Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JLY69

Calculation Name: 1TK1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TK1

Chain ID: A

ChEMBL ID:

UniProt ID: P11353

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptH
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646018.731525
FMO2-HF: Nuclear repulsion 2557799.814195
FMO2-HF: Total energy -88218.91733
FMO2-MP2: Total energy -88476.231928


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:8:ARG)


Summations of interaction energy for fragment #1(A:8:ARG)
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.
-57.348-54.9420.066-1.253-1.219-0.002
Interaction energy analysis for fragmet #1(A:8:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.968 / q_NPA : 0.978
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].
3A10LEU00.0230.0233.250-4.423-2.0170.066-1.253-1.219-0.002
4A11PRO00.0240.0065.557-1.971-1.9710.0000.0000.0000.000
5A12ILE00.1120.0586.5171.5901.5900.0000.0000.0000.000
6A13ARG10.9801.0058.92522.25422.2540.0000.0000.0000.000
7A14GLN0-0.039-0.0269.7300.1070.1070.0000.0000.0000.000
8A15GLN0-0.021-0.0116.0423.9243.9240.0000.0000.0000.000
9A16MET00.0290.02711.2111.1671.1670.0000.0000.0000.000
10A17GLU-1-0.807-0.90513.940-13.961-13.9610.0000.0000.0000.000
11A18ALA0-0.014-0.01813.9560.9850.9850.0000.0000.0000.000
12A19LEU0-0.015-0.00214.7500.8700.8700.0000.0000.0000.000
13A20ILE00.010-0.00416.5210.8850.8850.0000.0000.0000.000
14A21ARG10.8350.91219.29413.93713.9370.0000.0000.0000.000
15A22ARG10.9450.98614.81116.71916.7190.0000.0000.0000.000
16A23LYS10.8190.89719.18814.01314.0130.0000.0000.0000.000
17A24GLN0-0.019-0.01422.4030.2270.2270.0000.0000.0000.000
18A25ALA0-0.0200.00324.6090.4810.4810.0000.0000.0000.000
19A26GLU-1-0.823-0.91721.675-12.549-12.5490.0000.0000.0000.000
20A27ILE00.001-0.00424.9800.3950.3950.0000.0000.0000.000
21A28THR0-0.037-0.01827.9520.3950.3950.0000.0000.0000.000
22A29GLN00.0240.01327.7330.2540.2540.0000.0000.0000.000
23A30GLY00.0240.01330.1430.2630.2630.0000.0000.0000.000
24A31LEU0-0.033-0.01831.5860.2830.2830.0000.0000.0000.000
25A32GLU-1-0.815-0.90733.946-8.391-8.3910.0000.0000.0000.000
26A33SER0-0.137-0.06534.4000.2710.2710.0000.0000.0000.000
27A34ILE0-0.048-0.01936.3850.1730.1730.0000.0000.0000.000
28A35ASP-1-0.698-0.83438.846-7.072-7.0720.0000.0000.0000.000
29A36THR0-0.066-0.04340.6450.0500.0500.0000.0000.0000.000
30A37VAL0-0.0310.00340.1930.0540.0540.0000.0000.0000.000
31A38LYS10.8920.94536.8147.7517.7510.0000.0000.0000.000
32A39PHE0-0.024-0.03233.7900.0940.0940.0000.0000.0000.000
33A40HIS0-0.023-0.01135.779-0.105-0.1050.0000.0000.0000.000
34A41ALA00.0150.00832.5280.0570.0570.0000.0000.0000.000
