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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: 9Y5Z2

Calculation Name: 1T33-A-Xray315

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: 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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 221
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2508032.743981
FMO2-HF: Nuclear repulsion 2421547.699134
FMO2-HF: Total energy -86485.044847
FMO2-MP2: Total energy -86737.255192


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.
-3.905-5.73624.794-7.159-15.802-0.008
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 : 0.075 / q_NPA : 0.031
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].
3A3ILE 00.0250.0183.706-2.625-0.738-0.005-1.018-0.8630.000
4A4PRO 0-0.018-0.0145.599-0.525-0.5250.0000.0000.0000.000
5A5THR 0-0.0080.0076.6160.1750.1750.0000.0000.0000.000
6A6THR 00.0180.0108.4090.0390.0390.0000.0000.0000.000
7A7THR 0-0.007-0.00111.8590.0530.0530.0000.0000.0000.000
8A8THR 00.0950.03111.690-0.050-0.0500.0000.0000.0000.000
9A9LYS 10.9520.96612.1800.1670.1670.0000.0000.0000.000
10A10GLY 00.0340.02210.7950.0110.0110.0000.0000.0000.000
11A11GLU -1-0.908-0.9677.348-0.388-0.3880.0000.0000.0000.000
12A12GLN 00.0490.0347.5840.0350.0350.0000.0000.0000.000
13A13ALA 0-0.019-0.0119.2950.0290.0290.0000.0000.0000.000
14A14LYS 10.8800.9572.9362.2243.1300.147-0.253-0.8000.002
15A15SER 00.0370.0125.3220.0340.0340.0000.0000.0000.000
16A16GLN 0-0.013-0.0096.2720.0650.0650.0000.0000.0000.000
17A17LEU 0-0.020-0.0187.3420.0370.0370.0000.0000.0000.000
18A18ILE 00.0280.0202.0904.819-3.74812.285-0.846-2.871-0.002
19A19ALA 00.0010.0175.9020.0810.0810.0000.0000.0000.000
20A20ALA 00.005-0.0029.1290.0160.0160.0000.0000.0000.000
21A21ALA 00.009-0.0027.3380.0240.0240.0000.0000.0000.000
22A22LEU 00.0210.0097.3790.0260.0260.0000.0000.0000.000
23A23ALA 0-0.049-0.0089.8460.0180.0180.0000.0000.0000.000
24A24GLN 0-0.006-0.02012.8450.0090.0090.0000.0000.0000.000
25A25PHE 0-0.014-0.0098.4400.0120.0120.0000.0000.0000.000
26A26GLY 00.0090.00612.8880.0150.0150.0000.0000.0000.000
27A27GLU -1-0.898-0.94314.3880.0170.0170.0000.0000.0000.000
28A28TYR 0-0.018-0.01716.5800.0010.0010.0000.0000.0000.000
29A29GLY 0-0.0020.00515.2370.0050.0050.0000.0000.0000.000
30A30LEU 00.028-0.00812.144-0.016-0.0160.0000.0000.0000.000
31A31HIS 0-0.017-0.00615.728-0.003-0.0030.0000.0000.0000.000
32A32ALA 00.0030.02914.481-0.005-0.0050.0000.0000.0000.000
33A33THR 0-0.007-0.01015.909-0.005-0.0050.0000.0000.0000.000
34A34THR 00.0810.01912.685-0.004-0.0040.0000.0000.0000.000
35A35ARG 10.9450.97114.6560.0300.0300.0000.0000.0000.000
36A36ASP -1-0.867-0.93616.968-0.047-0.0470.0000.0000.0000.000
37A37ILE 00.0040.00210.281-0.004-0.0040.0000.0000.0000.000
