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: 39Z3L

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 OptHSide
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 -2647613.911441
FMO2-HF: Nuclear repulsion 2559393.616031
FMO2-HF: Total energy -88220.29541
FMO2-MP2: Total energy -88477.54908


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.
-57.77-55.4640.049-1.209-1.147-0.001
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 : 0.963 / q_NPA : 0.976
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].
3A10LEU00.0190.0153.341-4.086-1.7800.049-1.209-1.147-0.001
4A11PRO00.0270.0105.570-2.021-2.0210.0000.0000.0000.000
5A12ILE00.0960.0486.3691.5051.5050.0000.0000.0000.000
6A13ARG10.9660.9998.92421.39021.3900.0000.0000.0000.000
7A14GLN0-0.036-0.0319.8350.2330.2330.0000.0000.0000.000
8A15GLN0-0.014-0.0065.9123.4363.4360.0000.0000.0000.000
9A16MET00.0220.02311.2111.1161.1160.0000.0000.0000.000
10A17GLU-1-0.802-0.89913.947-13.735-13.7350.0000.0000.0000.000
11A18ALA0-0.008-0.01413.9370.9560.9560.0000.0000.0000.000
12A19LEU0-0.0230.00414.7180.8660.8660.0000.0000.0000.000
13A20ILE00.022-0.00216.5310.8750.8750.0000.0000.0000.000
14A21ARG10.8250.89819.29013.89413.8940.0000.0000.0000.000
15A22ARG10.8280.93115.34016.18116.1810.0000.0000.0000.000
16A23LYS10.8020.87819.39213.71813.7180.0000.0000.0000.000
17A24GLN0-0.019-0.02122.4140.2340.2340.0000.0000.0000.000
18A25ALA0-0.0200.00824.6070.4850.4850.0000.0000.0000.000
19A26GLU-1-0.812-0.91521.370-12.513-12.5130.0000.0000.0000.000
20A27ILE0-0.002-0.00724.7790.3940.3940.0000.0000.0000.000
21A28THR0-0.040-0.02727.9630.3810.3810.0000.0000.0000.000
22A29GLN00.0060.00627.8240.2270.2270.0000.0000.0000.000
23A30GLY00.0350.01630.1340.2580.2580.0000.0000.0000.000
24A31LEU0-0.029-0.01331.5780.2850.2850.0000.0000.0000.000
25A32GLU-1-0.778-0.87733.952-8.238-8.2380.0000.0000.0000.000
26A33SER0-0.136-0.06934.4300.2570.2570.0000.0000.0000.000
27A34ILE0-0.049-0.02136.3780.1670.1670.0000.0000.0000.000
28A35ASP-1-0.700-0.83738.845-7.046-7.0460.0000.0000.0000.000
29A36THR0-0.067-0.04940.6560.0620.0620.0000.0000.0000.000
30A37VAL0-0.0150.01540.6250.0590.0590.0000.0000.0000.000
31A38LYS10.8280.90636.0487.9277.9270.0000.0000.0000.000
32A39PHE0-0.014-0.03033.8360.0840.0840.0000.0000.0000.000
33A40HIS0-0.017-0.00535.779-0.096-0.0960.0000.0000.0000.000
34A41ALA0-0.025-0.03332.6020.1720.1720.0000.0000.0000.000
35A51GLY0-0.0120.02329.1700.0680.0680.0000.0000.0000.000
36A52GLY0-0.030-0.02330.0700.1000.1000.0000.0000.0000.000
37A53GLY00.039-0.00226.783-0.360-0.3600.0000.0000.0000.000
38A54THR0-0.053-0.03125.5350.3860.3860.0000.0000.0000.000
