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: VQ311

Calculation Name: 1T33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T33

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZQN9

Base Structure: X-ray

Registration Date: 2023-09-24

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2512442.488648
FMO2-HF: Nuclear repulsion 2425974.838676
FMO2-HF: Total energy -86467.649972
FMO2-MP2: Total energy -86719.596629


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.231-0.77512.478-6.103-13.831-0.013
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.032
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].
3A3ILE00.009-0.0023.070-3.562-1.3600.113-1.205-1.110-0.002
4A4PRO00.0200.0115.048-0.729-0.7290.0000.0000.0000.000
5A5THR0-0.036-0.0036.0330.2040.2040.0000.0000.0000.000
6A6THR00.0210.0098.3250.0620.0620.0000.0000.0000.000
7A7THR0-0.002-0.00511.6510.0730.0730.0000.0000.0000.000
8A8THR00.0890.03311.854-0.075-0.0750.0000.0000.0000.000
9A9LYS10.9460.97112.2200.2430.2430.0000.0000.0000.000
10A10GLY00.0490.02311.1280.0010.0010.0000.0000.0000.000
11A11GLU-1-0.873-0.9247.407-0.771-0.7710.0000.0000.0000.000
12A12GLN00.0320.0337.565-0.088-0.0880.0000.0000.0000.000
13A13ALA00.0000.0009.648-0.012-0.0120.0000.0000.0000.000
14A14LYS10.7860.8973.1933.0633.9000.043-0.272-0.6070.001
15A15SER00.015-0.0315.310-0.259-0.2590.0000.0000.0000.000
16A16GLN0-0.025-0.0086.2470.0610.0610.0000.0000.0000.000
17A17LEU0-0.020-0.0177.8200.0730.0730.0000.0000.0000.000
18A18ILE00.0050.0092.3570.626-0.9573.584-0.245-1.7570.000
19A19ALA00.0100.0086.0560.1690.1690.0000.0000.0000.000
20A20ALA0-0.0020.0009.0460.0870.0870.0000.0000.0000.000
21A21ALA00.005-0.0077.7450.0810.0810.0000.0000.0000.000
22A22LEU00.0240.0076.5980.1030.1030.0000.0000.0000.000
23A23ALA0-0.0340.0009.7610.0790.0790.0000.0000.0000.000
24A24GLN00.006-0.00713.0330.0510.0510.0000.0000.0000.000
25A25PHE0-0.014-0.0208.9350.0460.0460.0000.0000.0000.000
26A26GLY00.0180.01313.1720.0410.0410.0000.0000.0000.000
27A27GLU-1-0.855-0.91514.493-0.073-0.0730.0000.0000.0000.000
28A28TYR0-0.031-0.02216.8410.0160.0160.0000.0000.0000.000
29A29GLY00.0060.01214.9460.0150.0150.0000.0000.0000.000
30A30LEU0-0.018-0.02212.297-0.031-0.0310.0000.0000.0000.000
31A31HIS00.0180.01815.966-0.006-0.0060.0000.0000.0000.000
32A32ALA0-0.0040.02215.0890.0000.0000.0000.0000.0000.000
33A33THR0-0.033-0.05216.367-0.015-0.0150.0000.0000.0000.000
34A34THR00.0700.01313.315-0.013-0.0130.0000.0000.0000.000
35A35ARG10.8580.91115.3370.1280.1280.0000.0000.0000.000
36A36ASP-1-0.793-0.84717.513-0.171-0.1710.0000.0000.0000.000
37A37ILE00.0060.01010.922-0.006-0.0060.0000.0000.0000.000
