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: V62J1

Calculation Name: 2QYF-D-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2QYF

Chain ID: D

ChEMBL ID:

UniProt ID: Q15013

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2306318.690305
FMO2-HF: Nuclear repulsion 2225924.83156
FMO2-HF: Total energy -80393.858745
FMO2-MP2: Total energy -80622.791479


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(D:54:CYS)


Summations of interaction energy for fragment #1(D:54:CYS)
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.
-26.983-19.09811.533-9.153-10.268-0.095
Interaction energy analysis for fragmet #1(D:54:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.806 / q_NPA : 0.895
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].
3D56VAL00.0370.0243.5563.6185.7620.351-0.841-1.654-0.002
4D57PRO00.0110.0225.8131.5941.600-0.001-0.0050.0000.000
122D197ALA0-0.033-0.0053.1120.2840.7040.141-0.140-0.421-0.002
123D198ASP-1-0.921-0.9583.124-40.093-38.9930.086-0.645-0.541-0.006
124D199ALA0-0.029-0.0093.826-4.801-4.5670.001-0.025-0.2110.000
125D200PHE0-0.063-0.0524.5894.7684.812-0.001-0.008-0.0350.000
164D239HIS00.0130.0343.1980.3081.1150.038-0.314-0.531-0.002
165D240LYS10.8230.9113.81529.05430.1780.002-0.582-0.545-0.003
166D241LEU0-0.023-0.0161.852-46.408-44.87010.895-6.568-5.866-0.079
167D242THR00.0300.0173.43014.56515.0330.021-0.025-0.464-0.001
5D58VAL0-0.006-0.0149.4970.8530.8530.0000.0000.0000.000
6D59VAL0-0.0020.01312.2830.5770.5770.0000.0000.0000.000
7D60PHE00.006-0.01315.6760.1920.1920.0000.0000.0000.000
8D61PRO0-0.048-0.02618.6020.1960.1960.0000.0000.0000.000
9D62GLY00.0250.00621.8470.7100.7100.0000.0000.0000.000
10D63PRO0-0.034-0.01422.363-0.653-0.6530.0000.0000.0000.000
11D64VAL00.010-0.00120.494-0.051-0.0510.0000.0000.0000.000
12D65SER0-0.021-0.02123.7790.1370.1370.0000.0000.0000.000
13D66GLN00.0290.00223.421-0.862-0.8620.0000.0000.0000.000
14D67GLU-1-0.827-0.90223.406-12.465-12.4650.0000.0000.0000.000
15D68GLY00.022-0.00622.286-0.366-0.3660.0000.0000.0000.000
16D69CYS0-0.071-0.04019.045-0.844-0.8440.0000.0000.0000.000
17D70CYS00.0440.05118.781-0.994-0.9940.0000.0000.0000.000
18D71GLN0-0.009-0.02419.683-0.925-0.9250.0000.0000.0000.000
19D72PHE0-0.047-0.04115.310-0.594-0.5940.0000.0000.0000.000
20D73THR0-0.004-0.00414.948-1.670-1.6700.0000.0000.0000.000
21D74CYS0-0.021-0.01015.972-0.604-0.6040.0000.0000.0000.000
22D75GLU-1-0.823-0.90816.898-15.144-15.1440.0000.0000.0000.000
23D76LEU0-0.012-0.0049.265-0.735-0.7350.0000.0000.0000.000
24D77LEU00.0050.00612.814-1.195-1.1950.0000.0000.0000.000
25D78LYS10.7900.87614.93413.79513.7950.0000.0000.0000.000
26D79HIS0-0.0080.00310.5071.0071.0070.0000.0000.0000.000
27D80ILE0-0.004-0.0059.367-0.460-0.4600.0000.0000.0000.000
28D81MET0-0.046-0.01012.063-0.254-0.2540.0000.0000.0000.000
29D82TYR00.0120.02115.5920.4070.4070.0000.0000.0000.000
30D83GLN00.0120.00710.9651.4711.4710.0000.0000.0000.000
31D84ARG10.8070.8829.33527.34927.3490.0000.0000.0000.000
32D85GLN00.003-0.00613.2710.1180.1180.0000.0000.0000.000
33D86GLN0-0.020-0.01215.9721.6851.6850.0000.0000.0000.000
34D87LEU00.0480.03618.5360.7840.7840.0000.0000.0000.000
