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: M2V9Z

Calculation Name: 3DKT-D-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DKT

Chain ID: D

ChEMBL ID:

UniProt ID: Q9WZP2

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 264
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3394894.39444
FMO2-HF: Nuclear repulsion 3290055.147805
FMO2-HF: Total energy -104839.246635
FMO2-MP2: Total energy -105150.439603


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:4:MET)


Summations of interaction energy for fragment #1(D:4:MET)
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.
-121.339-114.1315.523-4.363-8.365-0.038
Interaction energy analysis for fragmet #1(D:4:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.908
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].
3D6PHE00.0190.0162.564-0.6742.9724.343-3.072-4.917-0.025
4D7LEU00.0030.0082.4407.2388.1360.563-0.295-1.165-0.003
6D9ARG10.7980.8434.55143.22443.351-0.001-0.011-0.1150.000
44D47GLY0-0.026-0.0085.611-0.101-0.065-0.001-0.006-0.0290.000
45D48TRP0-0.050-0.0444.319-0.2710.1340.015-0.081-0.3380.000
46D49GLU-1-0.933-0.9556.157-23.553-23.598-0.001-0.0040.0510.000
228D231GLN0-0.068-0.0452.298-3.176-1.1130.606-0.893-1.776-0.010
231D234SER0-0.064-0.0335.133-4.770-4.692-0.001-0.001-0.0760.000
5D8LYS10.9911.0115.46624.50724.5070.0000.0000.0000.000
7D10SER0-0.0090.0017.7082.2762.2760.0000.0000.0000.000
8D11PHE0-0.030-0.0189.4462.7242.7240.0000.0000.0000.000
9D12ALA00.0170.02211.4211.9801.9800.0000.0000.0000.000
10D13PRO0-0.087-0.04213.1740.0070.0070.0000.0000.0000.000
11D14LEU00.0140.00812.8691.0451.0450.0000.0000.0000.000
12D15THR0-0.023-0.03314.422-1.224-1.2240.0000.0000.0000.000
13D16GLU-1-0.898-0.96211.228-27.174-27.1740.0000.0000.0000.000
14D17LYS10.8050.91714.07317.36717.3670.0000.0000.0000.000
15D18GLN00.0730.02716.046-0.992-0.9920.0000.0000.0000.000
16D19TRP0-0.003-0.0119.970-1.206-1.2060.0000.0000.0000.000
17D20GLN00.0320.01112.0490.4270.4270.0000.0000.0000.000
18D21GLU-1-0.901-0.94212.952-15.927-15.9270.0000.0000.0000.000
19D22ILE0-0.013-0.00512.6980.5120.5120.0000.0000.0000.000
20D23ASP-1-0.812-0.8819.431-32.536-32.5360.0000.0000.0000.000
21D24ASN0-0.041-0.02412.406-0.512-0.5120.0000.0000.0000.000
22D25ARG10.8440.91115.57414.50714.5070.0000.0000.0000.000
23D26ALA00.0520.02313.4780.7640.7640.0000.0000.0000.000
24D27ARG10.9110.95810.91724.81524.8150.0000.0000.0000.000
25D28GLU-1-0.944-0.97315.120-13.783-13.7830.0000.0000.0000.000
26D29ILE00.0230.01818.4470.8770.8770.0000.0000.0000.000
27D30PHE00.0890.02613.3350.6190.6190.0000.0000.0000.000
28D31LYS10.9010.96917.25415.00815.0080.0000.0000.0000.000