38A38ALA0-0.001-0.00413.531-0.031-0.0310.0000.0000.0000.000
39A39ALA0-0.008-0.00214.637-0.001-0.0010.0000.0000.0000.000
40A40LEU0-0.037-0.00714.3750.0100.0100.0000.0000.0000.000
41A41ALA0-0.0140.00011.937-0.001-0.0010.0000.0000.0000.000
42A42GLY0-0.0030.01213.703-0.007-0.0070.0000.0000.0000.000
43A43GLN0-0.067-0.04312.0820.0030.0030.0000.0000.0000.000
44A44ASN00.006-0.00215.4310.0260.0260.0000.0000.0000.000
45A45ILE00.0420.00614.875-0.045-0.0450.0000.0000.0000.000
46A46ALA00.0130.00814.586-0.026-0.0260.0000.0000.0000.000
47A47ALA0-0.008-0.00412.121-0.014-0.0140.0000.0000.0000.000
48A48ILE00.0060.0079.728-0.110-0.1100.0000.0000.0000.000
49A49THR00.004-0.00210.044-0.073-0.0730.0000.0000.0000.000
50A50TYR0-0.048-0.01711.5680.0540.0540.0000.0000.0000.000
51A51TYR00.012-0.0016.9050.0470.0470.0000.0000.0000.000
52A52PHE0-0.005-0.0102.828-1.103-0.5670.094-0.128-0.5020.001
53A53GLY00.0410.0467.6480.2490.2490.0000.0000.0000.000
54A54SER0-0.063-0.0839.4000.0160.0160.0000.0000.0000.000
55A55LYS10.8220.9039.6270.0060.0060.0000.0000.0000.000
56A56GLU-1-0.768-0.90110.150-0.177-0.1770.0000.0000.0000.000
57A57ASP-1-0.860-0.8806.0830.2630.2630.0000.0000.0000.000
58A58LEU0-0.026-0.0115.173-0.379-0.315-0.001-0.002-0.0610.000
59A59TYR0-0.024-0.0376.360-0.156-0.1560.0000.0000.0000.000
60A60LEU00.0250.0104.202-0.1000.042-0.001-0.014-0.1270.000
61A61ALA0-0.034-0.0192.312-1.263-0.1611.238-0.657-1.6830.002
62A62CYS0-0.057-0.0232.753-2.362-0.6910.526-0.837-1.359-0.011
63A63ALA00.0240.0215.0600.1630.247-0.001-0.006-0.0770.000
64A64GLN0-0.061-0.0471.958-1.565-1.8286.084-1.785-4.0360.002
65A65TRP00.0250.0052.342-1.5710.4470.777-0.801-1.993-0.005
66A66ILE0-0.016-0.0134.038-0.244-0.1290.016-0.007-0.1240.000
67A67ALA00.0060.0127.152-0.072-0.0720.0000.0000.0000.000
68A68ASP-1-0.802-0.8944.5770.8981.3580.007-0.139-0.329-0.001
69A69PHE0-0.009-0.0067.379-0.267-0.2670.0000.0000.0000.000
70A70LEU00.001-0.0069.246-0.125-0.1250.0000.0000.0000.000
71A71GLY00.0590.02810.837-0.053-0.0530.0000.0000.0000.000
72A72GLU-1-0.854-0.92111.4340.0680.0680.0000.0000.0000.000
73A73LYS10.7720.89712.639-0.165-0.1650.0000.0000.0000.000
74A74PHE00.0080.00015.566-0.027-0.0270.0000.0000.0000.000
75A75ARG10.8220.90815.232-0.107-0.1070.0000.0000.0000.000
76A76PRO0-0.003-0.01317.242-0.011-0.0110.0000.0000.0000.000
77A77HIS0-0.038-0.01520.178-0.005-0.0050.0000.0000.0000.000
78A78ALA00.0840.03119.070-0.006-0.0060.0000.0000.0000.000
79A79GLU-1-0.819-0.88920.1070.0670.0670.0000.0000.0000.000
80A80LYS10.8820.94122.443-0.055-0.0550.0000.0000.0000.000
81A81ALA00.0420.03423.975-0.006-0.0060.0000.0000.0000.000
82A82GLU-1-0.809-0.90122.6060.1130.1130.0000.0000.0000.000