35D88PRO0-0.0050.00819.938-0.562-0.5620.0000.0000.0000.000
36D89LEU0-0.002-0.00621.6230.0600.0600.0000.0000.0000.000
37D90PRO00.000-0.00418.614-0.353-0.3530.0000.0000.0000.000
38D91TYR00.0670.02119.8130.6210.6210.0000.0000.0000.000
39D92GLU-1-0.796-0.91521.776-12.044-12.0440.0000.0000.0000.000
40D93GLN0-0.025-0.01522.3730.4740.4740.0000.0000.0000.000
41D94LEU0-0.043-0.01923.2630.3660.3660.0000.0000.0000.000
42D95LYS10.7590.88626.39811.49811.4980.0000.0000.0000.000
43D96HIS-1-0.944-0.94128.999-9.527-9.5270.0000.0000.0000.000
44D119VAL00.019-0.01037.0370.0110.0110.0000.0000.0000.000
45D120SER00.0420.01333.536-0.104-0.1040.0000.0000.0000.000
46D121SER00.0710.04332.726-0.257-0.2570.0000.0000.0000.000
47D122ARG11.0001.00032.9657.7387.7380.0000.0000.0000.000
48D123LYS10.9530.97531.4689.6259.6250.0000.0000.0000.000
49D124CYS00.0250.01528.032-0.341-0.3410.0000.0000.0000.000
50D125GLN00.0190.01328.727-0.209-0.2090.0000.0000.0000.000
51D126GLN0-0.040-0.02730.073-0.345-0.3450.0000.0000.0000.000
52D127ALA00.0050.00726.558-0.167-0.1670.0000.0000.0000.000
53D128LEU00.0230.01323.631-0.540-0.5400.0000.0000.0000.000
54D129ALA00.0440.02625.817-0.298-0.2980.0000.0000.0000.000
55D130GLU-1-0.891-0.95024.974-12.348-12.3480.0000.0000.0000.000
56D131LEU0-0.027-0.01219.414-0.336-0.3360.0000.0000.0000.000
57D132GLU-1-0.855-0.93123.201-11.115-11.1150.0000.0000.0000.000
58D133SER0-0.031-0.00825.8310.0510.0510.0000.0000.0000.000
59D134VAL0-0.032-0.03020.242-0.033-0.0330.0000.0000.0000.000
60D135LEU0-0.037-0.01519.723-0.297-0.2970.0000.0000.0000.000
61D136SER00.0630.04522.9400.0870.0870.0000.0000.0000.000
62D137HIS10.8450.90125.74111.25611.2560.0000.0000.0000.000
63D138LEU0-0.039-0.01519.160-0.246-0.2460.0000.0000.0000.000
64D139GLU-1-0.892-0.96223.141-11.883-11.8830.0000.0000.0000.000
65D140ASP-1-0.835-0.89725.669-10.473-10.4730.0000.0000.0000.000
66D141PHE0-0.044-0.02721.7590.0930.0930.0000.0000.0000.000
67D142PHE0-0.011-0.03318.611-0.090-0.0900.0000.0000.0000.000
68D143ALA00.0040.01424.7730.1560.1560.0000.0000.0000.000
69D144ARG10.8520.95628.16210.53210.5320.0000.0000.0000.000
70D145THR0-0.032-0.03024.8980.3560.3560.0000.0000.0000.000
71D146LEU0-0.0030.00923.959-0.336-0.3360.0000.0000.0000.000
72D147VAL00.0270.02018.7380.0430.0430.0000.0000.0000.000
73D148PRO0-0.0260.00718.833-0.636-0.6360.0000.0000.0000.000
74D149ARG10.8590.89011.91022.22922.2290.0000.0000.0000.000
75D150VAL00.0140.00914.1451.3401.3400.0000.0000.0000.000
76D151LEU0-0.042-0.01510.780-2.137-2.1370.0000.0000.0000.000
77D152ILE00.0210.01111.5772.1362.1360.0000.0000.0000.000
78D153LEU0-0.011-0.01311.284-2.578-2.5780.0000.0000.0000.000
79D154LEU00.0280.01911.5041.7331.7330.0000.0000.0000.000
80D155GLY00.0650.01413.997-0.812-0.8120.0000.0000.0000.000
81D156GLY0-0.036-0.01616.323-0.597-0.5970.0000.0000.0000.000
82D157ASN00.005-0.01217.5900.7250.7250.0000.0000.0000.000
83D158ALA00.0710.02216.816-0.904-0.9040.0000.0000.0000.000
84D159LEU00.0080.02116.320-0.836-0.8360.0000.0000.0000.000
85D160SER0-0.063-0.03715.479-0.419-0.4190.0000.0000.0000.000
86D161PRO00.0250.04511.8301.0791.0790.0000.0000.0000.000
