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: 16JMZ

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2016578.964964
FMO2-HF: Nuclear repulsion 1940416.64616
FMO2-HF: Total energy -76162.318804
FMO2-MP2: Total energy -76381.287515


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.
0.0380000000000012.250.027-0.938-1.3020.003
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 : 0.026 / 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].
3A2LYS10.9550.9823.2870.2381.9890.020-0.754-1.0170.003
4A3PRO00.0200.0116.1210.2940.2940.0000.0000.0000.000
5A4ARG10.8620.9153.0720.7581.2190.007-0.184-0.2850.000
6A5ILE0-0.0050.00610.6310.0750.0750.0000.0000.0000.000
7A6TYR0-0.001-0.00310.264-0.004-0.0040.0000.0000.0000.000
8A7VAL00.005-0.00315.3970.0030.0030.0000.0000.0000.000
9A8LYS10.9100.96018.859-0.032-0.0320.0000.0000.0000.000
10A9VAL0-0.036-0.02121.224-0.010-0.0100.0000.0000.0000.000
11A10LYS10.8470.93023.5690.0070.0070.0000.0000.0000.000
12A11PRO00.0810.03626.291-0.005-0.0050.0000.0000.0000.000
13A12GLU-1-0.875-0.94027.2880.0050.0050.0000.0000.0000.000
14A13ARG10.7950.88627.6810.0180.0180.0000.0000.0000.000
15A14LEU00.0470.03321.352-0.008-0.0080.0000.0000.0000.000
16A15GLY00.0230.00624.761-0.007-0.0070.0000.0000.0000.000
17A16ALA0-0.041-0.01527.246-0.005-0.0050.0000.0000.0000.000
18A17VAL00.0040.00221.650-0.006-0.0060.0000.0000.0000.000
19A18ILE0-0.0220.00321.546-0.011-0.0110.0000.0000.0000.000
20A19GLY00.0500.02223.520-0.009-0.0090.0000.0000.0000.000
21A20PRO00.014-0.00426.3470.0000.0000.0000.0000.0000.000
22A21ARG10.8750.93226.5660.0440.0440.0000.0000.0000.000
23A22GLY0-0.011-0.00423.061-0.007-0.0070.0000.0000.0000.000
24A23GLU-1-0.864-0.94623.156-0.065-0.0650.0000.0000.0000.000
25A24VAL00.0360.02624.290-0.006-0.0060.0000.0000.0000.000
26A25LYS10.9640.98517.0650.1010.1010.0000.0000.0000.000
27A26ALA0-0.017-0.01020.110-0.018-0.0180.0000.0000.0000.000
28A27GLU-1-0.839-0.91021.105-0.113-0.1130.0000.0000.0000.000
29A28ILE0-0.030-0.01519.480-0.005-0.0050.0000.0000.0000.000
30A29MET0-0.0380.01716.135-0.015-0.0150.0000.0000.0000.000
31A30ARG10.9060.94618.1100.1020.1020.0000.0000.0000.000
32A31ARG10.9160.95920.4800.0920.0920.0000.0000.0000.000
33A32THR0-0.051-0.02118.126-0.005-0.0050.0000.0000.0000.000
34A33GLY00.0760.06216.175-0.012-0.0120.0000.0000.0000.000
35A34THR0-0.042-0.04013.172-0.042-0.0420.0000.0000.0000.000
36A35VAL00.011-0.00210.7120.0320.0320.0000.0000.0000.000
37A36ILE0-0.011-0.02212.630-0.003-0.0030.0000.0000.0000.000
38A37THR0-0.035-0.02010.8630.0380.0380.0000.0000.0000.000
39A38VAL0-0.017-0.02814.0000.0130.0130.0000.0000.0000.000
40A39ASP-1-0.826-0.89315.8370.1140.1140.0000.0000.0000.000
41A40THR00.031-0.04417.542-0.001-0.0010.0000.0000.0000.000
42A41GLU-1-0.989-0.96620.5950.0820.0820.0000.0000.0000.000
43A42ASN00.0030.01617.627-0.010-0.0100.0000.0000.0000.000
44A43SER0-0.078-0.05121.010-0.007-0.0070.0000.0000.0000.000
