Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3QZ3L

Calculation Name: 1TUE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUE

Chain ID: B

ChEMBL ID:

UniProt ID: P06789

Base Structure: X-ray

Registration Date: 2023-03-13

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2106143.948119
FMO2-HF: Nuclear repulsion 2025543.653509
FMO2-HF: Total energy -80600.294609
FMO2-MP2: Total energy -80832.878481


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(B:0:HIS)


Summations of interaction energy for fragment #1(B:0:HIS)
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.
-37.202-34.2913.662-7.626-8.948-0.066
Interaction energy analysis for fragmet #1(B:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.026
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].
3B2GLN0-0.0150.0052.911-5.455-0.3981.189-2.109-4.1370.004
4B3THR00.0190.0083.6242.8573.1540.0090.030-0.3360.001
5B4PRO00.0480.0035.759-0.465-0.4650.0000.0000.0000.000
6B5LYS10.9140.9587.7492.5382.5380.0000.0000.0000.000
7B6GLU-1-0.803-0.8811.811-36.595-39.03712.464-5.547-4.475-0.071
8B7THR00.0490.0105.9680.9090.9090.0000.0000.0000.000
9B8LEU0-0.075-0.0318.3460.6420.6420.0000.0000.0000.000
10B9SER0-0.045-0.0278.3150.2010.2010.0000.0000.0000.000
11B10GLU-1-0.835-0.9117.376-2.219-2.2190.0000.0000.0000.000
12B11ARG10.9050.9319.9412.0632.0630.0000.0000.0000.000
13B12LEU0-0.008-0.00113.1600.1960.1960.0000.0000.0000.000
14B13SER0-0.055-0.03312.8790.1320.1320.0000.0000.0000.000
15B14ALA00.0370.02314.0160.1600.1600.0000.0000.0000.000
16B15LEU0-0.069-0.03715.8040.1370.1370.0000.0000.0000.000
17B16GLN0-0.018-0.04018.0810.0100.0100.0000.0000.0000.000
18B17ASP-1-0.834-0.90016.191-0.857-0.8570.0000.0000.0000.000
19B18LYS10.9510.97619.5470.6620.6620.0000.0000.0000.000
20B19ILE0-0.058-0.02921.7730.0550.0550.0000.0000.0000.000
21B20ILE00.0130.01021.8460.0430.0430.0000.0000.0000.000
22B21ASP-1-0.858-0.91922.545-0.418-0.4180.0000.0000.0000.000
23B22HIS0-0.080-0.05325.4070.0560.0560.0000.0000.0000.000
24B23TYR0-0.063-0.03727.2800.0130.0130.0000.0000.0000.000
25B24GLU-1-0.951-0.97326.828-0.317-0.3170.0000.0000.0000.000
26B25ASN0-0.104-0.06628.1020.0440.0440.0000.0000.0000.000
27B26ASP-1-0.874-0.92131.380-0.206-0.2060.0000.0000.0000.000
28B27SER0-0.013-0.01432.7090.0260.0260.0000.0000.0000.000
29B28LYS10.8650.91834.5550.1980.1980.0000.0000.0000.000
30B29ASP-1-0.770-0.84434.532-0.220-0.2200.0000.0000.0000.000
31B30ILE00.0620.01835.572-0.016-0.0160.0000.0000.0000.000
32B31ASP-1-0.855-0.91233.477-0.234-0.2340.0000.0000.0000.000
33B32SER0-0.063-0.04831.029-0.025-0.0250.0000.0000.0000.000
34B33GLN00.0410.02630.660-0.045-0.0450.0000.0000.0000.000
35B34ILE0-0.054-0.02331.321-0.024-0.0240.0000.0000.0000.000
36B35GLN0-0.022-0.00826.013-0.049-0.0490.0000.0000.0000.000
37B36TYR00.0400.02726.868-0.037-0.0370.0000.0000.0000.000
38B37TRP00.0380.00127.057-0.056-0.0560.0000.0000.0000.000
39B38GLN0-0.037-0.02625.822-0.038-0.0380.0000.0000.0000.000
40B39LEU0-0.019-0.00221.630-0.053-0.0530.0000.0000.0000.000
41B40ILE00.0290.03322.801-0.070-0.0700.0000.0000.0000.000