87D162LYS10.8780.94213.57221.70721.7070.0000.0000.0000.000
88D163GLU-1-0.834-0.8858.797-31.535-31.5350.0000.0000.0000.000
89D164PHE0-0.023-0.0098.1702.0822.0820.0000.0000.0000.000
90D165TYR00.037-0.0066.311-7.737-7.7370.0000.0000.0000.000
91D166GLU-1-0.819-0.8897.393-23.699-23.6990.0000.0000.0000.000
92D167LEU0-0.0030.0068.536-2.795-2.7950.0000.0000.0000.000
93D168ASP-1-0.832-0.88911.154-20.247-20.2470.0000.0000.0000.000
94D169LEU00.014-0.01013.056-0.206-0.2060.0000.0000.0000.000
95D170SER0-0.037-0.04416.0551.5261.5260.0000.0000.0000.000
96D171LEU0-0.022-0.00815.7811.0421.0420.0000.0000.0000.000
97D172LEU0-0.012-0.01217.0620.3880.3880.0000.0000.0000.000
98D173ALA00.018-0.01120.4090.3550.3550.0000.0000.0000.000
99D174PRO00.0300.02924.2440.0160.0160.0000.0000.0000.000
100D175TYR0-0.044-0.03626.2960.4740.4740.0000.0000.0000.000
101D176SER0-0.012-0.02528.5330.4610.4610.0000.0000.0000.000
102D177VAL00.0130.01629.031-0.312-0.3120.0000.0000.0000.000
103D178ASP-1-0.796-0.86225.716-11.010-11.0100.0000.0000.0000.000
104D179GLN00.0460.04126.043-0.616-0.6160.0000.0000.0000.000
105D180SER00.0920.04325.423-0.585-0.5850.0000.0000.0000.000
106D181LEU00.0110.00125.7040.2770.2770.0000.0000.0000.000
107D182SER0-0.017-0.01524.688-0.506-0.5060.0000.0000.0000.000
108D183THR00.0480.00520.641-0.638-0.6380.0000.0000.0000.000
109D184ALA00.0180.01620.441-0.683-0.6830.0000.0000.0000.000
110D185ALA0-0.051-0.02720.319-0.434-0.4340.0000.0000.0000.000
111D186CYS0-0.054-0.01318.161-0.622-0.6220.0000.0000.0000.000
112D187LEU00.0600.02416.243-1.227-1.2270.0000.0000.0000.000
113D188ARG10.9510.98115.25412.27512.2750.0000.0000.0000.000
114D189ARG10.9020.96114.08715.66915.6690.0000.0000.0000.000
115D190LEU00.0140.01611.686-1.162-1.1620.0000.0000.0000.000
116D191PHE00.0440.00710.454-2.022-2.0220.0000.0000.0000.000
117D192ARG10.9490.97610.39216.43616.4360.0000.0000.0000.000
118D193ALA0-0.015-0.0059.089-0.560-0.5600.0000.0000.0000.000
119D194ILE0-0.001-0.0105.884-2.341-2.3410.0000.0000.0000.000
120D195PHE0-0.022-0.0045.717-3.042-3.0420.0000.0000.0000.000
121D196MET0-0.043-0.0337.7930.1310.1310.0000.0000.0000.000
126D201SER00.0420.0526.5092.7252.7250.0000.0000.0000.000
127D202GLU-1-0.873-0.9287.919-33.906-33.9060.0000.0000.0000.000
128D203LEU00.0410.01510.7501.4431.4430.0000.0000.0000.000
129D204GLN0-0.087-0.03414.0601.5811.5810.0000.0000.0000.000
130D205ALA00.0530.03114.583-1.195-1.1950.0000.0000.0000.000
131D206PRO0-0.0070.01614.3030.5890.5890.0000.0000.0000.000
132D207PRO00.0180.00216.5070.9970.9970.0000.0000.0000.000
133D208LEU0-0.0060.01618.480-0.724-0.7240.0000.0000.0000.000
134D209MET0-0.074-0.04014.1630.1880.1880.0000.0000.0000.000
135D210GLY00.0320.02019.5130.6070.6070.0000.0000.0000.000
136D211THR00.003-0.02115.380-1.161-1.1610.0000.0000.0000.000
137D212VAL0-0.034-0.00716.9221.0691.0690.0000.0000.0000.000
138D213VAL00.0400.02116.207-1.302-1.3020.0000.0000.0000.000
139D214MET0-0.051-0.02616.3991.1471.1470.0000.0000.0000.000
140D215ALA00.0390.02816.644-1.206-1.2060.0000.0000.0000.000
141D216GLN00.007-0.00217.8490.2490.2490.0000.0000.0000.000
142D217GLY00.0750.02320.279-0.021-0.0210.0000.0000.0000.000