39A55SER00.0390.01428.243-0.228-0.2280.0000.0000.0000.000
40A56MET0-0.0040.03429.8580.2060.2060.0000.0000.0000.000
41A57VAL00.008-0.00832.453-0.052-0.0520.0000.0000.0000.000
42A58ILE00.0060.01835.8310.0510.0510.0000.0000.0000.000
43A59GLN0-0.061-0.05438.136-0.113-0.1130.0000.0000.0000.000
44A60ASP-1-0.868-0.92241.771-6.593-6.5930.0000.0000.0000.000
45A61GLY00.0250.01742.5390.0600.0600.0000.0000.0000.000
46A62THR0-0.065-0.03843.5450.1820.1820.0000.0000.0000.000
47A63THR0-0.091-0.05640.2750.1430.1430.0000.0000.0000.000
48A64PHE0-0.056-0.03336.658-0.041-0.0410.0000.0000.0000.000
49A65GLU-1-0.903-0.93640.909-6.561-6.5610.0000.0000.0000.000
50A66LYS10.9030.93539.2827.2937.2930.0000.0000.0000.000
51A67GLY00.0190.00736.248-0.053-0.0530.0000.0000.0000.000
52A68GLY0-0.012-0.00233.7370.1130.1130.0000.0000.0000.000
53A69VAL00.0220.00227.402-0.125-0.1250.0000.0000.0000.000
54A70ASN0-0.051-0.03127.5220.2030.2030.0000.0000.0000.000
55A71VAL00.0390.03221.993-0.326-0.3260.0000.0000.0000.000
56A72SER00.0200.01023.9660.4240.4240.0000.0000.0000.000
57A73VAL0-0.030-0.00519.745-0.471-0.4710.0000.0000.0000.000
58A74VAL0-0.019-0.00621.3910.5540.5540.0000.0000.0000.000
59A75TYR00.0410.02216.735-0.939-0.9390.0000.0000.0000.000
60A76GLY0-0.013-0.00721.8040.6350.6350.0000.0000.0000.000
61A77GLN00.017-0.00322.889-0.789-0.7890.0000.0000.0000.000
62A78LEU0-0.0180.01524.6970.3250.3250.0000.0000.0000.000
63A79SER00.0550.02227.231-0.164-0.1640.0000.0000.0000.000
64A80PRO00.0940.04629.840-0.156-0.1560.0000.0000.0000.000
65A81ALA0-0.019-0.01031.2810.0590.0590.0000.0000.0000.000
66A82ALA00.000-0.00229.9350.0900.0900.0000.0000.0000.000
67A83VAL00.0420.00226.547-0.056-0.0560.0000.0000.0000.000
68A84SER0-0.062-0.01929.182-0.028-0.0280.0000.0000.0000.000
69A85ALA0-0.035-0.02532.4940.0410.0410.0000.0000.0000.000
70A86MET0-0.022-0.01126.0450.0240.0240.0000.0000.0000.000
71A87LYS10.8440.92723.96411.97511.9750.0000.0000.0000.000
72A88ALA00.0160.01629.086-0.104-0.1040.0000.0000.0000.000
73A89ASP-1-0.878-0.93327.718-10.504-10.5040.0000.0000.0000.000
74A90HIS10.7610.86922.52211.73211.7320.0000.0000.0000.000
75A91LYS10.7990.87720.03514.39914.3990.0000.0000.0000.000
76A107ASP-1-0.913-0.97827.854-9.851-9.8510.0000.0000.0000.000
77A108GLY0-0.029-0.00427.811-0.069-0.0690.0000.0000.0000.000
78A109VAL0-0.017-0.01521.391-0.372-0.3720.0000.0000.0000.000
79A110LYS10.9540.98220.40913.90713.9070.0000.0000.0000.000
80A111PHE0-0.013-0.01019.106-0.522-0.5220.0000.0000.0000.000
81A112PHE00.0300.00915.8160.2490.2490.0000.0000.0000.000
82A113ALA00.0160.00518.324-0.235-0.2350.0000.0000.0000.000
83A114CYS0-0.066-0.01616.9020.1780.1780.0000.0000.0000.000