42B41ARG10.8820.93924.4560.3890.3890.0000.0000.0000.000
43B42TRP0-0.023-0.01220.122-0.038-0.0380.0000.0000.0000.000
44B43GLU-1-0.760-0.84319.519-0.791-0.7910.0000.0000.0000.000
45B44ASN0-0.076-0.06619.797-0.071-0.0710.0000.0000.0000.000
46B45ALA00.0000.00521.007-0.005-0.0050.0000.0000.0000.000
47B46ILE0-0.0060.00314.851-0.044-0.0440.0000.0000.0000.000
48B47PHE00.019-0.00417.069-0.092-0.0920.0000.0000.0000.000
49B48PHE0-0.052-0.01818.9050.0110.0110.0000.0000.0000.000
50B49ALA00.0590.02817.3280.0000.0000.0000.0000.0000.000
51B50ALA0-0.015-0.00414.994-0.066-0.0660.0000.0000.0000.000
52B51ARG10.8280.90515.9480.7360.7360.0000.0000.0000.000
53B52GLU-1-0.918-0.97118.932-0.675-0.6750.0000.0000.0000.000
54B53HIS0-0.098-0.04813.061-0.030-0.0300.0000.0000.0000.000
55B54GLY00.0060.00814.995-0.103-0.1030.0000.0000.0000.000
56B55ILE0-0.086-0.03811.662-0.064-0.0640.0000.0000.0000.000
57B56GLN00.0090.00315.0270.0450.0450.0000.0000.0000.000
58B57THR00.007-0.00614.7370.0110.0110.0000.0000.0000.000
59B58LEU00.009-0.00811.420-0.309-0.3090.0000.0000.0000.000
60B59ASN00.0470.04011.857-0.118-0.1180.0000.0000.0000.000
61B60HIS0-0.006-0.00213.3790.1580.1580.0000.0000.0000.000
62B61GLN00.0080.02216.0380.2120.2120.0000.0000.0000.000
63B62VAL0-0.009-0.01517.297-0.119-0.1190.0000.0000.0000.000
64B63VAL0-0.0020.01516.4280.0360.0360.0000.0000.0000.000
65B64PRO00.0290.02919.4480.0680.0680.0000.0000.0000.000
66B65ALA00.0270.02322.777-0.031-0.0310.0000.0000.0000.000
67B66TYR00.0560.01022.4040.0200.0200.0000.0000.0000.000
68B67ASN00.017-0.00225.852-0.021-0.0210.0000.0000.0000.000
69B68ILE00.0160.01826.6500.0190.0190.0000.0000.0000.000
70B69SER00.0450.02422.9530.0020.0020.0000.0000.0000.000
71B70LYS10.9580.97125.3730.4540.4540.0000.0000.0000.000
72B71SER0-0.0200.00627.8520.0260.0260.0000.0000.0000.000
73B72LYS10.9230.94624.3410.6160.6160.0000.0000.0000.000
74B73ALA0-0.0060.00026.0390.0080.0080.0000.0000.0000.000
75B74HIS0-0.044-0.01927.8750.0040.0040.0000.0000.0000.000
76B75LYS10.8430.89831.5940.3200.3200.0000.0000.0000.000
77B76ALA00.0320.02128.5920.0150.0150.0000.0000.0000.000
78B77ILE0-0.082-0.05029.1180.0090.0090.0000.0000.0000.000
79B78GLU-1-0.836-0.91631.905-0.264-0.2640.0000.0000.0000.000
80B79LEU00.0500.02533.6820.0170.0170.0000.0000.0000.000
81B80GLN0-0.0030.00829.832-0.013-0.0130.0000.0000.0000.000
82B81MET0-0.052-0.03233.6270.0150.0150.0000.0000.0000.000
83B82ALA00.0090.02036.3010.0160.0160.0000.0000.0000.000
84B83LEU00.0310.01234.6150.0120.0120.0000.0000.0000.000
85B84GLN00.003-0.00133.656-0.005-0.0050.0000.0000.0000.000
86B85GLY00.0230.01937.4940.0110.0110.0000.0000.0000.000
87B86LEU0-0.0010.00640.6750.0120.0120.0000.0000.0000.000
88B87ALA0-0.0110.00238.4720.0110.0110.0000.0000.0000.000
89B88GLN0-0.074-0.03840.0130.0060.0060.0000.0000.0000.000
90B89SER0-0.034-0.02042.8560.0110.0110.0000.0000.0000.000
91B90ALA0-0.005-0.02045.383-0.001-0.0010.0000.0000.0000.000
92B91TYR0-0.008-0.01846.0230.0040.0040.0000.0000.0000.000
93B92LYS10.8110.91337.4840.1900.1900.0000.0000.0000.000