35A51GLY0-0.0090.02329.1540.0670.0670.0000.0000.0000.000
36A52GLY0-0.032-0.02230.0550.1050.1050.0000.0000.0000.000
37A53GLY00.037-0.00526.768-0.369-0.3690.0000.0000.0000.000
38A54THR0-0.085-0.05125.6360.3880.3880.0000.0000.0000.000
39A55SER00.0280.00928.231-0.216-0.2160.0000.0000.0000.000
40A56MET00.0080.02429.8090.1820.1820.0000.0000.0000.000
41A57VAL00.000-0.00732.453-0.050-0.0500.0000.0000.0000.000
42A58ILE00.0040.01735.8220.0590.0590.0000.0000.0000.000
43A59GLN0-0.048-0.05138.1260.0440.0440.0000.0000.0000.000
44A60ASP-1-0.916-0.94341.762-6.572-6.5720.0000.0000.0000.000
45A61GLY00.0040.00542.5280.0570.0570.0000.0000.0000.000
46A62THR0-0.079-0.05243.5340.1740.1740.0000.0000.0000.000
47A63THR0-0.084-0.05040.1980.1450.1450.0000.0000.0000.000
48A64PHE0-0.046-0.02836.707-0.038-0.0380.0000.0000.0000.000
49A65GLU-1-0.882-0.92840.899-6.572-6.5720.0000.0000.0000.000
50A66LYS10.9450.95839.1097.3977.3970.0000.0000.0000.000
51A67GLY00.0180.00636.238-0.049-0.0490.0000.0000.0000.000
52A68GLY0-0.018-0.00433.7280.1180.1180.0000.0000.0000.000
53A69VAL00.0310.00627.379-0.124-0.1240.0000.0000.0000.000
54A70ASN0-0.028-0.02827.2240.2780.2780.0000.0000.0000.000
55A71VAL00.0230.01521.950-0.340-0.3400.0000.0000.0000.000
56A72SER00.0060.01223.9490.4310.4310.0000.0000.0000.000
57A73VAL0-0.028-0.00119.645-0.470-0.4700.0000.0000.0000.000
58A74VAL0-0.014-0.00421.3780.5680.5680.0000.0000.0000.000
59A75TYR00.0160.00916.815-0.937-0.9370.0000.0000.0000.000
60A76GLY0-0.006-0.00921.7910.6380.6380.0000.0000.0000.000
61A77GLN00.007-0.00422.879-0.663-0.6630.0000.0000.0000.000
62A78LEU0-0.0180.00924.3480.3170.3170.0000.0000.0000.000
63A79SER00.0610.03327.228-0.172-0.1720.0000.0000.0000.000
64A80PRO00.0930.03829.842-0.165-0.1650.0000.0000.0000.000
65A81ALA0-0.012-0.00631.2830.0590.0590.0000.0000.0000.000
66A82ALA0-0.004-0.00429.9520.0900.0900.0000.0000.0000.000
67A83VAL00.034-0.00226.517-0.067-0.0670.0000.0000.0000.000
68A84SER0-0.071-0.02529.189-0.013-0.0130.0000.0000.0000.000
69A85ALA0-0.019-0.01832.5030.0360.0360.0000.0000.0000.000
70A86MET0-0.032-0.01525.7350.0050.0050.0000.0000.0000.000
71A87LYS10.8860.96024.38211.91811.9180.0000.0000.0000.000
72A88ALA00.0200.01729.089-0.100-0.1000.0000.0000.0000.000
73A89ASP-1-0.896-0.95227.533-10.383-10.3830.0000.0000.0000.000
74A90HIS10.7860.89722.66111.87711.8770.0000.0000.0000.000
75A91LYS10.8490.92520.56614.12114.1210.0000.0000.0000.000
76A107ASP-1-0.893-0.96827.727-9.798-9.7980.0000.0000.0000.000
77A108GLY0-0.060-0.01527.812-0.054-0.0540.0000.0000.0000.000
78A109VAL0-0.012-0.01421.396-0.371-0.3710.0000.0000.0000.000
79A110LYS10.9680.98919.78814.51114.5110.0000.0000.0000.000
80A111PHE0-0.020-0.01119.105-0.547-0.5470.0000.0000.0000.000
