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

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FMODB ID: 3ZRQL

Calculation Name: 5XTB-O-Other547

Preferred Name: Mitochondrial complex I (NADH dehydrogenase)

Target Type: PROTEIN COMPLEX

Ligand Name: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | flavin mononucleotide | s-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate | iron/sulfur cluster | fe2/s2 (inorganic) cluster

Ligand 3-letter code: NDP | FMN | 8Q1 | SF4 | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XTB

Chain ID: O

ChEMBL ID: CHEMBL2363065

UniProt ID: O14561

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2163064.084299
FMO2-HF: Nuclear repulsion 2080165.781703
FMO2-HF: Total energy -82898.302596
FMO2-MP2: Total energy -83136.608952


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:36:GLY)


Summations of interaction energy for fragment #1(A:36: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.
-20.298-18.3380.004-0.833-1.132-0.003
Interaction energy analysis for fragmet #1(A:36:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.893 / q_NPA : 0.927
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].
3A38LEU0-0.0040.0123.3108.96710.8300.005-0.811-1.058-0.003
4A39PHE00.017-0.0085.3701.5341.631-0.001-0.022-0.0740.000
5A40VAL0-0.017-0.0057.2743.1663.1660.0000.0000.0000.000
6A41HIS10.9170.9739.00125.62625.6260.0000.0000.0000.000
7A42ARG10.9750.99010.59021.01021.0100.0000.0000.0000.000
8A43ASP-1-0.919-0.9559.329-27.964-27.9640.0000.0000.0000.000
9A44THR0-0.011-0.01812.2110.0320.0320.0000.0000.0000.000
10A45PRO0-0.0010.00812.0700.8800.8800.0000.0000.0000.000
11A46GLU-1-0.817-0.92515.111-17.554-17.5540.0000.0000.0000.000
12A47ASN0-0.033-0.01914.5441.0901.0900.0000.0000.0000.000
13A48ASN0-0.081-0.05113.006-0.380-0.3800.0000.0000.0000.000
14A49PRO00.0250.03516.298-0.788-0.7880.0000.0000.0000.000
15A50ASP-1-0.902-0.94918.930-13.904-13.9040.0000.0000.0000.000
16A51THR0-0.041-0.03119.6150.6930.6930.0000.0000.0000.000
17A52PRO0-0.0010.01121.495-0.338-0.3380.0000.0000.0000.000
18A53PHE00.000-0.01121.270-0.235-0.2350.0000.0000.0000.000
19A54ASP-1-0.807-0.88023.366-10.764-10.7640.0000.0000.0000.000
20A55PHE0-0.0440.00021.525-0.318-0.3180.0000.0000.0000.000
21A56THR00.0380.00126.2010.4730.4730.0000.0000.0000.000
22A57PRO00.0390.00529.199-0.100-0.1000.0000.0000.0000.000
23A58GLU-1-0.857-0.93430.684-9.512-9.5120.0000.0000.0000.000
24A59ASN0-0.029-0.00426.090-0.119-0.1190.0000.0000.0000.000
25A60TYR00.014-0.02828.261-0.107-0.1070.0000.0000.0000.000
26A61LYS10.8670.92230.2278.7538.7530.0000.0000.0000.000
27A62ARG10.9350.96627.21310.96510.9650.0000.0000.0000.000