94B93THR0-0.009-0.01841.827-0.006-0.0060.0000.0000.0000.000
95B94GLU-1-0.791-0.83343.850-0.144-0.1440.0000.0000.0000.000
96B95ASP-1-0.891-0.94641.771-0.168-0.1680.0000.0000.0000.000
97B96TRP0-0.063-0.04738.933-0.003-0.0030.0000.0000.0000.000
98B97THR0-0.018-0.03237.264-0.014-0.0140.0000.0000.0000.000
99B98LEU00.0540.02831.140-0.006-0.0060.0000.0000.0000.000
100B99GLN0-0.0050.00235.203-0.012-0.0120.0000.0000.0000.000
101B100ASP-1-0.812-0.87838.291-0.196-0.1960.0000.0000.0000.000
102B101THR0-0.050-0.04035.963-0.002-0.0020.0000.0000.0000.000
103B102CYS0-0.0360.01835.027-0.017-0.0170.0000.0000.0000.000
104B103GLU-1-0.778-0.89733.615-0.329-0.3290.0000.0000.0000.000
105B104GLU-1-0.941-0.97036.231-0.244-0.2440.0000.0000.0000.000
106B105LEU00.0160.01038.6340.0120.0120.0000.0000.0000.000
107B106TRP0-0.061-0.03138.4290.0140.0140.0000.0000.0000.000
108B107ASN0-0.014-0.02937.2290.0090.0090.0000.0000.0000.000
109B108THR0-0.036-0.00641.2780.0080.0080.0000.0000.0000.000
110B109GLU-1-0.802-0.87844.425-0.182-0.1820.0000.0000.0000.000
111B110PRO0-0.028-0.01847.7200.0040.0040.0000.0000.0000.000
112B111THR0-0.007-0.02143.628-0.005-0.0050.0000.0000.0000.000
113B112HIS0-0.063-0.03839.8650.0130.0130.0000.0000.0000.000
114B113CYS0-0.0340.00343.3310.0070.0070.0000.0000.0000.000
115B114PHE00.0120.00538.762-0.008-0.0080.0000.0000.0000.000
116B115LYS10.7810.87943.8330.2120.2120.0000.0000.0000.000
117B116LYS10.8360.92343.5740.1690.1690.0000.0000.0000.000
118B117GLY00.0290.01747.5770.0050.0050.0000.0000.0000.000
119B118GLY00.0340.00649.8290.0020.0020.0000.0000.0000.000
120B119GLN0-0.052-0.03250.7990.0040.0040.0000.0000.0000.000
121B120THR0-0.015-0.00954.433-0.003-0.0030.0000.0000.0000.000
122B121VAL00.0090.00255.3070.0050.0050.0000.0000.0000.000
123B122GLN00.0240.03256.765-0.001-0.0010.0000.0000.0000.000
124B123VAL0-0.008-0.01558.8330.0040.0040.0000.0000.0000.000
125B124TYR00.0020.00660.027-0.003-0.0030.0000.0000.0000.000
126B125PHE00.026-0.00858.3260.0020.0020.0000.0000.0000.000
127B126ASP-1-0.789-0.88563.901-0.102-0.1020.0000.0000.0000.000
128B127GLY0-0.0200.00767.2630.0030.0030.0000.0000.0000.000
129B128ASN0-0.061-0.04664.4310.0030.0030.0000.0000.0000.000
130B129LYS10.8100.89464.7210.0910.0910.0000.0000.0000.000
131B130ASP-1-0.887-0.92661.764-0.104-0.1040.0000.0000.0000.000
132B131ASN0-0.038-0.02460.230-0.008-0.0080.0000.0000.0000.000
133B132CYS0-0.050-0.02459.2180.0010.0010.0000.0000.0000.000
134B133MET0-0.0020.01952.018-0.006-0.0060.0000.0000.0000.000
135B134THR0-0.044-0.03653.3540.0060.0060.0000.0000.0000.000
136B135TYR0-0.047-0.05852.420-0.005-0.0050.0000.0000.0000.000
137B136VAL00.0050.00849.4060.0030.0030.0000.0000.0000.000
138B137ALA0-0.0070.00652.502-0.002-0.0020.0000.0000.0000.000
139B138TRP0-0.014-0.01746.5380.0010.0010.0000.0000.0000.000
140B139ASP-1-0.803-0.89252.124-0.122-0.1220.0000.0000.0000.000
141B140SER0-0.109-0.05550.1180.0050.0050.0000.0000.0000.000
142B141VAL0-0.0050.00349.060-0.007-0.0070.0000.0000.0000.000
143B142TYR0-0.049-0.07945.8150.0070.0070.0000.0000.0000.000
144B143TYR00.0350.01146.362-0.008-0.0080.0000.0000.0000.000
