FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: JYJ99

Calculation Name: 7A23-B-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: B

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2418616.019125
FMO2-HF: Nuclear repulsion 2332096.316891
FMO2-HF: Total energy -86519.702235
FMO2-MP2: Total energy -86766.907175


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:31:ALA)


Summations of interaction energy for fragment #1(A:31: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.
-37.869-33.9170.03-1.95-2.032-0.009
Interaction energy analysis for fragmet #1(A:31:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.919
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   
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].
3A33ASN0-0.010-0.0113.7001.1944.227-0.022-1.527-1.484-0.006
89A119ARG10.9110.9433.39949.66950.5680.053-0.417-0.535-0.003
90A120ALA0-0.051-0.0224.5140.5130.533-0.001-0.006-0.0130.000
4A34TYR00.0470.0455.7694.1984.1980.0000.0000.0000.000
5A35HIS0-0.037-0.0366.128-8.245-8.2450.0000.0000.0000.000
6A36LEU0-0.005-0.0097.6971.8171.8170.0000.0000.0000.000
7A37ASP-1-0.815-0.9049.947-21.778-21.7780.0000.0000.0000.000
8A38SER0-0.054-0.02410.773-0.489-0.4890.0000.0000.0000.000
9A39PRO0-0.052-0.04813.2140.6590.6590.0000.0000.0000.000
10A40ASP-1-0.853-0.89512.955-21.648-21.6480.0000.0000.0000.000
11A41ASN00.0680.0328.6252.5422.5420.0000.0000.0000.000
12A42LYS11.0071.00612.47316.31016.3100.0000.0000.0000.000
13A43PRO0-0.040-0.02414.4520.4590.4590.0000.0000.0000.000
14A44ASP-1-0.968-0.97616.589-13.669-13.6690.0000.0000.0000.000
15A45LEU0-0.0120.00416.5980.6530.6530.0000.0000.0000.000
16A46PRO0-0.001-0.00219.774-0.367-0.3670.0000.0000.0000.000
17A47TRP0-0.038-0.03117.354-0.110-0.1100.0000.0000.0000.000
18A48GLU-1-0.940-0.97620.765-11.652-11.6520.0000.0000.0000.000
19A49PHE0-0.006-0.00419.385-0.365-0.3650.0000.0000.0000.000
20A50SER00.0330.00923.1780.3180.3180.0000.0000.0000.000
21A51GLU-1-0.841-0.93325.535-10.442-10.4420.0000.0000.0000.000
22A52ALA0-0.021-0.00727.406-0.326-0.3260.0000.0000.0000.000
23A53ASN00.015-0.01422.9950.1060.1060.0000.0000.0000.000
24A54GLN00.0350.01525.721-0.056-0.0560.0000.0000.0000.000
25A55SER0-0.044-0.01727.5600.1940.1940.0000.0000.0000.000
26A56LYS10.8950.94324.94212.53512.5350.0000.0000.0000.000
27A57VAL00.0050.00223.170-0.114-0.1140.0000.0000.0000.000
28A58LYS10.9450.96825.5879.4079.4070.0000.0000.0000.000
29A59GLU-1-0.894-0.91228.778-10.152-10.1520.0000.0000.0000.000
30A60ILE00.0290.01922.5620.0730.0730.0000.0000.0000.000
31A61LEU0-0.043-0.04624.860-0.001-0.0010.0000.0000.0000.000
32A62SER0-0.119-0.05627.5680.3480.3480.0000.0000.0000.000
33A63TYR0-0.071-0.05426.9850.1520.1520.0000.0000.0000.000
34A64TYR0-0.026-0.01123.7700.1040.1040.0000.0000.0000.000