28A63ILE00.0240.01425.626-0.053-0.0530.0000.0000.0000.000
29A64GLU-1-0.791-0.86728.467-8.743-8.7430.0000.0000.0000.000
30A65ALA0-0.010-0.00731.7150.1720.1720.0000.0000.0000.000
31A66ILE0-0.028-0.01525.5680.0330.0330.0000.0000.0000.000
32A67VAL0-0.013-0.01329.429-0.017-0.0170.0000.0000.0000.000
33A68LYS10.8300.91331.1138.7268.7260.0000.0000.0000.000
34A69ASN0-0.026-0.00330.0700.4880.4880.0000.0000.0000.000
35A70TYR0-0.032-0.01327.012-0.218-0.2180.0000.0000.0000.000
36A71PRO00.016-0.00132.1430.2160.2160.0000.0000.0000.000
37A72GLU-1-0.762-0.86333.288-9.137-9.1370.0000.0000.0000.000
38A73GLY0-0.035-0.01234.326-0.083-0.0830.0000.0000.0000.000
39A74HIS0-0.039-0.02229.895-0.368-0.3680.0000.0000.0000.000
40A75LYS10.9010.92728.9849.1219.1210.0000.0000.0000.000
41A76ALA00.0120.00224.926-0.312-0.3120.0000.0000.0000.000
42A77ALA0-0.0030.00624.310-0.556-0.5560.0000.0000.0000.000
43A78ALA00.0140.00724.989-0.284-0.2840.0000.0000.0000.000
44A79VAL0-0.001-0.00219.246-0.306-0.3060.0000.0000.0000.000
45A80LEU00.0460.02418.213-0.393-0.3930.0000.0000.0000.000
46A81PRO00.0250.00219.529-0.517-0.5170.0000.0000.0000.000
47A82VAL0-0.0020.00421.857-0.001-0.0010.0000.0000.0000.000
48A83LEU00.0090.00815.719-0.131-0.1310.0000.0000.0000.000
49A84ASP-1-0.831-0.88317.439-16.391-16.3910.0000.0000.0000.000
50A85LEU0-0.047-0.01918.7770.0730.0730.0000.0000.0000.000
51A86ALA00.0210.00418.4420.2130.2130.0000.0000.0000.000
52A87GLN00.0580.04512.789-0.654-0.6540.0000.0000.0000.000
53A88ARG10.7700.87317.23215.24215.2420.0000.0000.0000.000
54A89GLN0-0.050-0.03220.3480.3980.3980.0000.0000.0000.000
55A90ASN0-0.066-0.03817.4330.6470.6470.0000.0000.0000.000
56A91GLY0-0.0110.00616.145-0.200-0.2000.0000.0000.0000.000
57A92TRP0-0.057-0.05710.446-0.606-0.6060.0000.0000.0000.000
58A93LEU0-0.009-0.00312.2351.5331.5330.0000.0000.0000.000
59A94PRO00.0190.02312.469-1.548-1.5480.0000.0000.0000.000
60A95ILE00.016-0.01314.2970.2550.2550.0000.0000.0000.000
61A96SER0-0.002-0.00615.5350.3110.3110.0000.0000.0000.000
62A97ALA00.0110.01016.9530.8070.8070.0000.0000.0000.000
63A98MET0-0.070-0.02711.2970.2810.2810.0000.0000.0000.000
64A99ASN00.0410.00817.5950.3860.3860.0000.0000.0000.000
65A100LYS10.9861.02420.63112.00412.0040.0000.0000.0000.000
66A101VAL00.014-0.01120.0290.5750.5750.0000.0000.0000.000
67A102ALA0-0.034-0.01621.3630.3560.3560.0000.0000.0000.000
68A103GLU-1-0.934-0.96523.120-11.278-11.2780.0000.0000.0000.000
69A104VAL0-0.068-0.03425.2670.4760.4760.0000.0000.0000.000
70A105LEU0-0.043-0.02823.7740.3360.3360.0000.0000.0000.000
71A106GLN0-0.030-0.00126.9360.3410.3410.0000.0000.0000.000
72A107VAL0-0.0230.00723.1760.1410.1410.0000.0000.0000.000
73A108PRO00.0180.00223.766-0.196-0.1960.0000.0000.0000.000
