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: KK4V3

Calculation Name: 1WKC-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WKC

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHW9

Base Structure: X-ray

Registration Date: 2025-10-03

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1822666.58285
FMO2-HF: Nuclear repulsion 1755924.671719
FMO2-HF: Total energy -66741.911132
FMO2-MP2: Total energy -66942.238463


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
96.608103.01413.68-6.111-13.974-0.045
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.920
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].
3A3LYS10.8630.8923.03227.47929.8870.131-1.236-1.304-0.008
5A5GLU-1-0.832-0.9052.300-72.966-70.5665.312-3.017-4.695-0.030
6A6LEU00.0110.0092.2972.6593.8653.688-0.797-4.097-0.007
7A7ARG11.0061.0093.48232.30232.3940.0180.092-0.2010.000
8A8ARG10.9290.9724.42834.80934.919-0.001-0.005-0.1040.000
9A9ARG10.9640.9782.71432.67532.6284.533-1.101-3.3840.000
152A152PRO0-0.075-0.0534.1680.2360.473-0.001-0.047-0.1890.000
4A4ALA0-0.017-0.0055.6214.7184.7180.0000.0000.0000.000
10A10ALA00.0540.0305.8472.1102.1100.0000.0000.0000.000
11A11ARG10.9560.9748.80023.04323.0430.0000.0000.0000.000
12A12ALA0-0.041-0.0198.8911.4311.4310.0000.0000.0000.000
13A13ALA0-0.013-0.00410.2341.0851.0850.0000.0000.0000.000
14A14TRP00.038-0.01211.8401.3631.3630.0000.0000.0000.000
15A15ARG10.8950.95712.87017.53417.5340.0000.0000.0000.000
16A16ARG10.9010.96510.87617.84917.8490.0000.0000.0000.000
17A17LEU0-0.0060.01216.1750.2750.2750.0000.0000.0000.000
18A18ASP-1-0.787-0.88719.080-10.604-10.6040.0000.0000.0000.000
19A19LEU00.0440.01019.430-0.013-0.0130.0000.0000.0000.000
20A20LYS10.9611.00122.0779.3279.3270.0000.0000.0000.000
21A21ALA0-0.026-0.01824.8460.2400.2400.0000.0000.0000.000
22A22LEU00.0250.00619.9360.1460.1460.0000.0000.0000.000
23A23SER0-0.036-0.02923.288-0.104-0.1040.0000.0000.0000.000
24A24ARG10.9410.97024.9239.2419.2410.0000.0000.0000.000
25A25ALA0-0.0070.01424.8530.1920.1920.0000.0000.0000.000
26A26VAL00.0410.01621.7430.1150.1150.0000.0000.0000.000
27A27GLY00.0100.00825.1770.0980.0980.0000.0000.0000.000
28A28ALA0-0.024-0.02328.3330.2280.2280.0000.0000.0000.000
29A29ALA00.0080.00826.6120.2320.2320.0000.0000.0000.000
30A30LEU00.000-0.01225.761-0.043-0.0430.0000.0000.0000.000
31A31LEU0-0.0360.00128.9540.1770.1770.0000.0000.0000.000
32A32PRO00.000-0.01131.5970.2380.2380.0000.0000.0000.000
33A33TRP00.0710.03627.7910.0960.0960.0000.0000.0000.000
34A34LEU0-0.033-0.02630.5230.0770.0770.0000.0000.0000.000
35A35ARG10.9130.95733.5688.1858.1850.0000.0000.0000.000
36A36GLU-1-0.947-0.96134.941-8.526-8.5260.0000.0000.0000.000
37A37ARG10.8610.93631.4539.6089.6080.0000.0000.0000.000
