FMO DATABASE

FMODB ID: 3GNGL

Calculation Name: 7A23-Q-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: Q

ChEMBL ID:

UniProt ID:

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-668392.149884
FMO2-HF: Nuclear repulsion	631373.111033
FMO2-HF: Total energy	-37019.038851
FMO2-MP2: Total energy	-37124.082252

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(Q:3:TRP)

Summations of interaction energy for fragment #1(Q:3:TRP)

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.
-22.569	-16.151	32.83	-14.682	-24.567	-0.092

Interaction energy analysis for fragmet #1(Q:3:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.882

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	Q	5	GLY	0	0.050	0.037	3.854	6.595	8.798	-0.020	-1.073	-1.110	-0.002
32	Q	34	LYS	1	0.898	0.968	3.255	27.390	27.812	0.017	-0.072	-0.367	0.000
33	Q	35	ASN	0	0.004	0.009	2.524	-20.213	-16.745	8.444	-3.434	-8.478	-0.001
34	Q	36	TYR	0	0.018	0.003	4.195	-8.807	-8.495	0.001	-0.078	-0.236	0.000
36	Q	38	ASP	-1	-0.796	-0.889	1.761	-79.134	-81.833	16.678	-7.284	-6.696	-0.077
37	Q	39	LEU	0	-0.076	-0.038	2.246	-10.787	-9.883	3.153	-1.251	-2.805	-0.011
38	Q	40	LYS	1	1.002	1.009	3.255	30.511	30.507	0.022	0.121	-0.139	-0.001
40	Q	42	LEU	0	0.014	0.012	3.057	1.486	2.117	0.143	-0.209	-0.565	-0.002
41	Q	43	ASN	0	-0.043	-0.033	4.765	5.938	5.951	-0.001	-0.003	-0.009	0.000
76	Q	79	GLU	-1	-0.894	-0.941	3.158	-40.850	-39.441	0.101	-0.606	-0.904	-0.005
80	Q	83	LEU	0	0.004	0.007	2.228	-1.818	-2.141	4.293	-0.789	-3.181	0.007
83	Q	86	LEU	0	0.017	-0.001	4.755	-0.225	-0.143	-0.001	-0.004	-0.077	0.000
4	Q	6	SER	0	-0.006	-0.025	5.817	5.720	5.720	0.000	0.000	0.000	0.000
5	Q	7	ILE	0	0.042	0.029	4.946	1.724	1.724	0.000	0.000	0.000	0.000
6	Q	8	SER	0	-0.054	-0.028	8.806	2.706	2.706	0.000	0.000	0.000	0.000
7	Q	9	LYS	1	0.907	0.968	10.713	27.309	27.309	0.000	0.000	0.000	0.000
8	Q	10	SER	0	-0.003	0.021	12.231	0.668	0.668	0.000	0.000	0.000	0.000
9	Q	11	MET	0	-0.047	-0.015	10.583	0.904	0.904	0.000	0.000	0.000	0.000
10	Q	12	LYS	1	0.844	0.945	13.941	15.260	15.260	0.000	0.000	0.000	0.000
11	Q	13	GLU	-1	-0.834	-0.922	13.518	-16.845	-16.845	0.000	0.000	0.000	0.000
12	Q	14	LEU	0	-0.014	-0.005	8.090	-0.444	-0.444	0.000	0.000	0.000	0.000
13	Q	15	ARG	1	0.760	0.846	12.195	15.668	15.668	0.000	0.000	0.000	0.000
14	Q	16	ILE	0	-0.025	-0.015	9.072	-0.414	-0.414	0.000	0.000	0.000	0.000
