FMO DATABASE

FMODB ID: 873VY

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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1473812.423137
FMO2-HF: Nuclear repulsion	1410707.94554
FMO2-HF: Total energy	-63104.477597
FMO2-MP2: Total energy	-63280.275737

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:65:ALA)

Summations of interaction energy for fragment #1(A:65:ALA)

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.
38.876	40.996	0.048	-0.827	-1.341	-0.003

Interaction energy analysis for fragmet #1(A:65:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / 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	67	PHE	0	0.001	0.003	3.015	4.622	6.350	0.048	-0.734	-1.042	-0.003
4	A	68	VAL	0	0.013	0.008	3.873	6.987	7.379	0.000	-0.093	-0.299	0.000
5	A	69	ILE	0	0.026	0.029	5.698	5.731	5.731	0.000	0.000	0.000	0.000
6	A	70	SER	0	0.050	0.020	7.480	4.682	4.682	0.000	0.000	0.000	0.000
7	A	71	LYS	1	0.895	0.961	8.514	26.441	26.441	0.000	0.000	0.000	0.000
8	A	72	VAL	0	0.013	0.005	9.879	3.037	3.037	0.000	0.000	0.000	0.000
9	A	73	ASP	-1	-0.731	-0.867	11.620	-22.069	-22.069	0.000	0.000	0.000	0.000
10	A	74	ASP	-1	-0.895	-0.958	12.453	-21.712	-21.712	0.000	0.000	0.000	0.000
11	A	75	LEU	0	-0.070	-0.027	14.290	1.691	1.691	0.000	0.000	0.000	0.000
12	A	76	MET	0	0.011	-0.003	15.854	1.075	1.075	0.000	0.000	0.000	0.000
13	A	77	ASN	0	-0.043	-0.023	17.096	1.382	1.382	0.000	0.000	0.000	0.000
14	A	78	TRP	0	0.046	0.012	18.593	0.870	0.870	0.000	0.000	0.000	0.000
15	A	79	ALA	0	0.011	0.005	20.147	0.855	0.855	0.000	0.000	0.000	0.000
16	A	80	ARG	1	0.901	0.949	20.528	15.636	15.636	0.000	0.000	0.000	0.000
17	A	81	THR	0	-0.034	-0.014	22.744	0.712	0.712	0.000	0.000	0.000	0.000
18	A	82	GLY	0	-0.026	-0.002	24.479	0.524	0.524	0.000	0.000	0.000	0.000
19	A	83	SER	0	-0.032	-0.016	26.187	0.461	0.461	0.000	0.000	0.000	0.000
20	A	84	ILE	0	0.015	0.019	27.406	-0.216	-0.216	0.000	0.000	0.000	0.000
21	A	85	TRP	0	0.000	-0.002	29.496	0.424	0.424	0.000	0.000	0.000	0.000
22	A	86	PRO	0	-0.010	-0.006	32.870	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	87	MET	0	0.030	0.022	35.479	0.256	0.256	0.000	0.000	0.000	0.000
24	A	88	THR	0	0.016	-0.009	38.292	-0.039	-0.039	0.000	0.000	0.000	0.000
25	A	89	PHE	0	0.014	0.012	40.643	0.260	0.260	0.000	0.000	0.000	0.000
26	A	90	GLY	0	0.047	-0.006	42.707	0.026	0.026	0.000	0.000	0.000	0.000
27	A	91	LEU	0	-0.055	-0.021	45.132	0.188	0.188	0.000	0.000	0.000	0.000
28	A	92	ALA	0	-0.010	-0.019	47.993	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	93	CYS	-1	-0.787	-0.865	49.656	-6.576	-6.576	0.000	0.000	0.000	0.000
30	A	94	CYS	0	-0.050	-0.046	44.850	-0.095	-0.095	0.000	0.000	0.000	0.000
31	A	95	ALA	0	0.028	0.012	45.096	-0.195	-0.195	0.000	0.000	0.000	0.000
32	A	96	VAL	0	-0.022	-0.010	46.365	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	97	GLU	-1	-0.823	-0.908	44.461	-7.011	-7.011	0.000	0.000	0.000	0.000
34	A	98	MET	0	-0.036	-0.003	41.031	-0.241	-0.241	0.000	0.000	0.000	0.000
