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

tag_button

FMODB ID: N18VQ

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098839.39304
FMO2-HF: Nuclear repulsion 2018240.559063
FMO2-HF: Total energy -80598.833977
FMO2-MP2: Total energy -80831.334656


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.
-34.703-29.9059.116-5.891-8.023-0.058
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 : -0.054 / q_NPA : -0.050
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].
3B2GLN0-0.002-0.0042.921-4.516-0.6991.518-1.733-3.602-0.001
4B3THR0-0.0010.0073.0914.8165.3700.014-0.096-0.4730.000
5B4PRO00.0700.0125.0650.0830.132-0.0010.000-0.0470.000
6B5LYS10.9520.9677.8223.0003.0000.0000.0000.0000.000
7B6GLU-1-0.826-0.9081.909-37.353-36.9757.585-4.062-3.901-0.057
8B7THR00.0090.0146.0620.8460.8460.0000.0000.0000.000
9B8LEU0-0.046-0.0358.1890.6630.6630.0000.0000.0000.000
10B9SER0-0.070-0.0918.5950.3690.3690.0000.0000.0000.000
11B10GLU-1-0.830-0.8897.274-2.866-2.8660.0000.0000.0000.000
12B11ARG10.9090.9469.9782.1852.1850.0000.0000.0000.000
13B12LEU0-0.014-0.00713.0940.2120.2120.0000.0000.0000.000
14B13SER00.0230.00212.9270.1660.1660.0000.0000.0000.000
15B14ALA00.0350.03914.3820.1510.1510.0000.0000.0000.000
16B15LEU0-0.087-0.04516.0600.1450.1450.0000.0000.0000.000
17B16GLN0-0.041-0.04918.1900.0280.0280.0000.0000.0000.000
18B17ASP-1-0.886-0.92517.420-0.878-0.8780.0000.0000.0000.000
19B18LYS10.9490.97419.0500.8470.8470.0000.0000.0000.000
20B19ILE0-0.057-0.02822.0630.0630.0630.0000.0000.0000.000
21B20ILE00.013-0.00522.8990.0520.0520.0000.0000.0000.000
22B21ASP-1-0.830-0.89923.254-0.505-0.5050.0000.0000.0000.000
23B22HIS0-0.138-0.07526.0760.0610.0610.0000.0000.0000.000
24B23TYR0-0.091-0.07227.4120.0200.0200.0000.0000.0000.000
25B24GLU-1-0.968-0.97327.033-0.395-0.3950.0000.0000.0000.000
26B25ASN0-0.073-0.04328.4770.0360.0360.0000.0000.0000.000
27B26ASP-1-0.952-0.96131.946-0.248-0.2480.0000.0000.0000.000
28B27SER0-0.063-0.04833.3640.0280.0280.0000.0000.0000.000
29B28LYS10.9590.96935.1910.2070.2070.0000.0000.0000.000
30B29ASP-1-0.855-0.90935.462-0.234-0.2340.0000.0000.0000.000
31B30ILE00.0730.02635.760-0.020-0.0200.0000.0000.0000.000
32B31ASP-1-0.919-0.96733.732-0.271-0.2710.0000.0000.0000.000
33B32SER0-0.067-0.02731.429-0.025-0.0250.0000.0000.0000.000
34B33GLN00.0660.03730.988-0.051-0.0510.0000.0000.0000.000
35B34ILE0-0.031-0.00931.353-0.027-0.0270.0000.0000.0000.000
36B35GLN00.002-0.00326.382-0.061-0.0610.0000.0000.0000.000
37B36TYR00.0530.05927.202-0.056-0.0560.0000.0000.0000.000
38B37TRP00.0430.00227.447-0.061-0.0610.0000.0000.0000.000
39B38GLN0-0.063-0.03426.161-0.041-0.0410.0000.0000.0000.000
40B39LEU0-0.0110.00122.051-0.062-0.0620.0000.0000.0000.000
41B40ILE00.0670.05023.041-0.075-0.0750.0000.0000.0000.000
42B41ARG10.8570.92324.7930.4560.4560.0000.0000.0000.000
43B42TRP0-0.036-0.01920.356-0.049-0.0490.0000.0000.0000.000
44B43GLU-1-0.854-0.91819.992-0.923-0.9230.0000.0000.0000.000