38A38GLY00.0320.03635.6320.0670.0670.0000.0000.0000.000
39A39PHE0-0.045-0.01630.9340.0520.0520.0000.0000.0000.000
40A40ARG10.9490.96836.0147.8217.8210.0000.0000.0000.000
41A41HIS0-0.042-0.01835.9720.3070.3070.0000.0000.0000.000
42A42ILE00.0500.03230.598-0.270-0.2700.0000.0000.0000.000
43A43LEU0-0.026-0.00727.1620.1190.1190.0000.0000.0000.000
44A44LEU00.0050.00527.169-0.343-0.3430.0000.0000.0000.000
45A45TYR0-0.027-0.05322.694-0.173-0.1730.0000.0000.0000.000
46A46HIS00.0440.01325.9310.2670.2670.0000.0000.0000.000
47A47PRO0-0.053-0.01223.281-0.381-0.3810.0000.0000.0000.000
48A48LEU00.0220.01420.2280.2380.2380.0000.0000.0000.000
49A49PRO00.001-0.02418.490-0.120-0.1200.0000.0000.0000.000
50A50HIS0-0.097-0.05813.996-1.257-1.2570.0000.0000.0000.000
51A51GLU-1-0.774-0.86416.473-14.830-14.8300.0000.0000.0000.000
52A52LEU00.0320.02019.2410.4440.4440.0000.0000.0000.000
53A53ASN00.0340.00922.0340.1100.1100.0000.0000.0000.000
54A54LEU00.0350.00223.8990.2280.2280.0000.0000.0000.000
55A55LEU00.0490.02927.3690.2000.2000.0000.0000.0000.000
56A56PRO0-0.001-0.00729.6690.2120.2120.0000.0000.0000.000
57A57LEU0-0.0100.00228.3210.1670.1670.0000.0000.0000.000
58A58MET0-0.063-0.03032.1520.2390.2390.0000.0000.0000.000
59A59GLU-1-0.952-0.96135.254-7.812-7.8120.0000.0000.0000.000
60A60ALA0-0.024-0.00834.3140.1560.1560.0000.0000.0000.000
61A61TYR0-0.066-0.06134.6990.1370.1370.0000.0000.0000.000
62A62PRO00.0460.03736.456-0.153-0.1530.0000.0000.0000.000
63A63ALA00.0250.02236.1990.0470.0470.0000.0000.0000.000
64A64ARG10.8980.94938.2727.6587.6580.0000.0000.0000.000
65A65TYR00.018-0.00132.040-0.325-0.3250.0000.0000.0000.000
66A66TYR0-0.042-0.02932.6490.1910.1910.0000.0000.0000.000
67A67LEU0-0.006-0.00228.796-0.287-0.2870.0000.0000.0000.000
68A68PRO0-0.0200.00426.1100.2150.2150.0000.0000.0000.000
69A69LYS10.8860.94628.7578.8048.8040.0000.0000.0000.000
70A70VAL0-0.005-0.00525.468-0.060-0.0600.0000.0000.0000.000
71A71ALA00.0230.01028.3760.3900.3900.0000.0000.0000.000
72A72GLY00.0380.02729.563-0.088-0.0880.0000.0000.0000.000
73A73LYS10.9690.97124.78811.89711.8970.0000.0000.0000.000
74A74GLY00.0390.02625.312-0.569-0.5690.0000.0000.0000.000
75A75LEU0-0.037-0.01523.709-0.075-0.0750.0000.0000.0000.000
76A76THR00.0340.01827.9360.2690.2690.0000.0000.0000.000
77A77VAL00.0620.03030.936-0.164-0.1640.0000.0000.0000.000
78A78HIS10.8310.91132.7709.0409.0400.0000.0000.0000.000
79A79PRO00.0300.02734.357-0.213-0.2130.0000.0000.0000.000
80A80PHE00.0090.01033.381-0.043-0.0430.0000.0000.0000.000
81A81GLY00.014-0.00535.8650.2450.2450.0000.0000.0000.000
82A82PRO00.0030.01137.358-0.182-0.1820.0000.0000.0000.000
83A83LEU00.0010.01833.543-0.083-0.0830.0000.0000.0000.000
84A84ALA00.0320.00637.7730.1670.1670.0000.0000.0000.000
