FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Z6K4N

Calculation Name: 1TKI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TKI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 321
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5280631.792032
FMO2-HF: Nuclear repulsion 5150572.096161
FMO2-HF: Total energy -130059.695871
FMO2-MP2: Total energy -130439.51019


3D Structure
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:18:LYS)


Summations of interaction energy for fragment #1(A:18:LYS)
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.
-86.845-89.55337.001-17.302-16.988-0.182
Interaction energy analysis for fragmet #1(A:18:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / 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].
3A20LEU0-0.020-0.0023.052-2.1481.9890.070-1.306-2.901-0.005
4A21TYR00.014-0.0122.2383.5526.0092.747-1.494-3.709-0.006
5A22GLU-1-0.813-0.8661.728-144.184-155.14232.301-13.080-8.262-0.153
6A23LYS10.7810.8735.09337.69837.759-0.001-0.003-0.0560.000
7A24TYR0-0.062-0.0517.4045.8745.8740.0000.0000.0000.000
8A25MET0-0.0170.0047.777-2.831-2.8310.0000.0000.0000.000
9A26ILE00.002-0.0046.1821.1721.1720.0000.0000.0000.000
10A27ALA0-0.016-0.0059.3120.8340.8340.0000.0000.0000.000
11A28GLU-1-0.731-0.83011.861-16.523-16.5230.0000.0000.0000.000
12A29ASP-1-0.931-0.96212.375-16.374-16.3740.0000.0000.0000.000
13A30LEU0-0.042-0.04013.7210.9610.9610.0000.0000.0000.000
14A31GLY00.0450.00014.5820.9110.9110.0000.0000.0000.000
15A32ARG10.8750.93012.09314.69114.6910.0000.0000.0000.000
16A33GLY00.1130.04113.9550.8180.8180.0000.0000.0000.000
17A34GLU-1-0.931-0.92914.235-13.056-13.0560.0000.0000.0000.000
18A35PHE00.0400.02112.816-0.361-0.3610.0000.0000.0000.000
19A36GLY00.0420.02210.132-1.297-1.2970.0000.0000.0000.000
20A37ILE0-0.069-0.0307.9921.3611.3610.0000.0000.0000.000
21A38VAL0-0.029-0.0019.717-1.303-1.3030.0000.0000.0000.000
22A39HIS00.0210.0158.8420.4520.4520.0000.0000.0000.000
23A40ARG10.8010.87411.86916.05016.0500.0000.0000.0000.000
24A41CYS0-0.030-0.00710.357-1.015-1.0150.0000.0000.0000.000
25A42VAL0-0.003-0.00411.8541.7721.7720.0000.0000.0000.000
26A43GLU-1-0.676-0.75712.082-21.763-21.7630.0000.0000.0000.000
27A44THR00.0370.00110.3072.1082.1080.0000.0000.0000.000
28A45SER0-0.004-0.00313.0800.7900.7900.0000.0000.0000.000
29A46SER0-0.090-0.09114.8751.3651.3650.0000.0000.0000.000
30A47LYS10.9280.96016.46217.23917.2390.0000.0000.0000.000
31A48LYS10.8630.94417.56217.97517.9750.0000.0000.0000.000
32A49THR0-0.006-0.00716.521-1.120-1.1200.0000.0000.0000.000
33A50TYR0-0.081-0.05814.3191.1171.1170.0000.0000.0000.000
