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: 8NJRY

Calculation Name: 1TUA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YE16

Base Structure: X-ray

Registration Date: 2023-09-26

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2020538.690022
FMO2-HF: Nuclear repulsion 1944374.788732
FMO2-HF: Total energy -76163.90129
FMO2-MP2: Total energy -76382.729211


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
0.0130000000000012.0920.014-0.974-1.1190.003
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.010
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].
3A2LYS10.8580.9203.561-0.1281.4560.012-0.749-0.8470.002
4A3PRO00.0230.0065.9920.2660.2660.0000.0000.0000.000
5A4ARG10.7990.8783.2351.9892.4840.002-0.225-0.2720.001
6A5ILE0-0.020-0.00210.6600.0910.0910.0000.0000.0000.000
7A6TYR00.0170.0129.710-0.031-0.0310.0000.0000.0000.000
8A7VAL0-0.018-0.01415.0870.0100.0100.0000.0000.0000.000
9A8LYS10.8670.92618.601-0.005-0.0050.0000.0000.0000.000
10A9VAL0-0.033-0.01820.895-0.009-0.0090.0000.0000.0000.000
11A10LYS10.8840.94723.3460.0300.0300.0000.0000.0000.000
12A11PRO00.0610.02126.142-0.006-0.0060.0000.0000.0000.000
13A12GLU-1-0.870-0.94327.162-0.022-0.0220.0000.0000.0000.000
14A13ARG10.7720.88427.4200.0410.0410.0000.0000.0000.000
15A14LEU00.0360.02520.824-0.009-0.0090.0000.0000.0000.000
16A15GLY00.0240.00724.379-0.009-0.0090.0000.0000.0000.000
17A16ALA0-0.025-0.01126.839-0.005-0.0050.0000.0000.0000.000
18A17VAL0-0.0050.00121.262-0.007-0.0070.0000.0000.0000.000
19A18ILE0-0.016-0.00421.031-0.015-0.0150.0000.0000.0000.000
20A19GLY00.0350.01623.063-0.010-0.0100.0000.0000.0000.000
21A20PRO00.0430.00726.0910.0010.0010.0000.0000.0000.000
22A21ARG10.8150.86826.4410.0650.0650.0000.0000.0000.000
23A22GLY00.0030.02022.586-0.008-0.0080.0000.0000.0000.000
24A23GLU-1-0.834-0.89622.501-0.095-0.0950.0000.0000.0000.000
25A24VAL00.0180.01424.369-0.007-0.0070.0000.0000.0000.000
26A25LYS10.9340.95716.5230.1700.1700.0000.0000.0000.000
27A26ALA0-0.012-0.01219.703-0.022-0.0220.0000.0000.0000.000
28A27GLU-1-0.808-0.88120.851-0.140-0.1400.0000.0000.0000.000
29A28ILE0-0.023-0.00719.167-0.005-0.0050.0000.0000.0000.000
30A29MET0-0.0170.04615.825-0.023-0.0230.0000.0000.0000.000
31A30ARG10.9050.94517.8750.1330.1330.0000.0000.0000.000
32A31ARG10.8580.91920.3010.1260.1260.0000.0000.0000.000
33A32THR0-0.045-0.02217.863-0.004-0.0040.0000.0000.0000.000
34A33GLY00.0990.07615.838-0.011-0.0110.0000.0000.0000.000
35A34THR0-0.057-0.05112.830-0.053-0.0530.0000.0000.0000.000
36A35VAL00.0280.00110.0950.0370.0370.0000.0000.0000.000
37A36ILE0-0.021-0.01412.238-0.014-0.0140.0000.0000.0000.000
38A37THR0-0.020-0.00610.1390.0540.0540.0000.0000.0000.000
39A38VAL0-0.020-0.03913.4350.0130.0130.0000.0000.0000.000
40A39ASP-1-0.802-0.86215.5560.0630.0630.0000.0000.0000.000
41A40THR00.044-0.01517.318-0.004-0.0040.0000.0000.0000.000
42A41GLU-1-0.979-0.96320.2390.0560.0560.0000.0000.0000.000
