0	0.091	0.036	23.166	-0.218	-0.218	0.000	0.000	0.000	0.000
18	A	32	GLY	0	-0.006	0.009	21.036	-0.226	-0.226	0.000	0.000	0.000	0.000
19	A	33	VAL	0	0.031	0.001	18.043	-0.855	-0.855	0.000	0.000	0.000	0.000
20	A	34	ARG	1	0.855	0.918	19.266	11.528	11.528	0.000	0.000	0.000	0.000
21	A	35	ASP	-1	-0.829	-0.924	20.368	-14.415	-14.415	0.000	0.000	0.000	0.000
22	A	36	PHE	0	-0.045	-0.041	12.015	-0.476	-0.476	0.000	0.000	0.000	0.000
23	A	37	ILE	0	-0.056	-0.031	16.477	-0.891	-0.891	0.000	0.000	0.000	0.000
24	A	38	GLU	-1	-0.877	-0.929	18.389	-13.092	-13.092	0.000	0.000	0.000	0.000
25	A	39	LYS	1	0.936	0.977	19.880	15.428	15.428	0.000	0.000	0.000	0.000
26	A	40	ARG	1	0.843	0.920	13.974	21.080	21.080	0.000	0.000	0.000	0.000
27	A	41	TYR	0	0.067	0.043	14.058	-1.304	-1.304	0.000	0.000	0.000	0.000
28	A	42	VAL	0	0.011	-0.012	13.452	-1.692	-1.692	0.000	0.000	0.000	0.000
29	A	43	GLU	-1	-0.834	-0.909	14.257	-19.372	-19.372	0.000	0.000	0.000	0.000
30	A	44	LEU	0	-0.026	-0.012	9.069	-1.222	-1.222	0.000	0.000	0.000	0.000
31	A	45	LYS	1	0.934	0.965	9.129	18.764	18.764	0.000	0.000	0.000	0.000
32	A	46	LYS	1	0.824	0.908	9.963	18.545	18.545	0.000	0.000	0.000	0.000
33	A	47	ALA	0	-0.046	-0.008	10.144	-0.107	-0.107	0.000	0.000	0.000	0.000
34	A	48	ASN	0	-0.015	-0.008	5.237	0.300	0.300	0.000	0.000	0.000	0.000
35	A	49	PRO	0	0.037	0.022	5.926	-3.089	-3.089	0.000	0.000	0.000	0.000
39	A	53	ILE	0	0.034	0.022	7.395	0.388	0.388	0.000	0.000	0.000	0.000
40	A	54	LEU	0	-0.051	-0.024	10.099	2.695	2.695	0.000	0.000	0.000	0.000
41	A	55	ILE	0	0.028	0.023	13.362	-0.297	-0.297	0.000	0.000	0.000	0.000
42	A	56	ARG	1	0.890	0.933	15.849	17.569	17.569	0.000	0.000	0.000	0.000
43	A	57	GLU	-1	-0.798	-0.900	18.559	-13.154	-13.154	0.000	0.000	0.000	0.000
44	A	59	SER	0	0.009	-0.005	21.655	-0.143	-0.143	0.000	0.000	0.000	0.000
45	A	60	ASP	-1	-0.860	-0.931	21.255	-14.563	-14.563	0.000	0.000	0.000	0.000
46	A	61	VAL	0	-0.019	-0.015	23.694	0.453	0.453	0.000	0.000	0.000	0.000
47	A	62	GLN	0	0.035	0.031	23.175	0.679	0.679	0.000	0.000	0.000	0.000
48	A	63	PRO	0	-0.005	0.006	19.172	-0.405	-0.405	0.000	0.000	0.000	0.000
49	A	64	LYS	1	0.798	0.902	17.435	14.809	14.809	0.000	0.000	0.000	0.000
50	A	65	LEU	0	0.021	0.007	9.842	-0.371	-0.371	0.000	0.000	0.000	0.000
51	A	66	TRP	0	-0.040	-0.048	12.228	0.466	0.466	0.000	0.000	0.000	0.000
52	A	67	ALA	0	0.000	-0.012	7.992	-2.252	-2.252	0.000	0.000	0.000	0.000
53	A	68	ARG	1	0.821	0.922	9.271	25.319	25.319	0.000	0.000	0.000	0.000
54	A	69	TYR	0	0.023	-0.007	5.651	-5.991	-5.991	0.000	0.000	0.000	0.000
56	A	71	PHE	0	-0.017	0.008	5.048	3.517	3.517	0.000	0.000	0.000	0.000
57	A	72	GLY	0	0.007	0.008	8.762	3.183	3.183	0.000	0.000	0.000	0.000
58	A	73	GLN	0	-0.040	-0.015	10.729	3.686	3.686	0.000	0.000	0.000	0.000
59	A	74	GLU	-1	-0.827	-0.915	11.435	-20.751	-20.751	0.000	0.000	0.000	0.000
60	A	75	THR	0	-0.023	-0.012	11.177	-0.528	-0.528	0.000	0.000	0.000	0.000
61	A	76	ASN	0	0.054	0.023	13.248	-1.231	-1.231	0.000	0.000	0.000	0.000
62	A	77	VAL	0	0.015	0.018	14.208	1.420	1.420	0.000	0.000	0.000	0.000
63	A	78	PRO	0	0.002	0.000	16.381	-0.721	-0.721	0.000	0.000	0.000	0.000
64	A	79	LEU	0	0.016	0.025	13.439	0.415	0.415	0.000	0.000	0.000	0.000
65	A	80	ASN	0	0.041	-0.010	17.365	0.080	0.080	0.000	0.000	0.000	0.000
66	A	81	ASN	0	-0.047	-0.028	20.927	0.136	0.136	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.007	0.027	17.058	0.071	0.071	0.000	0.000	0.000	0.000
68	A	83	SER	0	0.035	0.007	18.714	0.573	0.573	0.000	0.000	0.000	0.000
69	A	84	ALA	0	0.016	0.012	17.196	-1.010	-1.010	0.000	0.000	0.000	0.000
70	A	85	ASP	-1	-0.869	-0.924	15.247	-21.571	-21.571	0.000	0.000	0.000	0.000
71	A	86	GLN	0	0.034	0.027	14.093	-1.896	-1.896	0.000	0.000	0.000	0.000
72	A	87	VAL	0	0.058	0.017	13.530	-1.411	-1.411	0.000	0.000	0.000	0.000
73	A	88	THR	0	-0.015	-0.010	10.703	-1.675	-1.675	0.000	0.000	0.000	0.000
74	A	89	ARG	1	0.931	0.967	9.301	24.698	24.698	0.000	0.000	0.000	0.000
75	A	90	ALA	0	-0.006	0.001	9.698	-1.893	-1.893	0.000	0.000	0.000	0.000
76	A	91	LEU	0	-0.002	-0.012	7.425	-1.200	-1.200	0.000	0.000	0.000	0.000
77	A	92	GLU	-1	-0.885	-0.931	5.172	-39.735	-39.735	0.000	0.000	0.000	0.000
78	A	93	ASN	0	0.015	-0.005	5.335	-6.203	-6.203	0.000	0.000	0.000	0.000
79	A	94	VAL	0	-0.030	-0.031	7.360	-1.199	-1.199	0.000	0.000	0.000	0.000
83	A	98	LYS	1	0.893	0.968	7.153	26.343	26.343	0.000	0.000	0.000	0.000
84	A	99	ALA	-1	-0.817	-0.901	8.501	-29.304	-29.304	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:GLY)