83A83ARG10.7750.87923.661-0.067-0.0670.0000.0000.0000.000
84A84LEU0-0.0270.01028.069-0.006-0.0060.0000.0000.0000.000
85A85PHE00.029-0.01826.508-0.004-0.0040.0000.0000.0000.000
86A86SER0-0.050-0.00529.4080.0000.0000.0000.0000.0000.000
87A87GLN0-0.047-0.03931.267-0.007-0.0070.0000.0000.0000.000
88A88PRO0-0.028-0.02234.8980.0010.0010.0000.0000.0000.000
89A89ALA0-0.012-0.00737.9100.0000.0000.0000.0000.0000.000
90A90PRO0-0.0170.00333.769-0.002-0.0020.0000.0000.0000.000
91A91ASP-1-0.836-0.91435.8110.0330.0330.0000.0000.0000.000
92A92ARG10.9040.95435.285-0.033-0.0330.0000.0000.0000.000
93A93ASP-1-0.889-0.94736.1930.0310.0310.0000.0000.0000.000
94A94ALA0-0.007-0.00932.7540.0010.0010.0000.0000.0000.000
95A95ILE0-0.050-0.01931.4230.0030.0030.0000.0000.0000.000
96A96ARG10.7970.87331.110-0.025-0.0250.0000.0000.0000.000
97A97GLU-1-0.834-0.92231.7680.0290.0290.0000.0000.0000.000
98A98LEU0-0.073-0.02325.2920.0000.0000.0000.0000.0000.000
99A99ILE00.0280.00726.7860.0050.0050.0000.0000.0000.000
100A100LEU00.0510.03627.3860.0010.0010.0000.0000.0000.000
101A101LEU0-0.027-0.00725.007-0.002-0.0020.0000.0000.0000.000
102A102ALA00.0000.01023.1700.0000.0000.0000.0000.0000.000
103A103CYS0-0.011-0.00823.3750.0010.0010.0000.0000.0000.000
104A104LYS10.8890.94625.127-0.012-0.0120.0000.0000.0000.000
105A105ASN0-0.062-0.04920.675-0.006-0.0060.0000.0000.0000.000
106A106MET0-0.010-0.00420.1730.0010.0010.0000.0000.0000.000
107A107ILE00.0400.02321.195-0.006-0.0060.0000.0000.0000.000
108A108MET0-0.0240.00121.493-0.010-0.0100.0000.0000.0000.000
109A109LEU00.0100.01915.107-0.006-0.0060.0000.0000.0000.000
110A110LEU0-0.026-0.00818.242-0.008-0.0080.0000.0000.0000.000
111A111THR0-0.041-0.03020.522-0.007-0.0070.0000.0000.0000.000
112A112GLN0-0.043-0.02117.6370.0060.0060.0000.0000.0000.000
113A113GLU-1-0.748-0.88519.025-0.050-0.0500.0000.0000.0000.000
114A114ASP-1-0.903-0.93014.632-0.064-0.0640.0000.0000.0000.000
115A115THR00.0230.00413.735-0.023-0.0230.0000.0000.0000.000
116A116VAL0-0.0140.00114.8220.0090.0090.0000.0000.0000.000
117A117ASN00.027-0.00412.9190.0180.0180.0000.0000.0000.000
118A118LEU00.0510.03710.330-0.009-0.0090.0000.0000.0000.000
119A119SER00.0220.00812.2930.0210.0210.0000.0000.0000.000
120A120LYS10.7960.92115.4560.1210.1210.0000.0000.0000.000
121A121PHE00.004-0.0019.6270.0020.0020.0000.0000.0000.000
122A122ILE00.0150.00111.7860.0190.0190.0000.0000.0000.000
123A123SER0-0.002-0.01614.7800.0150.0150.0000.0000.0000.000
124A124ARG10.8530.92314.3580.0630.0630.0000.0000.0000.000
125A125GLU-1-0.741-0.83412.9500.0760.0760.0000.0000.0000.000
126A126GLN0-0.025-0.01716.3690.0190.0190.0000.0000.0000.000
