FMO DATABASE

FMODB ID: 1YZLZ

Calculation Name: 7A23-e-Other547

Preferred Name:

Target Type:

Ligand Name: cardiolipin | ubiquinone-10 | nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | phosphatidylinositol | (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate | flavin mononucleotide | iron/sulfur cluster | bicarbonate ion | fe2/s2 (inorganic) cluster | zinc ion

Ligand 3-letter code: CDL | U10 | NDP | T7X | PEV | FMN | SF4 | BCT | FES | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7A23

Chain ID: e

ChEMBL ID:

UniProt ID:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-540864.721027
FMO2-HF: Nuclear repulsion	508704.786508
FMO2-HF: Total energy	-32159.934518
FMO2-MP2: Total energy	-32255.017653

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:42:GLY)

Summations of interaction energy for fragment #1(A:42: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.
-92.106	-91.099	-0.01	-0.414	-0.583	-0.002

Interaction energy analysis for fragmet #1(A:42:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.916

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	44	PHE	0	0.030	0.016	3.856	0.674	1.681	-0.010	-0.414	-0.583	-0.002
4	A	45	LEU	0	0.028	0.017	6.618	0.791	0.791	0.000	0.000	0.000	0.000
5	A	46	ASP	-1	-0.836	-0.907	9.517	-19.771	-19.771	0.000	0.000	0.000	0.000
6	A	47	LYS	1	0.981	0.973	12.245	15.232	15.232	0.000	0.000	0.000	0.000
7	A	48	SER	0	0.013	-0.006	13.245	1.055	1.055	0.000	0.000	0.000	0.000
8	A	49	GLU	0	-0.038	-0.020	6.130	0.530	0.530	0.000	0.000	0.000	0.000
9	A	50	VAL	0	-0.009	0.001	11.419	0.645	0.645	0.000	0.000	0.000	0.000
10	A	51	THR	0	-0.034	-0.032	14.222	1.045	1.045	0.000	0.000	0.000	0.000
11	A	52	ASP	-1	-0.961	-0.962	11.934	-22.386	-22.386	0.000	0.000	0.000	0.000
12	A	53	ARG	1	0.877	0.961	11.925	22.827	22.827	0.000	0.000	0.000	0.000
13	A	54	VAL	0	-0.067	-0.033	14.596	1.109	1.109	0.000	0.000	0.000	0.000
14	A	55	LEU	0	-0.024	-0.027	17.416	1.071	1.071	0.000	0.000	0.000	0.000
15	A	56	SER	0	-0.056	-0.045	16.051	0.489	0.489	0.000	0.000	0.000	0.000
16	A	57	VAL	0	0.046	0.027	18.197	0.749	0.749	0.000	0.000	0.000	0.000
17	A	58	VAL	0	-0.108	-0.052	20.862	0.697	0.697	0.000	0.000	0.000	0.000
18	A	59	LYS	0	-0.019	0.002	18.478	0.545	0.545	0.000	0.000	0.000	0.000
19	A	60	ASN	0	-0.005	0.000	22.565	0.361	0.361	0.000	0.000	0.000	0.000
20	A	61	PHE	0	-0.030	-0.022	24.889	0.565	0.565	0.000	0.000	0.000	0.000
21	A	62	GLN	0	-0.048	-0.015	27.952	0.464	0.464	0.000	0.000	0.000	0.000
22	A	63	LYS	1	0.879	0.924	30.356	9.135	9.135	0.000	0.000	0.000	0.000
23	A	64	VAL	0	-0.029	-0.039	27.801	0.264	0.264	0.000	0.000	0.000	0.000
24	A	65	ASP	-1	-0.807	-0.902	29.509	-10.110	-10.110	0.000	0.000	0.000	0.000
25	A	66	PRO	0	0.027	-0.001	25.847	-0.106	-0.106	0.000	0.000	0.000	0.000
26	A	67	SER	0	-0.039	-0.011	26.714	-0.321	-0.321	0.000	0.000	0.000	0.000
27	A	68	LYS	1	0.768	0.893	29.313	8.857	8.857	0.000	0.000	0.000	0.000
28	A	69	VAL	0	-0.008	0.008	25.952	0.198	0.198	0.000	0.000	0.000	0.000
29	A	70	THR	0	0.021	0.008	25.090	-0.301	-0.301	0.000	0.000	0.000	0.000
30	A	71	PRO	0	0.052	0.001	21.591	0.212	0.212	0.000	0.000	0.000	0.000
31	A	72	LYS	1	0.928	0.977	23.850	10.194	10.194	0.000	0.000	0.000	0.000
32	A	73	ALA	0	-0.025	0.001	27.345	0.328	0.328	0.000	0.000	0.000	0.000
33	A	74	ASN	0	0.089	0.039	28.335	-0.447	-0.447	0.000	0.000	0.000	0.000
34	A	75	PHE	0	0.125	0.057	28.573	0.415	0.415	0.000	0.000	0.000	0.000
35	A	76	GLN	0	0.009	-0.005	30.587	0.244	0.244	0.000	0.000	0.000	0.000
36	A	77	ASN	0	-0.068	-0.019	32.300	0.060	0.060	0.000	0.000	0.000	0.000