35	A	99	MET	0	-0.026	-0.011	42.652	-0.110	-0.110	0.000	0.000	0.000	0.000
36	A	100	HIS	0	0.003	0.002	44.846	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	101	THR	0	-0.085	-0.064	38.897	-0.087	-0.087	0.000	0.000	0.000	0.000
38	A	102	GLY	0	0.012	0.012	39.915	-0.253	-0.253	0.000	0.000	0.000	0.000
39	A	103	ALA	0	-0.038	-0.004	41.768	0.057	0.057	0.000	0.000	0.000	0.000
40	A	104	ALA	0	0.026	-0.003	42.691	-0.114	-0.114	0.000	0.000	0.000	0.000
41	A	105	ARG	1	0.861	0.942	43.129	6.948	6.948	0.000	0.000	0.000	0.000
42	A	106	TYR	0	-0.059	-0.057	39.900	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	107	ASP	-1	-0.865	-0.914	37.944	-8.184	-8.184	0.000	0.000	0.000	0.000
44	A	108	LEU	0	0.009	-0.025	34.858	-0.282	-0.282	0.000	0.000	0.000	0.000
45	A	109	ASP	-1	-0.869	-0.931	34.667	-9.192	-9.192	0.000	0.000	0.000	0.000
46	A	110	ARG	1	0.884	0.949	33.682	8.903	8.903	0.000	0.000	0.000	0.000
47	A	111	PHE	0	-0.070	-0.036	30.334	-0.216	-0.216	0.000	0.000	0.000	0.000
48	A	112	GLY	0	0.083	0.053	30.435	-0.328	-0.328	0.000	0.000	0.000	0.000
49	A	113	ILE	0	-0.083	-0.047	31.225	-0.037	-0.037	0.000	0.000	0.000	0.000
50	A	114	ILE	0	0.018	0.018	33.744	0.318	0.318	0.000	0.000	0.000	0.000
51	A	115	PHE	0	-0.003	-0.018	36.029	-0.114	-0.114	0.000	0.000	0.000	0.000
52	A	116	ARG	1	0.905	0.965	35.467	8.940	8.940	0.000	0.000	0.000	0.000
53	A	117	PRO	0	0.007	0.001	39.008	0.048	0.048	0.000	0.000	0.000	0.000
54	A	118	SER	0	-0.014	-0.025	40.392	0.134	0.134	0.000	0.000	0.000	0.000
55	A	119	PRO	0	0.044	0.013	37.983	-0.178	-0.178	0.000	0.000	0.000	0.000
56	A	120	ARG	1	0.894	0.960	36.042	7.980	7.980	0.000	0.000	0.000	0.000
57	A	121	GLN	0	-0.001	0.001	31.416	-0.430	-0.430	0.000	0.000	0.000	0.000
58	A	122	SER	0	-0.005	-0.024	33.294	0.187	0.187	0.000	0.000	0.000	0.000
59	A	123	ASP	-1	-0.821	-0.891	27.526	-11.507	-11.507	0.000	0.000	0.000	0.000
60	A	124	CYS	0	-0.041	-0.011	30.392	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	125	MET	0	-0.008	0.009	32.884	0.339	0.339	0.000	0.000	0.000	0.000
62	A	126	ILE	0	0.033	0.015	36.143	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	127	VAL	0	-0.030	-0.015	38.358	0.255	0.255	0.000	0.000	0.000	0.000
64	A	128	ALA	0	0.029	0.015	41.120	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	129	GLY	0	0.052	0.036	43.841	0.123	0.123	0.000	0.000	0.000	0.000
66	A	130	THR	0	-0.030	-0.032	46.723	-0.063	-0.063	0.000	0.000	0.000	0.000
67	A	131	LEU	0	0.044	0.035	43.855	0.054	0.054	0.000	0.000	0.000	0.000
68	A	132	THR	0	0.012	-0.003	47.726	0.040	0.040	0.000	0.000	0.000	0.000
69	A	133	ASN	0	0.027	-0.008	49.862	-0.178	-0.178	0.000	0.000	0.000	0.000
70	A	134	LYS	1	0.957	0.972	50.765	5.714	5.714	0.000	0.000	0.000	0.000
71	A	135	MET	0	0.002	0.005	47.256	0.021	0.021	0.000	0.000	0.000	0.000
72	A	136	ALA	0	0.038	0.036	45.963	-0.158	-0.158	0.000	0.000	0.000	0.000
73	A	137	PRO	0	0.038	0.006	45.155	-0.176	-0.176	0.000	0.000	0.000	0.000
74	A	138	ALA	0	-0.059	-0.027	45.495	-0.106	-0.106	0.000	0.000	0.000	0.000