34A51MET0-0.007-0.00314.2090.1370.1370.0000.0000.0000.000
35A52ALA00.0160.0068.803-0.324-0.3240.0000.0000.0000.000
36A53LYS10.8300.91010.11817.57617.5760.0000.0000.0000.000
37A54PHE0-0.005-0.0013.085-0.665-0.2010.020-0.107-0.3770.000
38A55VAL00.010-0.0167.1802.6192.6190.0000.0000.0000.000
39A56LYS10.8670.9245.05423.73823.7380.0000.0000.0000.000
40A57VAL00.0190.0128.7351.7611.7610.0000.0000.0000.000
41A58LYS10.8640.92810.13518.22418.2240.0000.0000.0000.000
42A59GLY00.0130.01312.0661.2311.2310.0000.0000.0000.000
43A60THR00.012-0.01315.255-0.560-0.5600.0000.0000.0000.000
44A61ASP-1-0.834-0.91415.816-14.318-14.3180.0000.0000.0000.000
45A62GLN0-0.013-0.0259.5960.4990.4990.0000.0000.0000.000
46A63VAL0-0.030-0.01414.440-0.160-0.1600.0000.0000.0000.000
47A64LEU0-0.037-0.01617.8160.4940.4940.0000.0000.0000.000
48A65VAL00.0570.02612.4020.3130.3130.0000.0000.0000.000
49A66LYS10.8550.92312.31922.87622.8760.0000.0000.0000.000
50A67LYS10.9230.98416.45713.35413.3540.0000.0000.0000.000
51A68GLU-1-0.745-0.86616.074-16.013-16.0130.0000.0000.0000.000
52A69ILE00.018-0.00312.5330.3690.3690.0000.0000.0000.000
53A70SER0-0.043-0.03417.1150.2420.2420.0000.0000.0000.000
54A71ILE0-0.021-0.01020.4350.4780.4780.0000.0000.0000.000
55A72LEU0-0.002-0.00817.3250.2830.2830.0000.0000.0000.000
56A73ASN0-0.0070.01418.793-0.185-0.1850.0000.0000.0000.000
57A74ILE0-0.0220.00420.6530.1860.1860.0000.0000.0000.000
58A75ALA0-0.0130.00024.2860.5140.5140.0000.0000.0000.000
59A76ARG10.7830.87218.57716.04416.0440.0000.0000.0000.000
60A77HIS00.0830.03525.4640.1920.1920.0000.0000.0000.000
61A78ARG10.8410.91926.7899.0949.0940.0000.0000.0000.000
62A79ASN0-0.050-0.05127.965-0.060-0.0600.0000.0000.0000.000
63A80ILE00.0000.01723.1750.1090.1090.0000.0000.0000.000
64A81LEU0-0.031-0.00517.970-0.043-0.0430.0000.0000.0000.000
65A82HIS00.011-0.00519.5690.0610.0610.0000.0000.0000.000
66A83LEU00.0170.00513.948-0.516-0.5160.0000.0000.0000.000
67A84HIS0-0.046-0.01614.1681.3841.3840.0000.0000.0000.000
68A85GLU-1-0.755-0.83510.828-28.676-28.6760.0000.0000.0000.000
69A86SER0-0.015-0.01411.2621.1031.1030.0000.0000.0000.000
70A87PHE0-0.024-0.0056.586-0.749-0.7490.0000.0000.0000.000
71A88GLU-1-0.852-0.9297.943-22.332-22.3320.0000.0000.0000.000
72A89SER00.026-0.0065.110-1.164-1.1640.0000.0000.0000.000
73A90MET00.0120.0077.9192.9802.9800.0000.0000.0000.000
74A91GLU-1-0.857-0.9397.215-19.387-19.3870.0000.0000.0000.000
75A92GLU-1-0.838-0.8982.327-39.118-38.0851.865-1.296-1.602-0.018
76A93LEU0-0.0100.0006.228-1.435-1.4350.0000.0000.0000.000
77A94VAL0-0.021-0.0084.4160.5770.675-0.001-0.016-0.0810.000
78A95MET0-0.032-0.0067.4570.4580.4580.0000.0000.0000.000