35A65PRO00.0000.00029.4350.2120.2120.0000.0000.0000.000
36A66SER00.0200.01730.163-0.345-0.3450.0000.0000.0000.000
37A67ASN00.0290.00430.314-0.233-0.2330.0000.0000.0000.000
38A68TYR00.019-0.00827.142-0.036-0.0360.0000.0000.0000.000
39A69LYS10.8990.97526.13110.83810.8380.0000.0000.0000.000
40A70GLN00.008-0.00419.9250.1110.1110.0000.0000.0000.000
41A71SER0-0.030-0.03321.432-0.720-0.7200.0000.0000.0000.000
42A72ALA00.0050.00922.182-0.311-0.3110.0000.0000.0000.000
43A73VAL0-0.007-0.01216.233-0.452-0.4520.0000.0000.0000.000
44A74ILE00.0080.00815.696-0.854-0.8540.0000.0000.0000.000
45A75PRO00.0270.00117.009-0.646-0.6460.0000.0000.0000.000
46A76LEU00.0190.01719.278-0.076-0.0760.0000.0000.0000.000
47A77LEU0-0.010-0.00112.617-0.334-0.3340.0000.0000.0000.000
48A78ASP-1-0.801-0.88414.849-19.593-19.5930.0000.0000.0000.000
49A79LEU0-0.0080.00216.002-0.163-0.1630.0000.0000.0000.000
50A80ALA00.0110.00115.7310.2270.2270.0000.0000.0000.000
51A81GLN0-0.064-0.03010.5180.1750.1750.0000.0000.0000.000
52A82GLN0-0.088-0.06814.2520.6240.6240.0000.0000.0000.000
53A83GLN00.0180.02117.2520.7180.7180.0000.0000.0000.000
54A84ASN0-0.053-0.02014.6121.1361.1360.0000.0000.0000.000
55A85GLY00.0160.01215.130-0.841-0.8410.0000.0000.0000.000
56A86GLY00.032-0.00112.639-0.565-0.5650.0000.0000.0000.000
57A87TRP0-0.065-0.0558.562-2.748-2.7480.0000.0000.0000.000
58A88LEU00.0250.0079.3462.4742.4740.0000.0000.0000.000
59A89PRO0-0.0040.0029.579-2.674-2.6740.0000.0000.0000.000
60A90VAL00.029-0.00210.5260.8450.8450.0000.0000.0000.000
61A91SER00.0230.02412.6850.7030.7030.0000.0000.0000.000
62A92ALA00.0530.03714.1741.0801.0800.0000.0000.0000.000
63A93MET0-0.047-0.0188.4140.7670.7670.0000.0000.0000.000
64A94ASN00.0250.01814.6410.4350.4350.0000.0000.0000.000
65A95ALA00.0230.02617.6270.9290.9290.0000.0000.0000.000
66A96VAL00.0170.00616.8280.8270.8270.0000.0000.0000.000
67A97ALA0-0.016-0.01318.0480.6760.6760.0000.0000.0000.000
68A98LYS10.9130.95419.85513.69813.6980.0000.0000.0000.000
69A99VAL00.0250.01922.4160.5650.5650.0000.0000.0000.000
70A100ILE0-0.056-0.01920.2130.5010.5010.0000.0000.0000.000
71A101GLU-1-0.887-0.92023.491-10.473-10.4730.0000.0000.0000.000
72A102VAL0-0.020-0.00519.6740.1160.1160.0000.0000.0000.000
73A103ALA00.0060.00020.846-0.183-0.1830.0000.0000.0000.000
74A104PRO00.0440.00316.739-0.380-0.3800.0000.0000.0000.000
75A105ILE00.0130.02013.909-0.956-0.9560.0000.0000.0000.000
76A106ARG10.8660.91614.71514.86714.8670.0000.0000.0000.000
77A107VAL00.0140.01513.809-0.273-0.2730.0000.0000.0000.000
78A108TYR0-0.037-0.05110.989-1.442-1.4420.0000.0000.0000.000
79A109GLU-1-0.837-0.89010.174-20.398-20.3980.0000.0000.0000.000
80A110VAL00.0020.00910.858-1.386-1.3860.0000.0000.0000.000
81A111ALA00.0330.0059.386-0.975-0.9750.0000.0000.0000.000