84A115GLY00.0750.02319.991-0.268-0.2680.0000.0000.0000.000
85A116LEU0-0.0220.01621.7960.2790.2790.0000.0000.0000.000
86A117SER0-0.036-0.02423.885-0.018-0.0180.0000.0000.0000.000
87A118MET0-0.036-0.01027.2950.1260.1260.0000.0000.0000.000
88A119VAL0-0.012-0.00230.0880.0190.0190.0000.0000.0000.000
89A120ILE0-0.0090.00832.8470.0760.0760.0000.0000.0000.000
90A121HIS00.0410.02035.7900.0730.0730.0000.0000.0000.000
91A122PRO00.008-0.00938.9570.0600.0600.0000.0000.0000.000
92A123VAL00.0310.02741.4290.0850.0850.0000.0000.0000.000
93A124ASN0-0.035-0.01844.8190.1410.1410.0000.0000.0000.000
94A125PRO00.0240.00744.715-0.142-0.1420.0000.0000.0000.000
95A126HIS00.008-0.00445.642-0.150-0.1500.0000.0000.0000.000
96A127ALA0-0.0040.00640.979-0.102-0.1020.0000.0000.0000.000
97A128PRO0-0.020-0.00437.7570.0560.0560.0000.0000.0000.000
98A129THR00.0260.00936.774-0.018-0.0180.0000.0000.0000.000
99A130THR0-0.048-0.02232.384-0.141-0.1410.0000.0000.0000.000
100A131HIS0-0.061-0.05531.8810.2470.2470.0000.0000.0000.000
101A132LEU00.0040.02024.483-0.130-0.1300.0000.0000.0000.000
102A133ASN0-0.017-0.01624.710-0.258-0.2580.0000.0000.0000.000
103A134TYR00.0450.05119.861-0.126-0.1260.0000.0000.0000.000
104A135ARG10.8300.89319.96211.80311.8030.0000.0000.0000.000
105A136TYR0-0.033-0.04612.069-0.447-0.4470.0000.0000.0000.000
106A137PHE00.0010.00517.2940.6120.6120.0000.0000.0000.000
107A138GLU-1-0.750-0.85012.285-21.485-21.4850.0000.0000.0000.000
108A139THR00.019-0.00416.3230.8060.8060.0000.0000.0000.000
109A140TRP0-0.117-0.06812.598-0.940-0.9400.0000.0000.0000.000
110A141ASN0-0.070-0.05217.0730.5350.5350.0000.0000.0000.000
111A142GLN00.0150.00718.0650.4370.4370.0000.0000.0000.000
112A143ASP-1-0.871-0.92212.882-20.033-20.0330.0000.0000.0000.000
113A144GLY00.0090.01111.713-0.101-0.1010.0000.0000.0000.000
114A145THR0-0.115-0.0768.274-3.771-3.7710.0000.0000.0000.000
115A146PRO00.0000.00410.5090.9490.9490.0000.0000.0000.000
116A147GLN00.0330.02913.4440.8230.8230.0000.0000.0000.000
117A148THR0-0.049-0.02916.686-0.012-0.0120.0000.0000.0000.000
118A149TRP00.0350.01912.167-0.037-0.0370.0000.0000.0000.000
119A150TRP0-0.0090.01516.0380.1460.1460.0000.0000.0000.000
120A151PHE00.019-0.00411.941-0.054-0.0540.0000.0000.0000.000
121A152GLY00.0120.00317.7600.4310.4310.0000.0000.0000.000
122A153GLY0-0.048-0.04921.134-0.287-0.2870.0000.0000.0000.000
123A154GLY00.0070.01223.4050.1500.1500.0000.0000.0000.000
124A155ALA00.003-0.00525.4880.0320.0320.0000.0000.0000.000
125A156ASP-1-0.851-0.91628.366-8.712-8.7120.0000.0000.0000.000
126A157LEU00.0220.02832.0550.0390.0390.0000.0000.0000.000