79A96ILE00.0070.0119.0360.7130.7130.0000.0000.0000.000
80A97PHE00.0450.00512.5720.8150.8150.0000.0000.0000.000
81A98GLU-1-0.780-0.87016.124-13.627-13.6270.0000.0000.0000.000
82A99PHE0-0.010-0.01717.1320.1650.1650.0000.0000.0000.000
83A100ILE0-0.0390.00219.5570.7330.7330.0000.0000.0000.000
84A101SER00.020-0.00221.3200.0040.0040.0000.0000.0000.000
85A102GLY0-0.055-0.03023.8150.3750.3750.0000.0000.0000.000
86A103LEU0-0.029-0.00925.711-0.190-0.1900.0000.0000.0000.000
87A104ASP-1-0.692-0.79427.579-9.550-9.5500.0000.0000.0000.000
88A105ILE00.0360.01329.0670.1560.1560.0000.0000.0000.000
89A106PHE00.0520.01632.2010.2560.2560.0000.0000.0000.000
90A107GLU-1-0.769-0.84226.870-10.188-10.1880.0000.0000.0000.000
91A108ARG10.8110.91531.5438.9218.9210.0000.0000.0000.000
92A109ILE00.0090.02033.4820.1640.1640.0000.0000.0000.000
93A110ASN0-0.049-0.03033.8340.3020.3020.0000.0000.0000.000
94A111THR0-0.071-0.03133.8300.1480.1480.0000.0000.0000.000
95A112SER00.006-0.01136.4760.1610.1610.0000.0000.0000.000
96A113ALA0-0.0030.00237.2040.1370.1370.0000.0000.0000.000
97A114PHE0-0.045-0.03036.922-0.059-0.0590.0000.0000.0000.000
98A115GLU-1-0.889-0.93439.017-6.624-6.6240.0000.0000.0000.000
99A116LEU0-0.0050.00638.910-0.063-0.0630.0000.0000.0000.000
100A117ASN00.008-0.00241.3990.2010.2010.0000.0000.0000.000
101A118GLU-1-0.681-0.81342.441-6.570-6.5700.0000.0000.0000.000
102A119ARG10.8620.93242.5656.8976.8970.0000.0000.0000.000
103A120GLU-1-0.854-0.94537.399-8.192-8.1920.0000.0000.0000.000
104A121ILE0-0.0130.00638.520-0.241-0.2410.0000.0000.0000.000
105A122VAL00.0450.02338.972-0.179-0.1790.0000.0000.0000.000
106A123SER0-0.038-0.01037.991-0.202-0.2020.0000.0000.0000.000
107A124TYR0-0.023-0.01530.516-0.191-0.1910.0000.0000.0000.000
108A125VAL00.0370.00534.788-0.245-0.2450.0000.0000.0000.000
109A126HIS00.0000.00136.6260.0450.0450.0000.0000.0000.000
110A127GLN00.020-0.00932.875-0.406-0.4060.0000.0000.0000.000
111A128VAL0-0.0020.00331.648-0.304-0.3040.0000.0000.0000.000
112A129CYS0-0.019-0.00333.257-0.050-0.0500.0000.0000.0000.000
113A130GLU-1-0.833-0.91734.150-8.897-8.8970.0000.0000.0000.000
114A131ALA0-0.012-0.00129.691-0.103-0.1030.0000.0000.0000.000
115A132LEU00.004-0.00331.560-0.160-0.1600.0000.0000.0000.000
116A133GLN00.0640.04433.3200.1910.1910.0000.0000.0000.000
117A134PHE0-0.0050.00828.3050.0910.0910.0000.0000.0000.000
118A135LEU00.0090.01527.225-0.107-0.1070.0000.0000.0000.000
119A136HIS0-0.028-0.03831.2230.1670.1670.0000.0000.0000.000
120A137SER0-0.069-0.03134.2600.1020.1020.0000.0000.0000.000
121A138HIS0-0.039-0.02030.728-0.119-0.1190.0000.0000.0000.000
122A139ASN0-0.032-0.02232.056-0.073-0.0730.0000.0000.0000.000
