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: VQRJ1

Calculation Name: 1TF1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TF1

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACN4

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptHSide
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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1923486.131058
FMO2-HF: Nuclear repulsion 1852605.931181
FMO2-HF: Total energy -70880.199877
FMO2-MP2: Total energy -71082.538608


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.0053.3540.101-1.364-2.0960
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.000
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].
3A3GLU-1-0.803-0.8963.167-0.6291.2900.033-0.769-1.1840.002
4A4ASN0-0.048-0.0233.0090.0351.0300.029-0.369-0.655-0.001
5A5LEU00.0680.0244.600-0.153-0.127-0.001-0.012-0.0130.000
6A6TYR00.007-0.0117.5310.1680.1680.0000.0000.0000.000
7A7PHE0-0.0460.0043.366-0.673-0.2540.040-0.214-0.244-0.001
8A8GLN0-0.024-0.0385.9050.4130.4130.0000.0000.0000.000
9A9GLY00.0550.0347.1770.2150.2150.0000.0000.0000.000
10A10HIS00.016-0.0057.3740.2380.2380.0000.0000.0000.000
11A11MET0-0.030-0.00910.2580.2050.2050.0000.0000.0000.000
12A12ASP-1-0.820-0.89411.347-0.433-0.4330.0000.0000.0000.000
13A13VAL00.0180.01613.1120.0890.0890.0000.0000.0000.000
14A14LEU0-0.039-0.02814.7070.0690.0690.0000.0000.0000.000
15A15SER0-0.115-0.05316.1910.0560.0560.0000.0000.0000.000
16A16VAL00.0150.00817.7950.0350.0350.0000.0000.0000.000
17A17ALA00.0430.02019.3270.0310.0310.0000.0000.0000.000
18A18GLY00.0170.01421.0360.0210.0210.0000.0000.0000.000
19A19PRO0-0.047-0.05023.5810.0130.0130.0000.0000.0000.000
20A20PHE00.0360.02423.3530.0140.0140.0000.0000.0000.000
21A21MET00.0280.02922.0210.0040.0040.0000.0000.0000.000
22A22ARG10.9190.95425.7130.1410.1410.0000.0000.0000.000
23A23ARG10.9710.99128.8790.0770.0770.0000.0000.0000.000
24A24LEU00.0660.04226.1020.0070.0070.0000.0000.0000.000
25A25MET0-0.0040.03829.1430.0120.0120.0000.0000.0000.000
26A26LEU0-0.087-0.05030.7150.0070.0070.0000.0000.0000.000
27A27LEU0-0.040-0.02233.0200.0050.0050.0000.0000.0000.000
28A28SER00.008-0.00131.3440.0040.0040.0000.0000.0000.000
29A29GLY0-0.0260.00033.8550.0050.0050.0000.0000.0000.000
30A30GLU-1-0.775-0.88031.385-0.054-0.0540.0000.0000.0000.000
31A31THR0-0.037-0.03326.618-0.004-0.0040.0000.0000.0000.000
32A32VAL00.0010.01824.0470.0040.0040.0000.0000.0000.000
33A33ASN0-0.020-0.02621.730-0.019-0.0190.0000.0000.0000.000
34A34VAL00.0480.01816.5090.0120.0120.0000.0000.0000.000
35A35ALA0-0.007-0.00116.380-0.021-0.0210.0000.0000.0000.000
36A36ILE00.0220.01510.3240.0070.0070.0000.0000.0000.000
37A37ARG10.8450.90711.422-0.265-0.2650.0000.0000.0000.000
38A38ASN0-0.018-0.0197.960-0.129-0.1290.0000.0000.0000.000
39A39GLY00.0080.0079.801-0.018-0.0180.0000.0000.0000.000
40A40ASN0-0.017-0.01011.671-0.007-0.0070.0000.0000.0000.000
