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: NN8NQ

Calculation Name: 4TR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TR5

Chain ID: A

ChEMBL ID:

UniProt ID: W2E3J5

Base Structure: X-ray

Registration Date: 2023-09-22

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2308362.238305
FMO2-HF: Nuclear repulsion 2228146.954019
FMO2-HF: Total energy -80215.284286
FMO2-MP2: Total energy -80453.419389


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:14:GLU)


Summations of interaction energy for fragment #1(A:14:GLU)
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.
-226.348-225.94319.786-10.721-9.4680.097
Interaction energy analysis for fragmet #1(A:14:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.901 / q_NPA : -0.952
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].
3A16LEU00.0540.0282.8502.5525.5230.339-1.593-1.7170.000
4A17TYR0-0.067-0.0511.801-35.141-37.86319.448-9.115-7.6100.097
5A18PHE00.0320.0066.634-1.955-1.9550.0000.0000.0000.000
6A19GLN0-0.003-0.00810.222-0.028-0.0280.0000.0000.0000.000
7A20GLY00.0080.0249.509-0.838-0.8380.0000.0000.0000.000
8A21SER0-0.080-0.0529.4422.8622.8620.0000.0000.0000.000
9A22HIS00.0170.02710.695-2.604-2.6040.0000.0000.0000.000
10A23MET0-0.010-0.01913.504-2.115-2.1150.0000.0000.0000.000
11A24VAL0-0.014-0.01012.8191.9111.9110.0000.0000.0000.000
12A25GLY00.0440.02011.851-1.639-1.6390.0000.0000.0000.000
13A26GLU-1-0.832-0.9199.56128.92328.9230.0000.0000.0000.000
14A27LYS10.8920.9584.561-47.648-47.492-0.001-0.013-0.1410.000
15A28GLU-1-0.890-0.9558.09633.94833.9480.0000.0000.0000.000
16A29TYR00.0110.00610.367-1.364-1.3640.0000.0000.0000.000
17A30LYS10.9940.9966.520-39.300-39.3000.0000.0000.0000.000
18A31ALA0-0.012-0.0157.559-0.970-0.9700.0000.0000.0000.000
19A32TRP0-0.024-0.0269.272-1.607-1.6070.0000.0000.0000.000
20A33GLU-1-0.872-0.94612.90217.70817.7080.0000.0000.0000.000
21A34LYS10.8450.9258.273-31.212-31.2120.0000.0000.0000.000
22A35LYS10.8730.92310.807-27.478-27.4780.0000.0000.0000.000
23A36LEU0-0.049-0.00714.452-1.620-1.6200.0000.0000.0000.000
24A37ARG10.9250.95717.739-13.956-13.9560.0000.0000.0000.000
25A38ALA00.0540.01620.5610.0580.0580.0000.0000.0000.000
26A39ASN00.0380.00422.2620.0020.0020.0000.0000.0000.000
27A40GLU-1-0.819-0.89620.64415.18715.1870.0000.0000.0000.000
28A41LYS10.9801.00116.681-18.660-18.6600.0000.0000.0000.000
29A42GLU-1-0.881-0.94321.61812.42112.4210.0000.0000.0000.000
30A43LEU0-0.011-0.00325.193-0.413-0.4130.0000.0000.0000.000
31A44VAL00.0270.01621.097-0.352-0.3520.0000.0000.0000.000
32A45LYS10.9310.97222.995-13.335-13.3350.0000.0000.0000.000
33A46GLU-1-0.838-0.89825.47110.04110.0410.0000.0000.0000.000
34A47TYR0-0.017-0.01826.228-0.605-0.6050.0000.0000.0000.000
35A48THR0-0.058-0.04424.951-0.138-0.1380.0000.0000.0000.000
36A49ALA0-0.045-0.00527.462-0.242-0.2420.0000.0000.0000.000
37A50ASN0-0.006-0.00930.413-0.363-0.3630.0000.0000.0000.000
38A51ALA00.1040.05130.106-0.115-0.1150.0000.0000.0000.000
39A52LYS10.9280.94831.957-9.365-9.3650.0000.0000.0000.000
40A53PRO0-0.0010.00335.010-0.168-0.1680.0000.0000.0000.000
41A54PHE00.0350.02532.383-0.157-0.1570.0000.0000.0000.000
