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: 9Y622

Calculation Name: 1TUE-B-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2105137.084976
FMO2-HF: Nuclear repulsion 2024367.380811
FMO2-HF: Total energy -80769.704165
FMO2-MP2: Total energy -81002.725876


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:-1:ACE )


Summations of interaction energy for fragment #1(B:-1:ACE )
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.
0.8531.714-0.006-0.415-0.440
Interaction energy analysis for fragmet #1(B:-1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.015
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].
3B1MET 0-0.0300.0033.8521.0211.882-0.006-0.415-0.4400.000
4B2GLN 00.002-0.0026.9850.0960.0960.0000.0000.0000.000
5B3THR 0-0.0040.0069.2380.1680.1680.0000.0000.0000.000
6B4PRO 00.0710.01312.7260.0300.0300.0000.0000.0000.000
7B5LYS 10.9530.96715.5220.2440.2440.0000.0000.0000.000
8B6GLU -1-0.825-0.90710.334-0.749-0.7490.0000.0000.0000.000
9B7THR 00.0090.01411.6260.0260.0260.0000.0000.0000.000
10B8LEU 0-0.047-0.03513.4180.0460.0460.0000.0000.0000.000
11B9SER 0-0.069-0.09215.0710.0210.0210.0000.0000.0000.000
12B10GLU -1-0.831-0.88810.302-0.091-0.0910.0000.0000.0000.000
13B11ARG 10.9110.94614.3690.1000.1000.0000.0000.0000.000
14B12LEU 0-0.019-0.01017.1180.0150.0150.0000.0000.0000.000
15B13SER 00.0250.00316.8910.0060.0060.0000.0000.0000.000
16B14ALA 00.0360.04017.1930.0120.0120.0000.0000.0000.000
17B15LEU 0-0.086-0.04519.1240.0110.0110.0000.0000.0000.000
18B16GLN 0-0.042-0.04922.201-0.001-0.0010.0000.0000.0000.000
19B17ASP -1-0.886-0.92420.143-0.030-0.0300.0000.0000.0000.000
20B18LYS 10.9510.97521.047-0.010-0.0100.0000.0000.0000.000
21B19ILE 0-0.060-0.03024.9120.0030.0030.0000.0000.0000.000
22B20ILE 00.016-0.00526.5330.0010.0010.0000.0000.0000.000
23B21ASP -1-0.830-0.89925.0880.0110.0110.0000.0000.0000.000
24B22HIS 0-0.138-0.07528.4300.0010.0010.0000.0000.0000.000
25B23TYR 0-0.091-0.07231.222-0.001-0.0010.0000.0000.0000.000
26B24GLU -1-0.969-0.97329.295-0.001-0.0010.0000.0000.0000.000
27B25ASN 0-0.073-0.04329.9760.0020.0020.0000.0000.0000.000
28B26ASP -1-0.952-0.96133.8320.0020.0020.0000.0000.0000.000
29B27SER 0-0.064-0.04835.1330.0020.0020.0000.0000.0000.000
30B28LYS 10.9610.96837.113-0.009-0.0090.0000.0000.0000.000
31B29ASP -1-0.855-0.90937.0780.0170.0170.0000.0000.0000.000
32B30ILE 00.0720.02537.829-0.001-0.0010.0000.0000.0000.000
33B31ASP -1-0.918-0.96635.2640.0160.0160.0000.0000.0000.000
34B32SER 0-0.065-0.02633.4110.0010.0010.0000.0000.0000.000
35B33GLN 00.0630.03633.468-0.003-0.0030.0000.0000.0000.000
36B34ILE 0-0.030-0.00933.759-0.003-0.0030.0000.0000.0000.000
37B35GLN 00.003-0.00328.280-0.002-0.0020.0000.0000.0000.000
38B36TYR 00.0540.05930.083-0.003-0.0030.0000.0000.0000.000
39B37TRP 00.0420.00230.939-0.006-0.0060.0000.0000.0000.000
40B38GLN 0-0.064-0.03529.141-0.002-0.0020.0000.0000.0000.000
41B39LEU 0-0.0070.00225.080-0.003-0.0030.0000.0000.0000.000
42B40ILE 00.0610.04827.055-0.007-0.0070.0000.0000.0000.000
43B41ARG 10.8600.92529.3830.0030.0030.0000.0000.0000.000