29D32THR0-0.091-0.04818.5620.8480.8480.0000.0000.0000.000
30D33GLN00.0170.00020.3190.7140.7140.0000.0000.0000.000
31D34LEU00.0430.06015.1590.2730.2730.0000.0000.0000.000
32D35TYR0-0.017-0.03319.6310.1280.1280.0000.0000.0000.000
33D36GLY00.0450.02321.4880.3390.3390.0000.0000.0000.000
34D37ARG10.7790.85111.91219.80419.8040.0000.0000.0000.000
35D38LYS10.7680.90219.62112.30612.3060.0000.0000.0000.000
36D39PHE0-0.024-0.01822.7180.4150.4150.0000.0000.0000.000
37D40VAL0-0.0370.00820.0800.3190.3190.0000.0000.0000.000
38D41ASP-1-0.838-0.91420.183-12.966-12.9660.0000.0000.0000.000
39D42VAL00.022-0.01013.959-0.222-0.2220.0000.0000.0000.000
40D43GLU-1-0.811-0.87715.586-14.785-14.7850.0000.0000.0000.000
41D44GLY00.003-0.01212.062-0.698-0.6980.0000.0000.0000.000
42D45PRO0-0.049-0.0336.8680.4200.4200.0000.0000.0000.000
43D46TYR0-0.044-0.0358.555-0.356-0.3560.0000.0000.0000.000
47D50TYR0-0.027-0.0108.8442.4102.4100.0000.0000.0000.000
48D51ALA00.0560.02311.162-0.033-0.0330.0000.0000.0000.000
49D52ALA0-0.003-0.01014.2350.6290.6290.0000.0000.0000.000
50D53HIS10.8940.98416.64714.25314.2530.0000.0000.0000.000
51D54PRO0-0.038-0.03417.8970.6540.6540.0000.0000.0000.000
52D55LEU00.0390.00921.112-0.088-0.0880.0000.0000.0000.000
53D56GLY0-0.0370.00024.2970.2790.2790.0000.0000.0000.000
54D57GLU-1-0.849-0.91426.625-9.074-9.0740.0000.0000.0000.000
55D58VAL0-0.083-0.05628.477-0.300-0.3000.0000.0000.0000.000
56D59GLU-1-0.890-0.94230.904-8.791-8.7910.0000.0000.0000.000
57D60VAL0-0.028-0.02632.568-0.034-0.0340.0000.0000.0000.000
58D61LEU0-0.024-0.02332.8270.0170.0170.0000.0000.0000.000
59D62SER00.0090.01736.5760.0580.0580.0000.0000.0000.000
60D63ASP-1-0.783-0.85739.685-6.674-6.6740.0000.0000.0000.000
61D64GLU-1-1.006-1.02043.326-6.647-6.6470.0000.0000.0000.000
62D65ASN0-0.086-0.05045.8700.1900.1900.0000.0000.0000.000
63D66GLU-1-0.864-0.92039.922-7.326-7.3260.0000.0000.0000.000
64D67VAL00.002-0.00843.136-0.014-0.0140.0000.0000.0000.000
65D68VAL0-0.050-0.02738.282-0.040-0.0400.0000.0000.0000.000
66D69LYS10.8610.91938.5266.8496.8490.0000.0000.0000.000
67D70TRP0-0.064-0.02732.329-0.342-0.3420.0000.0000.0000.000
68D71GLY00.0610.02033.1640.1740.1740.0000.0000.0000.000
69D72LEU0-0.0070.00928.002-0.212-0.2120.0000.0000.0000.000
70D73ARG10.9310.96124.92510.40810.4080.0000.0000.0000.000
71D74LYS10.8700.94825.5858.9938.9930.0000.0000.0000.000
72D75SER0-0.046-0.03220.648-0.317-0.3170.0000.0000.0000.000
73D76LEU00.0230.01820.5050.3270.3270.0000.0000.0000.000
74D77PRO0-0.001-0.00518.505-0.673-0.6730.0000.0000.0000.000
75D78LEU0-0.041-0.02212.3590.1990.1990.0000.0000.0000.000
76D79ILE0-0.029-0.01116.0970.2650.2650.0000.0000.0000.000