37	A	78	ASP	0	-0.003	-0.002	33.039	0.408	0.408	0.000	0.000	0.000	0.000
38	A	79	LEU	0	-0.041	0.007	30.123	0.290	0.290	0.000	0.000	0.000	0.000
39	A	80	GLY	0	0.014	0.022	33.984	0.153	0.153	0.000	0.000	0.000	0.000
40	A	81	LEU	0	-0.026	-0.008	30.356	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	82	ASP	-1	-0.831	-0.919	34.320	-8.109	-8.109	0.000	0.000	0.000	0.000
42	A	83	SER	0	0.041	0.015	34.225	-0.398	-0.398	0.000	0.000	0.000	0.000
43	A	84	LEU	0	0.008	0.000	33.449	-0.241	-0.241	0.000	0.000	0.000	0.000
44	A	85	ASP	0	-0.025	-0.042	31.433	-0.281	-0.281	0.000	0.000	0.000	0.000
45	A	86	SER	0	-0.046	-0.037	30.003	-0.489	-0.489	0.000	0.000	0.000	0.000
46	A	87	VAL	0	0.016	0.001	28.605	-0.379	-0.379	0.000	0.000	0.000	0.000
47	A	88	GLU	-1	-0.866	-0.921	28.258	-10.582	-10.582	0.000	0.000	0.000	0.000
48	A	89	VAL	0	-0.018	-0.017	24.813	-0.385	-0.385	0.000	0.000	0.000	0.000
49	A	90	VAL	0	-0.014	-0.003	24.077	-0.571	-0.571	0.000	0.000	0.000	0.000
50	A	91	MET	0	-0.004	-0.004	23.365	-0.324	-0.324	0.000	0.000	0.000	0.000
51	A	92	ALA	0	-0.045	-0.020	23.433	-0.350	-0.350	0.000	0.000	0.000	0.000
52	A	93	LEU	0	-0.015	0.000	18.517	-0.501	-0.501	0.000	0.000	0.000	0.000
53	A	94	GLU	-1	-0.978	-0.989	18.734	-13.910	-13.910	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.985	-0.994	17.164	-16.195	-16.195	0.000	0.000	0.000	0.000
55	A	96	GLU	-1	-0.861	-0.902	15.488	-17.863	-17.863	0.000	0.000	0.000	0.000
56	A	97	PHE	0	0.028	-0.023	14.204	-1.770	-1.770	0.000	0.000	0.000	0.000
57	A	98	GLY	0	0.020	-0.001	14.923	1.064	1.064	0.000	0.000	0.000	0.000
58	A	99	PHE	0	0.060	0.012	16.132	-0.513	-0.513	0.000	0.000	0.000	0.000
59	A	100	GLU	0	-0.051	-0.050	18.321	-0.364	-0.364	0.000	0.000	0.000	0.000
60	A	101	ILE	0	0.054	0.046	20.306	0.020	0.020	0.000	0.000	0.000	0.000
61	A	102	PRO	0	-0.028	-0.023	23.025	0.239	0.239	0.000	0.000	0.000	0.000
62	A	103	ASP	-1	-0.866	-0.927	26.436	-9.934	-9.934	0.000	0.000	0.000	0.000
63	A	104	ASN	0	-0.021	-0.025	28.869	0.331	0.331	0.000	0.000	0.000	0.000
64	A	105	GLU	-1	-0.869	-0.928	27.350	-10.827	-10.827	0.000	0.000	0.000	0.000
65	A	106	ALA	0	0.009	0.005	27.363	-0.105	-0.105	0.000	0.000	0.000	0.000
66	A	107	ASP	-1	-0.852	-0.913	28.092	-9.716	-9.716	0.000	0.000	0.000	0.000
67	A	108	LYS	1	0.775	0.881	28.434	10.778	10.778	0.000	0.000	0.000	0.000
68	A	109	ILE	0	0.013	0.015	23.346	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	110	GLN	0	-0.001	-0.002	27.564	-0.128	-0.128	0.000	0.000	0.000	0.000
70	A	111	SER	0	-0.078	-0.064	27.656	0.168	0.168	0.000	0.000	0.000	0.000
71	A	112	ILE	0	0.051	0.050	22.231	-0.234	-0.234	0.000	0.000	0.000	0.000
72	A	113	ASP	-1	-0.924	-0.963	22.506	-13.569	-13.569	0.000	0.000	0.000	0.000
73	A	114	LEU	0	-0.025	-0.003	22.716	-0.528	-0.528	0.000	0.000	0.000	0.000
74	A	115	ALA	0	0.042	0.027	20.950	-0.327	-0.327	0.000	0.000	0.000	0.000
75	A	116	VAL	0	0.015	0.000	18.484	-0.866	-0.866	0.000	0.000	0.000	0.000
76	A	117	ASP	0	-0.060	-0.036	18.277	-0.809	-0.809	0.000	0.000	0.000	0.000
77	A	118	PHE	0	-0.006	0.013	19.439	-0.533	-0.533	0.000	0.000	0.000	0.000
78	A	119	ILE	0	-0.044	-0.004	12.428	-0.434	-0.434	0.000	0.000	0.000	0.000
79	A	120	ALA	0	-0.030	-0.027	14.952	-0.936	-0.936	0.000	0.000	0.000	0.000
80	A	121	SER	0	-0.043	-0.024	15.781	-0.317	-0.317	0.000	0.000	0.000	0.000
81	A	122	HIS	1	0.838	0.946	15.575	18.688	18.688	0.000	0.000	0.000	0.000
82	A	123	PRO	0	-0.037	-0.028	14.211	-1.135	-1.135	0.000	0.000	0.000	0.000
83	A	124	GLN	0	-0.089	-0.035	11.855	-0.379	-0.379	0.000	0.000	0.000	0.000
84	A	125	ALA	-1	-0.809	-0.876	8.241	-25.482	-25.482	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:GLY)