44B42TRP 0-0.036-0.01924.214-0.005-0.0050.0000.0000.0000.000
45B43GLU -1-0.855-0.91924.708-0.051-0.0510.0000.0000.0000.000
46B44ASN 0-0.032-0.04025.645-0.012-0.0120.0000.0000.0000.000
47B45ALA 0-0.0140.00125.748-0.004-0.0040.0000.0000.0000.000
48B46ILE 0-0.014-0.00520.183-0.007-0.0070.0000.0000.0000.000
49B47PHE 00.0280.00423.398-0.013-0.0130.0000.0000.0000.000
50B48PHE 0-0.032-0.01225.610-0.003-0.0030.0000.0000.0000.000
51B49ALA 00.0580.02122.874-0.004-0.0040.0000.0000.0000.000
52B50ALA 00.0120.01622.310-0.011-0.0110.0000.0000.0000.000
53B51ARG 10.8410.91423.2670.0680.0680.0000.0000.0000.000
54B52GLU -1-0.970-0.98925.769-0.066-0.0660.0000.0000.0000.000
55B53HIS 0-0.087-0.04020.648-0.007-0.0070.0000.0000.0000.000
56B54GLY 0-0.018-0.00222.906-0.015-0.0150.0000.0000.0000.000
57B55ILE 0-0.078-0.03019.514-0.012-0.0120.0000.0000.0000.000
58B56GLN 0-0.003-0.00323.4180.0060.0060.0000.0000.0000.000
59B57THR 0-0.020-0.01823.5330.0050.0050.0000.0000.0000.000
60B58LEU 00.023-0.00618.530-0.024-0.0240.0000.0000.0000.000
61B59ASN 00.0430.07817.609-0.014-0.0140.0000.0000.0000.000
62B60HIS 00.006-0.00320.1480.0170.0170.0000.0000.0000.000
63B61GLN 0-0.0130.01423.3290.0170.0170.0000.0000.0000.000
64B62VAL 00.0180.00125.101-0.010-0.0100.0000.0000.0000.000
65B63VAL 0-0.0160.01224.5070.0070.0070.0000.0000.0000.000
66B64PRO 00.0410.03527.3240.0030.0030.0000.0000.0000.000
67B65ALA 00.0300.01930.467-0.003-0.0030.0000.0000.0000.000
68B66TYR 00.0740.01329.1360.0030.0030.0000.0000.0000.000
69B67ASN 0-0.005-0.01333.0620.0000.0000.0000.0000.0000.000
70B68ILE 00.0140.01533.3960.0030.0030.0000.0000.0000.000
71B69SER 00.0490.01729.8850.0010.0010.0000.0000.0000.000
72B70LYS 10.9400.97232.0260.0380.0380.0000.0000.0000.000
73B71SER 0-0.021-0.00634.3350.0040.0040.0000.0000.0000.000
74B72LYS 11.0161.00431.9330.0410.0410.0000.0000.0000.000
75B73ALA 00.0170.01731.5920.0030.0030.0000.0000.0000.000
76B74HIS 0-0.014-0.00633.3240.0020.0020.0000.0000.0000.000
77B75LYS 10.9090.96436.8150.0190.0190.0000.0000.0000.000
78B76ALA 00.0250.02133.3080.0020.0020.0000.0000.0000.000
79B77ILE 0-0.064-0.04233.5580.0030.0030.0000.0000.0000.000
80B78GLU -1-0.860-0.91136.045-0.010-0.0100.0000.0000.0000.000
81B79LEU 00.0480.02537.8810.0020.0020.0000.0000.0000.000
82B80GLN 00.0300.02532.9420.0000.0000.0000.0000.0000.000
83B81MET 0-0.041-0.03237.0210.0030.0030.0000.0000.0000.000
84B82ALA 00.0060.02339.4790.0010.0010.0000.0000.0000.000
85B83LEU 00.0170.00337.9760.0010.0010.0000.0000.0000.000
86B84GLN 0-0.029-0.02635.1180.0000.0000.0000.0000.0000.000
87B85GLY 00.0360.03239.9460.0010.0010.0000.0000.0000.000
88B86LEU 0-0.0030.00743.5200.0010.0010.0000.0000.0000.000
89B87ALA 0-0.0030.00840.8010.0010.0010.0000.0000.0000.000
90B88GLN 0-0.064-0.03941.4340.0010.0010.0000.0000.0000.000
91B89SER 0-0.022-0.01444.9510.0000.0000.0000.0000.0000.000
92B90ALA 00.003-0.01547.6070.0010.0010.0000.0000.0000.000
93B91TYR 00.007-0.00848.6780.0000.0000.0000.0000.0000.000
94B92LYS 10.9441.00940.715-0.017-0.0170.0000.0000.0000.000
95B93THR 0-0.011-0.02243.8840.0000.0000.0000.0000.0000.000