41A41GLU-1-0.789-0.86013.917-0.026-0.0260.0000.0000.0000.000
42A42ALA00.0120.00614.302-0.019-0.0190.0000.0000.0000.000
43A43VAL0-0.028-0.00212.9930.0060.0060.0000.0000.0000.000
44A44LEU0-0.0050.00215.570-0.035-0.0350.0000.0000.0000.000
45A45ILE00.0130.00212.760-0.016-0.0160.0000.0000.0000.000
46A46GLY00.0280.01516.339-0.014-0.0140.0000.0000.0000.000
47A47GLN0-0.078-0.06319.2580.0170.0170.0000.0000.0000.000
48A48LEU0-0.052-0.01222.956-0.003-0.0030.0000.0000.0000.000
49A49GLU-1-0.769-0.86526.361-0.093-0.0930.0000.0000.0000.000
50A50CYS0-0.055-0.00229.2880.0020.0020.0000.0000.0000.000
51A51LYS10.9620.95232.5080.0770.0770.0000.0000.0000.000
52A52SER0-0.0140.00535.6730.0040.0040.0000.0000.0000.000
53A53MET00.012-0.00536.019-0.003-0.0030.0000.0000.0000.000
54A54VAL00.0200.03536.760-0.001-0.0010.0000.0000.0000.000
55A55ARG10.8210.86631.3060.0860.0860.0000.0000.0000.000
56A56MET00.0150.05624.4350.0000.0000.0000.0000.0000.000
57A57CYS0-0.001-0.01227.944-0.002-0.0020.0000.0000.0000.000
58A58ALA00.0310.03224.2100.0010.0010.0000.0000.0000.000
59A59PRO00.0510.03422.774-0.007-0.0070.0000.0000.0000.000
60A60LEU00.0210.01718.757-0.001-0.0010.0000.0000.0000.000
61A61GLY0-0.019-0.01816.4530.0030.0030.0000.0000.0000.000
62A62SER0-0.050-0.04217.5030.0210.0210.0000.0000.0000.000
63A63ARG10.7380.83712.3690.0780.0780.0000.0000.0000.000
64A64LEU00.006-0.00418.3020.0160.0160.0000.0000.0000.000
65A65PRO00.0410.03718.9610.0090.0090.0000.0000.0000.000
66A66LEU00.017-0.01415.912-0.014-0.0140.0000.0000.0000.000
67A67HIS0-0.028-0.02319.9940.0000.0000.0000.0000.0000.000
68A68ALA00.0140.00623.500-0.002-0.0020.0000.0000.0000.000
69A69SER00.0020.02422.015-0.012-0.0120.0000.0000.0000.000
70A70GLY00.005-0.01023.7500.0060.0060.0000.0000.0000.000
71A71ALA0-0.005-0.02120.0400.0020.0020.0000.0000.0000.000
72A72GLY00.005-0.00419.011-0.004-0.0040.0000.0000.0000.000
73A73LYS10.8220.88819.6220.0120.0120.0000.0000.0000.000
74A74ALA0-0.026-0.01320.8150.0110.0110.0000.0000.0000.000
75A75LEU0-0.046-0.02214.439-0.003-0.0030.0000.0000.0000.000
76A76LEU0-0.006-0.00216.7820.0290.0290.0000.0000.0000.000
77A77TYR00.0560.03119.1740.0100.0100.0000.0000.0000.000
78A78PRO0-0.023-0.01117.8890.0100.0100.0000.0000.0000.000
79A79LEU0-0.054-0.01614.5310.0190.0190.0000.0000.0000.000
80A80ALA00.0010.00318.340-0.014-0.0140.0000.0000.0000.000
81A81GLU-1-0.842-0.94120.0230.1150.1150.0000.0000.0000.000
82A82GLU-1-0.900-0.94920.2010.1810.1810.0000.0000.0000.000
83A83GLU-1-0.816-0.88913.9830.4300.4300.0000.0000.0000.000
84A84LEU0-0.014-0.01817.8960.0090.0090.0000.0000.0000.000
85A85MET0-0.013-0.00220.112-0.007-0.0070.0000.0000.0000.000
86A86SER0-0.043-0.02217.4790.0030.0030.0000.0000.0000.000
87A87ILE0-0.053-0.02415.5630.0070.0070.0000.0000.0000.000
88A88ILE00.0020.00018.067-0.012-0.0120.0000.0000.0000.000
89A89LEU0-0.0470.00021.019-0.013-0.0130.0000.0000.0000.000