43A42ASN0-0.047-0.04217.9420.0040.0040.0000.0000.0000.000
44A43SER0-0.035-0.02820.911-0.009-0.0090.0000.0000.0000.000
45A44MET0-0.027-0.00316.045-0.008-0.0080.0000.0000.0000.000
46A45VAL00.0080.00916.243-0.008-0.0080.0000.0000.0000.000
47A46ILE00.0070.00110.1880.0240.0240.0000.0000.0000.000
48A47VAL00.0140.01612.596-0.042-0.0420.0000.0000.0000.000
49A48GLU-1-0.765-0.8626.536-1.470-1.4700.0000.0000.0000.000
50A49PRO00.0320.0238.7190.0940.0940.0000.0000.0000.000
51A50GLU-1-0.926-0.9748.697-0.565-0.5650.0000.0000.0000.000
52A51ALA0-0.014-0.0128.778-0.085-0.0850.0000.0000.0000.000
53A52GLU-1-0.952-0.9877.502-0.653-0.6530.0000.0000.0000.000
54A53GLY00.0080.0089.3810.0570.0570.0000.0000.0000.000
55A54ILE0-0.052-0.00412.4980.0570.0570.0000.0000.0000.000
56A55PRO00.0160.02113.972-0.018-0.0180.0000.0000.0000.000
57A56PRO00.036-0.01215.2390.0010.0010.0000.0000.0000.000
58A57VAL00.0430.01916.6320.0050.0050.0000.0000.0000.000
59A58ASN00.0110.00416.9810.0320.0320.0000.0000.0000.000
60A59LEU00.0140.01012.2740.0100.0100.0000.0000.0000.000
61A60MET0-0.031-0.02115.8840.0170.0170.0000.0000.0000.000
62A61LYS10.8380.90818.8080.1350.1350.0000.0000.0000.000
63A62ALA00.0240.01317.2100.0170.0170.0000.0000.0000.000
64A63ALA00.000-0.00117.3560.0160.0160.0000.0000.0000.000
65A64GLU-1-0.774-0.89019.208-0.067-0.0670.0000.0000.0000.000
66A65VAL00.0110.01322.5560.0150.0150.0000.0000.0000.000
67A66VAL0-0.002-0.00119.2150.0140.0140.0000.0000.0000.000
68A67LYS10.8270.90222.5010.0900.0900.0000.0000.0000.000
69A68ALA00.0160.00724.1420.0120.0120.0000.0000.0000.000
70A69ILE0-0.019-0.00124.8730.0090.0090.0000.0000.0000.000
71A70SER00.0110.00424.5400.0110.0110.0000.0000.0000.000
72A71LEU0-0.029-0.02226.6670.0080.0080.0000.0000.0000.000
73A72GLY00.0200.01329.6970.0060.0060.0000.0000.0000.000
74A73PHE0-0.062-0.03130.3460.0010.0010.0000.0000.0000.000
75A74PRO0-0.0110.00230.702-0.001-0.0010.0000.0000.0000.000
76A75PRO00.0640.01527.556-0.001-0.0010.0000.0000.0000.000
77A76GLU-1-0.864-0.93829.202-0.074-0.0740.0000.0000.0000.000
78A77LYS10.8140.91431.7850.0490.0490.0000.0000.0000.000
79A78ALA0-0.001-0.00127.420-0.001-0.0010.0000.0000.0000.000
80A79PHE00.019-0.00524.943-0.006-0.0060.0000.0000.0000.000
81A80ARG10.8010.89827.8830.0560.0560.0000.0000.0000.000
82A81LEU0-0.044-0.02125.7260.0000.0000.0000.0000.0000.000
83A82LEU0-0.037-0.02622.473-0.009-0.0090.0000.0000.0000.000
84A83GLU-1-0.908-0.94325.438-0.088-0.0880.0000.0000.0000.000
85A84GLU-1-0.898-0.94627.880-0.101-0.1010.0000.0000.0000.000
86A85ASP-1-0.886-0.94529.200-0.076-0.0760.0000.0000.0000.000
87A86GLN0-0.062-0.01629.3670.0110.0110.0000.0000.0000.000
88A87ILE0-0.029-0.01627.770-0.009-0.0090.0000.0000.0000.000
89A88LEU0-0.002-0.01026.6420.0050.0050.0000.0000.0000.000
90A89VAL0-0.028-0.01229.3280.0020.0020.0000.0000.0000.000
91A90VAL0-0.001-0.01329.7440.0000.0000.0000.0000.0000.000
92A91VAL0-0.017-0.00532.9950.0020.0020.0000.0000.0000.000