96B94GLU -1-0.820-0.85845.5910.0050.0050.0000.0000.0000.000
97B95ASP -1-0.889-0.94444.0910.0090.0090.0000.0000.0000.000
98B96TRP 0-0.063-0.05541.670-0.002-0.0020.0000.0000.0000.000
99B97THR 00.0050.00140.1050.0000.0000.0000.0000.0000.000
100B98LEU 00.0660.03934.470-0.001-0.0010.0000.0000.0000.000
101B99GLN 0-0.0040.00138.727-0.002-0.0020.0000.0000.0000.000
102B100ASP -1-0.835-0.91842.0240.0000.0000.0000.0000.0000.000
103B101THR 0-0.085-0.06639.5720.0000.0000.0000.0000.0000.000
104B102CYS 0-0.0120.03039.302-0.001-0.0010.0000.0000.0000.000
105B103GLU -1-0.857-0.96338.905-0.020-0.0200.0000.0000.0000.000
106B104GLU -1-0.948-0.96940.977-0.014-0.0140.0000.0000.0000.000
107B105LEU 00.0200.01743.6910.0000.0000.0000.0000.0000.000
108B106TRP 0-0.071-0.04743.1480.0010.0010.0000.0000.0000.000
109B107ASN 0-0.044-0.05042.8320.0010.0010.0000.0000.0000.000
110B108THR 0-0.050-0.01946.4450.0000.0000.0000.0000.0000.000
111B109GLU -1-0.849-0.92249.517-0.008-0.0080.0000.0000.0000.000
112B110PRO 0-0.025-0.02652.7140.0000.0000.0000.0000.0000.000
113B111THR 00.0520.03848.6440.0000.0000.0000.0000.0000.000
114B112HIS 0-0.062-0.03545.2220.0010.0010.0000.0000.0000.000
115B113CYS 0-0.0370.00447.6160.0010.0010.0000.0000.0000.000
116B114PHE 00.0010.00442.565-0.001-0.0010.0000.0000.0000.000
117B115LYS 10.8030.89347.8980.0070.0070.0000.0000.0000.000
118B116LYS 10.8820.95346.847-0.003-0.0030.0000.0000.0000.000
119B117GLY 00.0280.01751.0600.0000.0000.0000.0000.0000.000
120B118GLY 00.017-0.00153.2800.0000.0000.0000.0000.0000.000
121B119GLN 0-0.011-0.00154.9140.0000.0000.0000.0000.0000.000
122B120THR 0-0.035-0.01758.5810.0000.0000.0000.0000.0000.000
123B121VAL 00.0230.01059.7510.0000.0000.0000.0000.0000.000
124B122GLN 0-0.0010.00761.7890.0000.0000.0000.0000.0000.000
125B123VAL 00.0230.01464.0680.0000.0000.0000.0000.0000.000
126B124TYR 0-0.032-0.00665.846-0.001-0.0010.0000.0000.0000.000
127B125PHE 00.0460.00864.1320.0000.0000.0000.0000.0000.000
128B126ASP -1-0.782-0.85469.741-0.008-0.0080.0000.0000.0000.000
129B127GLY 0-0.070-0.02473.3010.0000.0000.0000.0000.0000.000
130B128ASN 0-0.025-0.02270.7760.0000.0000.0000.0000.0000.000
131B129LYS 10.9170.95170.4110.0060.0060.0000.0000.0000.000
132B130ASP -1-0.912-0.95467.847-0.009-0.0090.0000.0000.0000.000
133B131ASN 0-0.0060.01065.971-0.001-0.0010.0000.0000.0000.000
134B132CYS 0-0.027-0.01964.9520.0000.0000.0000.0000.0000.000
135B133MET 0-0.0080.01357.716-0.001-0.0010.0000.0000.0000.000
136B134THR 0-0.036-0.02057.9030.0010.0010.0000.0000.0000.000
137B135TYR 0-0.063-0.08857.7410.0000.0000.0000.0000.0000.000
138B136VAL 00.0090.02354.1100.0000.0000.0000.0000.0000.000
139B137ALA 0-0.001-0.00457.0570.0000.0000.0000.0000.0000.000
140B138TRP 0-0.017-0.01451.0290.0010.0010.0000.0000.0000.000
141B139ASP -1-0.831-0.91755.6540.0000.0000.0000.0000.0000.000
142B140SER 0-0.119-0.06053.1360.0010.0010.0000.0000.0000.000
143B141VAL 00.0080.00352.705-0.001-0.0010.0000.0000.0000.000
144B142TYR 0-0.064-0.08149.1710.0010.0010.0000.0000.0000.000
145B143TYR 00.0570.01250.137-0.001-0.0010.0000.0000.0000.000
146B144MET 0-0.033-0.00747.5300.0010.0010.0000.0000.0000.000