123A140ILE0-0.037-0.01527.094-0.153-0.1530.0000.0000.0000.000
124A141GLY00.0250.02530.4120.2990.2990.0000.0000.0000.000
125A142HIS0-0.036-0.04825.064-0.071-0.0710.0000.0000.0000.000
126A143PHE00.013-0.02627.289-0.248-0.2480.0000.0000.0000.000
127A144ASP-1-0.771-0.85125.127-10.871-10.8710.0000.0000.0000.000
128A145ILE00.0030.01427.685-0.164-0.1640.0000.0000.0000.000
129A146ARG10.8180.89525.83710.36110.3610.0000.0000.0000.000
130A147PRO00.0450.01529.056-0.285-0.2850.0000.0000.0000.000
131A148GLU-1-0.781-0.87825.973-9.900-9.9000.0000.0000.0000.000
132A149ASN0-0.047-0.02924.490-0.624-0.6240.0000.0000.0000.000
133A150ILE0-0.022-0.00725.353-0.337-0.3370.0000.0000.0000.000
134A151ILE00.0080.00323.3700.3390.3390.0000.0000.0000.000
135A152TYR0-0.006-0.02126.721-0.082-0.0820.0000.0000.0000.000
136A153GLN00.0490.01426.0280.0720.0720.0000.0000.0000.000
137A154THR00.0390.00225.655-0.243-0.2430.0000.0000.0000.000
138A155ARG10.9540.97325.68210.63010.6300.0000.0000.0000.000
139A156ARG10.9480.98030.2989.7289.7280.0000.0000.0000.000
140A157SER0-0.0170.00430.4170.3740.3740.0000.0000.0000.000
141A158SER00.0890.04932.467-0.077-0.0770.0000.0000.0000.000
142A159THR0-0.0110.01329.2890.0910.0910.0000.0000.0000.000
143A160ILE0-0.0330.00229.433-0.268-0.2680.0000.0000.0000.000
144A161LYS10.8000.87924.02712.26312.2630.0000.0000.0000.000
145A162ILE00.0250.02224.8370.0050.0050.0000.0000.0000.000
146A163ILE0-0.043-0.03620.548-0.479-0.4790.0000.0000.0000.000
147A164GLU-1-0.754-0.84420.066-13.886-13.8860.0000.0000.0000.000
148A165PHE00.009-0.02320.6390.4690.4690.0000.0000.0000.000
149A166GLY00.0090.00120.318-0.033-0.0330.0000.0000.0000.000
150A167GLN0-0.052-0.03521.0530.2940.2940.0000.0000.0000.000
151A168ALA0-0.0120.01524.1300.3960.3960.0000.0000.0000.000
152A169ARG10.8970.94824.68010.30110.3010.0000.0000.0000.000
153A170GLN0-0.009-0.00527.0490.1020.1020.0000.0000.0000.000
154A171LEU0-0.038-0.00829.763-0.024-0.0240.0000.0000.0000.000
155A172LYS10.8700.92031.5229.5849.5840.0000.0000.0000.000
156A173PRO00.042-0.00133.4860.0580.0580.0000.0000.0000.000
157A174GLY0-0.0010.00436.090-0.141-0.1410.0000.0000.0000.000
158A175ASP-1-0.870-0.90530.566-9.841-9.8410.0000.0000.0000.000
159A176ASN0-0.032-0.02432.8700.4020.4020.0000.0000.0000.000
160A177PHE0-0.050-0.02628.742-0.319-0.3190.0000.0000.0000.000
161A178ARG10.9490.97227.5159.9619.9610.0000.0000.0000.000
162A179LEU00.0030.02028.046-0.300-0.3000.0000.0000.0000.000
163A180LEU0-0.020-0.02024.1310.2090.2090.0000.0000.0000.000
164A181PHE00.0280.01527.709-0.157-0.1570.0000.0000.0000.000
165A182THR00.0250.00027.8120.1260.1260.0000.0000.0000.000
166A183ALA00.0290.02030.5060.1380.1380.0000.0000.0000.000