85A85PRO0-0.015-0.00238.500-0.183-0.1830.0000.0000.0000.000
86A86GLY00.0020.01239.5600.1760.1760.0000.0000.0000.000
87A87PRO00.0220.01537.9450.1360.1360.0000.0000.0000.000
88A88PHE00.0280.00438.738-0.134-0.1340.0000.0000.0000.000
89A89GLY0-0.031-0.02835.091-0.080-0.0800.0000.0000.0000.000
90A90LEU0-0.051-0.01533.589-0.316-0.3160.0000.0000.0000.000
91A91LEU00.0250.00132.9080.1740.1740.0000.0000.0000.000
92A92GLU-1-0.866-0.91934.139-8.517-8.5170.0000.0000.0000.000
93A93PRO0-0.029-0.01733.5010.1940.1940.0000.0000.0000.000
94A94THR0-0.017-0.02936.3710.0730.0730.0000.0000.0000.000
95A95THR0-0.022-0.00737.4060.1420.1420.0000.0000.0000.000
96A96PRO00.0750.03438.880-0.184-0.1840.0000.0000.0000.000
97A97PRO0-0.062-0.02636.876-0.193-0.1930.0000.0000.0000.000
98A98GLU-1-0.844-0.93436.483-7.755-7.7550.0000.0000.0000.000
99A99ASP-1-0.839-0.92435.603-9.057-9.0570.0000.0000.0000.000
100A100PRO00.010-0.01330.9140.0140.0140.0000.0000.0000.000
101A101ARG10.8720.91932.6519.2549.2540.0000.0000.0000.000
102A102VAL0-0.054-0.00735.2500.1220.1220.0000.0000.0000.000
103A103LEU0-0.044-0.01330.3190.0490.0490.0000.0000.0000.000
104A104ASP-1-0.791-0.89133.447-8.806-8.8060.0000.0000.0000.000
105A105LEU0-0.040-0.01127.683-0.239-0.2390.0000.0000.0000.000
106A106VAL0-0.015-0.01124.7340.0920.0920.0000.0000.0000.000
107A107VAL00.0110.00724.052-0.383-0.3830.0000.0000.0000.000
108A108VAL0-0.040-0.02419.022-0.054-0.0540.0000.0000.0000.000
109A109PRO00.0630.06418.939-0.385-0.3850.0000.0000.0000.000
110A110GLY00.023-0.01315.045-0.541-0.5410.0000.0000.0000.000
111A111LEU0-0.045-0.01410.7850.1560.1560.0000.0000.0000.000
112A112ALA00.0470.0169.429-0.270-0.2700.0000.0000.0000.000
113A113PHE00.0140.02011.480-0.024-0.0240.0000.0000.0000.000
114A114ASP-1-0.786-0.86310.464-24.573-24.5730.0000.0000.0000.000
115A115ARG10.9320.94612.38520.00820.0080.0000.0000.0000.000
116A116GLU-1-0.915-0.95913.402-19.615-19.6150.0000.0000.0000.000
117A117GLY00.0520.03215.6670.5320.5320.0000.0000.0000.000
118A118TYR0-0.030-0.01512.4980.3580.3580.0000.0000.0000.000
119A119ARG10.8950.93813.02116.53416.5340.0000.0000.0000.000
120A120LEU0-0.049-0.0237.074-1.237-1.2370.0000.0000.0000.000
121A121GLY00.0150.00110.9031.3691.3690.0000.0000.0000.000
122A122HIS0-0.059-0.05212.729-2.235-2.2350.0000.0000.0000.000
123A123GLY0-0.038-0.02414.0310.5850.5850.0000.0000.0000.000
124A124GLN00.0070.00814.7980.4590.4590.0000.0000.0000.000
125A125GLY00.0410.02717.2210.7560.7560.0000.0000.0000.000
126A126PHE0-0.011-0.01618.5750.2940.2940.0000.0000.0000.000
127A127TYR00.0490.01219.1220.2500.2500.0000.0000.0000.000
128A128ASP-1-0.823-0.90916.911-17.989-17.9890.0000.0000.0000.000
129A129ARG10.7700.87920.00714.43514.4350.0000.0000.0000.000