15	Q	17	LEU	0	0.007	0.017	13.754	0.205	0.205	0.000	0.000	0.000	0.000
16	Q	18	LEU	0	0.017	0.007	13.585	0.158	0.158	0.000	0.000	0.000	0.000
17	Q	19	CYS	0	0.004	0.020	17.178	1.451	1.451	0.000	0.000	0.000	0.000
18	Q	20	GLN	0	-0.024	-0.004	18.550	-0.448	-0.448	0.000	0.000	0.000	0.000
19	Q	21	SER	0	-0.017	-0.026	19.232	-0.338	-0.338	0.000	0.000	0.000	0.000
20	Q	22	SER	0	-0.004	0.022	20.588	0.465	0.465	0.000	0.000	0.000	0.000
21	Q	23	PRO	0	0.053	0.024	19.521	-0.641	-0.641	0.000	0.000	0.000	0.000
22	Q	24	ALA	0	0.107	0.062	18.429	-0.616	-0.616	0.000	0.000	0.000	0.000
23	Q	25	SER	0	-0.013	-0.030	16.013	-0.004	-0.004	0.000	0.000	0.000	0.000
24	Q	26	ALA	0	0.029	0.023	14.822	-0.991	-0.991	0.000	0.000	0.000	0.000
25	Q	27	PRO	0	0.030	0.016	11.390	-1.159	-1.159	0.000	0.000	0.000	0.000
26	Q	28	THR	0	0.062	0.030	10.115	-1.474	-1.474	0.000	0.000	0.000	0.000
27	Q	29	ARG	1	0.903	0.951	10.933	14.565	14.565	0.000	0.000	0.000	0.000
28	Q	30	THR	0	-0.084	-0.051	8.941	-1.547	-1.547	0.000	0.000	0.000	0.000
29	Q	31	PHE	0	0.028	-0.005	5.943	-2.059	-2.059	0.000	0.000	0.000	0.000
30	Q	32	VAL	0	0.002	-0.005	6.364	-4.205	-4.205	0.000	0.000	0.000	0.000
31	Q	33	GLU	-1	-0.913	-0.966	7.660	-26.382	-26.382	0.000	0.000	0.000	0.000
35	Q	37	LYS	1	0.997	0.999	5.775	28.877	28.877	0.000	0.000	0.000	0.000
39	Q	41	SER	0	-0.079	-0.041	5.465	3.663	3.663	0.000	0.000	0.000	0.000
42	Q	44	PRO	0	0.040	0.023	7.608	1.817	1.817	0.000	0.000	0.000	0.000
43	Q	45	LYS	1	0.901	0.938	10.498	20.242	20.242	0.000	0.000	0.000	0.000
44	Q	46	LEU	0	0.036	0.034	8.640	1.214	1.214	0.000	0.000	0.000	0.000
45	Q	47	PRO	0	-0.011	-0.009	11.454	-1.050	-1.050	0.000	0.000	0.000	0.000
46	Q	48	ILE	0	0.004	0.000	6.835	-0.533	-0.533	0.000	0.000	0.000	0.000
47	Q	49	LEU	0	-0.029	-0.011	11.179	0.272	0.272	0.000	0.000	0.000	0.000
48	Q	50	ILE	0	0.027	0.021	10.344	-0.203	-0.203	0.000	0.000	0.000	0.000
49	Q	51	ARG	1	0.886	0.932	14.323	18.188	18.188	0.000	0.000	0.000	0.000
50	Q	52	GLU	-1	-0.823	-0.904	17.707	-17.571	-17.571	0.000	0.000	0.000	0.000
51	Q	54	SER	0	0.030	-0.007	23.431	-0.072	-0.072	0.000	0.000	0.000	0.000
52	Q	55	GLY	0	0.021	0.005	24.289	0.377	0.377	0.000	0.000	0.000	0.000
53	Q	56	VAL	0	-0.010	-0.010	22.044	0.196	0.196	0.000	0.000	0.000	0.000
54	Q	57	GLN	0	0.045	0.011	21.685	-0.758	-0.758	0.000	0.000	0.000	0.000
55	Q	58	PRO	0	-0.014	0.009	16.120	-0.324	-0.324	0.000	0.000	0.000	0.000