42A55ASN00.0510.01030.498-0.057-0.0570.0000.0000.0000.000
43A56THR0-0.028-0.00734.343-0.145-0.1450.0000.0000.0000.000
44A57TYR0-0.061-0.02636.323-0.328-0.3280.0000.0000.0000.000
45A58LEU00.0260.01032.107-0.146-0.1460.0000.0000.0000.000
46A59ARG10.8660.92634.262-9.353-9.3530.0000.0000.0000.000
47A60ALA0-0.040-0.00638.238-0.151-0.1510.0000.0000.0000.000
48A61ASN0-0.039-0.01840.044-0.348-0.3480.0000.0000.0000.000
49A62GLU-1-0.905-0.94838.5627.9227.9220.0000.0000.0000.000
50A63GLY0-0.065-0.04335.5100.1180.1180.0000.0000.0000.000
51A64LYS10.9360.97435.860-7.481-7.4810.0000.0000.0000.000
52A65LEU0-0.045-0.02833.5960.0200.0200.0000.0000.0000.000
53A66GLY00.0200.00838.255-0.157-0.1570.0000.0000.0000.000
54A67PHE0-0.0130.00441.024-0.182-0.1820.0000.0000.0000.000
55A68LYS10.9270.96539.803-8.069-8.0690.0000.0000.0000.000
56A69PRO00.1070.05938.9920.2910.2910.0000.0000.0000.000
57A70GLU-1-0.850-0.94137.6868.7718.7710.0000.0000.0000.000
58A71ILE0-0.043-0.02035.3500.2950.2950.0000.0000.0000.000
59A72ASP-1-0.739-0.88334.2809.0099.0090.0000.0000.0000.000
60A73LYS10.8880.94633.535-8.349-8.3490.0000.0000.0000.000
61A74LYS10.8490.91230.712-9.477-9.4770.0000.0000.0000.000
62A75ILE00.0370.02429.3790.4600.4600.0000.0000.0000.000
63A76LEU00.0140.01529.0590.4020.4020.0000.0000.0000.000
64A77LYS10.9050.95227.075-10.593-10.5930.0000.0000.0000.000
65A78LEU00.0090.01024.0950.6520.6520.0000.0000.0000.000
66A79ASP-1-0.771-0.86924.12112.17512.1750.0000.0000.0000.000
67A80GLU-1-0.886-0.93923.69813.54013.5400.0000.0000.0000.000
68A81ALA00.0050.01120.7320.7980.7980.0000.0000.0000.000
69A82LEU0-0.005-0.01119.2401.1421.1420.0000.0000.0000.000
70A83LYS10.8690.94119.536-12.303-12.3030.0000.0000.0000.000
71A84LYS10.7980.91915.921-16.159-16.1590.0000.0000.0000.000
72A85SER0-0.0140.00613.3271.4231.4230.0000.0000.0000.000
73A86LYS10.9590.98613.778-19.495-19.4950.0000.0000.0000.000
74A87LEU00.0020.01113.1622.0682.0680.0000.0000.0000.000
75A88SER00.0330.0149.002-2.062-2.0620.0000.0000.0000.000
76A89GLU-1-0.908-0.96310.74926.87126.8710.0000.0000.0000.000
77A90THR0-0.042-0.03113.939-0.409-0.4090.0000.0000.0000.000
78A91VAL00.0330.03414.7980.3850.3850.0000.0000.0000.000
79A92GLN0-0.009-0.01917.601-1.479-1.4790.0000.0000.0000.000
80A93VAL0-0.0140.01019.6290.4920.4920.0000.0000.0000.000
81A94TYR0-0.034-0.04221.877-0.878-0.8780.0000.0000.0000.000
82A95ARG10.8390.90725.291-10.707-10.7070.0000.0000.0000.000
83A96GLY00.0240.03228.273-0.207-0.2070.0000.0000.0000.000
84A97ASP-1-0.863-0.94531.29910.10710.1070.0000.0000.0000.000
85A98ASP-1-0.825-0.92034.4928.3788.3780.0000.0000.0000.000
86A99THR0-0.006-0.01938.2420.1120.1120.0000.0000.0000.000
87A100SER0-0.003-0.01439.730-0.083-0.0830.0000.0000.0000.000
88A101ILE0-0.026-0.00834.219-0.062-0.0620.0000.0000.0000.000
89A102PHE0-0.008-0.00138.1980.0610.0610.0000.0000.0000.000
90A103GLY00.0380.03241.130-0.145-0.1450.0000.0000.0000.000
91A104LYS10.9670.93743.650-6.908-6.9080.0000.0000.0000.000
92A105GLU-1-0.926-0.93847.2796.6376.6370.0000.0000.0000.000
93A106PHE00.0520.01444.465-0.083-0.0830.0000.0000.0000.000
94A107GLN0-0.062-0.01044.1580.0210.0210.0000.0000.0000.000
95A108ASN00.016-0.00545.2510.1520.1520.0000.0000.0000.000
