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: QLQNY

Calculation Name: 5K0Y-f-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5K0Y

Chain ID: f

ChEMBL ID:

UniProt ID: O75821

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-05

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2447328.942668
FMO2-HF: Nuclear repulsion 2365343.955469
FMO2-HF: Total energy -81984.987199
FMO2-MP2: Total energy -82223.416894


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-10.627-6.7080.626-1.752-2.792-0.01
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.885
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].
3A4ALA00.0180.0113.552-1.6990.163-0.001-0.897-0.964-0.003
4A5LEU00.0200.0102.548-3.642-3.0770.551-0.342-0.774-0.004
5A6ASP-1-0.835-0.9125.397-28.762-28.719-0.001-0.001-0.0400.000
7A8LEU0-0.046-0.0203.464-1.610-1.1840.019-0.154-0.290-0.001
58A59LEU00.0360.0193.469-1.438-1.2010.008-0.063-0.1820.000
62A63ARG10.9280.9433.47852.39053.1760.050-0.295-0.542-0.002
6A7VAL0-0.006-0.0078.5990.9790.9790.0000.0000.0000.000
8A9GLN0-0.068-0.0325.817-1.297-1.2970.0000.0000.0000.000
9A10MET0-0.049-0.0067.8773.3453.3450.0000.0000.0000.000
10A11LYS10.9020.93510.77520.48720.4870.0000.0000.0000.000
11A12GLU-1-0.853-0.93313.862-14.630-14.6300.0000.0000.0000.000
12A13GLU-1-0.883-0.94516.468-17.593-17.5930.0000.0000.0000.000
13A14ASP-1-0.750-0.88113.231-20.912-20.9120.0000.0000.0000.000
14A15VAL0-0.0080.00115.7950.4710.4710.0000.0000.0000.000
15A16LEU00.0390.01218.0550.6920.6920.0000.0000.0000.000
16A17LYS10.8930.97018.19115.61415.6140.0000.0000.0000.000
17A18PHE00.022-0.01114.3570.3140.3140.0000.0000.0000.000
18A19LEU0-0.0030.02020.1450.4920.4920.0000.0000.0000.000
19A20ALA00.0100.00823.3080.4910.4910.0000.0000.0000.000
20A21ALA0-0.0020.00322.7760.4040.4040.0000.0000.0000.000
21A22GLY00.0010.00924.8490.0630.0630.0000.0000.0000.000
22A23THR0-0.081-0.06320.629-0.141-0.1410.0000.0000.0000.000
23A24HIS00.0420.01122.106-0.459-0.4590.0000.0000.0000.000
24A25LEU0-0.039-0.01323.0730.0960.0960.0000.0000.0000.000
25A26GLY00.0750.03726.138-0.161-0.1610.0000.0000.0000.000
26A27GLY0-0.0080.00226.6420.4100.4100.0000.0000.0000.000
27A28THR0-0.031-0.04529.779-0.137-0.1370.0000.0000.0000.000
28A29ASN0-0.0240.00531.2670.4350.4350.0000.0000.0000.000
29A30LEU00.0170.00530.294-0.304-0.3040.0000.0000.0000.000
30A31ASP-1-0.876-0.94925.999-11.685-11.6850.0000.0000.0000.000
31A32PHE00.0200.00827.2990.1620.1620.0000.0000.0000.000
32A33GLN0-0.014-0.01522.575-0.443-0.4430.0000.0000.0000.000
33A34MET00.0050.01420.197-0.963-0.9630.0000.0000.0000.000