38A38ALA 0-0.018-0.01213.193-0.012-0.0120.0000.0000.0000.000
39A39ALA 0-0.028-0.01914.2370.0000.0000.0000.0000.0000.000
40A40LEU 0-0.042-0.01014.1580.0020.0020.0000.0000.0000.000
41A41ALA 0-0.0130.00011.4890.0030.0030.0000.0000.0000.000
42A42GLY 0-0.0120.00913.484-0.009-0.0090.0000.0000.0000.000
43A43GLN 0-0.046-0.02111.370-0.019-0.0190.0000.0000.0000.000
44A44ASN 00.0280.00714.7550.0160.0160.0000.0000.0000.000
45A45ILE 00.0430.00614.563-0.022-0.0220.0000.0000.0000.000
46A46ALA 0-0.017-0.01114.698-0.007-0.0070.0000.0000.0000.000
47A47ALA 0-0.012-0.00511.727-0.011-0.0110.0000.0000.0000.000
48A48ILE 00.0130.0069.618-0.063-0.0630.0000.0000.0000.000
49A49THR 0-0.0040.0009.871-0.026-0.0260.0000.0000.0000.000
50A50TYR 0-0.047-0.01611.1170.0370.0370.0000.0000.0000.000
51A51TYR 0-0.017-0.0136.4570.0250.0250.0000.0000.0000.000
52A52PHE 0-0.020-0.0262.692-0.998-0.3770.261-0.138-0.7450.001
53A53GLY 00.0450.0497.3180.1950.1950.0000.0000.0000.000
54A54SER 0-0.037-0.0369.2930.0010.0010.0000.0000.0000.000
55A55LYS 10.8970.9539.445-0.050-0.0500.0000.0000.0000.000
56A56GLU -1-0.869-0.9509.864-0.003-0.0030.0000.0000.0000.000
57A57ASP -1-0.854-0.9095.7190.4060.4060.0000.0000.0000.000
58A58LEU 0-0.069-0.0314.879-0.430-0.3300.000-0.004-0.0960.000
59A59TYR 0-0.043-0.0515.637-0.111-0.1110.0000.0000.0000.000
60A60LEU 00.0440.0164.420-0.0800.0470.000-0.010-0.1160.000
61A61ALA 0-0.032-0.0092.067-1.201-1.0503.591-1.222-2.5200.008
62A62CYS 0-0.055-0.0153.073-0.3571.3060.426-0.611-1.478-0.010
63A63ALA 00.0270.0215.0400.2210.2970.000-0.006-0.0690.000
64A64GLN 0-0.059-0.0451.851-0.860-2.0467.596-2.348-4.062-0.003
65A65TRP 00.0280.0033.387-2.048-0.1950.453-0.639-1.668-0.003
66A66ILE 0-0.030-0.0154.235-0.637-0.6640.0350.114-0.1220.000
67A67ALA 0-0.0120.0047.087-0.122-0.1220.0000.0000.0000.000
68A68ASP -1-0.852-0.9354.045-1.912-1.4070.005-0.175-0.335-0.001
69A69PHE 0-0.033-0.0177.555-0.105-0.1050.0000.0000.0000.000
70A70LEU 00.000-0.0239.428-0.084-0.0840.0000.0000.0000.000
71A71GLY 00.0420.02011.030-0.028-0.0280.0000.0000.0000.000
72A72GLU -1-0.958-0.98910.988-0.104-0.1040.0000.0000.0000.000
73A73LYS 10.9080.96012.845-0.050-0.0500.0000.0000.0000.000
74A74PHE 0-0.021-0.00915.484-0.006-0.0060.0000.0000.0000.000
75A75ARG 10.9471.01214.5120.0780.0780.0000.0000.0000.000
76A76PRO 0-0.017-0.02716.8400.0020.0020.0000.0000.0000.000
77A77HIS 0-0.023-0.01520.2300.0030.0030.0000.0000.0000.000
78A78ALA 00.0790.04718.8640.0020.0020.0000.0000.0000.000
79A79GLU -1-0.915-0.96319.195-0.054-0.0540.0000.0000.0000.000
80A80LYS 10.8210.91322.0760.0160.0160.0000.0000.0000.000
81A81ALA 00.0580.02324.0650.0010.0010.0000.0000.0000.000
82A82GLU -1-0.862-0.93222.3900.0070.0070.0000.0000.0000.000
83A83ARG 10.8820.93524.3950.0240.0240.0000.0000.0000.000
84A84LEU 0-0.063-0.01327.7760.0000.0000.0000.0000.0000.000
