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: LZGM9

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2650150.873006
FMO2-HF: Nuclear repulsion 2561929.866766
FMO2-HF: Total energy -88221.00624
FMO2-MP2: Total energy -88478.099209


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.
-58.981-56.8280.024-1.138-1.0390.001
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 : 0.959 / q_NPA : 0.974
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].
3A10LEU00.0230.0113.386-3.330-1.1770.024-1.138-1.0390.001
4A11PRO00.0310.0146.147-1.542-1.5420.0000.0000.0000.000
5A12ILE00.0680.0396.5921.9441.9440.0000.0000.0000.000
6A13ARG10.8940.9689.03020.62120.6210.0000.0000.0000.000
7A14GLN0-0.012-0.01210.1330.3220.3220.0000.0000.0000.000
8A15GLN0-0.022-0.0126.2313.1853.1850.0000.0000.0000.000
9A16MET00.0330.03011.3721.1521.1520.0000.0000.0000.000
10A17GLU-1-0.804-0.91114.320-13.751-13.7510.0000.0000.0000.000
11A18ALA0-0.016-0.01314.1180.9590.9590.0000.0000.0000.000
12A19LEU0-0.0100.00815.1010.8820.8820.0000.0000.0000.000
13A20ILE0-0.009-0.01016.9500.8910.8910.0000.0000.0000.000
14A21ARG10.8350.90419.19013.89313.8930.0000.0000.0000.000
15A22ARG10.7950.88815.92915.57315.5730.0000.0000.0000.000
16A23LYS10.7600.86619.60513.64713.6470.0000.0000.0000.000
17A24GLN0-0.040-0.04022.7080.2540.2540.0000.0000.0000.000
18A25ALA00.0040.02824.7960.4740.4740.0000.0000.0000.000
19A26GLU-1-0.790-0.89621.080-12.711-12.7110.0000.0000.0000.000
20A27ILE0-0.001-0.00624.7770.3610.3610.0000.0000.0000.000
21A28THR0-0.036-0.03227.9120.3810.3810.0000.0000.0000.000
22A29GLN00.0190.00327.8130.2090.2090.0000.0000.0000.000
23A30GLY00.0180.01630.2020.2360.2360.0000.0000.0000.000
24A31LEU0-0.030-0.01231.5510.2830.2830.0000.0000.0000.000
25A32GLU-1-0.768-0.88634.025-8.138-8.1380.0000.0000.0000.000
26A33SER0-0.125-0.06034.6030.2430.2430.0000.0000.0000.000
27A34ILE0-0.041-0.02136.5520.1540.1540.0000.0000.0000.000
28A35ASP-1-0.643-0.80139.178-7.009-7.0090.0000.0000.0000.000
29A36THR0-0.133-0.07041.0000.1220.1220.0000.0000.0000.000
30A37VAL0-0.0170.01241.1320.0210.0210.0000.0000.0000.000
31A38LYS10.8310.90036.3127.8777.8770.0000.0000.0000.000
32A39PHE0-0.002-0.01733.9700.0740.0740.0000.0000.0000.000
33A40HIS0-0.013-0.00235.832-0.086-0.0860.0000.0000.0000.000
34A41ALA0-0.028-0.02932.7610.1160.1160.0000.0000.0000.000
35A51GLY00.0030.00929.157-0.001-0.0010.0000.0000.0000.000
36A52GLY0-0.025-0.01130.0550.1680.1680.0000.0000.0000.000
37A53GLY00.0110.00026.940-0.351-0.3510.0000.0000.0000.000
38A54THR0-0.031-0.00725.2590.4340.4340.0000.0000.0000.000
39A55SER00.0460.01428.112-0.212-0.2120.0000.0000.0000.000