34A35GLU-1-0.869-0.92921.827-12.152-12.1520.0000.0000.0000.000
35A36GLN00.004-0.01218.8970.2740.2740.0000.0000.0000.000
36A37TYR0-0.030-0.01616.046-1.507-1.5070.0000.0000.0000.000
37A38ILE0-0.0080.01818.663-0.394-0.3940.0000.0000.0000.000
38A39TYR0-0.039-0.01419.192-0.097-0.0970.0000.0000.0000.000
39A40LYS10.9310.95621.19112.43212.4320.0000.0000.0000.000
40A41ARG10.9490.98625.0399.2959.2950.0000.0000.0000.000
41A42LYS10.9440.98428.2809.4669.4660.0000.0000.0000.000
42A43SER00.021-0.00830.580-0.020-0.0200.0000.0000.0000.000
43A44ASP-1-0.901-0.95034.301-8.198-8.1980.0000.0000.0000.000
44A45GLY0-0.035-0.01033.2830.1000.1000.0000.0000.0000.000
45A46ILE00.0120.00428.677-0.060-0.0600.0000.0000.0000.000
46A47TYR0-0.0090.00325.6890.0100.0100.0000.0000.0000.000
47A48ILE00.0020.01022.3110.0100.0100.0000.0000.0000.000
48A49ILE00.0410.02919.333-0.241-0.2410.0000.0000.0000.000
49A50ASN00.003-0.00416.168-0.574-0.5740.0000.0000.0000.000
50A51LEU00.0580.03515.464-0.850-0.8500.0000.0000.0000.000
51A52LYS10.9040.9449.95123.59923.5990.0000.0000.0000.000
52A53ARG10.8700.92411.22117.31617.3160.0000.0000.0000.000
53A54THR00.004-0.00813.066-0.447-0.4470.0000.0000.0000.000
54A55TRP0-0.008-0.0046.6861.4931.4930.0000.0000.0000.000
55A56GLU-1-0.851-0.9217.729-28.601-28.6010.0000.0000.0000.000
56A57LYS10.8830.9488.70018.28418.2840.0000.0000.0000.000
57A58LEU00.0200.01811.220-0.026-0.0260.0000.0000.0000.000
59A60LEU0-0.067-0.0396.850-2.578-2.5780.0000.0000.0000.000
60A61ALA00.0210.0118.2840.4360.4360.0000.0000.0000.000
61A62ALA00.0060.0008.9550.9110.9110.0000.0000.0000.000
63A64ALA0-0.0220.0048.2920.3490.3490.0000.0000.0000.000
64A65ILE0-0.0020.00411.6611.7681.7680.0000.0000.0000.000
65A66VAL0-0.031-0.0099.3481.1681.1680.0000.0000.0000.000
66A67ALA00.003-0.00610.737-0.132-0.1320.0000.0000.0000.000
67A68ILE0-0.0260.00312.3881.2511.2510.0000.0000.0000.000
68A69GLU-1-0.919-0.96014.964-20.485-20.4850.0000.0000.0000.000
69A70ASN0-0.043-0.01017.7250.9440.9440.0000.0000.0000.000
70A71PRO00.0040.00818.494-0.493-0.4930.0000.0000.0000.000
71A72ALA00.0440.02519.5350.0650.0650.0000.0000.0000.000
72A73ASP-1-0.844-0.90720.508-14.718-14.7180.0000.0000.0000.000
73A74VAL00.0130.00217.133-0.486-0.4860.0000.0000.0000.000
74A75SER0-0.0020.00220.5350.6840.6840.0000.0000.0000.000
75A76VAL0-0.040-0.01419.963-0.359-0.3590.0000.0000.0000.000
76A77ILE0-0.019-0.02022.5810.6700.6700.0000.0000.0000.000
77A78SER00.013-0.00124.714-0.382-0.3820.0000.0000.0000.000
78A79SER0-0.041-0.03127.1610.3880.3880.0000.0000.0000.000
79A80ARG10.9340.96927.33810.88510.8850.0000.0000.0000.000
80A81ASN00.0350.00129.979-0.178-0.1780.0000.0000.0000.000