74A109PRO00.0600.00420.314-0.471-0.4710.0000.0000.0000.000
75A110MET0-0.0090.01116.358-0.790-0.7900.0000.0000.0000.000
76A111ARG10.9070.95517.76113.29413.2940.0000.0000.0000.000
77A112VAL00.0240.02116.947-0.639-0.6390.0000.0000.0000.000
78A113TYR00.0150.00014.277-1.018-1.0180.0000.0000.0000.000
79A114GLU-1-0.849-0.91613.203-18.427-18.4270.0000.0000.0000.000
80A115VAL0-0.012-0.00413.738-1.448-1.4480.0000.0000.0000.000
81A116ALA00.0310.00712.905-0.979-0.9790.0000.0000.0000.000
82A117THR0-0.085-0.0638.433-3.358-3.3580.0000.0000.0000.000
83A118PHE0-0.050-0.0249.125-3.499-3.4990.0000.0000.0000.000
84A119TYR00.0050.00211.207-0.793-0.7930.0000.0000.0000.000
85A120THR00.001-0.0177.7710.3580.3580.0000.0000.0000.000
86A121MET00.0260.0279.160-2.211-2.2110.0000.0000.0000.000
87A122TYR0-0.031-0.00811.0061.1681.1680.0000.0000.0000.000
88A123ASN0-0.015-0.0048.685-5.123-5.1230.0000.0000.0000.000
89A124ARG10.9460.9665.96337.35237.3520.0000.0000.0000.000
90A125LYS10.8730.9465.35334.61134.6110.0000.0000.0000.000
91A126PRO00.0230.0168.2110.2740.2740.0000.0000.0000.000
92A127VAL00.0070.00610.299-1.696-1.6960.0000.0000.0000.000
93A128GLY00.0100.00712.5611.2791.2790.0000.0000.0000.000
94A129LYS10.8770.94415.89513.11813.1180.0000.0000.0000.000
95A130TYR0-0.023-0.02017.7910.8080.8080.0000.0000.0000.000
96A131HIS00.0030.0109.9310.8080.8080.0000.0000.0000.000
97A132ILE0-0.024-0.01514.4540.7520.7520.0000.0000.0000.000
98A133GLN00.0310.00912.809-0.685-0.6850.0000.0000.0000.000
99A134VAL0-0.0100.00913.9351.0221.0220.0000.0000.0000.000
100A135CYS0-0.0140.01414.409-1.045-1.0450.0000.0000.0000.000
101A136THR00.1020.04114.1011.2371.2370.0000.0000.0000.000
102A137THR00.002-0.01515.6100.7120.7120.0000.0000.0000.000
103A138THR00.0390.00617.4910.6670.6670.0000.0000.0000.000
104A139PRO0-0.0090.00020.8280.4890.4890.0000.0000.0000.000
105A140CYS00.0100.00020.0820.4420.4420.0000.0000.0000.000
106A141MET0-0.0060.00817.8780.5680.5680.0000.0000.0000.000
107A142LEU0-0.001-0.00921.6440.4460.4460.0000.0000.0000.000
108A143ARG10.7940.90424.73811.57811.5780.0000.0000.0000.000
109A144ASN00.0200.00323.885-0.301-0.3010.0000.0000.0000.000
110A145SER00.012-0.02918.6770.2050.2050.0000.0000.0000.000
111A146ASP-1-0.874-0.92617.780-17.877-17.8770.0000.0000.0000.000
112A147SER0-0.030-0.00919.553-0.051-0.0510.0000.0000.0000.000
113A148ILE0-0.032-0.03219.9080.3390.3390.0000.0000.0000.000
114A149LEU00.0310.01413.987-0.248-0.2480.0000.0000.0000.000
115A150GLU-1-0.911-0.96117.507-15.026-15.0260.0000.0000.0000.000
116A151ALA0-0.059-0.02419.6720.3870.3870.0000.0000.0000.000
117A152ILE00.0120.00617.1970.2390.2390.0000.0000.0000.000
118A153GLN00.0060.00316.236-0.255-0.2550.0000.0000.0000.000