143D218HIS00.0290.01723.9340.0630.0630.0000.0000.0000.000
144D219ARG10.8980.93127.17810.65810.6580.0000.0000.0000.000
145D220ASN0-0.023-0.01129.1480.1360.1360.0000.0000.0000.000
146D221CYS0-0.072-0.01828.2760.2330.2330.0000.0000.0000.000
147D222GLY00.0230.00931.0590.0860.0860.0000.0000.0000.000
148D223GLU-1-0.843-0.92326.815-11.143-11.1430.0000.0000.0000.000
149D224ASP-1-0.943-0.97130.224-9.627-9.6270.0000.0000.0000.000
150D225TRP00.0050.01324.538-0.068-0.0680.0000.0000.0000.000
151D226PHE0-0.039-0.04821.005-0.343-0.3430.0000.0000.0000.000
152D227ARG10.9710.98225.48711.49711.4970.0000.0000.0000.000
153D228PRO00.0440.02324.916-0.649-0.6490.0000.0000.0000.000
154D229LYS10.8300.92021.82913.54513.5450.0000.0000.0000.000
155D230LEU00.0490.01523.172-0.562-0.5620.0000.0000.0000.000
156D231ASN00.0100.00024.090-0.274-0.2740.0000.0000.0000.000
157D232TYR0-0.018-0.02515.512-0.309-0.3090.0000.0000.0000.000
158D233ARG10.8880.94417.48514.57214.5720.0000.0000.0000.000
159D234VAL00.0280.02511.2440.2610.2610.0000.0000.0000.000
160D235PRO00.0000.01111.838-0.014-0.0140.0000.0000.0000.000
161D236SER00.0160.00610.876-2.363-2.3630.0000.0000.0000.000
162D237ARG10.9290.95410.29119.22519.2250.0000.0000.0000.000
163D238GLY00.0530.0248.9690.8600.8600.0000.0000.0000.000
168D243VAL0-0.008-0.0105.657-2.646-2.6460.0000.0000.0000.000
169D244THR00.0300.0067.9342.4672.4670.0000.0000.0000.000
170D245LEU0-0.028-0.01410.8870.6490.6490.0000.0000.0000.000
171D246SER00.011-0.00314.0250.8680.8680.0000.0000.0000.000
172D247CYS0-0.0510.00216.9240.0610.0610.0000.0000.0000.000
173D248GLY00.0250.01818.9680.7420.7420.0000.0000.0000.000
174D249ARG10.8950.94220.49612.93912.9390.0000.0000.0000.000
175D250PRO00.0110.02021.919-0.487-0.4870.0000.0000.0000.000
176D251SER0-0.012-0.02623.0180.4690.4690.0000.0000.0000.000
177D252ILE0-0.0080.01521.8090.5400.5400.0000.0000.0000.000
178D253ARG10.9640.98725.05610.15210.1520.0000.0000.0000.000
179D254THR00.0350.00525.028-0.272-0.2720.0000.0000.0000.000
180D255THR0-0.015-0.00924.680-0.434-0.4340.0000.0000.0000.000
181D256ALA0-0.030-0.01224.4330.1560.1560.0000.0000.0000.000
182D257TRP0-0.004-0.01820.9400.1810.1810.0000.0000.0000.000
183D258GLU-1-0.881-0.92823.763-11.296-11.2960.0000.0000.0000.000
184D259ASP-1-0.862-0.92826.087-10.549-10.5490.0000.0000.0000.000
185D260TYR0-0.050-0.01822.7620.1170.1170.0000.0000.0000.000
186D261ILE0-0.019-0.00223.141-0.342-0.3420.0000.0000.0000.000
187D262TRP00.009-0.00314.505-0.147-0.1470.0000.0000.0000.000
188D263PHE00.0110.00521.1320.7410.7410.0000.0000.0000.000
189D264GLN0-0.014-0.02620.411-0.776-0.7760.0000.0000.0000.000
190D265ALA00.0550.04121.1980.6960.6960.0000.0000.0000.000
191D266PRO0-0.082-0.03023.099-0.138-0.1380.0000.0000.0000.000
192D267VAL0-0.018-0.00924.8730.3960.3960.0000.0000.0000.000
193D268THR0-0.052-0.02620.723-0.674-0.6740.0000.0000.0000.000
194D269PHE00.0580.03819.3330.2930.2930.0000.0000.0000.000
195D270LYS10.9430.96321.08411.66011.6600.0000.0000.0000.000
196D271GLY00.0310.02320.4370.2490.2490.0000.0000.0000.000
197D272PHE0-0.090-0.06921.3190.5750.5750.0000.0000.0000.000
198D273ARG0-0.068-0.05018.5493.3633.3630.0000.0000.0000.000