56	Q	59	GLN	0	0.012	0.002	17.132	-0.104	-0.104	0.000	0.000	0.000	0.000
57	Q	60	MET	0	-0.054	-0.015	9.006	-1.310	-1.310	0.000	0.000	0.000	0.000
58	Q	61	TRP	0	0.023	-0.009	14.212	0.786	0.786	0.000	0.000	0.000	0.000
59	Q	62	ALA	0	-0.008	-0.010	13.083	-1.622	-1.622	0.000	0.000	0.000	0.000
60	Q	63	ARG	1	0.905	0.976	14.839	16.687	16.687	0.000	0.000	0.000	0.000
61	Q	64	TYR	0	0.001	-0.029	14.130	-0.624	-0.624	0.000	0.000	0.000	0.000
62	Q	65	ASP	-1	-0.856	-0.959	18.147	-13.598	-13.598	0.000	0.000	0.000	0.000
63	Q	66	MET	0	0.016	0.023	20.607	0.284	0.284	0.000	0.000	0.000	0.000
64	Q	67	GLY	0	-0.020	-0.017	22.511	0.405	0.405	0.000	0.000	0.000	0.000
65	Q	68	VAL	0	-0.007	0.011	20.679	-0.011	-0.011	0.000	0.000	0.000	0.000
66	Q	69	GLU	-1	-0.776	-0.878	19.337	-15.572	-15.572	0.000	0.000	0.000	0.000
67	Q	70	ARG	1	0.897	0.960	16.716	16.340	16.340	0.000	0.000	0.000	0.000
68	Q	71	CYS	0	-0.004	0.007	17.470	-0.666	-0.666	0.000	0.000	0.000	0.000
69	Q	72	VAL	0	-0.003	-0.004	14.940	0.362	0.362	0.000	0.000	0.000	0.000
70	Q	73	ASN	0	0.019	0.014	16.822	-0.287	-0.287	0.000	0.000	0.000	0.000
71	Q	74	LEU	0	-0.005	-0.024	12.846	-0.638	-0.638	0.000	0.000	0.000	0.000
72	Q	75	ASP	-1	-0.893	-0.941	15.806	-14.876	-14.876	0.000	0.000	0.000	0.000
73	Q	76	GLY	0	0.013	0.005	17.262	0.193	0.193	0.000	0.000	0.000	0.000
74	Q	77	LEU	0	-0.070	-0.015	12.267	-0.396	-0.396	0.000	0.000	0.000	0.000
75	Q	78	THR	0	0.054	0.017	10.419	-0.727	-0.727	0.000	0.000	0.000	0.000
77	Q	80	PRO	0	0.058	0.012	5.090	-1.497	-1.497	0.000	0.000	0.000	0.000
78	Q	81	GLN	0	-0.014	-0.015	6.085	0.158	0.158	0.000	0.000	0.000	0.000
79	Q	82	ILE	0	0.004	0.016	8.601	0.141	0.141	0.000	0.000	0.000	0.000
81	Q	84	LYS	1	0.909	0.971	6.580	22.404	22.404	0.000	0.000	0.000	0.000
82	Q	85	ALA	0	0.083	0.034	9.071	0.386	0.386	0.000	0.000	0.000	0.000
84	Q	87	GLU	-1	-0.930	-0.959	7.604	-32.324	-32.324	0.000	0.000	0.000	0.000
85	Q	88	ASN	0	-0.014	-0.021	8.957	1.405	1.405	0.000	0.000	0.000	0.000
86	Q	89	LEU	0	0.009	0.022	11.121	1.490	1.490	0.000	0.000	0.000	0.000
87	Q	90	VAL	0	0.014	-0.003	7.382	0.816	0.816	0.000	0.000	0.000	0.000
88	Q	91	LYS	1	0.860	0.909	10.822	20.918	20.918	0.000	0.000	0.000	0.000
89	Q	92	SER	0	-0.044	-0.018	13.503	1.810	1.810	0.000	0.000	0.000	0.000
90	Q	93	GLY	0	-0.019	-0.004	14.880	1.009	1.009	0.000	0.000	0.000	0.000
91	Q	94	ALA	-1	-0.895	-0.920	14.984	-17.568	-17.568	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(Q:3:TRP)