45B44ASN0-0.032-0.04120.196-0.084-0.0840.0000.0000.0000.000
46B45ALA0-0.0140.00221.159-0.011-0.0110.0000.0000.0000.000
47B46ILE0-0.015-0.00515.269-0.060-0.0600.0000.0000.0000.000
48B47PHE00.0310.00517.010-0.130-0.1300.0000.0000.0000.000
49B48PHE0-0.030-0.01119.0090.0250.0250.0000.0000.0000.000
50B49ALA00.0540.02016.7690.0050.0050.0000.0000.0000.000
51B50ALA00.0120.01614.922-0.080-0.0800.0000.0000.0000.000
52B51ARG10.8450.91515.9060.8090.8090.0000.0000.0000.000
53B52GLU-1-0.966-0.98818.831-0.787-0.7870.0000.0000.0000.000
54B53HIS0-0.094-0.04313.571-0.009-0.0090.0000.0000.0000.000
55B54GLY0-0.015-0.00114.713-0.127-0.1270.0000.0000.0000.000
56B55ILE0-0.078-0.03011.534-0.108-0.1080.0000.0000.0000.000
57B56GLN00.000-0.00114.9340.0790.0790.0000.0000.0000.000
58B57THR0-0.022-0.01915.3000.0430.0430.0000.0000.0000.000
59B58LEU00.024-0.00511.412-0.318-0.3180.0000.0000.0000.000
60B59ASN00.0420.07811.615-0.159-0.1590.0000.0000.0000.000
61B60HIS00.005-0.00413.6140.2020.2020.0000.0000.0000.000
62B61GLN0-0.0100.01516.3200.2230.2230.0000.0000.0000.000
63B62VAL00.0150.00017.593-0.114-0.1140.0000.0000.0000.000
64B63VAL0-0.0120.01316.6130.0420.0420.0000.0000.0000.000
65B64PRO00.0370.03419.6680.0790.0790.0000.0000.0000.000
66B65ALA00.0310.02022.851-0.037-0.0370.0000.0000.0000.000
67B66TYR00.0750.01321.6720.0240.0240.0000.0000.0000.000
68B67ASN0-0.008-0.01525.761-0.019-0.0190.0000.0000.0000.000
69B68ILE00.0150.01626.6670.0230.0230.0000.0000.0000.000
70B69SER00.0510.01823.232-0.014-0.0140.0000.0000.0000.000
71B70LYS10.9390.97225.5580.5170.5170.0000.0000.0000.000
72B71SER0-0.023-0.00628.1570.0240.0240.0000.0000.0000.000
73B72LYS11.0161.00425.9480.6350.6350.0000.0000.0000.000
74B73ALA00.0180.01826.2670.0070.0070.0000.0000.0000.000
75B74HIS0-0.012-0.00528.1890.0030.0030.0000.0000.0000.000
76B75LYS10.9040.96331.7410.3670.3670.0000.0000.0000.000
77B76ALA00.0270.02129.0390.0180.0180.0000.0000.0000.000
78B77ILE0-0.063-0.04129.2070.0120.0120.0000.0000.0000.000
79B78GLU-1-0.859-0.91132.021-0.296-0.2960.0000.0000.0000.000
80B79LEU00.0450.02434.0490.0190.0190.0000.0000.0000.000
81B80GLN00.0320.02629.901-0.012-0.0120.0000.0000.0000.000
82B81MET0-0.045-0.03433.6340.0150.0150.0000.0000.0000.000
83B82ALA00.0060.02336.2100.0180.0180.0000.0000.0000.000
84B83LEU00.0190.00434.7200.0140.0140.0000.0000.0000.000
85B84GLN0-0.028-0.02632.6650.0060.0060.0000.0000.0000.000
86B85GLY00.0320.03137.3880.0120.0120.0000.0000.0000.000
87B86LEU0-0.0040.00840.7600.0130.0130.0000.0000.0000.000
88B87ALA00.0060.01138.6260.0130.0130.0000.0000.0000.000
89B88GLN0-0.069-0.04139.5940.0090.0090.0000.0000.0000.000
90B89SER0-0.022-0.01343.0550.0130.0130.0000.0000.0000.000
91B90ALA00.002-0.01545.778-0.001-0.0010.0000.0000.0000.000
92B91TYR00.006-0.00846.2970.0040.0040.0000.0000.0000.000
93B92LYS10.9451.00839.6140.1940.1940.0000.0000.0000.000
94B93THR0-0.011-0.02142.058-0.007-0.0070.0000.0000.0000.000
95B94GLU-1-0.822-0.85844.038-0.167-0.1670.0000.0000.0000.000
96B95ASP-1-0.888-0.94442.103-0.193-0.1930.0000.0000.0000.000