40A56MET00.0090.04129.8530.1940.1940.0000.0000.0000.000
41A57VAL0-0.013-0.02132.379-0.048-0.0480.0000.0000.0000.000
42A58ILE00.0250.02035.8130.0570.0570.0000.0000.0000.000
43A59GLN0-0.064-0.06038.384-0.133-0.1330.0000.0000.0000.000
44A60ASP-1-0.845-0.90742.049-6.570-6.5700.0000.0000.0000.000
45A61GLY00.0130.01742.5680.0760.0760.0000.0000.0000.000
46A62THR0-0.075-0.04443.5900.1620.1620.0000.0000.0000.000
47A63THR0-0.087-0.06040.4790.1590.1590.0000.0000.0000.000
48A64PHE0-0.041-0.03236.863-0.037-0.0370.0000.0000.0000.000
49A65GLU-1-0.890-0.92741.153-6.530-6.5300.0000.0000.0000.000
50A66LYS10.8840.91539.6797.2517.2510.0000.0000.0000.000
51A67GLY00.0090.00536.615-0.063-0.0630.0000.0000.0000.000
52A68GLY0-0.0060.00434.0340.1140.1140.0000.0000.0000.000
53A69VAL00.0190.00527.758-0.130-0.1300.0000.0000.0000.000
54A70ASN0-0.027-0.01727.7810.0860.0860.0000.0000.0000.000
55A71VAL00.0120.01322.336-0.270-0.2700.0000.0000.0000.000
56A72SER00.0120.00824.2660.3030.3030.0000.0000.0000.000
57A73VAL0-0.027-0.01519.725-0.494-0.4940.0000.0000.0000.000
58A74VAL0-0.027-0.00121.3580.5550.5550.0000.0000.0000.000
59A75TYR00.0550.03016.671-0.999-0.9990.0000.0000.0000.000
60A76GLY0-0.011-0.00321.6350.6200.6200.0000.0000.0000.000
61A77GLN00.000-0.01622.778-0.866-0.8660.0000.0000.0000.000
62A78LEU0-0.0090.02024.8820.4080.4080.0000.0000.0000.000
63A79SER00.0560.02427.379-0.176-0.1760.0000.0000.0000.000
64A80PRO00.0740.02930.076-0.120-0.1200.0000.0000.0000.000
65A81ALA0-0.021-0.00931.3430.0340.0340.0000.0000.0000.000
66A82ALA00.0050.00529.9760.0850.0850.0000.0000.0000.000
67A83VAL00.023-0.00626.402-0.080-0.0800.0000.0000.0000.000
68A84SER0-0.042-0.01728.860-0.074-0.0740.0000.0000.0000.000
69A85ALA0-0.025-0.01632.0360.0410.0410.0000.0000.0000.000
70A86MET0-0.025-0.00626.2010.0850.0850.0000.0000.0000.000
71A87LYS10.8830.94924.54711.48911.4890.0000.0000.0000.000
72A88ALA0-0.016-0.00728.494-0.185-0.1850.0000.0000.0000.000
73A89ASP-1-0.857-0.91328.038-10.524-10.5240.0000.0000.0000.000
74A90HIS10.7570.86722.94311.58911.5890.0000.0000.0000.000
75A91LYS10.7540.84620.17214.56414.5640.0000.0000.0000.000
76A107ASP-1-0.875-0.95828.318-9.911-9.9110.0000.0000.0000.000
77A108GLY0-0.046-0.01727.792-0.146-0.1460.0000.0000.0000.000
78A109VAL0-0.020-0.00521.348-0.339-0.3390.0000.0000.0000.000
79A110LYS10.9540.97620.57013.75313.7530.0000.0000.0000.000
80A111PHE0-0.034-0.01418.984-0.430-0.4300.0000.0000.0000.000
81A112PHE00.0270.00915.9690.2090.2090.0000.0000.0000.000
82A113ALA00.0120.00718.376-0.219-0.2190.0000.0000.0000.000
83A114CYS0-0.067-0.01417.0580.1630.1630.0000.0000.0000.000