81A112PHE00.0420.01415.9710.2090.2090.0000.0000.0000.000
82A113ALA00.0150.00318.322-0.241-0.2410.0000.0000.0000.000
83A114CYS0-0.066-0.01216.9100.1420.1420.0000.0000.0000.000
84A115GLY00.0730.02219.986-0.269-0.2690.0000.0000.0000.000
85A116LEU0-0.0210.01621.7900.2880.2880.0000.0000.0000.000
86A117SER0-0.046-0.02923.8770.1220.1220.0000.0000.0000.000
87A118MET0-0.024-0.00327.2880.1350.1350.0000.0000.0000.000
88A119VAL00.0060.00930.0800.0090.0090.0000.0000.0000.000
89A120ILE0-0.0070.00732.8630.0740.0740.0000.0000.0000.000
90A121HIS00.0190.00735.7820.0510.0510.0000.0000.0000.000
91A122PRO00.005-0.01139.1170.0510.0510.0000.0000.0000.000
92A123VAL00.0350.02841.4200.0870.0870.0000.0000.0000.000
93A124ASN0-0.034-0.01544.8050.1390.1390.0000.0000.0000.000
94A125PRO00.0190.00644.706-0.146-0.1460.0000.0000.0000.000
95A126HIS00.0330.02645.633-0.152-0.1520.0000.0000.0000.000
96A127ALA00.0050.00640.927-0.102-0.1020.0000.0000.0000.000
97A128PRO0-0.027-0.00737.7060.0620.0620.0000.0000.0000.000
98A129THR00.0240.00636.751-0.017-0.0170.0000.0000.0000.000
99A130THR0-0.054-0.02532.369-0.143-0.1430.0000.0000.0000.000
100A131HIS0-0.027-0.01231.5740.1850.1850.0000.0000.0000.000
101A132LEU00.0120.02224.609-0.123-0.1230.0000.0000.0000.000
102A133ASN0-0.017-0.02424.603-0.293-0.2930.0000.0000.0000.000
103A134TYR00.0560.05419.832-0.122-0.1220.0000.0000.0000.000
104A135ARG10.8650.92719.93511.90311.9030.0000.0000.0000.000
105A136TYR0-0.043-0.06612.221-0.416-0.4160.0000.0000.0000.000
106A137PHE0-0.0010.00417.2910.6450.6450.0000.0000.0000.000
107A138GLU-1-0.750-0.84012.207-21.868-21.8680.0000.0000.0000.000
108A139THR00.019-0.00716.3280.8470.8470.0000.0000.0000.000
109A140TRP0-0.127-0.05813.312-0.816-0.8160.0000.0000.0000.000
110A141ASN0-0.096-0.07217.0690.6040.6040.0000.0000.0000.000
111A142GLN00.0350.02217.8190.3720.3720.0000.0000.0000.000
112A143ASP-1-0.867-0.91012.944-20.753-20.7530.0000.0000.0000.000
113A144GLY00.0090.00111.295-0.020-0.0200.0000.0000.0000.000
114A145THR0-0.103-0.0698.120-3.660-3.6600.0000.0000.0000.000
115A146PRO0-0.0030.00010.3511.0861.0860.0000.0000.0000.000
116A147GLN00.0330.02613.4530.9590.9590.0000.0000.0000.000
117A148THR0-0.041-0.03016.656-0.035-0.0350.0000.0000.0000.000
118A149TRP00.0330.02511.9150.0490.0490.0000.0000.0000.000
119A150TRP0-0.0010.01216.0400.2450.2450.0000.0000.0000.000
120A151PHE00.018-0.00411.915-0.056-0.0560.0000.0000.0000.000
121A152GLY0-0.002-0.00317.7570.4460.4460.0000.0000.0000.000
122A153GLY0-0.052-0.04521.129-0.302-0.3020.0000.0000.0000.000
123A154GLY00.0120.01723.4000.1590.1590.0000.0000.0000.000
124A155ALA00.000-0.00625.4820.0280.0280.0000.0000.0000.000
125A156ASP-1-0.885-0.94228.358-8.888-8.8880.0000.0000.0000.000