81A82THR0-0.022-0.02228.2930.0120.0120.0000.0000.0000.000
82A83GLY00.0310.01926.383-0.317-0.3170.0000.0000.0000.000
83A84GLN0-0.0070.00526.688-0.146-0.1460.0000.0000.0000.000
84A85ARG10.8450.93128.09910.45510.4550.0000.0000.0000.000
85A86ALA00.0070.00823.534-0.228-0.2280.0000.0000.0000.000
86A87VAL00.0350.00923.236-0.461-0.4610.0000.0000.0000.000
87A88LEU00.0010.01424.497-0.193-0.1930.0000.0000.0000.000
88A89LYS10.8950.95024.19610.95710.9570.0000.0000.0000.000
89A90PHE00.0450.01616.318-0.285-0.2850.0000.0000.0000.000
90A91ALA0-0.015-0.00521.243-0.457-0.4570.0000.0000.0000.000
91A92ALA0-0.039-0.01823.669-0.059-0.0590.0000.0000.0000.000
92A93ALA0-0.044-0.01320.3630.0110.0110.0000.0000.0000.000
93A94THR0-0.041-0.02816.945-0.685-0.6850.0000.0000.0000.000
94A95GLY00.0420.02519.376-0.358-0.3580.0000.0000.0000.000
95A96ALA0-0.031-0.01020.1820.0630.0630.0000.0000.0000.000
96A97THR00.009-0.01822.0320.7390.7390.0000.0000.0000.000
97A98PRO0-0.033-0.01824.942-0.202-0.2020.0000.0000.0000.000
98A99ILE0-0.037-0.01326.5810.5070.5070.0000.0000.0000.000
99A100ALA00.0400.01927.975-0.237-0.2370.0000.0000.0000.000
100A101GLY0-0.028-0.00430.1260.3650.3650.0000.0000.0000.000
101A102ARG10.9310.94832.3197.8987.8980.0000.0000.0000.000
102A103PHE00.0510.02029.0140.1080.1080.0000.0000.0000.000
103A104THR0-0.006-0.00532.6070.1410.1410.0000.0000.0000.000
104A105PRO0-0.031-0.02035.051-0.132-0.1320.0000.0000.0000.000
105A106GLY00.0020.02435.0460.2530.2530.0000.0000.0000.000
106A107THR0-0.086-0.03332.094-0.015-0.0150.0000.0000.0000.000
107A108PHE00.0280.01726.858-0.266-0.2660.0000.0000.0000.000
108A109THR00.0120.00331.315-0.031-0.0310.0000.0000.0000.000
109A110ASN0-0.046-0.03234.722-0.105-0.1050.0000.0000.0000.000
110A111GLN00.0460.01836.372-0.165-0.1650.0000.0000.0000.000
111A112ILE0-0.0230.00039.3050.0720.0720.0000.0000.0000.000
112A113GLN0-0.007-0.00737.6620.2700.2700.0000.0000.0000.000
113A114ALA0-0.030-0.01340.6250.0030.0030.0000.0000.0000.000
114A115ALA0-0.015-0.01235.497-0.043-0.0430.0000.0000.0000.000
115A116PHE00.0080.00731.1430.0500.0500.0000.0000.0000.000
116A117ARG10.8580.90928.66710.08010.0800.0000.0000.0000.000
117A118GLU-1-0.898-0.94827.504-10.515-10.5150.0000.0000.0000.000
118A119PRO0-0.077-0.02323.322-0.392-0.3920.0000.0000.0000.000
119A120ARG10.9580.97915.12518.26718.2670.0000.0000.0000.000
120A121LEU0-0.063-0.03015.442-0.446-0.4460.0000.0000.0000.000
121A122LEU00.0060.01419.8690.4090.4090.0000.0000.0000.000
122A123VAL0-0.002-0.00317.287-0.782-0.7820.0000.0000.0000.000
123A124VAL00.0060.00719.9900.6520.6520.0000.0000.0000.000