127A127LEU0-0.041-0.02219.1430.0030.0030.0000.0000.0000.000
128A128SER0-0.075-0.03418.471-0.005-0.0050.0000.0000.0000.000
129A129PRO0-0.0090.01516.415-0.004-0.0040.0000.0000.0000.000
130A130THR0-0.032-0.03312.5010.0040.0040.0000.0000.0000.000
131A131SER00.032-0.0049.777-0.016-0.0160.0000.0000.0000.000
132A132ALA0-0.029-0.0128.7810.0520.0520.0000.0000.0000.000
133A133TYR0-0.005-0.0189.8120.0330.0330.0000.0000.0000.000
134A134GLN0-0.084-0.04211.8980.0090.0090.0000.0000.0000.000
135A135LEU0-0.0020.0134.480-0.0590.012-0.001-0.005-0.0660.000
136A136VAL00.007-0.0079.2100.0140.0140.0000.0000.0000.000
137A137HIS0-0.0100.00010.776-0.022-0.0220.0000.0000.0000.000
138A138GLU-1-0.876-0.93611.8450.3780.3780.0000.0000.0000.000
139A139GLN0-0.051-0.0207.2910.0170.0170.0000.0000.0000.000
140A140VAL0-0.042-0.01911.295-0.013-0.0130.0000.0000.0000.000
141A141ILE0-0.025-0.00713.944-0.032-0.0320.0000.0000.0000.000
142A142ASP-1-0.846-0.90916.3540.1450.1450.0000.0000.0000.000
143A143PRO00.0200.00315.375-0.022-0.0220.0000.0000.0000.000
144A144LEU00.0290.02617.993-0.019-0.0190.0000.0000.0000.000
145A145HIS00.0480.02919.938-0.023-0.0230.0000.0000.0000.000
146A146THR0-0.0110.01121.625-0.019-0.0190.0000.0000.0000.000
147A147HIS0-0.060-0.05620.995-0.008-0.0080.0000.0000.0000.000
148A148LEU00.012-0.00222.780-0.011-0.0110.0000.0000.0000.000
149A149THR0-0.050-0.03025.828-0.009-0.0090.0000.0000.0000.000
150A150ARG10.8510.90326.126-0.106-0.1060.0000.0000.0000.000
151A151LEU0-0.0240.00226.548-0.006-0.0060.0000.0000.0000.000
152A152VAL00.017-0.00429.653-0.006-0.0060.0000.0000.0000.000
153A153ALA0-0.005-0.00631.682-0.004-0.0040.0000.0000.0000.000
154A154ALA0-0.015-0.00332.844-0.003-0.0030.0000.0000.0000.000
155A155TYR0-0.042-0.02634.320-0.004-0.0040.0000.0000.0000.000
156A156THR0-0.009-0.01536.158-0.002-0.0020.0000.0000.0000.000
157A157GLY00.0010.01837.541-0.002-0.0020.0000.0000.0000.000
158A158CYS0-0.075-0.03136.055-0.001-0.0010.0000.0000.0000.000
159A159ASP-1-0.799-0.90233.4380.0730.0730.0000.0000.0000.000
160A160ALA00.0210.00429.5870.0000.0000.0000.0000.0000.000
161A161ASN0-0.072-0.04729.2490.0140.0140.0000.0000.0000.000
162A162ASP-1-0.773-0.83130.6760.0580.0580.0000.0000.0000.000
163A163THR00.0470.00530.7480.0020.0020.0000.0000.0000.000
164A164ARG10.8520.88831.746-0.051-0.0510.0000.0000.0000.000
165A165MET00.0260.04431.848-0.004-0.0040.0000.0000.0000.000
166A166ILE00.0430.02626.5890.0000.0000.0000.0000.0000.000
167A167LEU0-0.014-0.01228.7290.0000.0000.0000.0000.0000.000
168A168HIS0-0.031-0.02730.762-0.005-0.0050.0000.0000.0000.000
169A169THR0-0.012-0.00926.985-0.004-0.0040.0000.0000.0000.000
170A170HIS0-0.027-0.02523.489-0.006-0.0060.0000.0000.0000.000