119A154LYS10.8710.92918.18112.85812.8580.0000.0000.0000.000
120A155LYS10.7790.88921.94412.23512.2350.0000.0000.0000.000
121A156LEU0-0.043-0.02217.6800.2210.2210.0000.0000.0000.000
122A157GLY0-0.0070.00519.592-0.028-0.0280.0000.0000.0000.000
123A158ILE0-0.053-0.01713.455-0.160-0.1600.0000.0000.0000.000
124A159LYS10.8820.93412.57418.19018.1900.0000.0000.0000.000
125A160VAL00.003-0.01910.096-2.477-2.4770.0000.0000.0000.000
126A161GLY00.0230.0197.5690.3680.3680.0000.0000.0000.000
127A162GLU-1-0.910-0.9408.331-23.869-23.8690.0000.0000.0000.000
128A163THR0-0.008-0.01410.4881.1491.1490.0000.0000.0000.000
129A164THR00.0100.02412.7250.8930.8930.0000.0000.0000.000
130A165PRO00.0370.01116.329-0.009-0.0090.0000.0000.0000.000
131A166ASP-1-0.927-0.97618.782-13.605-13.6050.0000.0000.0000.000
132A167LYS10.8740.93517.31616.02316.0230.0000.0000.0000.000
133A168LEU00.0020.02618.391-0.115-0.1150.0000.0000.0000.000
134A169PHE00.0490.00316.638-0.373-0.3730.0000.0000.0000.000
135A170THR00.001-0.02311.305-0.927-0.9270.0000.0000.0000.000
136A171LEU0-0.0130.01612.5290.2970.2970.0000.0000.0000.000
137A172ILE0-0.043-0.0226.295-3.122-3.1220.0000.0000.0000.000
138A173GLU-1-0.914-0.9399.220-26.912-26.9120.0000.0000.0000.000
139A174VAL0-0.042-0.0309.709-3.349-3.3490.0000.0000.0000.000
140A175GLU-1-0.833-0.90611.423-21.010-21.0100.0000.0000.0000.000
141A176CYS0-0.082-0.03713.6810.9390.9390.0000.0000.0000.000
142A177LEU00.0400.02015.2280.2100.2100.0000.0000.0000.000
143A178GLY00.018-0.00518.4320.6140.6140.0000.0000.0000.000
144A179ALA00.0080.01221.8510.6070.6070.0000.0000.0000.000
145A180CYS0-0.056-0.04522.3720.1470.1470.0000.0000.0000.000
146A181VAL0-0.0080.00224.7670.1640.1640.0000.0000.0000.000
147A182ASN0-0.025-0.01527.1450.5650.5650.0000.0000.0000.000
148A183ALA00.0070.00925.9580.2800.2800.0000.0000.0000.000
149A184PRO00.0310.03021.460-0.397-0.3970.0000.0000.0000.000
150A185MET0-0.0100.00219.8220.6600.6600.0000.0000.0000.000
151A186VAL00.013-0.00918.431-1.038-1.0380.0000.0000.0000.000
152A187GLN00.0010.00317.9780.7480.7480.0000.0000.0000.000
153A188ILE00.0240.01317.468-1.201-1.2010.0000.0000.0000.000
154A189ASN00.007-0.00117.4860.7270.7270.0000.0000.0000.000
155A190ASP-1-0.838-0.91019.252-15.435-15.4350.0000.0000.0000.000
156A191ASN0-0.097-0.04421.3071.5611.5610.0000.0000.0000.000
157A192TYR00.0610.03021.515-0.413-0.4130.0000.0000.0000.000
158A193TYR00.0540.01122.6380.4460.4460.0000.0000.0000.000
159A194GLU-1-0.811-0.90023.531-12.655-12.6550.0000.0000.0000.000
160A195ASP-1-0.803-0.87725.814-10.006-10.0060.0000.0000.0000.000
161A196LEU0-0.0360.01323.2790.2640.2640.0000.0000.0000.000
162A197THR00.0270.01626.326-0.107-0.1070.0000.0000.0000.000