85A85PHE 00.032-0.00126.6030.0020.0020.0000.0000.0000.000
86A86SER 0-0.099-0.03029.6520.0010.0010.0000.0000.0000.000
87A87GLN 00.023-0.00631.4950.0000.0000.0000.0000.0000.000
88A88PRO 0-0.026-0.01735.0160.0010.0010.0000.0000.0000.000
89A89ALA 0-0.003-0.00837.7120.0010.0010.0000.0000.0000.000
90A90PRO 0-0.028-0.00433.602-0.001-0.0010.0000.0000.0000.000
91A91ASP -1-0.864-0.93135.5610.0010.0010.0000.0000.0000.000
92A92ARG 10.9160.94835.533-0.008-0.0080.0000.0000.0000.000
93A93ASP -1-0.883-0.94736.4720.0030.0030.0000.0000.0000.000
94A94ALA 00.0450.02532.8790.0000.0000.0000.0000.0000.000
95A95ILE 0-0.049-0.02131.6160.0000.0000.0000.0000.0000.000
96A96ARG 10.8580.92331.311-0.004-0.0040.0000.0000.0000.000
97A97GLU -1-0.937-0.97631.5140.0000.0000.0000.0000.0000.000
98A98LEU 0-0.041-0.01225.8520.0000.0000.0000.0000.0000.000
99A99ILE 00.0160.00527.0180.0020.0020.0000.0000.0000.000
100A100LEU 00.0240.01427.5760.0020.0020.0000.0000.0000.000
101A101LEU 0-0.016-0.00624.7140.0000.0000.0000.0000.0000.000
102A102ALA 00.0050.02023.1710.0010.0010.0000.0000.0000.000
103A103CYS 00.0150.00323.2660.0040.0040.0000.0000.0000.000
104A104LYS 10.9930.99825.0620.0020.0020.0000.0000.0000.000
105A105ASN 0-0.079-0.06220.574-0.001-0.0010.0000.0000.0000.000
106A106MET 00.0080.01120.4020.0060.0060.0000.0000.0000.000
107A107ILE 00.0220.01721.4250.0040.0040.0000.0000.0000.000
108A108MET 0-0.031-0.00721.659-0.001-0.0010.0000.0000.0000.000
109A109LEU 0-0.0020.00215.5970.0020.0020.0000.0000.0000.000
110A110LEU 0-0.053-0.04018.9910.0050.0050.0000.0000.0000.000
111A111THR 0-0.048-0.01721.116-0.003-0.0030.0000.0000.0000.000
112A112GLN 0-0.0090.00917.8030.0040.0040.0000.0000.0000.000
113A113GLU -1-0.877-0.97819.4210.0190.0190.0000.0000.0000.000
114A114ASP -1-0.934-0.95415.4540.0420.0420.0000.0000.0000.000
115A115THR 00.0350.01514.3910.0180.0180.0000.0000.0000.000
116A116VAL 0-0.022-0.00815.5490.0070.0070.0000.0000.0000.000
117A117ASN 00.033-0.00912.806-0.002-0.0020.0000.0000.0000.000
118A118LEU 00.0300.03811.3630.0010.0010.0000.0000.0000.000
119A119SER 00.0160.00212.798-0.001-0.0010.0000.0000.0000.000
120A120LYS 10.8360.94215.398-0.017-0.0170.0000.0000.0000.000
121A121PHE 00.012-0.0039.4920.0020.0020.0000.0000.0000.000
122A122ILE 00.0100.00412.4850.0020.0020.0000.0000.0000.000
123A123SER 0-0.001-0.01215.081-0.005-0.0050.0000.0000.0000.000
124A124ARG 10.8940.95915.563-0.046-0.0460.0000.0000.0000.000
125A125GLU -1-0.743-0.85513.0960.1080.1080.0000.0000.0000.000
126A126GLN 0-0.026-0.00116.5040.0050.0050.0000.0000.0000.000
127A127LEU 0-0.044-0.02319.093-0.003-0.0030.0000.0000.0000.000
128A128SER 0-0.077-0.02919.081-0.001-0.0010.0000.0000.0000.000
129A129PRO 00.0030.01516.3420.0030.0030.0000.0000.0000.000
130A130THR 0-0.026-0.03512.5200.0090.0090.0000.0000.0000.000