127A158THR0-0.054-0.03635.3920.1100.1100.0000.0000.0000.000
128A159PRO00.0270.01038.6490.0470.0470.0000.0000.0000.000
129A160SER0-0.026-0.01241.5610.0470.0470.0000.0000.0000.000
130A161TYR0-0.024-0.05445.0540.0860.0860.0000.0000.0000.000
131A162LEU0-0.039-0.01742.237-0.156-0.1560.0000.0000.0000.000
132A163TYR0-0.009-0.01242.7640.1660.1660.0000.0000.0000.000
133A164GLU-1-0.833-0.92040.743-7.559-7.5590.0000.0000.0000.000
134A165GLU-1-0.782-0.88540.190-7.043-7.0430.0000.0000.0000.000
135A166ASP-1-0.789-0.85538.435-7.525-7.5250.0000.0000.0000.000
136A167GLY00.0210.00136.576-0.249-0.2490.0000.0000.0000.000
137A168GLN0-0.053-0.04235.349-0.311-0.3110.0000.0000.0000.000
138A169LEU0-0.0090.00233.674-0.216-0.2160.0000.0000.0000.000
139A170PHE00.0330.00430.415-0.315-0.3150.0000.0000.0000.000
140A171HIS0-0.037-0.01030.635-0.590-0.5900.0000.0000.0000.000
141A172GLN0-0.066-0.02530.111-0.107-0.1070.0000.0000.0000.000
142A173LEU00.0270.01028.306-0.289-0.2890.0000.0000.0000.000
143A174HIS0-0.047-0.04025.581-0.653-0.6530.0000.0000.0000.000
144A175LYS10.8550.91225.2169.6189.6180.0000.0000.0000.000
145A176ASP-1-0.858-0.91625.565-10.435-10.4350.0000.0000.0000.000
146A177ALA0-0.070-0.03121.903-0.427-0.4270.0000.0000.0000.000
147A178LEU00.018-0.01720.919-0.578-0.5780.0000.0000.0000.000
148A179ASP-1-0.804-0.90321.439-11.357-11.3570.0000.0000.0000.000
149A180LYS10.7720.89719.27312.98112.9810.0000.0000.0000.000
150A181HIS0-0.108-0.04714.735-1.043-1.0430.0000.0000.0000.000
151A182ASP-1-0.756-0.88418.517-14.269-14.2690.0000.0000.0000.000
152A183THR00.0140.02021.3640.1340.1340.0000.0000.0000.000
153A184ALA0-0.0190.00023.8480.4820.4820.0000.0000.0000.000
154A185LEU0-0.046-0.01119.1780.3360.3360.0000.0000.0000.000
155A186TYR00.0850.03023.8080.4440.4440.0000.0000.0000.000
156A187PRO0-0.048-0.03726.5780.3050.3050.0000.0000.0000.000
157A188ARG10.7850.86121.85112.80312.8030.0000.0000.0000.000
158A189PHE00.0310.00720.9500.1660.1660.0000.0000.0000.000
159A190LYS10.8610.95626.8939.1539.1530.0000.0000.0000.000
160A191LYS10.9470.97430.1068.5388.5380.0000.0000.0000.000
161A207GLY00.0250.01240.7210.0660.0660.0000.0000.0000.000
162A208ILE0-0.027-0.00135.5480.0360.0360.0000.0000.0000.000
163A209GLY00.0090.01634.983-0.125-0.1250.0000.0000.0000.000
164A210GLY00.0540.00631.2420.0170.0170.0000.0000.0000.000
165A211ILE0-0.028-0.00924.3090.0430.0430.0000.0000.0000.000
166A212PHE0-0.007-0.01626.4280.0020.0020.0000.0000.0000.000
167A213PHE00.0150.01719.367-0.058-0.0580.0000.0000.0000.000
168A214ASP-1-0.775-0.90022.597-12.038-12.0380.0000.0000.0000.000
169A215ASP-1-0.808-0.86821.205-13.293-13.2930.0000.0000.0000.000
170A216TYR0-0.0080.00917.059-0.270-0.2700.0000.0000.0000.000