45A44MET0-0.019-0.00316.324-0.011-0.0110.0000.0000.0000.000
46A45VAL0-0.0090.00016.617-0.004-0.0040.0000.0000.0000.000
47A46ILE00.0050.00610.1910.0150.0150.0000.0000.0000.000
48A47VAL00.0030.00413.319-0.031-0.0310.0000.0000.0000.000
49A48GLU-1-0.854-0.9326.997-0.737-0.7370.0000.0000.0000.000
50A49PRO00.0050.0158.4520.0670.0670.0000.0000.0000.000
51A50GLU-1-0.928-0.9728.918-0.425-0.4250.0000.0000.0000.000
52A51ALA0-0.019-0.0179.047-0.049-0.0490.0000.0000.0000.000
53A52GLU-1-0.964-0.9967.736-0.586-0.5860.0000.0000.0000.000
54A53GLY0-0.0020.0049.3530.0440.0440.0000.0000.0000.000
55A54ILE0-0.0470.00512.3580.0520.0520.0000.0000.0000.000
56A55PRO00.0020.00713.831-0.016-0.0160.0000.0000.0000.000
57A56PRO00.0640.00215.3170.0000.0000.0000.0000.0000.000
58A57VAL00.0430.02016.6540.0090.0090.0000.0000.0000.000
59A58ASN00.0060.00116.9270.0270.0270.0000.0000.0000.000
60A59LEU00.0180.01612.4530.0090.0090.0000.0000.0000.000
61A60MET0-0.036-0.03415.9640.0180.0180.0000.0000.0000.000
62A61LYS10.9350.98518.7960.1090.1090.0000.0000.0000.000
63A62ALA00.0320.02817.4600.0150.0150.0000.0000.0000.000
64A63ALA0-0.016-0.01417.6390.0150.0150.0000.0000.0000.000
65A64GLU-1-0.909-0.96319.464-0.041-0.0410.0000.0000.0000.000
66A65VAL0-0.0100.00222.7210.0130.0130.0000.0000.0000.000
67A66VAL00.0050.00019.4190.0110.0110.0000.0000.0000.000
68A67LYS10.9800.99422.6750.0390.0390.0000.0000.0000.000
69A68ALA00.0140.00024.3180.0090.0090.0000.0000.0000.000
70A69ILE0-0.0130.00624.9770.0060.0060.0000.0000.0000.000
71A70SER00.0040.00524.8900.0080.0080.0000.0000.0000.000
72A71LEU0-0.031-0.02826.9970.0050.0050.0000.0000.0000.000
73A72GLY0-0.0030.01129.9290.0030.0030.0000.0000.0000.000
74A73PHE0-0.066-0.03130.5560.0000.0000.0000.0000.0000.000
75A74PRO0-0.036-0.01130.680-0.001-0.0010.0000.0000.0000.000
76A75PRO00.1030.02528.050-0.001-0.0010.0000.0000.0000.000
77A76GLU-1-0.879-0.94029.462-0.050-0.0500.0000.0000.0000.000
78A77LYS10.8870.94931.8670.0320.0320.0000.0000.0000.000
79A78ALA00.0180.01027.511-0.001-0.0010.0000.0000.0000.000
80A79PHE00.020-0.00125.005-0.005-0.0050.0000.0000.0000.000
81A80ARG10.9050.96227.8970.0400.0400.0000.0000.0000.000
82A81LEU0-0.051-0.02726.033-0.001-0.0010.0000.0000.0000.000
83A82LEU0-0.059-0.03722.407-0.007-0.0070.0000.0000.0000.000
84A83GLU-1-0.953-0.97625.560-0.068-0.0680.0000.0000.0000.000
85A84GLU-1-0.944-0.97528.085-0.078-0.0780.0000.0000.0000.000
86A85ASP-1-0.897-0.95528.959-0.058-0.0580.0000.0000.0000.000
87A86GLN0-0.0300.00929.4240.0100.0100.0000.0000.0000.000
88A87ILE0-0.036-0.02128.343-0.006-0.0060.0000.0000.0000.000
89A88LEU00.013-0.00726.7480.0040.0040.0000.0000.0000.000
90A89VAL0-0.020-0.00729.5340.0020.0020.0000.0000.0000.000
91A90VAL0-0.006-0.01629.9130.0000.0000.0000.0000.0000.000
92A91VAL0-0.023-0.01132.8750.0020.0020.0000.0000.0000.000
93A92ASP-1-0.794-0.90133.6060.0060.0060.0000.0000.0000.000