124A125THR0-0.061-0.04121.545-0.354-0.3540.0000.0000.0000.000
125A126ASP-1-0.788-0.90923.678-11.266-11.2660.0000.0000.0000.000
126A127PRO00.0270.02324.0810.4270.4270.0000.0000.0000.000
127A128ARG10.7960.88726.71610.22010.2200.0000.0000.0000.000
128A129ALA0-0.033-0.00129.3640.3800.3800.0000.0000.0000.000
129A130ASP-1-0.722-0.84926.332-11.261-11.2610.0000.0000.0000.000
130A131HIS00.0550.01728.435-0.410-0.4100.0000.0000.0000.000
131A132GLN0-0.027-0.01230.4660.1930.1930.0000.0000.0000.000
132A133PRO0-0.0030.00327.0870.0020.0020.0000.0000.0000.000
133A134LEU0-0.0150.01424.815-0.143-0.1430.0000.0000.0000.000
134A135THR0-0.026-0.02827.451-0.009-0.0090.0000.0000.0000.000
135A136GLU-1-0.652-0.81930.606-9.546-9.5460.0000.0000.0000.000
136A137ALA00.0220.00825.6040.0700.0700.0000.0000.0000.000
137A138SER0-0.086-0.05027.766-0.040-0.0400.0000.0000.0000.000
138A139TYR0-0.039-0.02628.6660.1840.1840.0000.0000.0000.000
139A140VAL0-0.021-0.00928.5850.2590.2590.0000.0000.0000.000
140A141ASN0-0.063-0.02426.3150.0380.0380.0000.0000.0000.000
141A142LEU00.0330.02923.940-0.422-0.4220.0000.0000.0000.000
142A143PRO00.0050.01819.1070.1280.1280.0000.0000.0000.000
143A144THR00.002-0.01420.7870.0540.0540.0000.0000.0000.000
144A145ILE00.0140.02514.911-0.302-0.3020.0000.0000.0000.000
145A146ALA00.014-0.00618.1680.7990.7990.0000.0000.0000.000
146A147LEU0-0.036-0.00518.401-0.582-0.5820.0000.0000.0000.000
147A148CYS0-0.055-0.03320.2270.8670.8670.0000.0000.0000.000
148A149ASN00.0610.02021.769-0.708-0.7080.0000.0000.0000.000
149A150THR00.0080.00024.550-0.011-0.0110.0000.0000.0000.000
150A151ASP-1-0.779-0.87726.700-10.147-10.1470.0000.0000.0000.000
151A152SER0-0.054-0.03325.1730.3090.3090.0000.0000.0000.000
152A153PRO0-0.024-0.00626.724-0.126-0.1260.0000.0000.0000.000
153A154LEU00.0580.00622.545-0.247-0.2470.0000.0000.0000.000
154A155ARG10.9170.96124.2559.9439.9430.0000.0000.0000.000
155A156TYR00.0480.00824.7850.2700.2700.0000.0000.0000.000
156A157VAL0-0.0040.01419.935-0.125-0.1250.0000.0000.0000.000
157A158ASP-1-0.888-0.94118.099-15.024-15.0240.0000.0000.0000.000
158A159ILE0-0.060-0.04611.966-0.918-0.9180.0000.0000.0000.000
159A160ALA00.0540.02816.0940.3730.3730.0000.0000.0000.000
160A161ILE0-0.032-0.03014.438-1.047-1.0470.0000.0000.0000.000
161A162PRO0-0.029-0.00715.7150.8480.8480.0000.0000.0000.000
162A163CYS0-0.043-0.02218.358-0.343-0.3430.0000.0000.0000.000
163A164ASN00.1070.06320.9960.5350.5350.0000.0000.0000.000
164A165ASN0-0.070-0.06922.1410.1920.1920.0000.0000.0000.000
165A166LYS10.8040.92224.15411.39111.3910.0000.0000.0000.000
166A167GLY0-0.013-0.00828.0020.2400.2400.0000.0000.0000.000