77D80GLU-1-0.902-0.94811.196-23.779-23.7790.0000.0000.0000.000
78D81LEU0-0.061-0.02112.9741.3381.3380.0000.0000.0000.000
79D82ARG10.8880.92610.83721.24521.2450.0000.0000.0000.000
80D83ALA00.0100.01913.9001.1581.1580.0000.0000.0000.000
81D84THR0-0.010-0.02014.941-0.835-0.8350.0000.0000.0000.000
82D85PHE0-0.013-0.00313.4550.8130.8130.0000.0000.0000.000
83D86THR00.0410.02417.343-0.693-0.6930.0000.0000.0000.000
84D87LEU0-0.031-0.00317.0510.4890.4890.0000.0000.0000.000
85D88ASP-1-0.831-0.91420.502-12.475-12.4750.0000.0000.0000.000
86D89LEU00.0310.00319.431-0.389-0.3890.0000.0000.0000.000
87D90TRP00.0400.02622.124-0.043-0.0430.0000.0000.0000.000
88D91GLU-1-0.738-0.84924.257-11.564-11.5640.0000.0000.0000.000
89D92LEU00.0250.00217.673-0.107-0.1070.0000.0000.0000.000
90D93ASP-1-0.896-0.95221.588-13.877-13.8770.0000.0000.0000.000
91D94ASN0-0.080-0.04923.2350.5130.5130.0000.0000.0000.000
92D95LEU00.0120.02619.1400.3150.3150.0000.0000.0000.000
93D96GLU-1-0.823-0.90419.992-15.747-15.7470.0000.0000.0000.000
94D97ARG10.7550.88523.47512.14012.1400.0000.0000.0000.000
95D98GLY0-0.0010.00625.8330.5120.5120.0000.0000.0000.000
96D99LYS10.7680.87526.39311.66811.6680.0000.0000.0000.000
97D100PRO0-0.017-0.01625.482-0.428-0.4280.0000.0000.0000.000
98D101ASN0-0.011-0.00124.920-0.329-0.3290.0000.0000.0000.000
99D102VAL00.0190.00521.8640.3760.3760.0000.0000.0000.000
100D103ASP-1-0.882-0.92223.731-12.322-12.3220.0000.0000.0000.000
101D104LEU00.018-0.00318.313-0.413-0.4130.0000.0000.0000.000
102D105SER0-0.016-0.03320.982-0.504-0.5040.0000.0000.0000.000
103D106SER00.006-0.01021.379-0.191-0.1910.0000.0000.0000.000
104D107LEU0-0.0110.01114.931-0.429-0.4290.0000.0000.0000.000
105D108GLU-1-0.823-0.90418.473-13.453-13.4530.0000.0000.0000.000
106D109GLU-1-0.964-0.98220.588-11.898-11.8980.0000.0000.0000.000
107D110THR00.003-0.00416.7450.2250.2250.0000.0000.0000.000
108D111VAL0-0.021-0.02015.444-0.324-0.3240.0000.0000.0000.000
109D112ARG10.8980.95417.67012.76312.7630.0000.0000.0000.000
110D113LYS10.8270.90420.23312.36912.3690.0000.0000.0000.000
111D114VAL00.0040.00014.3240.1640.1640.0000.0000.0000.000
112D115ALA0-0.005-0.01217.814-0.003-0.0030.0000.0000.0000.000
113D116GLU-1-0.871-0.92319.064-11.743-11.7430.0000.0000.0000.000
114D117PHE00.0020.00918.2780.4000.4000.0000.0000.0000.000
115D118GLU-1-0.763-0.88015.506-16.615-16.6150.0000.0000.0000.000
116D119ASP-1-0.699-0.84018.858-12.686-12.6860.0000.0000.0000.000
117D120GLU-1-0.851-0.89122.204-10.338-10.3380.0000.0000.0000.000
118D121VAL0-0.033-0.00620.1470.4570.4570.0000.0000.0000.000
119D122ILE00.0100.02018.9680.2670.2670.0000.0000.0000.000
120D123PHE00.013-0.01722.9870.4720.4720.0000.0000.0000.000