82A112THR0-0.138-0.0946.169-4.191-4.1910.0000.0000.0000.000
83A113PHE0-0.0280.0036.238-3.213-3.2130.0000.0000.0000.000
84A114TYR00.0140.0038.8180.1950.1950.0000.0000.0000.000
85A115SER00.009-0.0036.814-0.799-0.7990.0000.0000.0000.000
86A116MET00.0060.0157.361-1.868-1.8680.0000.0000.0000.000
87A117PHE00.0100.0178.8710.3230.3230.0000.0000.0000.000
88A118ASN0-0.034-0.0056.099-7.720-7.7200.0000.0000.0000.000
91A121LYS10.8800.9316.26123.54123.5410.0000.0000.0000.000
92A122VAL00.0030.0087.062-2.232-2.2320.0000.0000.0000.000
93A123GLY0-0.019-0.0049.4041.9451.9450.0000.0000.0000.000
94A124LYS10.8450.91212.97317.36717.3670.0000.0000.0000.000
95A125TYR00.0030.00314.9010.7290.7290.0000.0000.0000.000
96A126HIS00.0070.0067.7621.4481.4480.0000.0000.0000.000
97A127LEU00.0310.01812.4570.8280.8280.0000.0000.0000.000
98A128LEU00.0040.0149.655-1.345-1.3450.0000.0000.0000.000
99A129VAL00.0370.02213.1911.7421.7420.0000.0000.0000.000
100A130CYS0-0.0360.00213.955-1.108-1.1080.0000.0000.0000.000
101A131GLY00.0820.04414.7060.7560.7560.0000.0000.0000.000
102A132THR00.031-0.00215.6950.7420.7420.0000.0000.0000.000
103A133THR00.0110.00017.6970.3200.3200.0000.0000.0000.000
104A134PRO00.002-0.00820.8970.3460.3460.0000.0000.0000.000
105A135CYS00.0260.01919.4200.3560.3560.0000.0000.0000.000
106A136MET0-0.045-0.00919.7070.1660.1660.0000.0000.0000.000
107A137ILE0-0.059-0.04021.3200.3410.3410.0000.0000.0000.000
108A138ARG10.8880.94224.16611.28811.2880.0000.0000.0000.000
109A139GLY00.0960.05524.4370.1170.1170.0000.0000.0000.000
110A140SER0-0.047-0.04418.285-0.103-0.1030.0000.0000.0000.000
111A141ARG10.9920.99218.28214.75314.7530.0000.0000.0000.000
112A142ASP-1-0.875-0.91719.763-13.360-13.3600.0000.0000.0000.000
113A143ILE0-0.073-0.03019.5660.0600.0600.0000.0000.0000.000
114A144GLU-1-0.825-0.90213.125-23.119-23.1190.0000.0000.0000.000
115A145SER0-0.048-0.04317.654-0.525-0.5250.0000.0000.0000.000
116A146ALA00.0310.01519.626-0.091-0.0910.0000.0000.0000.000
117A147LEU0-0.032-0.00216.1240.1640.1640.0000.0000.0000.000
118A148LEU0-0.046-0.02213.130-0.464-0.4640.0000.0000.0000.000
119A149ASP-1-0.940-0.97417.023-14.214-14.2140.0000.0000.0000.000
120A150HIS0-0.015-0.00420.394-0.023-0.0230.0000.0000.0000.000
121A151LEU0-0.050-0.02515.2770.1920.1920.0000.0000.0000.000
122A152GLY0-0.022-0.00218.0660.0990.0990.0000.0000.0000.000
123A153VAL0-0.065-0.03712.357-0.407-0.4070.0000.0000.0000.000
124A154LYS10.8670.92710.35326.70426.7040.0000.0000.0000.000
125A155ARG10.8120.8618.50726.96026.9600.0000.0000.0000.000
126A156GLY00.0370.0306.6401.1821.1820.0000.0000.0000.000
127A157GLU-1-0.962-0.9686.858-30.680-30.6800.0000.0000.0000.000
128A158VAL0-0.0100.0028.9592.0732.0730.0000.0000.0000.000
129A159THR0-0.008-0.01710.9781.3741.3740.0000.0000.0000.000