94A93LEU00.007-0.02235.7350.0010.0010.0000.0000.0000.000
95A94LYS10.9640.99735.810-0.015-0.0150.0000.0000.0000.000
96A95GLN0-0.043-0.01335.1690.0010.0010.0000.0000.0000.000
97A96VAL0-0.033-0.00239.1800.0000.0000.0000.0000.0000.000
98A97VAL0-0.073-0.04942.3190.0010.0010.0000.0000.0000.000
99A98GLY00.0360.02340.9460.0010.0010.0000.0000.0000.000
100A99ASP-1-0.898-0.95839.5590.0190.0190.0000.0000.0000.000
101A100SER0-0.037-0.01241.8980.0000.0000.0000.0000.0000.000
102A101GLN00.0900.02941.528-0.001-0.0010.0000.0000.0000.000
103A102ASN0-0.003-0.01544.754-0.002-0.0020.0000.0000.0000.000
104A103HIS00.0460.03646.635-0.002-0.0020.0000.0000.0000.000
105A104LEU00.0550.05140.224-0.002-0.0020.0000.0000.0000.000
106A105LYS10.9400.95244.376-0.004-0.0040.0000.0000.0000.000
107A106ARG10.9050.94346.213-0.005-0.0050.0000.0000.0000.000
108A107ILE00.0280.02043.010-0.001-0.0010.0000.0000.0000.000
109A108LYS10.8860.95440.3820.0000.0000.0000.0000.0000.000
110A109GLY00.0090.01444.796-0.001-0.0010.0000.0000.0000.000
111A110ARG10.8780.94448.1970.0040.0040.0000.0000.0000.000
112A111ILE00.0420.02842.222-0.001-0.0010.0000.0000.0000.000
113A112ILE0-0.0240.00643.288-0.002-0.0020.0000.0000.0000.000
114A113GLY00.0160.00245.968-0.001-0.0010.0000.0000.0000.000
115A114GLU-1-0.912-0.96349.532-0.007-0.0070.0000.0000.0000.000
116A115GLY00.0330.00950.579-0.001-0.0010.0000.0000.0000.000
117A116GLY0-0.027-0.03546.929-0.001-0.0010.0000.0000.0000.000
118A117ARG10.9590.98147.2200.0100.0100.0000.0000.0000.000
119A118ALA00.0050.01647.930-0.001-0.0010.0000.0000.0000.000
120A119ARG10.8880.95040.8030.0190.0190.0000.0000.0000.000
121A120ARG10.8970.95444.1140.0160.0160.0000.0000.0000.000
122A121THR00.0300.02845.752-0.001-0.0010.0000.0000.0000.000
123A122ILE0-0.004-0.00842.629-0.001-0.0010.0000.0000.0000.000
124A123GLU-1-0.835-0.90040.020-0.026-0.0260.0000.0000.0000.000
125A124GLU-1-0.927-0.96442.600-0.022-0.0220.0000.0000.0000.000
126A125MET0-0.097-0.03845.2300.0000.0000.0000.0000.0000.000
127A126THR0-0.052-0.05341.065-0.001-0.0010.0000.0000.0000.000
128A127ASP-1-0.922-0.94839.875-0.038-0.0380.0000.0000.0000.000
129A128THR0-0.030-0.01137.249-0.002-0.0020.0000.0000.0000.000
130A129TYR0-0.071-0.02433.8550.0010.0010.0000.0000.0000.000
131A130ILE00.016-0.01436.1980.0000.0000.0000.0000.0000.000
132A131ASN0-0.048-0.02834.6740.0020.0020.0000.0000.0000.000
133A132VAL0-0.016-0.01436.5350.0010.0010.0000.0000.0000.000
134A133GLY00.0810.05035.4070.0000.0000.0000.0000.0000.000
135A134GLU-1-0.974-0.99735.2080.0090.0090.0000.0000.0000.000
136A135TYR00.008-0.01531.6210.0010.0010.0000.0000.0000.000
137A136GLU-1-0.818-0.88730.8890.0000.0000.0000.0000.0000.000
138A137VAL0-0.032-0.02235.188-0.001-0.0010.0000.0000.0000.000
139A138ALA0-0.0080.01231.8960.0000.0000.0000.0000.0000.000
140A139ILE0-0.005-0.01433.4720.0000.0000.0000.0000.0000.000
141A140ILE00.0230.01530.660-0.002-0.0020.0000.0000.0000.000