84A115GLY00.0960.03020.133-0.219-0.2190.0000.0000.0000.000
85A116LEU0-0.0290.01321.6330.3080.3080.0000.0000.0000.000
86A117SER0-0.048-0.03424.099-0.027-0.0270.0000.0000.0000.000
87A118MET0-0.0170.00827.6710.1730.1730.0000.0000.0000.000
88A119VAL0-0.022-0.00630.2630.0270.0270.0000.0000.0000.000
89A120ILE0-0.0100.00033.1670.0560.0560.0000.0000.0000.000
90A121HIS00.0340.01236.0860.0990.0990.0000.0000.0000.000
91A122PRO00.008-0.00839.1920.0610.0610.0000.0000.0000.000
92A123VAL00.0240.03141.8460.0750.0750.0000.0000.0000.000
93A124ASN0-0.029-0.01645.1380.1570.1570.0000.0000.0000.000
94A125PRO00.0150.00545.142-0.143-0.1430.0000.0000.0000.000
95A126HIS00.005-0.00246.221-0.143-0.1430.0000.0000.0000.000
96A127ALA00.0080.00541.260-0.105-0.1050.0000.0000.0000.000
97A128PRO0-0.025-0.00638.1830.0430.0430.0000.0000.0000.000
98A129THR00.0290.02037.318-0.023-0.0230.0000.0000.0000.000
99A130THR0-0.068-0.03832.813-0.139-0.1390.0000.0000.0000.000
100A131HIS0-0.043-0.05132.3900.2560.2560.0000.0000.0000.000
101A132LEU00.0000.01124.950-0.113-0.1130.0000.0000.0000.000
102A133ASN0-0.020-0.01424.888-0.249-0.2490.0000.0000.0000.000
103A134TYR00.0400.02920.211-0.135-0.1350.0000.0000.0000.000
104A135ARG10.7870.87520.47511.65711.6570.0000.0000.0000.000
105A136TYR0-0.029-0.04711.992-0.481-0.4810.0000.0000.0000.000
106A137PHE00.0140.01017.1170.6750.6750.0000.0000.0000.000
107A138GLU-1-0.729-0.84312.143-21.574-21.5740.0000.0000.0000.000
108A139THR0-0.008-0.01115.8950.7620.7620.0000.0000.0000.000
109A140TRP0-0.046-0.04312.239-0.957-0.9570.0000.0000.0000.000
110A141ASN0-0.029-0.03617.2920.7940.7940.0000.0000.0000.000
111A142GLN0-0.018-0.01417.7720.2660.2660.0000.0000.0000.000
112A143ASP-1-0.844-0.90713.227-19.938-19.9380.0000.0000.0000.000
113A144GLY00.0230.02511.221-0.316-0.3160.0000.0000.0000.000
114A145THR0-0.122-0.0897.940-4.250-4.2500.0000.0000.0000.000
115A146PRO0-0.0170.00410.4340.9100.9100.0000.0000.0000.000
116A147GLN00.0220.00513.2350.7700.7700.0000.0000.0000.000
117A148THR0-0.035-0.01216.5170.2360.2360.0000.0000.0000.000
118A149TRP00.0110.00512.255-0.058-0.0580.0000.0000.0000.000
119A150TRP0-0.0250.00715.7800.0650.0650.0000.0000.0000.000
120A151PHE00.019-0.00312.368-0.041-0.0410.0000.0000.0000.000
121A152GLY00.007-0.00317.9310.4270.4270.0000.0000.0000.000
122A153GLY0-0.040-0.03321.071-0.352-0.3520.0000.0000.0000.000
123A154GLY00.0020.00823.2860.2540.2540.0000.0000.0000.000
124A155ALA00.0130.01426.134-0.039-0.0390.0000.0000.0000.000
125A156ASP-1-0.848-0.89728.730-8.550-8.5500.0000.0000.0000.000
126A157LEU00.0240.03332.4760.0500.0500.0000.0000.0000.000
127A158THR0-0.025-0.03635.7960.1330.1330.0000.0000.0000.000