130A160LYS10.9390.95614.69717.25217.2520.0000.0000.0000.000
131A161ASP-1-0.850-0.91717.151-15.059-15.0590.0000.0000.0000.000
132A162GLY0-0.024-0.01215.2370.4870.4870.0000.0000.0000.000
133A163LEU0-0.0030.00915.649-0.705-0.7050.0000.0000.0000.000
134A164PHE00.0750.02914.602-0.425-0.4250.0000.0000.0000.000
135A165SER00.001-0.0109.277-1.741-1.7410.0000.0000.0000.000
136A166VAL00.0370.03510.7101.4261.4260.0000.0000.0000.000
137A167GLY0-0.015-0.0128.703-3.668-3.6680.0000.0000.0000.000
138A168GLU-1-0.840-0.9059.078-21.787-21.7870.0000.0000.0000.000
139A169MET0-0.038-0.0199.261-3.122-3.1220.0000.0000.0000.000
140A170GLU-1-0.865-0.93711.650-19.420-19.4200.0000.0000.0000.000
141A171CYS0-0.058-0.03114.0290.5440.5440.0000.0000.0000.000
142A172MET00.0770.04013.922-0.224-0.2240.0000.0000.0000.000
143A173GLY0-0.001-0.00317.9130.5470.5470.0000.0000.0000.000
144A174CYS0-0.102-0.05921.3310.5520.5520.0000.0000.0000.000
145A175CYS00.0170.01222.108-0.451-0.4510.0000.0000.0000.000
146A176VAL00.003-0.01024.3650.2500.2500.0000.0000.0000.000
147A177ASN0-0.055-0.03925.9150.7930.7930.0000.0000.0000.000
148A178ALA0-0.0080.00424.826-0.390-0.3900.0000.0000.0000.000
149A179PRO00.0220.03422.493-0.517-0.5170.0000.0000.0000.000
150A180MET0-0.061-0.03118.7360.1070.1070.0000.0000.0000.000
151A181ILE00.0370.00817.078-0.760-0.7600.0000.0000.0000.000
152A182THR00.0400.01015.6951.0501.0500.0000.0000.0000.000
153A183VAL0-0.048-0.01816.225-0.875-0.8750.0000.0000.0000.000
154A184ALA00.0080.00114.1620.6290.6290.0000.0000.0000.000
155A185ASP-1-0.802-0.85215.876-15.480-15.4800.0000.0000.0000.000
156A186TYR00.0380.02012.604-0.318-0.3180.0000.0000.0000.000
157A187SER0-0.072-0.07217.3020.1230.1230.0000.0000.0000.000
158A188ASN0-0.043-0.02720.034-0.041-0.0410.0000.0000.0000.000
159A189GLY00.1010.05719.429-0.191-0.1910.0000.0000.0000.000
160A190SER0-0.045-0.00820.0650.8220.8220.0000.0000.0000.000
161A191GLU-1-0.865-0.92421.830-11.229-11.2290.0000.0000.0000.000
162A192GLY0-0.050-0.03624.1710.2200.2200.0000.0000.0000.000
163A193TYR0-0.068-0.01516.447-0.634-0.6340.0000.0000.0000.000
164A194THR0-0.010-0.02320.8920.4920.4920.0000.0000.0000.000
165A195TYR00.0390.02213.061-0.310-0.3100.0000.0000.0000.000
166A196ASN0-0.0130.00519.2080.2780.2780.0000.0000.0000.000
167A197TYR00.0440.01917.955-0.739-0.7390.0000.0000.0000.000
168A198PHE00.0080.01021.0640.8260.8260.0000.0000.0000.000
169A199GLU-1-0.793-0.88922.210-12.304-12.3040.0000.0000.0000.000
170A200ASP-1-0.805-0.90124.520-10.384-10.3840.0000.0000.0000.000
171A201VAL0-0.0310.00122.0290.4170.4170.0000.0000.0000.000
172A202THR00.0550.00725.4560.0850.0850.0000.0000.0000.000
173A203PRO00.0430.00124.361-0.126-0.1260.0000.0000.0000.000
174A204GLU-1-0.848-0.89625.163-10.383-10.3830.0000.0000.0000.000