121D124ARG10.7760.85026.18910.75110.7510.0000.0000.0000.000
122D125GLY00.0020.02024.3660.2060.2060.0000.0000.0000.000
123D126CYS0-0.031-0.02622.7990.2050.2050.0000.0000.0000.000
124D127GLU-1-0.879-0.93725.406-9.525-9.5250.0000.0000.0000.000
125D128LYS10.8960.93325.43910.55110.5510.0000.0000.0000.000
126D129SER00.0080.00621.246-0.136-0.1360.0000.0000.0000.000
127D130GLY00.0040.00522.777-0.294-0.2940.0000.0000.0000.000
128D131VAL0-0.038-0.00521.9280.0730.0730.0000.0000.0000.000
129D132LYS10.8650.95924.8629.0819.0810.0000.0000.0000.000
130D133GLY00.0490.02426.184-0.154-0.1540.0000.0000.0000.000
131D134LEU0-0.001-0.01525.7690.4220.4220.0000.0000.0000.000
132D135LEU0-0.030-0.03328.8960.3190.3190.0000.0000.0000.000
133D136SER0-0.0140.00930.5840.2890.2890.0000.0000.0000.000
134D137PHE0-0.059-0.03729.0610.1760.1760.0000.0000.0000.000
135D138GLU-1-0.779-0.88434.153-7.770-7.7700.0000.0000.0000.000
136D139GLU-1-0.905-0.97535.897-8.220-8.2200.0000.0000.0000.000
137D140ARG10.7750.91135.0828.2178.2170.0000.0000.0000.000
138D141LYS10.8500.93337.5967.7577.7570.0000.0000.0000.000
139D142ILE0-0.049-0.02339.5440.2330.2330.0000.0000.0000.000
140D143GLU-1-0.885-0.94042.131-6.751-6.7510.0000.0000.0000.000
141D144CYS0-0.043-0.02742.395-0.041-0.0410.0000.0000.0000.000
142D145GLY00.0030.01144.4280.0260.0260.0000.0000.0000.000
143D146SER0-0.009-0.03144.692-0.218-0.2180.0000.0000.0000.000
144D147THR0-0.067-0.03146.2830.0220.0220.0000.0000.0000.000
145D148PRO00.0360.00945.334-0.069-0.0690.0000.0000.0000.000
146D149LYS10.9360.96045.9715.7705.7700.0000.0000.0000.000
147D150ASP-1-0.733-0.85946.734-6.308-6.3080.0000.0000.0000.000
148D151LEU00.0200.02939.600-0.075-0.0750.0000.0000.0000.000
149D152LEU0-0.020-0.01842.843-0.109-0.1090.0000.0000.0000.000
150D153GLU-1-0.907-0.95744.814-6.328-6.3280.0000.0000.0000.000
151D154ALA00.0190.00942.014-0.020-0.0200.0000.0000.0000.000
152D155ILE00.0040.00639.262-0.094-0.0940.0000.0000.0000.000
153D156VAL0-0.003-0.00641.479-0.064-0.0640.0000.0000.0000.000
154D157ARG10.8980.96344.1796.5546.5540.0000.0000.0000.000
155D158ALA00.0210.01138.687-0.015-0.0150.0000.0000.0000.000
156D159LEU00.003-0.00138.125-0.070-0.0700.0000.0000.0000.000
157D160SER0-0.068-0.03840.6710.0510.0510.0000.0000.0000.000
158D161ILE0-0.056-0.02539.8340.0880.0880.0000.0000.0000.000
159D162PHE00.0140.00635.0200.0000.0000.0000.0000.0000.000
160D163SER0-0.0170.00438.866-0.031-0.0310.0000.0000.0000.000
161D164LYS10.8910.94341.4776.7296.7290.0000.0000.0000.000
162D165ASP-1-0.864-0.91538.206-7.493-7.4930.0000.0000.0000.000
163D166GLY0-0.052-0.02138.409-0.142-0.1420.0000.0000.0000.000