128A159PRO0-0.018-0.01138.8060.0800.0800.0000.0000.0000.000
129A160SER00.0180.01441.8200.0590.0590.0000.0000.0000.000
130A161TYR0-0.009-0.03445.1390.1170.1170.0000.0000.0000.000
131A162LEU0-0.060-0.03142.638-0.173-0.1730.0000.0000.0000.000
132A163TYR00.007-0.01042.9060.1610.1610.0000.0000.0000.000
133A164GLU-1-0.816-0.90540.199-7.617-7.6170.0000.0000.0000.000
134A165GLU-1-0.790-0.88540.093-7.005-7.0050.0000.0000.0000.000
135A166ASP-1-0.780-0.86038.174-7.535-7.5350.0000.0000.0000.000
136A167GLY00.0170.00836.502-0.248-0.2480.0000.0000.0000.000
137A168GLN0-0.034-0.03935.436-0.305-0.3050.0000.0000.0000.000
138A169LEU0-0.0150.00533.622-0.231-0.2310.0000.0000.0000.000
139A170PHE00.0340.00330.812-0.311-0.3110.0000.0000.0000.000
140A171HIS0-0.049-0.01630.717-0.566-0.5660.0000.0000.0000.000
141A172GLN0-0.055-0.03030.146-0.128-0.1280.0000.0000.0000.000
142A173LEU00.0130.00228.278-0.287-0.2870.0000.0000.0000.000
143A174HIS0-0.035-0.03925.850-0.614-0.6140.0000.0000.0000.000
144A175LYS10.7990.88025.2829.7019.7010.0000.0000.0000.000
145A176ASP-1-0.810-0.88925.170-10.430-10.4300.0000.0000.0000.000
146A177ALA0-0.069-0.02422.073-0.405-0.4050.0000.0000.0000.000
147A178LEU00.0360.00220.842-0.595-0.5950.0000.0000.0000.000
148A179ASP-1-0.779-0.90520.974-11.433-11.4330.0000.0000.0000.000
149A180LYS10.7560.88918.83212.90312.9030.0000.0000.0000.000
150A181HIS0-0.075-0.03814.525-1.082-1.0820.0000.0000.0000.000
151A182ASP-1-0.753-0.86618.109-13.922-13.9220.0000.0000.0000.000
152A183THR0-0.008-0.00221.2940.1090.1090.0000.0000.0000.000
153A184ALA0-0.033-0.00824.0790.5230.5230.0000.0000.0000.000
154A185LEU0-0.050-0.01419.0330.2480.2480.0000.0000.0000.000
155A186TYR00.0920.03623.6650.4510.4510.0000.0000.0000.000
156A187PRO0-0.059-0.04626.4730.3080.3080.0000.0000.0000.000
157A188ARG10.7810.86521.66512.85012.8500.0000.0000.0000.000
158A189PHE00.0280.01621.0760.0280.0280.0000.0000.0000.000
159A190LYS10.8810.96026.9979.1179.1170.0000.0000.0000.000
160A191LYS10.9230.96330.1708.6068.6060.0000.0000.0000.000
161A207GLY00.0220.01040.9460.0570.0570.0000.0000.0000.000
162A208ILE0-0.024-0.00135.8230.0530.0530.0000.0000.0000.000
163A209GLY00.0060.01535.097-0.125-0.1250.0000.0000.0000.000
164A210GLY00.0520.00531.3200.0210.0210.0000.0000.0000.000
165A211ILE0-0.032-0.00624.5240.0480.0480.0000.0000.0000.000
166A212PHE0-0.009-0.01926.6440.0070.0070.0000.0000.0000.000
167A213PHE00.0240.02119.378-0.062-0.0620.0000.0000.0000.000
168A214ASP-1-0.744-0.88222.779-12.121-12.1210.0000.0000.0000.000
169A215ASP-1-0.776-0.85121.326-13.212-13.2120.0000.0000.0000.000
170A216TYR0-0.0120.00516.888-0.293-0.2930.0000.0000.0000.000