167A168ALA00.0340.00427.716-0.375-0.3750.0000.0000.0000.000
168A169HIS00.0940.04626.143-0.317-0.3170.0000.0000.0000.000
169A170SER0-0.028-0.02323.581-0.410-0.4100.0000.0000.0000.000
170A171VAL0-0.021-0.00622.268-0.651-0.6510.0000.0000.0000.000
171A172GLY00.0260.00422.088-0.474-0.4740.0000.0000.0000.000
172A173LEU00.0050.01219.045-0.394-0.3940.0000.0000.0000.000
173A174MET0-0.0030.00316.201-0.972-0.9720.0000.0000.0000.000
174A175TRP00.0130.00417.011-1.110-1.1100.0000.0000.0000.000
175A176TRP0-0.010-0.00616.886-0.936-0.9360.0000.0000.0000.000
176A177MET0-0.054-0.02414.143-1.022-1.0220.0000.0000.0000.000
177A178LEU0-0.0050.00013.223-1.579-1.5790.0000.0000.0000.000
178A179ALA00.0100.00713.567-1.104-1.1040.0000.0000.0000.000
179A180ARG10.8320.91311.79522.44122.4410.0000.0000.0000.000
180A181GLU-1-0.851-0.9248.174-33.803-33.8030.0000.0000.0000.000
181A182VAL0-0.010-0.01910.018-2.053-2.0530.0000.0000.0000.000
182A183LEU0-0.009-0.00111.935-0.336-0.3360.0000.0000.0000.000
183A184ARG10.7260.8668.92231.13331.1330.0000.0000.0000.000
184A185MET0-0.008-0.0066.105-0.503-0.5030.0000.0000.0000.000
185A186ARG10.8700.9319.02321.70721.7070.0000.0000.0000.000
186A187GLY00.0240.01012.4071.2941.2940.0000.0000.0000.000
187A188THR0-0.028-0.00915.6000.5380.5380.0000.0000.0000.000
188A189ILE0-0.0360.01814.3350.7740.7740.0000.0000.0000.000
189A190SER00.002-0.00312.6110.1710.1710.0000.0000.0000.000
190A191ARG10.9500.96510.96719.75519.7550.0000.0000.0000.000
191A192GLU-1-0.836-0.9216.135-42.326-42.3260.0000.0000.0000.000
192A193HIS0-0.031-0.0159.4031.8241.8240.0000.0000.0000.000
193A194PRO0-0.015-0.01212.541-0.784-0.7840.0000.0000.0000.000
194A195TRP00.0400.01314.3380.2380.2380.0000.0000.0000.000
195A196GLU-1-0.879-0.94417.438-16.300-16.3000.0000.0000.0000.000
196A197VAL0-0.049-0.00220.7770.8630.8630.0000.0000.0000.000
197A198MET00.0310.02621.216-0.597-0.5970.0000.0000.0000.000
198A199PRO0-0.027-0.01921.327-0.003-0.0030.0000.0000.0000.000
199A200ASP-1-0.816-0.93323.083-11.622-11.6220.0000.0000.0000.000
200A201LEU0-0.034-0.00324.5510.4810.4810.0000.0000.0000.000
201A202TYR0-0.015-0.02220.5850.2480.2480.0000.0000.0000.000
202A203PHE00.0180.00423.6880.3320.3320.0000.0000.0000.000
203A204TYR0-0.022-0.01126.845-0.163-0.1630.0000.0000.0000.000
204A205ARG10.7540.84930.1928.2858.2850.0000.0000.0000.000
205A206ASP-1-0.849-0.91533.050-9.177-9.1770.0000.0000.0000.000
206A207PRO0-0.052-0.04034.8590.0600.0600.0000.0000.0000.000
207A208GLU-1-0.819-0.88237.893-8.363-8.3630.0000.0000.0000.000
208A209GLU-2-1.921-1.93840.033-14.669-14.6690.0000.0000.0000.000