75	A	139	LEU	0	0.043	0.016	40.785	-0.105	-0.105	0.000	0.000	0.000	0.000
76	A	140	ARG	1	0.783	0.861	36.583	8.344	8.344	0.000	0.000	0.000	0.000
77	A	141	LYS	1	0.963	0.982	40.365	6.758	6.758	0.000	0.000	0.000	0.000
78	A	142	VAL	0	-0.028	-0.007	40.004	-0.076	-0.076	0.000	0.000	0.000	0.000
79	A	143	TYR	0	0.095	0.021	32.214	-0.124	-0.124	0.000	0.000	0.000	0.000
80	A	144	ASP	-1	-0.801	-0.876	35.770	-8.849	-8.849	0.000	0.000	0.000	0.000
81	A	145	GLN	0	-0.109	-0.054	35.836	-0.108	-0.108	0.000	0.000	0.000	0.000
82	A	146	MET	0	-0.030	0.015	33.195	0.137	0.137	0.000	0.000	0.000	0.000
83	A	147	PRO	0	0.000	-0.005	29.577	-0.070	-0.070	0.000	0.000	0.000	0.000
84	A	148	GLU	-1	-0.927	-0.964	25.361	-12.791	-12.791	0.000	0.000	0.000	0.000
85	A	149	PRO	0	-0.053	-0.027	24.478	-0.064	-0.064	0.000	0.000	0.000	0.000
86	A	150	ARG	1	0.844	0.947	26.382	9.915	9.915	0.000	0.000	0.000	0.000
87	A	151	TRP	0	0.032	-0.007	24.408	-0.322	-0.322	0.000	0.000	0.000	0.000
88	A	152	VAL	0	-0.019	-0.019	30.723	0.342	0.342	0.000	0.000	0.000	0.000
89	A	153	ILE	0	-0.008	-0.003	32.752	-0.136	-0.136	0.000	0.000	0.000	0.000
90	A	154	SER	0	-0.015	-0.001	35.722	0.197	0.197	0.000	0.000	0.000	0.000
91	A	155	MET	0	-0.007	0.000	38.839	-0.122	-0.122	0.000	0.000	0.000	0.000
92	A	156	GLY	0	0.113	0.047	41.179	0.188	0.188	0.000	0.000	0.000	0.000
93	A	157	SER	0	-0.066	-0.048	43.773	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	158	CYS	0	-0.091	-0.033	45.511	0.071	0.071	0.000	0.000	0.000	0.000
95	A	159	ALA	0	0.042	0.052	42.598	0.033	0.033	0.000	0.000	0.000	0.000
96	A	160	ASN	0	-0.005	-0.009	40.260	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	161	GLY	0	0.046	0.032	41.518	-0.102	-0.102	0.000	0.000	0.000	0.000
98	A	162	GLY	0	0.003	-0.022	44.134	0.062	0.062	0.000	0.000	0.000	0.000
99	A	163	GLY	0	-0.011	0.001	47.189	0.109	0.109	0.000	0.000	0.000	0.000
100	A	164	TYR	0	-0.013	-0.010	48.635	0.070	0.070	0.000	0.000	0.000	0.000
101	A	165	TYR	0	0.034	0.007	51.627	0.157	0.157	0.000	0.000	0.000	0.000
102	A	166	HIS	0	-0.006	0.008	48.137	-0.095	-0.095	0.000	0.000	0.000	0.000
103	A	167	TYR	0	0.033	0.004	51.330	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	168	SER	0	0.009	0.022	54.487	0.138	0.138	0.000	0.000	0.000	0.000
105	A	169	TYR	0	0.055	0.026	54.719	-0.120	-0.120	0.000	0.000	0.000	0.000
106	A	170	SER	0	-0.048	-0.028	54.764	-0.046	-0.046	0.000	0.000	0.000	0.000
107	A	171	VAL	0	0.005	0.020	49.877	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	172	VAL	0	0.010	0.018	45.607	0.031	0.031	0.000	0.000	0.000	0.000
109	A	173	ARG	1	0.809	0.888	47.043	6.285	6.285	0.000	0.000	0.000	0.000
110	A	174	GLY	0	0.057	0.046	43.207	-0.109	-0.109	0.000	0.000	0.000	0.000
111	A	175	CYS	0	-0.077	-0.054	40.386	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	176	ASP	-1	-0.725	-0.845	37.199	-8.783	-8.783	0.000	0.000	0.000	0.000
113	A	177	ARG	1	0.842	0.935	39.644	7.065	7.065	0.000	0.000	0.000	0.000
114	A	178	ILE	0	-0.071	-0.029	41.276	0.131	0.131	0.000	0.000	0.000	0.000