96A109SER00.0310.03148.306-0.096-0.0960.0000.0000.0000.000
97A110ILE0-0.040-0.03243.090-0.017-0.0170.0000.0000.0000.000
98A111TYR0-0.065-0.08740.4200.1300.1300.0000.0000.0000.000
99A112GLN00.0290.01346.370-0.130-0.1300.0000.0000.0000.000
100A113GLY00.0120.01049.040-0.010-0.0100.0000.0000.0000.000
101A114ASN0-0.005-0.01843.6750.1180.1180.0000.0000.0000.000
102A115LYS10.9500.98944.698-6.711-6.7110.0000.0000.0000.000
103A116VAL00.0220.01441.659-0.068-0.0680.0000.0000.0000.000
104A117ASN00.0410.03045.018-0.098-0.0980.0000.0000.0000.000
105A118ARG10.9050.92745.007-7.062-7.0620.0000.0000.0000.000
106A119GLU-1-0.915-0.96147.5306.1516.1510.0000.0000.0000.000
107A120LEU0-0.025-0.00947.5980.0270.0270.0000.0000.0000.000
108A121PHE00.0190.00939.6780.1060.1060.0000.0000.0000.000
109A122ARG10.9110.95444.184-6.506-6.5060.0000.0000.0000.000
110A123LYS11.0401.02545.888-6.235-6.2350.0000.0000.0000.000
111A124LEU0-0.0160.01140.9080.0770.0770.0000.0000.0000.000
112A125ARG10.8880.93740.472-7.327-7.3270.0000.0000.0000.000
113A126ASP-1-0.911-0.95641.7217.2157.2150.0000.0000.0000.000
114A127GLU-1-0.968-0.96742.5867.4157.4150.0000.0000.0000.000
115A128TYR0-0.050-0.03338.2720.2280.2280.0000.0000.0000.000
116A129GLN00.0300.00637.2440.3980.3980.0000.0000.0000.000
117A130GLY0-0.016-0.00936.735-0.190-0.1900.0000.0000.0000.000
118A131LYS10.8970.96137.352-7.539-7.5390.0000.0000.0000.000
119A132ILE0-0.002-0.00333.2300.3090.3090.0000.0000.0000.000
120A133ARG10.9170.96334.074-8.625-8.6250.0000.0000.0000.000
121A134THR00.0380.00132.8080.3990.3990.0000.0000.0000.000
122A135GLU-1-0.827-0.88230.5729.6179.6170.0000.0000.0000.000
123A136TYR00.006-0.00731.5820.3850.3850.0000.0000.0000.000
124A137GLY0-0.004-0.00132.2010.0630.0630.0000.0000.0000.000
125A138TYR0-0.006-0.03126.3070.0370.0370.0000.0000.0000.000
126A139LEU0-0.0230.00126.563-0.330-0.3300.0000.0000.0000.000
127A140SER0-0.008-0.00724.7460.4710.4710.0000.0000.0000.000
128A141THR0-0.049-0.02822.328-0.367-0.3670.0000.0000.0000.000
129A142SER0-0.008-0.00822.0960.4080.4080.0000.0000.0000.000
130A143ILE00.0370.01915.863-0.289-0.2890.0000.0000.0000.000
131A144VAL0-0.016-0.00319.447-0.175-0.1750.0000.0000.0000.000
132A145SER00.0280.03217.3061.2591.2590.0000.0000.0000.000
133A146ASN00.0480.00618.7410.3630.3630.0000.0000.0000.000
134A147GLN0-0.012-0.00521.597-1.177-1.1770.0000.0000.0000.000
135A148GLN00.0260.02023.7780.1450.1450.0000.0000.0000.000
136A149PHE0-0.039-0.03125.116-0.522-0.5220.0000.0000.0000.000
137A150ALA00.012-0.00329.0380.0340.0340.0000.0000.0000.000
138A151MET00.0080.00431.625-0.108-0.1080.0000.0000.0000.000
139A152ARG10.8820.96333.205-9.654-9.6540.0000.0000.0000.000
140A153PRO00.0610.03735.7960.0640.0640.0000.0000.0000.000
141A154VAL00.0010.01634.476-0.043-0.0430.0000.0000.0000.000
142A155LEU00.0120.02028.4770.2450.2450.0000.0000.0000.000
143A156THR00.004-0.00628.923-0.184-0.1840.0000.0000.0000.000
144A157THR0-0.089-0.03625.3360.2290.2290.0000.0000.0000.000
145A158LEU00.0310.01524.312-0.303-0.3030.0000.0000.0000.000
146A159LYS10.9650.99222.267-12.127-12.1270.0000.0000.0000.000
147A160VAL00.011-0.00319.402-0.569-0.5690.0000.0000.0000.000
148A161PRO00.0210.01619.2350.8750.8750.0000.0000.0000.000