145B144MET0-0.0050.00644.291-0.001-0.0010.0000.0000.0000.000
146B145THR00.001-0.02347.0040.0020.0020.0000.0000.0000.000
147B146ASP-1-0.854-0.93748.667-0.151-0.1510.0000.0000.0000.000
148B147ALA0-0.082-0.03849.869-0.001-0.0010.0000.0000.0000.000
149B148GLY0-0.024-0.01145.990-0.001-0.0010.0000.0000.0000.000
150B149THR0-0.0190.00845.057-0.007-0.0070.0000.0000.0000.000
151B150TRP00.0080.01042.169-0.003-0.0030.0000.0000.0000.000
152B151ASP-1-0.843-0.93046.776-0.125-0.1250.0000.0000.0000.000
153B152LYS10.7940.91149.6710.1320.1320.0000.0000.0000.000
154B153THR0-0.062-0.02051.3760.0080.0080.0000.0000.0000.000
155B154ALA00.0460.02253.137-0.004-0.0040.0000.0000.0000.000
156B155THR0-0.043-0.01053.853-0.001-0.0010.0000.0000.0000.000
157B156CYS0-0.081-0.02156.1530.0060.0060.0000.0000.0000.000
158B157VAL00.0340.00958.731-0.004-0.0040.0000.0000.0000.000
159B158SER0-0.046-0.03260.9110.0050.0050.0000.0000.0000.000
160B159HIS00.0510.01562.727-0.002-0.0020.0000.0000.0000.000
161B160ARG10.8200.88859.6720.1140.1140.0000.0000.0000.000
162B161GLY00.0360.00559.290-0.003-0.0030.0000.0000.0000.000
163B162LEU0-0.0160.02154.3140.0050.0050.0000.0000.0000.000
164B163TYR00.021-0.00255.995-0.002-0.0020.0000.0000.0000.000
165B164TYR00.0590.03550.2520.0010.0010.0000.0000.0000.000
166B165VAL0-0.007-0.00156.0100.0010.0010.0000.0000.0000.000
167B166LYS10.8370.91651.1490.1430.1430.0000.0000.0000.000
168B167GLU-1-0.757-0.88852.951-0.135-0.1350.0000.0000.0000.000
169B168GLY0-0.0030.00456.6190.0030.0030.0000.0000.0000.000
170B169TYR0-0.034-0.01557.2810.0050.0050.0000.0000.0000.000
171B170ASN0-0.019-0.01357.655-0.004-0.0040.0000.0000.0000.000
172B171THR0-0.005-0.00552.9160.0000.0000.0000.0000.0000.000
173B172PHE0-0.035-0.03555.193-0.001-0.0010.0000.0000.0000.000
174B173TYR0-0.008-0.01551.074-0.004-0.0040.0000.0000.0000.000
175B174ILE00.0030.01351.293-0.005-0.0050.0000.0000.0000.000
176B175GLU-1-0.776-0.85954.713-0.116-0.1160.0000.0000.0000.000
177B176PHE00.0240.00257.087-0.001-0.0010.0000.0000.0000.000
178B177LYS10.8230.90759.8620.1120.1120.0000.0000.0000.000
179B178SER0-0.006-0.02056.8890.0010.0010.0000.0000.0000.000
180B179GLU-1-0.790-0.84754.452-0.149-0.1490.0000.0000.0000.000
181B180CYS00.0120.02357.8930.0010.0010.0000.0000.0000.000
182B181GLU-1-0.880-0.92060.225-0.112-0.1120.0000.0000.0000.000
183B182LYS10.8210.90552.4750.1480.1480.0000.0000.0000.000
184B183TYR0-0.017-0.00752.714-0.006-0.0060.0000.0000.0000.000
185B184GLY00.0480.04359.1210.0010.0010.0000.0000.0000.000
186B185ASN0-0.115-0.06761.3510.0020.0020.0000.0000.0000.000
187B186THR00.001-0.01964.5690.0030.0030.0000.0000.0000.000
188B187GLY0-0.027-0.00766.4000.0030.0030.0000.0000.0000.000
189B188THR0-0.078-0.04567.3320.0020.0020.0000.0000.0000.000
190B189TRP0-0.002-0.02663.439-0.002-0.0020.0000.0000.0000.000
191B190GLU-1-0.830-0.89664.629-0.088-0.0880.0000.0000.0000.000
192B191VAL00.0000.00261.394-0.002-0.0020.0000.0000.0000.000
193B192HIS0-0.072-0.04462.2320.0030.0030.0000.0000.0000.000
194B193PHE00.0050.00458.671-0.003-0.0030.0000.0000.0000.000