115	A	179	VAL	0	-0.009	-0.013	37.074	-0.049	-0.049	0.000	0.000	0.000	0.000
116	A	180	PRO	0	0.025	0.038	33.029	0.132	0.132	0.000	0.000	0.000	0.000
117	A	181	VAL	0	-0.003	-0.003	34.328	-0.128	-0.128	0.000	0.000	0.000	0.000
118	A	182	ASP	-1	-0.806	-0.876	29.675	-11.127	-11.127	0.000	0.000	0.000	0.000
119	A	183	ILE	0	-0.058	-0.034	30.061	-0.215	-0.215	0.000	0.000	0.000	0.000
120	A	184	TYR	0	-0.031	-0.041	33.231	0.178	0.178	0.000	0.000	0.000	0.000
121	A	185	VAL	0	-0.006	-0.002	36.780	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	186	PRO	0	0.001	0.007	37.802	0.217	0.217	0.000	0.000	0.000	0.000
123	A	187	GLY	0	0.063	0.028	40.827	0.036	0.036	0.000	0.000	0.000	0.000
124	A	188	CYS	0	-0.041	-0.029	44.495	-0.049	-0.049	0.000	0.000	0.000	0.000
125	A	189	PRO	0	0.079	0.035	46.809	-0.069	-0.069	0.000	0.000	0.000	0.000
126	A	190	PRO	0	-0.033	-0.026	41.701	0.006	0.006	0.000	0.000	0.000	0.000
127	A	191	THR	0	0.041	0.027	42.700	0.091	0.091	0.000	0.000	0.000	0.000
128	A	192	ALA	0	0.059	0.024	41.906	-0.208	-0.208	0.000	0.000	0.000	0.000
129	A	193	GLU	-1	-0.851	-0.912	39.063	-7.815	-7.815	0.000	0.000	0.000	0.000
130	A	194	ALA	0	-0.025	-0.009	37.819	-0.260	-0.260	0.000	0.000	0.000	0.000
131	A	195	LEU	0	0.012	-0.007	37.318	-0.235	-0.235	0.000	0.000	0.000	0.000
132	A	196	LEU	0	0.018	0.014	34.385	-0.280	-0.280	0.000	0.000	0.000	0.000
133	A	197	TYR	0	0.006	0.002	31.806	-0.316	-0.316	0.000	0.000	0.000	0.000
134	A	198	GLY	0	0.010	-0.002	32.585	-0.335	-0.335	0.000	0.000	0.000	0.000
135	A	199	LEU	0	0.030	0.002	32.037	-0.319	-0.319	0.000	0.000	0.000	0.000
136	A	200	LEU	0	0.023	0.014	29.263	-0.422	-0.422	0.000	0.000	0.000	0.000
137	A	201	GLN	0	-0.059	-0.029	28.037	-0.693	-0.693	0.000	0.000	0.000	0.000
138	A	202	LEU	0	0.005	0.004	27.825	-0.377	-0.377	0.000	0.000	0.000	0.000
139	A	203	GLN	0	0.037	0.011	25.664	-0.454	-0.454	0.000	0.000	0.000	0.000
140	A	204	LYS	1	0.915	0.962	23.732	11.325	11.325	0.000	0.000	0.000	0.000
141	A	205	LYS	1	0.791	0.882	23.115	11.022	11.022	0.000	0.000	0.000	0.000
142	A	206	ILE	0	-0.019	0.002	21.812	-0.543	-0.543	0.000	0.000	0.000	0.000
143	A	207	ASN	0	-0.060	-0.040	19.411	-1.253	-1.253	0.000	0.000	0.000	0.000
144	A	208	ARG	1	0.886	0.940	18.486	13.120	13.120	0.000	0.000	0.000	0.000
145	A	209	ARG	1	0.820	0.919	18.980	14.589	14.589	0.000	0.000	0.000	0.000
146	A	210	LYS	1	0.914	0.963	12.786	21.914	21.914	0.000	0.000	0.000	0.000
147	A	211	ASP	-1	-0.741	-0.855	15.010	-16.568	-16.568	0.000	0.000	0.000	0.000
148	A	212	PHE	0	-0.032	-0.021	9.214	0.220	0.220	0.000	0.000	0.000	0.000
149	A	213	LEU	0	0.000	-0.020	9.596	-0.743	-0.743	0.000	0.000	0.000	0.000
150	A	214	HIS	0	-0.035	-0.030	11.818	-0.068	-0.068	0.000	0.000	0.000	0.000
151	A	215	TRP	0	-0.043	0.002	12.645	0.421	0.421	0.000	0.000	0.000	0.000
152	A	216	TRP	0	-0.078	-0.045	7.387	-2.527	-2.527	0.000	0.000	0.000	0.000
153	A	217	ASN	-1	-0.985	-0.967	12.024	-22.857	-22.857	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:65:ALA)