131A131SER 00.020-0.0019.301-0.008-0.0080.0000.0000.0000.000
132A132ALA 0-0.036-0.0218.7880.0170.0170.0000.0000.0000.000
133A133TYR 00.009-0.0119.8570.0050.0050.0000.0000.0000.000
134A134GLN 0-0.046-0.01111.988-0.013-0.0130.0000.0000.0000.000
135A135LEU 00.0150.0204.534-0.0440.0160.000-0.003-0.0570.000
136A136VAL 0-0.003-0.0139.184-0.034-0.0340.0000.0000.0000.000
137A137HIS 00.001-0.00710.576-0.022-0.0220.0000.0000.0000.000
138A138GLU -1-0.862-0.94411.7320.2110.2110.0000.0000.0000.000
139A139GLN 0-0.0190.0116.956-0.025-0.0250.0000.0000.0000.000
140A140VAL 0-0.026-0.01411.178-0.023-0.0230.0000.0000.0000.000
141A141ILE 0-0.0340.01713.908-0.007-0.0070.0000.0000.0000.000
142A142ASP -1-0.889-0.94616.0610.0640.0640.0000.0000.0000.000
143A143PRO 0-0.0110.02015.379-0.009-0.0090.0000.0000.0000.000
144A144LEU 00.0360.01617.968-0.006-0.0060.0000.0000.0000.000
145A145HIS 00.0350.02619.805-0.003-0.0030.0000.0000.0000.000
146A146THR 0-0.017-0.02521.206-0.004-0.0040.0000.0000.0000.000
147A147HIS 00.001-0.00321.426-0.006-0.0060.0000.0000.0000.000
148A148LEU 00.0110.00823.015-0.003-0.0030.0000.0000.0000.000
149A149THR 0-0.034-0.01925.761-0.001-0.0010.0000.0000.0000.000
150A150ARG 10.8690.93226.547-0.033-0.0330.0000.0000.0000.000
151A151LEU 0-0.021-0.00426.740-0.002-0.0020.0000.0000.0000.000
152A152VAL 00.017-0.00129.912-0.002-0.0020.0000.0000.0000.000
153A153ALA 0-0.049-0.01431.551-0.001-0.0010.0000.0000.0000.000
154A154ALA 00.0160.00532.646-0.001-0.0010.0000.0000.0000.000
155A155TYR 0-0.052-0.02134.139-0.001-0.0010.0000.0000.0000.000
156A156THR 0-0.059-0.02535.956-0.001-0.0010.0000.0000.0000.000
157A157GLY 00.0200.02637.2660.0000.0000.0000.0000.0000.000
158A158CYS 0-0.050-0.03236.0930.0010.0010.0000.0000.0000.000
159A159ASP -1-0.855-0.94134.0500.0260.0260.0000.0000.0000.000
160A160ALA 00.012-0.01329.7330.0010.0010.0000.0000.0000.000
161A161ASN 0-0.028-0.01829.2020.0050.0050.0000.0000.0000.000
162A162ASP -1-0.804-0.87231.0440.0300.0300.0000.0000.0000.000
163A163THR 00.0720.01931.1050.0010.0010.0000.0000.0000.000
164A164ARG 10.8620.90831.731-0.024-0.0240.0000.0000.0000.000
165A165MET 00.0270.03831.973-0.001-0.0010.0000.0000.0000.000
166A166ILE 00.0180.01026.5550.0000.0000.0000.0000.0000.000
167A167LEU 0-0.040-0.03028.6560.0010.0010.0000.0000.0000.000
168A168HIS 0-0.014-0.00830.878-0.001-0.0010.0000.0000.0000.000
169A169THR 00.0170.00726.809-0.002-0.0020.0000.0000.0000.000
170A170HIS 0-0.024-0.01623.503-0.001-0.0010.0000.0000.0000.000
171A171ALA 0-0.015-0.00427.5410.0000.0000.0000.0000.0000.000
172A172LEU 00.001-0.00228.651-0.001-0.0010.0000.0000.0000.000
173A173LEU 0-0.0080.00123.493-0.001-0.0010.0000.0000.0000.000
174A174GLY 00.0040.00226.0140.0010.0010.0000.0000.0000.000
175A175GLU -1-0.869-0.91627.6870.0170.0170.0000.0000.0000.000
176A176VAL 0-0.023-0.00924.063-0.001-0.0010.0000.0000.0000.000