142A141GLY00.0480.01732.8300.0020.0020.0000.0000.0000.000
143A142ASP-1-0.785-0.86932.954-0.041-0.0410.0000.0000.0000.000
144A143TYR00.027-0.01032.7250.0040.0040.0000.0000.0000.000
145A144GLU-1-0.875-0.95434.455-0.027-0.0270.0000.0000.0000.000
146A145ARG10.8150.89138.0000.0380.0380.0000.0000.0000.000
147A146ALA00.0110.00734.7740.0030.0030.0000.0000.0000.000
148A147MET0-0.019-0.01135.7140.0030.0030.0000.0000.0000.000
149A148ALA0-0.0140.00138.0350.0030.0030.0000.0000.0000.000
150A149ALA00.014-0.00139.0410.0020.0020.0000.0000.0000.000
151A150LYS10.9100.96434.8000.0150.0150.0000.0000.0000.000
152A151GLN00.0870.05739.4370.0010.0010.0000.0000.0000.000
153A152ALA0-0.017-0.01442.5910.0020.0020.0000.0000.0000.000
154A153ILE0-0.022-0.02340.1880.0020.0020.0000.0000.0000.000
155A154GLU-1-0.879-0.95239.654-0.007-0.0070.0000.0000.0000.000
156A155MET0-0.019-0.01043.1450.0010.0010.0000.0000.0000.000
157A156LEU0-0.084-0.04345.9290.0010.0010.0000.0000.0000.000
158A157ALA0-0.043-0.01743.5230.0010.0010.0000.0000.0000.000
159A158GLU-1-0.923-0.95745.617-0.001-0.0010.0000.0000.0000.000
160A159GLY0-0.043-0.01448.0430.0010.0010.0000.0000.0000.000
161A160ARG10.9180.97750.2820.0040.0040.0000.0000.0000.000
162A161MET00.003-0.01052.1190.0000.0000.0000.0000.0000.000
163A162HIS00.0470.00349.7620.0000.0000.0000.0000.0000.000
164A163SER00.0100.00852.575-0.001-0.0010.0000.0000.0000.000
165A164THR0-0.040-0.01852.6180.0000.0000.0000.0000.0000.000
166A165VAL00.0500.02947.756-0.001-0.0010.0000.0000.0000.000
167A166TYR00.0650.02148.931-0.001-0.0010.0000.0000.0000.000
168A167ARG10.9750.98751.2440.0090.0090.0000.0000.0000.000
169A168HIS0-0.037-0.02046.6660.0000.0000.0000.0000.0000.000
170A169LEU00.0430.01444.303-0.001-0.0010.0000.0000.0000.000
171A170GLU-1-0.943-0.96647.889-0.018-0.0180.0000.0000.0000.000
172A171ARG10.8540.92250.3190.0110.0110.0000.0000.0000.000
173A172ILE00.0640.03744.411-0.001-0.0010.0000.0000.0000.000
174A173MET00.0270.02242.939-0.002-0.0020.0000.0000.0000.000
175A174ARG10.9210.96846.4980.0160.0160.0000.0000.0000.000
176A175GLU-1-0.947-0.97546.613-0.020-0.0200.0000.0000.0000.000
177A176ILE00.0290.01041.821-0.001-0.0010.0000.0000.0000.000
178A177LYS11.0161.00944.6510.0250.0250.0000.0000.0000.000
179A178ARG10.8820.95646.1290.0190.0190.0000.0000.0000.000
180A179ARG10.8990.95043.0270.0250.0250.0000.0000.0000.000
181A180GLU-1-0.800-0.88040.795-0.035-0.0350.0000.0000.0000.000
182A181ARG10.9480.98344.4940.0220.0220.0000.0000.0000.000
183A182LEU0-0.067-0.04047.6000.0000.0000.0000.0000.0000.000
184A183LYS10.9710.99040.7540.0330.0330.0000.0000.0000.000
185A184MET0-0.008-0.00443.6660.0000.0000.0000.0000.0000.000
186A185TRP00.016-0.01445.8210.0010.0010.0000.0000.0000.000
187A186ALA0-0.035-0.01747.5180.0000.0000.0000.0000.0000.000
188A187ARG10.8940.96841.8010.0380.0380.0000.0000.0000.000
189A188GLU-1-0.954-0.96445.070-0.036-0.0360.0000.0000.0000.000