90A90GLN0-0.068-0.04415.5450.0140.0140.0000.0000.0000.000
91A91THR0-0.038-0.02118.140-0.008-0.0080.0000.0000.0000.000
92A92GLY0-0.0180.01020.532-0.019-0.0190.0000.0000.0000.000
93A93LEU0-0.025-0.02423.5290.0000.0000.0000.0000.0000.000
94A94GLN00.0220.01925.301-0.002-0.0020.0000.0000.0000.000
95A95GLN00.0030.00627.049-0.001-0.0010.0000.0000.0000.000
96A96PHE0-0.067-0.04623.957-0.003-0.0030.0000.0000.0000.000
97A97THR0-0.032-0.03429.921-0.003-0.0030.0000.0000.0000.000
98A98PRO0-0.008-0.02133.2000.0040.0040.0000.0000.0000.000
99A99THR00.0070.00834.6050.0030.0030.0000.0000.0000.000
100A100THR0-0.031-0.00628.4690.0000.0000.0000.0000.0000.000
101A101LEU00.0090.01428.6680.0030.0030.0000.0000.0000.000
102A102VAL00.013-0.00728.7170.0030.0030.0000.0000.0000.000
103A103ASP-1-0.837-0.90530.3390.0440.0440.0000.0000.0000.000
104A104MET00.0180.00123.511-0.005-0.0050.0000.0000.0000.000
105A105PRO00.005-0.00628.845-0.001-0.0010.0000.0000.0000.000
106A106THR0-0.010-0.02031.314-0.002-0.0020.0000.0000.0000.000
107A107LEU00.0000.01223.994-0.004-0.0040.0000.0000.0000.000
108A108LEU00.0300.01224.965-0.004-0.0040.0000.0000.0000.000
109A109LYS10.8090.89527.763-0.047-0.0470.0000.0000.0000.000
110A110ASP-1-0.861-0.92428.2200.0060.0060.0000.0000.0000.000
111A111LEU0-0.020-0.02422.654-0.006-0.0060.0000.0000.0000.000
112A112GLU-1-0.821-0.90126.2610.0450.0450.0000.0000.0000.000
113A113GLN0-0.025-0.00528.223-0.007-0.0070.0000.0000.0000.000
114A114ALA00.0040.00225.965-0.005-0.0050.0000.0000.0000.000
115A115ARG10.8480.92921.314-0.071-0.0710.0000.0000.0000.000
116A116GLU-1-0.978-0.97226.2080.0120.0120.0000.0000.0000.000
117A117LEU0-0.039-0.02029.774-0.004-0.0040.0000.0000.0000.000
118A118GLY0-0.011-0.00226.120-0.006-0.0060.0000.0000.0000.000
119A119TYR0-0.031-0.00725.889-0.011-0.0110.0000.0000.0000.000
120A120THR00.0130.01624.2190.0070.0070.0000.0000.0000.000
121A121VAL00.030-0.00427.171-0.009-0.0090.0000.0000.0000.000
122A122ASP-1-0.803-0.87827.362-0.024-0.0240.0000.0000.0000.000
123A123LYS10.8750.92129.351-0.002-0.0020.0000.0000.0000.000
124A124GLU-1-0.783-0.86032.342-0.016-0.0160.0000.0000.0000.000
125A125GLU-1-0.781-0.84729.2030.0040.0040.0000.0000.0000.000
126A126HIS00.0130.01324.633-0.004-0.0040.0000.0000.0000.000
127A127VAL0-0.009-0.02228.0240.0000.0000.0000.0000.0000.000
128A128VAL00.0240.00430.6880.0000.0000.0000.0000.0000.000
129A129GLY0-0.0050.00134.469-0.003-0.0030.0000.0000.0000.000
130A130LEU0-0.086-0.02928.052-0.005-0.0050.0000.0000.0000.000
131A131ASN00.0480.01631.6750.0060.0060.0000.0000.0000.000
132A132CYS0-0.086-0.05126.364-0.011-0.0110.0000.0000.0000.000
133A133ILE0-0.0020.01927.9940.0080.0080.0000.0000.0000.000
134A134ALA0-0.032-0.02522.783-0.012-0.0120.0000.0000.0000.000
135A135SER0-0.008-0.01723.1020.0110.0110.0000.0000.0000.000
136A136ALA0-0.0010.00518.780-0.018-0.0180.0000.0000.0000.000
137A137ILE0-0.026-0.00816.5580.0030.0030.0000.0000.0000.000