130A130PHE00.0550.02023.5990.2550.2550.0000.0000.0000.000
131A131LEU0-0.018-0.02620.3880.4560.4560.0000.0000.0000.000
132A132LYS10.8740.95521.02714.75414.7540.0000.0000.0000.000
133A133GLU-1-0.897-0.93526.274-10.548-10.5480.0000.0000.0000.000
134A134VAL0-0.0060.01127.1140.4790.4790.0000.0000.0000.000
135A135ARG10.8750.92328.51410.41510.4150.0000.0000.0000.000
136A136ALA00.0430.04629.1930.2960.2960.0000.0000.0000.000
137A137ALA0-0.026-0.00228.584-0.291-0.2910.0000.0000.0000.000
138A138THR0-0.040-0.03923.665-0.254-0.2540.0000.0000.0000.000
139A139VAL00.0240.00023.2730.0550.0550.0000.0000.0000.000
140A140GLY00.0130.01319.2730.0150.0150.0000.0000.0000.000
141A141VAL0-0.038-0.01020.2080.1220.1220.0000.0000.0000.000
142A142VAL0-0.031-0.03314.625-0.504-0.5040.0000.0000.0000.000
143A143PRO00.0230.01316.3190.3030.3030.0000.0000.0000.000
144A144GLN00.0600.01816.243-0.633-0.6330.0000.0000.0000.000
145A145ALA0-0.037-0.01614.109-0.785-0.7850.0000.0000.0000.000
146A146LEU0-0.075-0.04410.883-1.286-1.2860.0000.0000.0000.000
147A147LEU00.0390.03912.281-1.079-1.0790.0000.0000.0000.000
148A148PHE0-0.056-0.0366.161-0.580-0.5800.0000.0000.0000.000
149A149PRO00.009-0.0167.4001.1501.1500.0000.0000.0000.000
150A150ALA00.0330.0178.361-1.128-1.1280.0000.0000.0000.000
151A151LEU0-0.058-0.0276.758-5.225-5.2250.0000.0000.0000.000
153A153ARG10.9560.9996.84125.81625.8160.0000.0000.0000.000
154A154ASP-1-0.815-0.89310.479-30.031-30.0310.0000.0000.0000.000
155A155PRO0-0.025-0.03012.6171.2391.2390.0000.0000.0000.000
156A156TRP0-0.018-0.00313.3321.6651.6650.0000.0000.0000.000
157A157ASP-1-0.831-0.89312.383-24.422-24.4220.0000.0000.0000.000
158A158VAL0-0.053-0.03515.9850.5690.5690.0000.0000.0000.000
159A159PRO0-0.058-0.00717.054-0.296-0.2960.0000.0000.0000.000
160A160VAL0-0.017-0.01318.1880.8350.8350.0000.0000.0000.000
161A161ASP-1-0.761-0.88720.270-12.316-12.3160.0000.0000.0000.000
162A162HIS10.8060.90022.67812.21812.2180.0000.0000.0000.000
163A163LEU00.0200.02517.277-0.521-0.5210.0000.0000.0000.000
164A164ALA00.0040.00221.1660.6360.6360.0000.0000.0000.000
165A165THR0-0.0050.00319.480-0.398-0.3980.0000.0000.0000.000
166A166GLU-1-0.788-0.92120.021-12.988-12.9880.0000.0000.0000.000
167A167ALA0-0.030-0.00523.3760.4440.4440.0000.0000.0000.000
168A168GLY00.0140.01125.0910.3820.3820.0000.0000.0000.000
169A169VAL0-0.050-0.02124.537-0.528-0.5280.0000.0000.0000.000
170A170GLU-1-0.920-0.95619.847-14.064-14.0640.0000.0000.0000.000
171A171ALA0-0.038-0.03823.843-0.082-0.0820.0000.0000.0000.000
172A172VAL0-0.0300.01118.929-0.263-0.2630.0000.0000.0000.000
173A173LYS10.9360.96220.43814.57514.5750.0000.0000.0000.000
174A174ARG10.9350.96221.01710.97410.9740.0000.0000.0000.000
175A175PRO-1-0.905-0.93919.747-13.986-13.9860.0000.0000.0000.000