93A92ASP-1-0.813-0.89833.626-0.008-0.0080.0000.0000.0000.000
94A93LEU00.010-0.01035.5860.0020.0020.0000.0000.0000.000
95A94LYS10.8910.93936.401-0.002-0.0020.0000.0000.0000.000
96A95GLN0-0.035-0.02035.6250.0000.0000.0000.0000.0000.000
97A96VAL0-0.038-0.00939.1530.0000.0000.0000.0000.0000.000
98A97VAL0-0.070-0.04242.1810.0010.0010.0000.0000.0000.000
99A98GLY00.0520.02940.6030.0010.0010.0000.0000.0000.000
100A99ASP-1-0.839-0.91738.6800.0070.0070.0000.0000.0000.000
101A100SER00.0010.01141.4060.0000.0000.0000.0000.0000.000
102A101GLN00.0750.02140.285-0.002-0.0020.0000.0000.0000.000
103A102ASN00.010-0.01344.268-0.002-0.0020.0000.0000.0000.000
104A103HIS00.0300.02546.397-0.002-0.0020.0000.0000.0000.000
105A104LEU00.0450.04039.878-0.002-0.0020.0000.0000.0000.000
106A105LYS10.9540.96544.2050.0040.0040.0000.0000.0000.000
107A106ARG10.8820.94946.1290.0030.0030.0000.0000.0000.000
108A107ILE00.0250.01643.128-0.001-0.0010.0000.0000.0000.000
109A108LYS10.8560.91839.5400.0140.0140.0000.0000.0000.000
110A109GLY00.0080.01144.512-0.002-0.0020.0000.0000.0000.000
111A110ARG10.8020.88847.7450.0120.0120.0000.0000.0000.000
112A111ILE00.0400.01541.890-0.001-0.0010.0000.0000.0000.000
113A112ILE0-0.0190.00442.848-0.002-0.0020.0000.0000.0000.000
114A113GLY00.0250.00945.774-0.001-0.0010.0000.0000.0000.000
115A114GLU-1-0.819-0.89849.355-0.016-0.0160.0000.0000.0000.000
116A115GLY00.0400.02149.987-0.001-0.0010.0000.0000.0000.000
117A116GLY00.0090.00646.678-0.002-0.0020.0000.0000.0000.000
118A117ARG10.8140.88347.0630.0170.0170.0000.0000.0000.000
119A118ALA0-0.0040.01347.698-0.001-0.0010.0000.0000.0000.000
120A119ARG10.8510.90339.6850.0330.0330.0000.0000.0000.000
121A120ARG10.8710.94343.3280.0260.0260.0000.0000.0000.000
122A121THR00.0320.01645.078-0.001-0.0010.0000.0000.0000.000
123A122ILE0-0.010-0.00742.087-0.001-0.0010.0000.0000.0000.000
124A123GLU-1-0.767-0.83639.207-0.042-0.0420.0000.0000.0000.000
125A124GLU-1-0.902-0.96842.057-0.032-0.0320.0000.0000.0000.000
126A125MET0-0.078-0.03544.9810.0000.0000.0000.0000.0000.000
127A126THR0-0.036-0.05641.025-0.001-0.0010.0000.0000.0000.000
128A127ASP-1-0.833-0.87538.836-0.054-0.0540.0000.0000.0000.000
129A128THR0-0.007-0.01337.020-0.002-0.0020.0000.0000.0000.000
130A129TYR0-0.040-0.02233.5370.0040.0040.0000.0000.0000.000
131A130ILE00.008-0.00635.7830.0000.0000.0000.0000.0000.000
132A131ASN0-0.060-0.01934.3230.0030.0030.0000.0000.0000.000
133A132VAL00.001-0.01236.4740.0010.0010.0000.0000.0000.000
134A133GLY00.1090.07434.7490.0000.0000.0000.0000.0000.000
135A134GLU-1-0.937-0.97534.972-0.003-0.0030.0000.0000.0000.000
136A135TYR0-0.034-0.02731.1410.0030.0030.0000.0000.0000.000
137A136GLU-1-0.776-0.85131.065-0.018-0.0180.0000.0000.0000.000
138A137VAL0-0.056-0.03034.915-0.001-0.0010.0000.0000.0000.000
139A138ALA0-0.0010.00731.7180.0000.0000.0000.0000.0000.000
140A139ILE0-0.007-0.00933.1530.0010.0010.0000.0000.0000.000