126A157LEU00.0450.02332.0480.0540.0540.0000.0000.0000.000
127A158THR0-0.083-0.04535.3850.0950.0950.0000.0000.0000.000
128A159PRO00.0220.00638.6420.0450.0450.0000.0000.0000.000
129A160SER0-0.049-0.01641.5530.0280.0280.0000.0000.0000.000
130A161TYR0-0.018-0.06045.0460.0980.0980.0000.0000.0000.000
131A162LEU0-0.041-0.02342.210-0.160-0.1600.0000.0000.0000.000
132A163TYR0-0.008-0.02342.7100.1640.1640.0000.0000.0000.000
133A164GLU-1-0.840-0.93040.719-7.577-7.5770.0000.0000.0000.000
134A165GLU-1-0.831-0.91840.182-7.045-7.0450.0000.0000.0000.000
135A166ASP-1-0.792-0.86438.430-7.556-7.5560.0000.0000.0000.000
136A167GLY00.0190.00336.567-0.251-0.2510.0000.0000.0000.000
137A168GLN0-0.043-0.03735.341-0.327-0.3270.0000.0000.0000.000
138A169LEU0-0.0140.00533.550-0.213-0.2130.0000.0000.0000.000
139A170PHE00.019-0.00530.289-0.309-0.3090.0000.0000.0000.000
140A171HIS0-0.042-0.00830.627-0.560-0.5600.0000.0000.0000.000
141A172GLN0-0.043-0.00830.103-0.058-0.0580.0000.0000.0000.000
142A173LEU00.0220.00728.300-0.290-0.2900.0000.0000.0000.000
143A174HIS0-0.029-0.02525.566-0.647-0.6470.0000.0000.0000.000
144A175LYS10.8520.91225.2089.6479.6470.0000.0000.0000.000
145A176ASP-1-0.861-0.92125.557-10.536-10.5360.0000.0000.0000.000
146A177ALA0-0.082-0.03521.795-0.424-0.4240.0000.0000.0000.000
147A178LEU00.015-0.02020.874-0.582-0.5820.0000.0000.0000.000
148A179ASP-1-0.808-0.90221.432-11.391-11.3910.0000.0000.0000.000
149A180LYS10.8370.93219.40012.84612.8460.0000.0000.0000.000
150A181HIS0-0.117-0.05514.871-1.059-1.0590.0000.0000.0000.000
151A182ASP-1-0.817-0.94218.511-14.258-14.2580.0000.0000.0000.000
152A183THR00.0240.02921.3600.1460.1460.0000.0000.0000.000
153A184ALA0-0.0190.00123.8690.4950.4950.0000.0000.0000.000
154A185LEU0-0.044-0.01619.0840.3410.3410.0000.0000.0000.000
155A186TYR00.045-0.00223.8040.4320.4320.0000.0000.0000.000
156A187PRO0-0.052-0.03926.5730.3160.3160.0000.0000.0000.000
157A188ARG10.8140.90822.10012.79512.7950.0000.0000.0000.000
158A189PHE00.0360.00520.9530.1450.1450.0000.0000.0000.000
159A190LYS10.8970.98026.8889.0719.0710.0000.0000.0000.000
160A191LYS10.9380.96930.1018.5198.5190.0000.0000.0000.000
161A207GLY00.0220.00940.7170.0710.0710.0000.0000.0000.000
162A208ILE0-0.026-0.00235.5060.0400.0400.0000.0000.0000.000
163A209GLY00.0130.01834.975-0.123-0.1230.0000.0000.0000.000
164A210GLY00.0560.00631.2350.0240.0240.0000.0000.0000.000
165A211ILE0-0.035-0.01024.1830.0540.0540.0000.0000.0000.000
166A212PHE0-0.002-0.01226.442-0.001-0.0010.0000.0000.0000.000
167A213PHE00.0130.01619.334-0.068-0.0680.0000.0000.0000.000
168A214ASP-1-0.811-0.93922.640-12.085-12.0850.0000.0000.0000.000
169A215ASP-1-0.845-0.90521.222-13.360-13.3600.0000.0000.0000.000
