FMO DATABASE

FMODB ID: N62QQ

Calculation Name: 7B0N-K-Other547

Preferred Name:

Target Type:

Ligand Name: cardiolipin | nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | 1,2-distearoyl-sn-glycerophosphoethanolamine | diundecyl phosphatidyl choline | ~{s}-[2-[3-[[(2~{r})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{s})-3-oxidanyltetradecanethioate | flavin mononucleotide | dodecyl-beta-d-maltoside | iron/sulfur cluster | n-formylmethionine | fe2/s2 (inorganic) cluster | zinc ion

Ligand 3-letter code: CDL | NDP | 3PE | PLC | EHZ | FMN | LMT | SF4 | FME | FES | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7B0N

Chain ID: K

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-536158.479716
FMO2-HF: Nuclear repulsion	502335.506557
FMO2-HF: Total energy	-33822.973159
FMO2-MP2: Total energy	-33922.452913

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:1:MET)

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

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.
9.453	17.392	5.899	-4.446	-9.394	-0.028

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.880 / q_NPA : 0.931

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	3	ILE	0	0.063	0.039	3.460	2.060	3.544	0.003	-0.519	-0.969	0.000
4	A	4	GLY	0	0.037	0.029	3.048	7.877	8.289	0.004	-0.108	-0.308	0.000
5	A	5	THR	0	0.010	-0.008	3.679	6.240	6.855	0.005	-0.173	-0.448	0.000
38	A	38	LEU	0	0.004	0.003	4.156	-2.412	-2.289	-0.001	-0.019	-0.104	0.000
39	A	39	ILE	0	-0.135	-0.066	2.191	-24.591	-22.535	2.384	-1.990	-2.450	-0.016
40	A	40	LEU	0	-0.018	0.007	3.622	-0.653	-0.345	0.007	-0.005	-0.309	-0.001
42	A	42	ARG	1	0.882	0.945	2.596	47.014	49.551	3.498	-1.584	-4.451	-0.011
43	A	43	ASN	0	0.010	-0.009	4.335	-0.406	-0.002	-0.001	-0.048	-0.355	0.000
6	A	6	ILE	0	-0.023	-0.009	5.795	6.041	6.041	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.037	0.019	7.456	3.719	3.719	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.024	0.036	8.291	3.281	3.281	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.015	0.003	9.674	2.968	2.968	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.007	-0.008	11.748	2.415	2.415	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.022	-0.007	12.515	2.092	2.092	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.035	0.014	14.000	1.503	1.503	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.028	-0.018	15.377	1.404	1.404	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.001	-0.001	17.393	1.130	1.130	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.018	-0.022	18.497	0.978	0.978	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.029	-0.007	19.784	0.873	0.873	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.050	-0.026	20.358	0.852	0.852	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.018	-0.009	23.338	0.760	0.760	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.944	0.969	24.926	11.461	11.461	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.949	0.983	25.680	12.213	12.213	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.031	0.010	26.795	0.097	0.097	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.148	0.081	26.814	-0.410	-0.410	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.014	0.010	24.554	-0.460	-0.460	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.002	-0.011	22.228	-0.542	-0.542	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.028	0.024	20.816	-0.836	-0.836	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.016	0.004	20.589	-0.547	-0.547	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.007	-0.006	17.970	-0.667	-0.667	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.056	-0.027	16.436	-1.106	-1.106	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.019	0.022	15.520	-1.399	-1.399	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.805	-0.879	15.010	-18.493	-18.493	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.030	-0.040	12.566	-1.205	-1.205	0.000	0.000	0.000	0.000
32	A	32	MET	0	-0.038	-0.013	10.850	-3.218	-3.218	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.020	0.019	10.440	-3.304	-3.304	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.001	0.004	9.070	-2.002	-2.002	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.000	-0.010	6.703	-4.033	-4.033	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.015	-0.002	5.616	-9.124	-9.124	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.062	0.024	6.835	-4.526	-4.526	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.052	0.022	6.671	2.137	2.137	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.019	-0.010	6.558	3.747	3.747	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.011	0.007	8.171	2.022	2.022	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.054	-0.035	5.569	0.964	0.964	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.059	-0.029	8.729	0.757	0.757	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.905	-0.931	11.874	-18.463	-18.463	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.843	-0.893	12.898	-18.071	-18.071	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.021	0.013	13.306	-1.358	-1.358	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.024	-0.037	14.696	0.018	0.018	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.008	-0.010	10.657	-0.208	-0.208	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.009	-0.014	11.543	-0.911	-0.911	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.026	-0.004	12.862	0.577	0.577	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.016	-0.002	12.377	0.547	0.547	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.036	0.015	10.897	0.116	0.116	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.008	-0.003	12.819	0.612	0.612	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.003	0.002	16.302	0.929	0.929	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.009	-0.002	12.188	0.713	0.713	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.030	-0.013	13.747	0.550	0.550	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.029	-0.012	16.670	0.849	0.849	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.025	-0.016	18.657	0.725	0.725	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.047	0.033	16.746	0.611	0.611	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.019	0.013	18.908	0.629	0.629	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.037	-0.024	21.682	0.754	0.754	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.906	-0.953	19.293	-15.567	-15.567	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.002	-0.036	20.971	0.820	0.820	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.043	-0.010	23.375	0.572	0.572	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.005	0.008	26.444	0.563	0.563	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.044	0.028	26.062	0.455	0.455	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.007	-0.012	25.541	0.434	0.434	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.076	-0.040	28.724	0.523	0.523	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.005	-0.005	29.091	0.429	0.429	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.006	0.009	28.671	0.328	0.328	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.021	0.008	31.763	0.343	0.343	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.035	-0.020	34.600	0.432	0.432	0.000	0.000	0.000	0.000
77	A	77	TYR	0	0.012	-0.001	34.206	0.350	0.350	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.013	0.008	35.626	0.274	0.274	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.924	0.959	37.395	8.004	8.004	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.033	-0.008	40.081	0.225	0.225	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.880	0.950	37.977	8.602	8.602	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.002	0.016	40.796	0.105	0.105	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.036	-0.030	38.086	-0.055	-0.055	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.015	0.011	31.891	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.013	-0.003	34.848	-0.144	-0.144	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.013	-0.029	32.332	-0.065	-0.065	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.034	-0.016	31.614	-0.246	-0.246	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.029	0.000	33.676	0.174	0.174	0.000	0.000	0.000	0.000
89	A	89	ILE	-1	-0.942	-0.967	29.553	-10.380	-10.380	0.000	0.000	0.000	0.000

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