163A198ALA00.0750.02025.776-0.205-0.2050.0000.0000.0000.000
164A199LYS10.9230.95326.8319.7049.7040.0000.0000.0000.000
165A200ASP-1-0.844-0.92827.644-10.825-10.8250.0000.0000.0000.000
166A201ILE0-0.0050.01622.067-0.158-0.1580.0000.0000.0000.000
167A202GLU-1-0.915-0.95024.970-11.997-11.9970.0000.0000.0000.000
168A203GLU-1-0.911-0.95227.137-9.993-9.9930.0000.0000.0000.000
169A204ILE00.0240.00523.200-0.038-0.0380.0000.0000.0000.000
170A205ILE0-0.045-0.03320.426-0.275-0.2750.0000.0000.0000.000
171A206ASP-1-0.860-0.91724.257-11.402-11.4020.0000.0000.0000.000
172A207GLU-1-0.834-0.94027.623-10.529-10.5290.0000.0000.0000.000
173A208LEU0-0.056-0.02421.1980.0400.0400.0000.0000.0000.000
174A209LYS10.8770.92923.83912.49612.4960.0000.0000.0000.000
175A210ALA0-0.0140.01027.3210.3050.3050.0000.0000.0000.000
176A211GLY0-0.013-0.01429.3750.4150.4150.0000.0000.0000.000
177A212LYS10.8790.94528.51910.02010.0200.0000.0000.0000.000
178A213ILE00.0170.03525.1710.2720.2720.0000.0000.0000.000
179A214PRO0-0.025-0.00128.747-0.124-0.1240.0000.0000.0000.000
180A215LYS10.8510.90125.43112.01412.0140.0000.0000.0000.000
181A216PRO0-0.0180.00228.5860.1360.1360.0000.0000.0000.000
182A217GLY00.0770.04427.974-0.361-0.3610.0000.0000.0000.000
183A218PRO0-0.069-0.05028.328-0.259-0.2590.0000.0000.0000.000
184A219ARG10.9210.97628.28211.13511.1350.0000.0000.0000.000
185A220SER0-0.078-0.07430.8080.3650.3650.0000.0000.0000.000
186A221GLY00.0220.02033.2450.2660.2660.0000.0000.0000.000
187A222ARG10.8000.89731.7269.9829.9820.0000.0000.0000.000
188A223PHE00.0400.01333.263-0.263-0.2630.0000.0000.0000.000
189A224SER00.0290.00933.9440.0070.0070.0000.0000.0000.000
190A225CYS0-0.040-0.02231.548-0.077-0.0770.0000.0000.0000.000
191A226GLU-1-0.896-0.93433.069-8.194-8.1940.0000.0000.0000.000
192A227PRO0-0.049-0.04036.149-0.049-0.0490.0000.0000.0000.000
193A228ALA00.0630.01537.6850.2070.2070.0000.0000.0000.000
194A229GLY0-0.056-0.02439.6810.1890.1890.0000.0000.0000.000
195A230GLY0-0.012-0.01641.5240.0980.0980.0000.0000.0000.000
196A231LEU0-0.057-0.00240.5180.1240.1240.0000.0000.0000.000
197A232THR00.0680.03542.0730.1520.1520.0000.0000.0000.000
198A233SER0-0.043-0.02540.335-0.080-0.0800.0000.0000.0000.000
199A234LEU0-0.0120.00140.9580.1780.1780.0000.0000.0000.000
200A235THR00.0230.00644.5040.0280.0280.0000.0000.0000.000
201A236GLU-1-0.935-0.96447.654-6.082-6.0820.0000.0000.0000.000
202A237PRO00.004-0.00648.082-0.107-0.1070.0000.0000.0000.000
203A238PRO0-0.052-0.01248.791-0.058-0.0580.0000.0000.0000.000
204A239LYS10.9710.98046.2096.7126.7120.0000.0000.0000.000
205A240GLY00.0680.03949.404-0.039-0.0390.0000.0000.0000.000
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