171A171ALA0-0.030-0.01627.641-0.003-0.0030.0000.0000.0000.000
172A172LEU0-0.007-0.00328.922-0.004-0.0040.0000.0000.0000.000
173A173LEU0-0.002-0.00123.798-0.002-0.0020.0000.0000.0000.000
174A174GLY00.0150.00725.909-0.002-0.0020.0000.0000.0000.000
175A175GLU-1-0.871-0.92527.6310.0210.0210.0000.0000.0000.000
176A176VAL0-0.023-0.01423.504-0.005-0.0050.0000.0000.0000.000
177A177LEU00.012-0.00721.190-0.005-0.0050.0000.0000.0000.000
178A178ALA00.0080.02124.200-0.006-0.0060.0000.0000.0000.000
179A179PHE00.001-0.00326.154-0.006-0.0060.0000.0000.0000.000
180A180ARG10.7940.88417.4100.0100.0100.0000.0000.0000.000
181A181LEU0-0.008-0.02220.469-0.008-0.0080.0000.0000.0000.000
182A182GLY00.0310.03023.593-0.003-0.0030.0000.0000.0000.000
183A183LYS10.8200.91622.7070.0410.0410.0000.0000.0000.000
184A184GLU-1-0.881-0.94826.268-0.031-0.0310.0000.0000.0000.000
185A185THR0-0.079-0.05228.5670.0020.0020.0000.0000.0000.000
186A186ILE00.0320.01428.8990.0010.0010.0000.0000.0000.000
187A187LEU00.0110.02727.1850.0000.0000.0000.0000.0000.000
188A188LEU00.0130.00731.4220.0010.0010.0000.0000.0000.000
189A189ARG10.8290.92134.1140.0050.0050.0000.0000.0000.000
190A190THR0-0.024-0.03833.5340.0010.0010.0000.0000.0000.000
191A191GLY0-0.031-0.00135.6960.0000.0000.0000.0000.0000.000
192A192TRP0-0.018-0.00730.651-0.002-0.0020.0000.0000.0000.000
193A193PRO00.0110.00231.4230.0000.0000.0000.0000.0000.000
194A194GLN0-0.039-0.02426.539-0.007-0.0070.0000.0000.0000.000
195A195PHE00.0140.00624.3230.0040.0040.0000.0000.0000.000
196A196ASP-1-0.794-0.89226.722-0.027-0.0270.0000.0000.0000.000
197A197GLU-1-0.835-0.91326.788-0.001-0.0010.0000.0000.0000.000
198A198GLU-1-0.837-0.90528.537-0.013-0.0130.0000.0000.0000.000
199A199LYS10.7560.86029.8010.0210.0210.0000.0000.0000.000
200A200ALA00.0050.00826.5360.0030.0030.0000.0000.0000.000
201A201GLU-1-0.923-0.96928.3620.0010.0010.0000.0000.0000.000
202A202LEU0-0.026-0.01031.5170.0030.0030.0000.0000.0000.000
203A203ILE0-0.0090.00827.6380.0020.0020.0000.0000.0000.000
204A204TYR0-0.006-0.01929.0840.0020.0020.0000.0000.0000.000
205A205GLN0-0.0130.00430.6820.0030.0030.0000.0000.0000.000
206A206THR0-0.038-0.02333.3040.0010.0010.0000.0000.0000.000
207A207VAL00.0190.00328.8550.0020.0020.0000.0000.0000.000
208A208THR0-0.015-0.01732.1630.0040.0040.0000.0000.0000.000
209A209CYS0-0.049-0.01733.7600.0010.0010.0000.0000.0000.000
210A210HIS0-0.062-0.04434.166-0.002-0.0020.0000.0000.0000.000
211A211ILE00.0330.00929.7360.0020.0020.0000.0000.0000.000
212A212ASP-1-0.781-0.87134.2350.0290.0290.0000.0000.0000.000
213A213LEU0-0.063-0.02737.1000.0000.0000.0000.0000.0000.000
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