170A216TYR00.0050.00916.783-0.131-0.1310.0000.0000.0000.000
171A217ASP-1-0.859-0.95715.394-16.383-16.3830.0000.0000.0000.000
172A218GLU-1-0.835-0.90215.576-14.428-14.4280.0000.0000.0000.000
173A219ARG10.8810.94013.34816.22716.2270.0000.0000.0000.000
174A220ASP-1-0.799-0.8867.080-34.012-34.0120.0000.0000.0000.000
175A221PRO00.027-0.0047.6411.1541.1540.0000.0000.0000.000
176A222GLN0-0.038-0.0295.420-2.238-2.2380.0000.0000.0000.000
177A223GLU-1-0.913-0.9647.785-21.098-21.0980.0000.0000.0000.000
178A224ILE0-0.057-0.01310.9131.6381.6380.0000.0000.0000.000
179A225LEU0-0.019-0.0138.6371.3371.3370.0000.0000.0000.000
180A226LYS10.8990.96411.75317.93217.9320.0000.0000.0000.000
181A227MET00.0050.02413.4211.1461.1460.0000.0000.0000.000
182A228VAL0-0.007-0.01015.6771.0931.0930.0000.0000.0000.000
183A229GLU-1-0.957-0.98814.711-16.405-16.4050.0000.0000.0000.000
184A230ASP-1-0.811-0.89017.313-14.542-14.5420.0000.0000.0000.000
185A231CYS0-0.074-0.04619.4310.8680.8680.0000.0000.0000.000
186A232PHE00.008-0.01919.1380.7000.7000.0000.0000.0000.000
187A233ASP-1-0.878-0.92420.650-12.649-12.6490.0000.0000.0000.000
188A234ALA0-0.0090.01023.3140.4310.4310.0000.0000.0000.000
189A235PHE0-0.0110.00025.6420.5460.5460.0000.0000.0000.000
190A236LEU0-0.003-0.00127.1660.3770.3770.0000.0000.0000.000
191A237PRO00.0220.01727.5300.4350.4350.0000.0000.0000.000
192A238SER0-0.0180.00329.7710.4060.4060.0000.0000.0000.000
193A239TYR00.0290.00031.6300.3170.3170.0000.0000.0000.000
194A240LEU00.006-0.00132.1350.3010.3010.0000.0000.0000.000
195A241THR0-0.065-0.04334.0910.3450.3450.0000.0000.0000.000
196A242ILE0-0.038-0.01635.0820.2620.2620.0000.0000.0000.000
197A243VAL00.018-0.00637.1890.2450.2450.0000.0000.0000.000
198A244LYS10.9440.97437.0658.1138.1130.0000.0000.0000.000
199A245ARG10.8020.90338.9887.7227.7220.0000.0000.0000.000
200A246ARG10.8300.89642.0687.0707.0700.0000.0000.0000.000
201A247LYS10.8450.90941.5347.0357.0350.0000.0000.0000.000
202A248ASP-1-0.841-0.89144.510-6.485-6.4850.0000.0000.0000.000
203A249MET0-0.082-0.01847.1110.0820.0820.0000.0000.0000.000
204A250PRO00.0310.00549.425-0.014-0.0140.0000.0000.0000.000
205A251TYR0-0.0070.00149.316-0.041-0.0410.0000.0000.0000.000
206A252THR0-0.019-0.00453.2210.0450.0450.0000.0000.0000.000
207A253LYS11.0090.97654.1325.3215.3210.0000.0000.0000.000
208A254GLU-1-0.854-0.92754.638-5.282-5.2820.0000.0000.0000.000
209A255GLU-1-0.809-0.85652.617-5.764-5.7640.0000.0000.0000.000
210A256GLN0-0.004-0.01148.3770.0210.0210.0000.0000.0000.000
211A257GLN0-0.011-0.00950.603-0.032-0.0320.0000.0000.0000.000
212A258TRP00.0090.01152.539-0.049-0.0490.0000.0000.0000.000
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