177A177LEU 0-0.002-0.02321.6720.0000.0000.0000.0000.0000.000
178A178ALA 00.0220.03124.6320.0010.0010.0000.0000.0000.000
179A179PHE 00.0080.00026.739-0.001-0.0010.0000.0000.0000.000
180A180ARG 10.8410.93618.158-0.045-0.0450.0000.0000.0000.000
181A181LEU 0-0.013-0.02420.9600.0000.0000.0000.0000.0000.000
182A182GLY 0-0.0020.00824.192-0.001-0.0010.0000.0000.0000.000
183A183LYS 10.9080.96422.720-0.020-0.0200.0000.0000.0000.000
184A184GLU -1-0.867-0.93926.8610.0080.0080.0000.0000.0000.000
185A185THR 0-0.041-0.01729.004-0.002-0.0020.0000.0000.0000.000
186A186ILE 00.0320.01129.404-0.001-0.0010.0000.0000.0000.000
187A187LEU 0-0.0070.01527.602-0.001-0.0010.0000.0000.0000.000
188A188LEU 00.0070.00731.844-0.002-0.0020.0000.0000.0000.000
189A189ARG 10.8640.93234.562-0.010-0.0100.0000.0000.0000.000
190A190THR 0-0.048-0.03733.976-0.001-0.0010.0000.0000.0000.000
191A191GLY 0-0.0120.00835.906-0.001-0.0010.0000.0000.0000.000
192A192TRP 0-0.040-0.02531.602-0.001-0.0010.0000.0000.0000.000
193A193PRO 00.0100.00532.0990.0010.0010.0000.0000.0000.000
194A194GLN 00.010-0.00527.1970.0000.0000.0000.0000.0000.000
195A195PHE 0-0.006-0.01325.179-0.001-0.0010.0000.0000.0000.000
196A196ASP -1-0.788-0.88127.5060.0000.0000.0000.0000.0000.000
197A197GLU -1-0.904-0.96627.225-0.001-0.0010.0000.0000.0000.000
198A198GLU -1-0.864-0.92929.104-0.002-0.0020.0000.0000.0000.000
199A199LYS 10.7730.87930.547-0.001-0.0010.0000.0000.0000.000
200A200ALA 0-0.0040.00027.3380.0020.0020.0000.0000.0000.000
201A201GLU -1-0.946-0.97229.1650.0000.0000.0000.0000.0000.000
202A202LEU 0-0.013-0.00732.0310.0010.0010.0000.0000.0000.000
203A203ILE 0-0.0140.00428.3820.0010.0010.0000.0000.0000.000
204A204TYR 00.0150.00328.9960.0010.0010.0000.0000.0000.000
205A205GLN 0-0.0150.00530.9980.0000.0000.0000.0000.0000.000
206A206THR 0-0.043-0.02733.6180.0000.0000.0000.0000.0000.000
207A207VAL 00.0360.00929.2970.0000.0000.0000.0000.0000.000
208A208THR 0-0.036-0.02032.4150.0000.0000.0000.0000.0000.000
209A209CYS 0-0.054-0.01633.8210.0000.0000.0000.0000.0000.000
210A210HIS 0-0.044-0.05734.617-0.001-0.0010.0000.0000.0000.000
211A211ILE 00.0240.00729.9900.0010.0010.0000.0000.0000.000
212A212ASP -1-0.797-0.88134.4990.0080.0080.0000.0000.0000.000
213A213LEU 0-0.057-0.03037.4660.0000.0000.0000.0000.0000.000
214A214ILE 0-0.008-0.00435.1580.0000.0000.0000.0000.0000.000
215A215LEU 0-0.0020.00033.5880.0000.0000.0000.0000.0000.000
216A216HIS 0-0.003-0.00437.4850.0000.0000.0000.0000.0000.000
217A217GLY 0-0.029-0.00840.9080.0000.0000.0000.0000.0000.000
218A218LEU 0-0.037-0.02136.3250.0000.0000.0000.0000.0000.000
219A219THR 0-0.046-0.02540.1520.0000.0000.0000.0000.0000.000
220A220GLN 0-0.043-0.00941.588-0.001-0.0010.0000.0000.0000.000
221A221NME 0-0.027-0.00544.5170.0010.0010.0000.0000.0000.000