171A217ASP-1-0.782-0.90815.456-16.112-16.1120.0000.0000.0000.000
172A218GLU-1-0.811-0.86815.207-14.555-14.5550.0000.0000.0000.000
173A219ARG10.8260.90312.99216.17916.1790.0000.0000.0000.000
174A220ASP-1-0.810-0.8986.491-34.332-34.3320.0000.0000.0000.000
175A221PRO00.0290.0037.9801.2561.2560.0000.0000.0000.000
176A222GLN0-0.039-0.0175.348-2.069-2.0690.0000.0000.0000.000
177A223GLU-1-0.892-0.9547.769-20.061-20.0610.0000.0000.0000.000
178A224ILE0-0.025-0.00710.8971.4531.4530.0000.0000.0000.000
179A225LEU0-0.019-0.0048.8391.2901.2900.0000.0000.0000.000
180A226LYS10.8130.91311.88617.35417.3540.0000.0000.0000.000
181A227MET00.0130.02613.5061.1501.1500.0000.0000.0000.000
182A228VAL00.0270.00515.8181.0561.0560.0000.0000.0000.000
183A229GLU-1-0.813-0.89315.974-15.515-15.5150.0000.0000.0000.000
184A230ASP-1-0.795-0.89117.445-14.093-14.0930.0000.0000.0000.000
185A231CYS0-0.063-0.03719.6350.7710.7710.0000.0000.0000.000
186A232PHE00.019-0.00619.3590.6280.6280.0000.0000.0000.000
187A233ASP-1-0.838-0.90820.895-12.217-12.2170.0000.0000.0000.000
188A234ALA0-0.0030.01823.5180.3520.3520.0000.0000.0000.000
189A235PHE00.0070.01125.9140.4820.4820.0000.0000.0000.000
190A236LEU00.0030.00627.2920.3740.3740.0000.0000.0000.000
191A237PRO00.0160.00427.3870.3980.3980.0000.0000.0000.000
192A238SER0-0.0120.00829.9050.3680.3680.0000.0000.0000.000
193A239TYR00.027-0.01231.7680.2920.2920.0000.0000.0000.000
194A240LEU00.0050.00732.0890.2760.2760.0000.0000.0000.000
195A241THR0-0.058-0.04034.0360.3180.3180.0000.0000.0000.000
196A242ILE0-0.055-0.02034.9500.2390.2390.0000.0000.0000.000
197A243VAL00.0220.01137.3700.2290.2290.0000.0000.0000.000
198A244LYS10.9370.96836.1578.2128.2120.0000.0000.0000.000
199A245ARG10.7820.89038.8877.6527.6520.0000.0000.0000.000
200A246ARG10.7930.84841.9617.0287.0280.0000.0000.0000.000
201A247LYS10.8290.90142.1546.9196.9190.0000.0000.0000.000
202A248ASP-1-0.813-0.87044.624-6.469-6.4690.0000.0000.0000.000
203A249MET0-0.056-0.00347.3790.0860.0860.0000.0000.0000.000
204A250PRO00.0310.00249.608-0.012-0.0120.0000.0000.0000.000
205A251TYR0-0.0210.00349.940-0.038-0.0380.0000.0000.0000.000
206A252THR0-0.011-0.01653.4410.0470.0470.0000.0000.0000.000
207A253LYS11.0170.99254.2335.2075.2070.0000.0000.0000.000
208A254GLU-1-0.873-0.93254.953-5.287-5.2870.0000.0000.0000.000
209A255GLU-1-0.768-0.83552.846-5.680-5.6800.0000.0000.0000.000
210A256GLN0-0.010-0.00748.8420.0300.0300.0000.0000.0000.000
211A257GLN0-0.021-0.02250.793-0.053-0.0530.0000.0000.0000.000
212A258TRP0-0.0040.00252.703-0.054-0.0540.0000.0000.0000.000
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