138A138TYR00.013-0.00816.068-0.003-0.0030.0000.0000.0000.000
139A139ASP-1-0.799-0.87812.198-0.079-0.0790.0000.0000.0000.000
140A140ASP-1-0.865-0.96315.122-0.065-0.0650.0000.0000.0000.000
141A141VAL0-0.103-0.04213.7090.0210.0210.0000.0000.0000.000
142A142GLY0-0.0030.01216.6560.0220.0220.0000.0000.0000.000
143A143SER0-0.111-0.06512.3450.0260.0260.0000.0000.0000.000
144A144VAL00.0090.00314.427-0.041-0.0410.0000.0000.0000.000
145A145VAL0-0.050-0.03610.7230.0040.0040.0000.0000.0000.000
146A146ALA0-0.014-0.01112.126-0.093-0.0930.0000.0000.0000.000
147A147ALA00.0160.02614.8110.0480.0480.0000.0000.0000.000
148A148ILE0-0.012-0.00118.446-0.027-0.0270.0000.0000.0000.000
149A149SER0-0.012-0.01521.3480.0190.0190.0000.0000.0000.000
150A150ILE00.0070.01524.356-0.011-0.0110.0000.0000.0000.000
151A151SER00.018-0.02126.4900.0030.0030.0000.0000.0000.000
152A152GLY00.0120.00328.785-0.005-0.0050.0000.0000.0000.000
153A153PRO00.002-0.00232.2610.0030.0030.0000.0000.0000.000
154A154SER0-0.012-0.02135.508-0.001-0.0010.0000.0000.0000.000
155A155SER0-0.022-0.00736.7550.0010.0010.0000.0000.0000.000
156A156ARG10.7280.82035.0480.0530.0530.0000.0000.0000.000
157A157LEU0-0.039-0.00631.6270.0000.0000.0000.0000.0000.000
158A158THR00.029-0.02336.1620.0000.0000.0000.0000.0000.000
159A159GLU-1-0.847-0.93837.818-0.018-0.0180.0000.0000.0000.000
160A160ASP-1-0.926-0.92338.869-0.023-0.0230.0000.0000.0000.000
161A161ARG10.8150.89735.9580.0410.0410.0000.0000.0000.000
162A162PHE0-0.002-0.00334.548-0.003-0.0030.0000.0000.0000.000
163A163VAL00.0360.02733.920-0.002-0.0020.0000.0000.0000.000
164A164SER00.0200.00734.765-0.003-0.0030.0000.0000.0000.000
165A165GLN00.003-0.01632.489-0.008-0.0080.0000.0000.0000.000
166A166GLY00.0640.03330.246-0.006-0.0060.0000.0000.0000.000
167A167GLU-1-0.870-0.92429.750-0.027-0.0270.0000.0000.0000.000
168A168LEU0-0.0040.01130.765-0.004-0.0040.0000.0000.0000.000
169A169VAL0-0.017-0.00725.622-0.009-0.0090.0000.0000.0000.000
170A170ARG10.7980.87825.9860.0220.0220.0000.0000.0000.000
171A171ASP-1-0.828-0.89526.099-0.046-0.0460.0000.0000.0000.000
172A172THR0-0.028-0.02324.929-0.006-0.0060.0000.0000.0000.000
173A173ALA00.0190.01121.832-0.013-0.0130.0000.0000.0000.000
174A174ARG10.8550.94021.9750.0350.0350.0000.0000.0000.000
175A175ASP-1-0.900-0.95423.484-0.081-0.0810.0000.0000.0000.000
176A176ILE0-0.049-0.02918.962-0.010-0.0100.0000.0000.0000.000
177A177SER00.011-0.00518.795-0.018-0.0180.0000.0000.0000.000
178A178THR0-0.038-0.01819.6330.0000.0000.0000.0000.0000.000
179A179ALA0-0.032-0.02721.500-0.001-0.0010.0000.0000.0000.000
180A180LEU0-0.039-0.01113.912-0.012-0.0120.0000.0000.0000.000
181A181GLY00.0610.04817.168-0.013-0.0130.0000.0000.0000.000
182A182LEU0-0.096-0.04818.9350.0200.0200.0000.0000.0000.000
183A183LYS10.8490.92718.0750.0840.0840.0000.0000.0000.000
184A184ALA0-0.0060.00720.1450.0160.0160.0000.0000.0000.000