141A140ILE00.0160.01030.227-0.003-0.0030.0000.0000.0000.000
142A141GLY00.0730.03432.5730.0040.0040.0000.0000.0000.000
143A142ASP-1-0.743-0.83632.555-0.056-0.0560.0000.0000.0000.000
144A143TYR00.0400.00432.5880.0040.0040.0000.0000.0000.000
145A144GLU-1-0.827-0.89734.498-0.036-0.0360.0000.0000.0000.000
146A145ARG10.7800.84037.4380.0510.0510.0000.0000.0000.000
147A146ALA00.0180.00734.5300.0030.0030.0000.0000.0000.000
148A147MET0-0.0060.00035.8220.0030.0030.0000.0000.0000.000
149A148ALA0-0.0110.00138.0020.0030.0030.0000.0000.0000.000
150A149ALA0-0.001-0.00638.6730.0030.0030.0000.0000.0000.000
151A150LYS10.8220.89635.6070.0280.0280.0000.0000.0000.000
152A151GLN00.0750.04939.1730.0020.0020.0000.0000.0000.000
153A152ALA0-0.006-0.00842.4440.0020.0020.0000.0000.0000.000
154A153ILE00.007-0.00939.6140.0020.0020.0000.0000.0000.000
155A154GLU-1-0.788-0.89438.822-0.020-0.0200.0000.0000.0000.000
156A155MET0-0.034-0.01242.9550.0020.0020.0000.0000.0000.000
157A156LEU0-0.068-0.03645.6120.0010.0010.0000.0000.0000.000
158A157ALA0-0.010-0.00543.1150.0010.0010.0000.0000.0000.000
159A158GLU-1-0.822-0.88045.231-0.010-0.0100.0000.0000.0000.000
160A159GLY0-0.029-0.00447.8740.0010.0010.0000.0000.0000.000
161A160ARG10.8000.88149.4820.0110.0110.0000.0000.0000.000
162A161MET00.0440.02251.693-0.001-0.0010.0000.0000.0000.000
163A162HIS00.0980.05349.2950.0000.0000.0000.0000.0000.000
164A163SER0-0.0080.00952.661-0.001-0.0010.0000.0000.0000.000
165A164THR0-0.034-0.02353.0870.0000.0000.0000.0000.0000.000
166A165VAL00.0440.02547.538-0.001-0.0010.0000.0000.0000.000
167A166TYR00.0760.02048.849-0.001-0.0010.0000.0000.0000.000
168A167ARG10.8660.94250.7890.0150.0150.0000.0000.0000.000
169A168HIS0-0.017-0.02246.5040.0010.0010.0000.0000.0000.000
170A169LEU00.0440.02144.106-0.001-0.0010.0000.0000.0000.000
171A170GLU-1-0.842-0.92847.495-0.029-0.0290.0000.0000.0000.000
172A171ARG10.8660.94049.9960.0180.0180.0000.0000.0000.000
173A172ILE00.0600.03344.1330.0000.0000.0000.0000.0000.000
174A173MET00.0370.03042.525-0.002-0.0020.0000.0000.0000.000
175A174ARG10.9320.96746.2330.0220.0220.0000.0000.0000.000
176A175GLU-1-0.900-0.92946.488-0.028-0.0280.0000.0000.0000.000
177A176ILE00.0340.01941.8360.0000.0000.0000.0000.0000.000
178A177LYS10.8860.94844.8200.0310.0310.0000.0000.0000.000
179A178ARG10.8870.95146.3210.0250.0250.0000.0000.0000.000
180A179ARG10.7480.82142.3290.0340.0340.0000.0000.0000.000
181A180GLU-1-0.822-0.87540.931-0.046-0.0460.0000.0000.0000.000
182A181ARG10.9320.98044.3770.0290.0290.0000.0000.0000.000
183A182LEU0-0.047-0.02947.5720.0000.0000.0000.0000.0000.000
184A183LYS10.9660.98340.3550.0430.0430.0000.0000.0000.000
185A184MET0-0.0020.00644.4260.0000.0000.0000.0000.0000.000
186A185TRP00.008-0.03145.7390.0010.0010.0000.0000.0000.000
187A186ALA0-0.0230.00047.2250.0010.0010.0000.0000.0000.000
188A187ARG10.7690.86641.1330.0480.0480.0000.0000.0000.000
189A188GLU-1-0.806-0.85644.684-0.045-0.0450.0000.0000.0000.000