97B96TRP0-0.061-0.05439.239-0.002-0.0020.0000.0000.0000.000
98B97THR00.0070.00237.501-0.015-0.0150.0000.0000.0000.000
99B98LEU00.0640.03731.348-0.004-0.0040.0000.0000.0000.000
100B99GLN0-0.008-0.00135.527-0.011-0.0110.0000.0000.0000.000
101B100ASP-1-0.834-0.91838.556-0.225-0.2250.0000.0000.0000.000
102B101THR0-0.083-0.06436.323-0.003-0.0030.0000.0000.0000.000
103B102CYS0-0.0130.03035.339-0.020-0.0200.0000.0000.0000.000
104B103GLU-1-0.856-0.96333.676-0.382-0.3820.0000.0000.0000.000
105B104GLU-1-0.948-0.97036.465-0.278-0.2780.0000.0000.0000.000
106B105LEU00.0140.01538.9430.0140.0140.0000.0000.0000.000
107B106TRP0-0.067-0.04638.5390.0150.0150.0000.0000.0000.000
108B107ASN0-0.044-0.05037.4780.0110.0110.0000.0000.0000.000
109B108THR0-0.048-0.01741.5280.0090.0090.0000.0000.0000.000
110B109GLU-1-0.851-0.92244.755-0.203-0.2030.0000.0000.0000.000
111B110PRO0-0.024-0.02448.0360.0040.0040.0000.0000.0000.000
112B111THR00.0510.03643.856-0.003-0.0030.0000.0000.0000.000
113B112HIS0-0.062-0.03540.4980.0160.0160.0000.0000.0000.000
114B113CYS0-0.0390.00343.4610.0100.0100.0000.0000.0000.000
115B114PHE00.0000.00439.123-0.010-0.0100.0000.0000.0000.000
116B115LYS10.8070.89344.2040.2400.2400.0000.0000.0000.000
117B116LYS10.8840.95444.2190.1900.1900.0000.0000.0000.000
118B117GLY00.0270.01747.7960.0060.0060.0000.0000.0000.000
119B118GLY00.017-0.00249.7680.0040.0040.0000.0000.0000.000
120B119GLN0-0.011-0.00151.2480.0050.0050.0000.0000.0000.000
121B120THR0-0.037-0.01854.700-0.002-0.0020.0000.0000.0000.000
122B121VAL00.0230.01155.7310.0060.0060.0000.0000.0000.000
123B122GLN00.0020.00857.190-0.001-0.0010.0000.0000.0000.000
124B123VAL00.0310.01659.1820.0050.0050.0000.0000.0000.000
125B124TYR0-0.033-0.00760.598-0.003-0.0030.0000.0000.0000.000
126B125PHE00.0400.00658.5960.0040.0040.0000.0000.0000.000
127B126ASP-1-0.788-0.85564.087-0.114-0.1140.0000.0000.0000.000
128B127GLY0-0.061-0.02167.5690.0030.0030.0000.0000.0000.000
129B128ASN0-0.027-0.02364.7740.0040.0040.0000.0000.0000.000
130B129LYS10.9170.95264.8660.1020.1020.0000.0000.0000.000
131B130ASP-1-0.913-0.95562.357-0.121-0.1210.0000.0000.0000.000
132B131ASN0-0.0060.01060.022-0.008-0.0080.0000.0000.0000.000
133B132CYS0-0.025-0.01959.4680.0010.0010.0000.0000.0000.000
134B133MET0-0.0100.01452.156-0.006-0.0060.0000.0000.0000.000
135B134THR0-0.035-0.02053.2710.0050.0050.0000.0000.0000.000
136B135TYR0-0.064-0.08852.976-0.005-0.0050.0000.0000.0000.000
137B136VAL00.0100.02349.9160.0040.0040.0000.0000.0000.000
138B137ALA0-0.001-0.00352.851-0.002-0.0020.0000.0000.0000.000
139B138TRP0-0.018-0.01446.9720.0010.0010.0000.0000.0000.000
140B139ASP-1-0.831-0.91852.253-0.141-0.1410.0000.0000.0000.000
141B140SER0-0.116-0.06050.0690.0060.0060.0000.0000.0000.000
142B141VAL00.0010.00249.160-0.008-0.0080.0000.0000.0000.000
143B142TYR0-0.059-0.08045.9500.0080.0080.0000.0000.0000.000
144B143TYR00.0540.01146.678-0.009-0.0090.0000.0000.0000.000
145B144MET0-0.029-0.00744.174-0.001-0.0010.0000.0000.0000.000