167A184PRO00.0380.02433.120-0.136-0.1360.0000.0000.0000.000
168A185GLU-1-0.710-0.84535.534-7.855-7.8550.0000.0000.0000.000
169A186TYR0-0.052-0.03833.2090.0490.0490.0000.0000.0000.000
170A187TYR0-0.074-0.04729.098-0.162-0.1620.0000.0000.0000.000
171A188ALA00.0800.04335.5430.1600.1600.0000.0000.0000.000
172A189PRO00.0310.02238.686-0.106-0.1060.0000.0000.0000.000
173A190GLU-1-0.734-0.84138.059-7.541-7.5410.0000.0000.0000.000
174A191VAL0-0.055-0.03233.891-0.121-0.1210.0000.0000.0000.000
175A192HIS0-0.010-0.00636.133-0.077-0.0770.0000.0000.0000.000
176A193GLN00.0150.00738.7440.1010.1010.0000.0000.0000.000
177A194HIS0-0.056-0.00135.898-0.126-0.1260.0000.0000.0000.000
178A195ASP-1-0.759-0.86438.342-7.105-7.1050.0000.0000.0000.000
179A196VAL0-0.062-0.04637.699-0.242-0.2420.0000.0000.0000.000
180A197VAL00.0160.02333.2790.1410.1410.0000.0000.0000.000
181A198SER0-0.037-0.03336.4030.0550.0550.0000.0000.0000.000
182A199THR00.0770.02834.571-0.034-0.0340.0000.0000.0000.000
183A200ALA00.0500.03036.116-0.056-0.0560.0000.0000.0000.000
184A201THR0-0.031-0.03434.6850.0760.0760.0000.0000.0000.000
185A202ASP-1-0.766-0.86331.900-9.388-9.3880.0000.0000.0000.000
186A203MET0-0.057-0.00834.461-0.122-0.1220.0000.0000.0000.000
187A204TRP00.0600.03637.4260.1330.1330.0000.0000.0000.000
188A205SER0-0.044-0.02432.9790.0280.0280.0000.0000.0000.000
189A206LEU0-0.035-0.03035.108-0.038-0.0380.0000.0000.0000.000
190A207GLY00.0610.02736.5010.0780.0780.0000.0000.0000.000
191A208THR00.022-0.01237.2130.1840.1840.0000.0000.0000.000
192A209LEU0-0.045-0.01332.7880.0360.0360.0000.0000.0000.000
193A210VAL0-0.021-0.01836.6230.0280.0280.0000.0000.0000.000
194A211TYR00.0330.00139.7350.0810.0810.0000.0000.0000.000
195A212VAL0-0.022-0.00336.2190.0990.0990.0000.0000.0000.000
196A213LEU0-0.055-0.02435.357-0.001-0.0010.0000.0000.0000.000
197A214LEU0-0.007-0.00139.2870.0690.0690.0000.0000.0000.000
198A215SER0-0.011-0.01042.4090.1310.1310.0000.0000.0000.000
199A216GLY0-0.051-0.03240.0520.0750.0750.0000.0000.0000.000
200A217ILE0-0.031-0.02841.119-0.010-0.0100.0000.0000.0000.000
201A218ASN0-0.015-0.00938.2390.0570.0570.0000.0000.0000.000
202A219PRO00.0250.00940.3860.1060.1060.0000.0000.0000.000
203A220PHE00.0450.02140.9310.0870.0870.0000.0000.0000.000
204A221LEU0-0.068-0.02441.673-0.002-0.0020.0000.0000.0000.000
205A222ALA00.0730.03343.8230.1340.1340.0000.0000.0000.000
206A223GLU-1-0.912-0.95744.071-6.105-6.1050.0000.0000.0000.000
207A224THR0-0.019-0.01243.516-0.073-0.0730.0000.0000.0000.000
208A225ASN00.001-0.01137.060-0.018-0.0180.0000.0000.0000.000
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