175A205LYS10.8660.92626.24910.20810.2080.0000.0000.0000.000
176A206VAL00.0080.00920.370-0.205-0.2050.0000.0000.0000.000
177A207VAL00.0290.02122.597-0.426-0.4260.0000.0000.0000.000
178A208GLU-1-0.869-0.94424.177-10.675-10.6750.0000.0000.0000.000
179A209ILE0-0.060-0.03721.5400.1440.1440.0000.0000.0000.000
180A210VAL00.0170.00919.368-0.142-0.1420.0000.0000.0000.000
181A211GLU-1-0.897-0.96421.946-11.709-11.7090.0000.0000.0000.000
182A212LYS10.8870.93725.17211.21211.2120.0000.0000.0000.000
183A213LEU0-0.0040.01219.9770.1190.1190.0000.0000.0000.000
184A214ARG10.8060.91220.77914.20114.2010.0000.0000.0000.000
185A215LYS10.7840.89323.20610.90510.9050.0000.0000.0000.000
186A216GLY00.0160.02824.9970.3560.3560.0000.0000.0000.000
187A217GLU-1-0.835-0.90926.026-10.823-10.8230.0000.0000.0000.000
188A218LYS10.8950.92623.69712.44012.4400.0000.0000.0000.000
189A219PRO0-0.032-0.01024.4820.5100.5100.0000.0000.0000.000
190A220PRO00.0000.00926.857-0.200-0.2000.0000.0000.0000.000
191A221HIS00.0130.00624.702-0.327-0.3270.0000.0000.0000.000
192A222GLY00.0240.02025.5130.4970.4970.0000.0000.0000.000
193A223THR0-0.033-0.02826.754-0.210-0.2100.0000.0000.0000.000
194A224GLN0-0.074-0.04026.0120.3870.3870.0000.0000.0000.000
195A225ASN0-0.023-0.01729.0260.4150.4150.0000.0000.0000.000
196A226PRO00.0930.05131.8590.0680.0680.0000.0000.0000.000
197A227LYS10.8550.92235.2448.7638.7630.0000.0000.0000.000
198A228ARG10.7650.88629.81810.23710.2370.0000.0000.0000.000
199A229ILE00.0020.01034.915-0.070-0.0700.0000.0000.0000.000
200A230LYS11.0411.00430.4889.2659.2650.0000.0000.0000.000
201A231CYS0-0.028-0.00829.6790.2550.2550.0000.0000.0000.000
202A232GLY00.0210.02031.1520.1900.1900.0000.0000.0000.000
203A233PRO0-0.023-0.02434.133-0.170-0.1700.0000.0000.0000.000
204A234GLU-1-0.879-0.95234.579-8.359-8.3590.0000.0000.0000.000
205A235GLY00.0390.02836.2160.0330.0330.0000.0000.0000.000
206A236GLY00.0220.01239.3000.2130.2130.0000.0000.0000.000
207A237ASN0-0.032-0.02538.701-0.019-0.0190.0000.0000.0000.000
208A238LYS10.8850.93539.7547.8957.8950.0000.0000.0000.000
209A239THR00.0200.01239.9840.0860.0860.0000.0000.0000.000
210A240LEU0-0.0120.00139.5160.1580.1580.0000.0000.0000.000
211A241LEU0-0.019-0.01542.282-0.078-0.0780.0000.0000.0000.000
212A242GLY0-0.0130.00545.2040.1120.1120.0000.0000.0000.000
213A243GLU-1-0.907-0.95745.930-6.843-6.8430.0000.0000.0000.000
214A244PRO0-0.043-0.02143.2380.0760.0760.0000.0000.0000.000
215A245LYS10.9620.98646.0076.1306.1300.0000.0000.0000.000
216A246PRO00.006-0.00747.705-0.095-0.0950.0000.0000.0000.000
217A247PRO0-0.053-0.01247.0060.1120.1120.0000.0000.0000.000
218A248GLN0-0.045-0.03350.024-0.036-0.0360.0000.0000.0000.000
219A249PHE-1-0.891-0.93347.034-6.039-6.0390.0000.0000.0000.000