149A162LYS10.9850.99114.383-20.367-20.3670.0000.0000.0000.000
150A163GLY0-0.051-0.02616.429-0.867-0.8670.0000.0000.0000.000
151A164ALA0-0.0160.00217.991-0.656-0.6560.0000.0000.0000.000
152A165HIS0-0.007-0.01017.8860.5860.5860.0000.0000.0000.000
153A166ALA0-0.002-0.01217.498-0.846-0.8460.0000.0000.0000.000
154A167GLY00.0330.03617.2810.9380.9380.0000.0000.0000.000
155A168TYR0-0.019-0.00814.1410.1900.1900.0000.0000.0000.000
156A169VAL00.005-0.00117.480-0.027-0.0270.0000.0000.0000.000
157A170ASP-1-0.846-0.92018.31517.60517.6050.0000.0000.0000.000
158A171LYS10.8200.89919.737-13.579-13.5790.0000.0000.0000.000
159A172ILE0-0.051-0.00217.684-0.804-0.8040.0000.0000.0000.000
160A173SER0-0.029-0.05421.873-0.374-0.3740.0000.0000.0000.000
161A174GLN00.023-0.00823.6480.0300.0300.0000.0000.0000.000
162A175TYR00.0140.02124.9480.1230.1230.0000.0000.0000.000
163A176LYS10.8880.94326.139-11.313-11.3130.0000.0000.0000.000
164A177GLY00.0360.07424.1270.0980.0980.0000.0000.0000.000
165A178GLN00.0230.00120.1650.2280.2280.0000.0000.0000.000
166A179TYR00.0820.04414.5490.0910.0910.0000.0000.0000.000
167A180GLU-1-0.869-0.93318.45212.86612.8660.0000.0000.0000.000
168A181LEU0-0.0030.00717.0240.9800.9800.0000.0000.0000.000
169A182LEU0-0.046-0.02619.631-0.989-0.9890.0000.0000.0000.000
170A183LEU0-0.004-0.00921.5820.4690.4690.0000.0000.0000.000
171A184PRO00.0430.01222.308-0.492-0.4920.0000.0000.0000.000
172A185ARG10.8260.91625.054-10.764-10.7640.0000.0000.0000.000
173A186ASN0-0.054-0.04228.581-0.030-0.0300.0000.0000.0000.000
174A187THR00.0100.01526.3750.1620.1620.0000.0000.0000.000
175A188LYS10.9590.97728.573-10.704-10.7040.0000.0000.0000.000
176A189TYR00.004-0.00628.5240.4270.4270.0000.0000.0000.000
177A190LYS10.9290.96930.078-9.863-9.8630.0000.0000.0000.000
178A191ILE00.0170.00831.1950.3450.3450.0000.0000.0000.000
179A192ASP-1-0.828-0.83129.51810.54110.5410.0000.0000.0000.000
180A193LYS10.9330.95933.062-9.206-9.2060.0000.0000.0000.000
181A194MET0-0.0060.00434.1820.1890.1890.0000.0000.0000.000
182A195TYR0-0.125-0.09131.583-0.362-0.3620.0000.0000.0000.000
183A196ILE00.0100.00837.3520.1290.1290.0000.0000.0000.000
184A197ILE0-0.0010.00232.894-0.017-0.0170.0000.0000.0000.000
185A198VAL00.0110.00237.361-0.099-0.0990.0000.0000.0000.000
186A199ASN0-0.0060.00035.4080.0760.0760.0000.0000.0000.000
187A200LYS11.0040.99038.882-7.930-7.9300.0000.0000.0000.000
188A201GLY0-0.011-0.00840.6060.0770.0770.0000.0000.0000.000
189A202SER00.0160.00938.903-0.041-0.0410.0000.0000.0000.000
190A203GLU-1-0.815-0.88640.2117.3887.3880.0000.0000.0000.000
191A204THR00.0360.06834.3010.0090.0090.0000.0000.0000.000
192A205ILE0-0.033-0.01437.279-0.047-0.0470.0000.0000.0000.000
193A206LYS10.8900.94428.838-10.585-10.5850.0000.0000.0000.000
194A207ILE00.012-0.00332.378-0.219-0.2190.0000.0000.0000.000
195A208GLU-1-0.847-0.91429.57211.04411.0440.0000.0000.0000.000
196A209ALA00.009-0.00128.780-0.329-0.3290.0000.0000.0000.000
197A210THR0-0.060-0.10325.5390.6670.6670.0000.0000.0000.000
198A211VAL0-0.022-0.00424.002-0.448-0.4480.0000.0000.0000.000
199A212GLN0-0.013-0.01325.3710.5110.5110.0000.0000.0000.000
200A213PRO00.0000.00923.448-0.176-0.1760.0000.0000.0000.000