171A217ASP-1-0.817-0.92115.392-16.086-16.0860.0000.0000.0000.000
172A218GLU-1-0.793-0.86015.574-14.264-14.2640.0000.0000.0000.000
173A219ARG10.8310.89613.39315.98315.9830.0000.0000.0000.000
174A220ASP-1-0.809-0.8906.935-33.594-33.5940.0000.0000.0000.000
175A221PRO00.0350.0017.7381.1281.1280.0000.0000.0000.000
176A222GLN0-0.035-0.0235.511-2.371-2.3710.0000.0000.0000.000
177A223GLU-1-0.876-0.9517.791-20.525-20.5250.0000.0000.0000.000
178A224ILE0-0.043-0.00810.9191.5671.5670.0000.0000.0000.000
179A225LEU0-0.016-0.0088.6521.2771.2770.0000.0000.0000.000
180A226LYS10.8240.93011.76717.73417.7340.0000.0000.0000.000
181A227MET00.0190.02813.4301.1601.1600.0000.0000.0000.000
182A228VAL00.0170.00415.6891.0901.0900.0000.0000.0000.000
183A229GLU-1-0.819-0.90415.399-16.033-16.0330.0000.0000.0000.000
184A230ASP-1-0.795-0.89317.323-14.272-14.2720.0000.0000.0000.000
185A231CYS0-0.069-0.04119.4410.8190.8190.0000.0000.0000.000
186A232PHE00.017-0.01419.1590.6760.6760.0000.0000.0000.000
187A233ASP-1-0.852-0.90820.620-12.414-12.4140.0000.0000.0000.000
188A234ALA0-0.0090.01323.3250.4040.4040.0000.0000.0000.000
189A235PHE0-0.004-0.00225.6530.5330.5330.0000.0000.0000.000
190A236LEU00.0030.00727.3860.3830.3830.0000.0000.0000.000
191A237PRO00.0340.01927.5600.4140.4140.0000.0000.0000.000
192A238SER0-0.0190.00129.7720.3930.3930.0000.0000.0000.000
193A239TYR00.025-0.00731.6400.2930.2930.0000.0000.0000.000
194A240LEU0-0.0010.00032.2090.2940.2940.0000.0000.0000.000
195A241THR0-0.061-0.03834.1560.3370.3370.0000.0000.0000.000
196A242ILE0-0.043-0.01935.0580.2520.2520.0000.0000.0000.000
197A243VAL00.010-0.00637.1850.2400.2400.0000.0000.0000.000
198A244LYS10.9440.97236.6198.1508.1500.0000.0000.0000.000
199A245ARG10.7950.89439.1287.6637.6630.0000.0000.0000.000
200A246ARG10.8190.86942.1817.0347.0340.0000.0000.0000.000
201A247LYS10.8200.89641.8756.9506.9500.0000.0000.0000.000
202A248ASP-1-0.820-0.87344.520-6.493-6.4930.0000.0000.0000.000
203A249MET0-0.078-0.01447.2430.0830.0830.0000.0000.0000.000
204A250PRO00.0480.00949.436-0.014-0.0140.0000.0000.0000.000
205A251TYR0-0.0220.00149.508-0.046-0.0460.0000.0000.0000.000
206A252THR0-0.030-0.01853.2310.0420.0420.0000.0000.0000.000
207A253LYS11.0010.97354.1415.2545.2540.0000.0000.0000.000
208A254GLU-1-0.851-0.93054.647-5.281-5.2810.0000.0000.0000.000
209A255GLU-1-0.783-0.84752.650-5.703-5.7030.0000.0000.0000.000
210A256GLN0-0.016-0.01748.3010.0170.0170.0000.0000.0000.000
211A257GLN0-0.014-0.01150.611-0.037-0.0370.0000.0000.0000.000
212A258TRP00.0090.01152.546-0.048-0.0480.0000.0000.0000.000
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