147B145THR 0-0.010-0.01050.442-0.001-0.0010.0000.0000.0000.000
148B146ASP -1-0.897-0.95451.688-0.001-0.0010.0000.0000.0000.000
149B147ALA 0-0.091-0.04752.2120.0000.0000.0000.0000.0000.000
150B148GLY 0-0.029-0.01548.4860.0010.0010.0000.0000.0000.000
151B149THR 0-0.033-0.00947.7450.0010.0010.0000.0000.0000.000
152B150TRP 00.000-0.00245.574-0.001-0.0010.0000.0000.0000.000
153B151ASP -1-0.894-0.94249.9430.0040.0040.0000.0000.0000.000
154B152LYS 10.8430.92052.566-0.005-0.0050.0000.0000.0000.000
155B153THR 0-0.067-0.03054.3230.0000.0000.0000.0000.0000.000
156B154ALA 00.0500.03456.6210.0000.0000.0000.0000.0000.000
157B155THR 0-0.043-0.02457.5240.0000.0000.0000.0000.0000.000
158B156CYS 0-0.080-0.03660.0060.0000.0000.0000.0000.0000.000
159B157VAL 00.0500.02363.259-0.001-0.0010.0000.0000.0000.000
160B158SER 0-0.035-0.02465.2880.0000.0000.0000.0000.0000.000
161B159HIS 00.0430.01567.5800.0000.0000.0000.0000.0000.000
162B160ARG 10.8430.92065.4240.0050.0050.0000.0000.0000.000
163B161GLY 00.0560.01964.266-0.001-0.0010.0000.0000.0000.000
164B162LEU 0-0.045-0.00359.2150.0010.0010.0000.0000.0000.000
165B163TYR 00.0020.00060.4480.0000.0000.0000.0000.0000.000
166B164TYR 00.0720.04154.7400.0000.0000.0000.0000.0000.000
167B165VAL 0-0.007-0.01060.0140.0000.0000.0000.0000.0000.000
168B166LYS 10.9730.98753.3180.0040.0040.0000.0000.0000.000
169B167GLU -1-0.833-0.92156.4510.0000.0000.0000.0000.0000.000
170B168GLY 0-0.013-0.00459.9420.0000.0000.0000.0000.0000.000
171B169TYR 0-0.019-0.00761.4890.0000.0000.0000.0000.0000.000
172B170ASN 0-0.032-0.01161.6610.0000.0000.0000.0000.0000.000
173B171THR 0-0.018-0.01257.4580.0000.0000.0000.0000.0000.000
174B172PHE 0-0.030-0.02759.7680.0000.0000.0000.0000.0000.000
175B173TYR 00.0090.00055.8060.0000.0000.0000.0000.0000.000
176B174ILE 00.0010.01056.769-0.001-0.0010.0000.0000.0000.000
177B175GLU -1-0.805-0.90160.040-0.005-0.0050.0000.0000.0000.000
178B176PHE 00.031-0.00262.536-0.001-0.0010.0000.0000.0000.000
179B177LYS 10.9630.98865.4580.0070.0070.0000.0000.0000.000
180B178SER 00.008-0.00562.1920.0000.0000.0000.0000.0000.000
181B179GLU -1-0.853-0.87860.259-0.010-0.0100.0000.0000.0000.000
182B180CYS 00.0290.02363.7380.0000.0000.0000.0000.0000.000
183B181GLU -1-1.035-1.01166.730-0.009-0.0090.0000.0000.0000.000
184B182LYS 10.8520.91658.4720.0110.0110.0000.0000.0000.000
185B183TYR 0-0.031-0.01658.898-0.001-0.0010.0000.0000.0000.000
186B184GLY 00.0260.02965.6310.0000.0000.0000.0000.0000.000
187B185ASN 0-0.075-0.03168.6750.0000.0000.0000.0000.0000.000
188B186THR 00.017-0.02571.3540.0000.0000.0000.0000.0000.000
189B187GLY 0-0.042-0.02272.7810.0000.0000.0000.0000.0000.000
190B188THR 0-0.079-0.04773.7030.0000.0000.0000.0000.0000.000
191B189TRP 0-0.003-0.01569.182-0.001-0.0010.0000.0000.0000.000
192B190GLU -1-0.907-0.93770.626-0.004-0.0040.0000.0000.0000.000
193B191VAL 0-0.009-0.01066.3230.0000.0000.0000.0000.0000.000
194B192HIS 0-0.093-0.05667.4260.0000.0000.0000.0000.0000.000
195B193PHE 00.018-0.00862.4860.0000.0000.0000.0000.0000.000
196B194NME 0-0.0090.01566.8660.0000.0000.0000.0000.0000.000