164D167ILE0-0.052-0.02233.582-0.201-0.2010.0000.0000.0000.000
165D168GLU-1-0.870-0.94335.151-7.620-7.6200.0000.0000.0000.000
166D169GLY0-0.002-0.00832.052-0.252-0.2520.0000.0000.0000.000
167D170PRO0-0.0070.00929.8620.2620.2620.0000.0000.0000.000
168D171TYR0-0.009-0.01131.580-0.179-0.1790.0000.0000.0000.000
169D172THR0-0.058-0.05628.8020.1230.1230.0000.0000.0000.000
170D173LEU0-0.0270.00132.0530.0850.0850.0000.0000.0000.000
171D174VAL00.0140.00928.391-0.104-0.1040.0000.0000.0000.000
172D175ILE0-0.036-0.02531.3190.2740.2740.0000.0000.0000.000
173D176ASN00.0750.03632.668-0.027-0.0270.0000.0000.0000.000
174D177THR00.014-0.01431.8510.1760.1760.0000.0000.0000.000
175D178ASP-1-0.885-0.93634.528-8.243-8.2430.0000.0000.0000.000
176D179ARG10.7920.86537.6568.0298.0290.0000.0000.0000.000
177D180TRP00.0070.00636.6140.1740.1740.0000.0000.0000.000
178D181ILE0-0.023-0.01537.0070.1900.1900.0000.0000.0000.000
179D182ASN0-0.036-0.02440.2580.2600.2600.0000.0000.0000.000
180D183PHE00.0300.01440.7550.1400.1400.0000.0000.0000.000
181D184LEU0-0.026-0.01141.3850.1410.1410.0000.0000.0000.000
182D185LYS10.8680.95243.7377.0737.0730.0000.0000.0000.000
183D186GLU-1-0.892-0.95746.932-6.377-6.3770.0000.0000.0000.000
184D187GLU-1-0.946-0.97645.585-6.308-6.3080.0000.0000.0000.000
185D188ALA0-0.034-0.00746.921-0.099-0.0990.0000.0000.0000.000
186D189GLY0-0.037-0.02147.9090.1200.1200.0000.0000.0000.000
187D190HIS0-0.074-0.03049.3960.1890.1890.0000.0000.0000.000
188D191TYR0-0.087-0.09145.1910.0920.0920.0000.0000.0000.000
189D192PRO0-0.0120.00143.105-0.021-0.0210.0000.0000.0000.000
190D193LEU00.0570.03341.547-0.004-0.0040.0000.0000.0000.000
191D194GLU-1-0.861-0.94238.001-7.661-7.6610.0000.0000.0000.000
192D195LYS10.9600.98939.4347.1327.1320.0000.0000.0000.000
193D196ARG10.9630.98841.1936.5156.5150.0000.0000.0000.000
194D197VAL00.0030.00537.7900.0720.0720.0000.0000.0000.000
195D198GLU-1-0.912-0.95835.566-8.466-8.4660.0000.0000.0000.000
196D199GLU-1-0.859-0.92638.412-6.995-6.9950.0000.0000.0000.000
197D200CYS0-0.072-0.03441.6490.1200.1200.0000.0000.0000.000
198D201LEU0-0.040-0.01135.1890.0280.0280.0000.0000.0000.000
199D202ARG10.8490.91937.4947.3837.3830.0000.0000.0000.000
200D203GLY0-0.023-0.00337.109-0.072-0.0720.0000.0000.0000.000
201D204GLY00.0110.01233.982-0.237-0.2370.0000.0000.0000.000
202D205LYS10.8100.89925.86311.14411.1440.0000.0000.0000.000
203D206ILE00.0190.00532.6340.0500.0500.0000.0000.0000.000
204D207ILE0-0.047-0.02326.419-0.249-0.2490.0000.0000.0000.000
205D208THR00.0000.00130.1140.1110.1110.0000.0000.0000.000
206D209THR0-0.022-0.02226.802-0.363-0.3630.0000.0000.0000.000
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