146B145THR0-0.013-0.01047.1060.0000.0000.0000.0000.0000.000
147B146ASP-1-0.895-0.95348.440-0.164-0.1640.0000.0000.0000.000
148B147ALA0-0.091-0.04849.021-0.003-0.0030.0000.0000.0000.000
149B148GLY0-0.030-0.01645.586-0.002-0.0020.0000.0000.0000.000
150B149THR0-0.026-0.00644.957-0.006-0.0060.0000.0000.0000.000
151B150TRP0-0.009-0.00642.147-0.002-0.0020.0000.0000.0000.000
152B151ASP-1-0.891-0.94147.115-0.144-0.1440.0000.0000.0000.000
153B152LYS10.8400.91949.8380.1500.1500.0000.0000.0000.000
154B153THR0-0.064-0.02951.4460.0090.0090.0000.0000.0000.000
155B154ALA00.0450.03253.398-0.005-0.0050.0000.0000.0000.000
156B155THR0-0.038-0.02253.850-0.001-0.0010.0000.0000.0000.000
157B156CYS0-0.079-0.03656.3550.0070.0070.0000.0000.0000.000
158B157VAL00.0500.02359.271-0.004-0.0040.0000.0000.0000.000
159B158SER0-0.035-0.02461.2740.0050.0050.0000.0000.0000.000
160B159HIS00.0420.01463.088-0.003-0.0030.0000.0000.0000.000
161B160ARG10.8450.92060.4940.1270.1270.0000.0000.0000.000
162B161GLY00.0520.01759.505-0.003-0.0030.0000.0000.0000.000
163B162LEU0-0.0380.00054.7210.0040.0040.0000.0000.0000.000
164B163TYR00.0040.00056.305-0.003-0.0030.0000.0000.0000.000
165B164TYR00.0640.03950.6950.0010.0010.0000.0000.0000.000
166B165VAL0-0.003-0.00956.2450.0000.0000.0000.0000.0000.000
167B166LYS10.9680.98649.4570.1750.1750.0000.0000.0000.000
168B167GLU-1-0.829-0.92153.128-0.147-0.1470.0000.0000.0000.000
169B168GLY0-0.015-0.00556.6350.0030.0030.0000.0000.0000.000
170B169TYR0-0.019-0.00657.6920.0060.0060.0000.0000.0000.000
171B170ASN0-0.031-0.01157.855-0.006-0.0060.0000.0000.0000.000
172B171THR0-0.018-0.01253.361-0.001-0.0010.0000.0000.0000.000
173B172PHE0-0.025-0.02555.6210.0000.0000.0000.0000.0000.000
174B173TYR00.005-0.00251.220-0.002-0.0020.0000.0000.0000.000
175B174ILE00.0010.01151.855-0.005-0.0050.0000.0000.0000.000
176B175GLU-1-0.805-0.90155.106-0.131-0.1310.0000.0000.0000.000
177B176PHE00.030-0.00157.652-0.002-0.0020.0000.0000.0000.000
178B177LYS10.9660.98960.1930.1210.1210.0000.0000.0000.000
179B178SER00.005-0.00756.3540.0010.0010.0000.0000.0000.000
180B179GLU-1-0.851-0.87754.566-0.168-0.1680.0000.0000.0000.000
181B180CYS00.0290.02357.9790.0020.0020.0000.0000.0000.000
182B181GLU-1-1.036-1.01360.590-0.130-0.1300.0000.0000.0000.000
183B182LYS10.8510.91552.3110.1710.1710.0000.0000.0000.000
184B183TYR0-0.026-0.01452.884-0.007-0.0070.0000.0000.0000.000
185B184GLY00.0220.02959.4450.0020.0020.0000.0000.0000.000
186B185ASN0-0.071-0.03062.1990.0000.0000.0000.0000.0000.000
187B186THR00.012-0.02665.0490.0040.0040.0000.0000.0000.000
188B187GLY0-0.040-0.02166.8190.0030.0030.0000.0000.0000.000
189B188THR0-0.077-0.04667.8420.0020.0020.0000.0000.0000.000
190B189TRP0-0.006-0.01663.829-0.003-0.0030.0000.0000.0000.000
191B190GLU-1-0.906-0.93665.406-0.098-0.0980.0000.0000.0000.000
192B191VAL0-0.002-0.00761.724-0.004-0.0040.0000.0000.0000.000
193B192HIS0-0.093-0.05362.8480.0030.0030.0000.0000.0000.000
194B193PHE00.0060.00558.762-0.002-0.0020.0000.0000.0000.000