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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: K2G83

Calculation Name: 2A2J-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine

ligand 3-letter code: CME

PDB ID: 2A2J

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIJ1

Base Structure: X-ray

Registration Date: 2023-09-27

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2180681.249629
FMO2-HF: Nuclear repulsion 2100745.857207
FMO2-HF: Total energy -79935.392422
FMO2-MP2: Total energy -80169.172732


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:24:PRO)


Summations of interaction energy for fragment #1(A:24:PRO)
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.
-25.204-22.77519.978-8.968-13.4370.02
Interaction energy analysis for fragmet #1(A:24:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.005
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].
3A26LYS10.8510.9233.631-1.3770.683-0.009-0.945-1.106-0.001
4A27ASP-1-0.720-0.8324.882-0.893-0.8930.0000.0000.0000.000
5A28GLY0-0.0150.0035.9380.4080.4080.0000.0000.0000.000
6A29CME0-0.062-0.0035.7440.4790.4790.0000.0000.0000.000
7A30GLY00.0600.0304.058-1.069-0.9020.000-0.038-0.1290.000
8A31ASP-1-0.867-0.9355.2840.5060.5060.0000.0000.0000.000
9A32LEU0-0.038-0.0116.404-0.087-0.0870.0000.0000.0000.000
10A33ASP-1-0.826-0.9199.4100.4370.4370.0000.0000.0000.000
11A34PHE0-0.012-0.02412.381-0.016-0.0160.0000.0000.0000.000
12A35ASP-1-0.803-0.89213.777-0.146-0.1460.0000.0000.0000.000
13A36TRP0-0.072-0.0348.4380.0200.0200.0000.0000.0000.000
14A37LEU0-0.069-0.05115.1070.0180.0180.0000.0000.0000.000
15A38ASP-1-0.876-0.91518.414-0.026-0.0260.0000.0000.0000.000
16A39ASP-1-0.962-0.96820.537-0.090-0.0900.0000.0000.0000.000
17A40GLY00.0000.00021.7500.0060.0060.0000.0000.0000.000
18A41TRP00.021-0.01919.660-0.004-0.0040.0000.0000.0000.000
19A42LEU0-0.0310.00520.0140.0000.0000.0000.0000.0000.000
20A43THR00.020-0.00620.738-0.008-0.0080.0000.0000.0000.000
21A44LEU00.0220.03213.907-0.031-0.0310.0000.0000.0000.000
22A45LEU0-0.020-0.01216.960-0.011-0.0110.0000.0000.0000.000
23A46ARG10.7890.87118.691-0.006-0.0060.0000.0000.0000.000
24A47ARG10.8440.89813.3170.3810.3810.0000.0000.0000.000
25A48TRP0-0.001-0.01710.191-0.015-0.0150.0000.0000.0000.000
26A49LEU00.0060.01815.481-0.011-0.0110.0000.0000.0000.000
27A50ASN0-0.031-0.01318.373-0.003-0.0030.0000.0000.0000.000
28A51ASP-1-0.804-0.87113.112-0.430-0.4300.0000.0000.0000.000
29A52ALA0-0.003-0.00215.137-0.044-0.0440.0000.0000.0000.000
30A53GLN00.017-0.00215.963-0.001-0.0010.0000.0000.0000.000
31A54ARG10.9010.95316.5710.3820.3820.0000.0000.0000.000
32A55ALA0-0.026-0.00414.273-0.037-0.0370.0000.0000.0000.000
33A56GLY00.0000.00816.2340.0020.0020.0000.0000.0000.000
34A57VAL0-0.045-0.01215.2550.0340.0340.0000.0000.0000.000
35A58SER0-0.002-0.01618.2650.0030.0030.0000.0000.0000.000
36A59GLU-1-0.933-0.96620.9720.0510.0510.0000.0000.0000.000
37A60PRO00.0430.04819.1270.0320.0320.0000.0000.0000.000
38A61ASN0-0.010-0.02119.8950.0120.0120.0000.0000.0000.000
39A62ALA0-0.028-0.02422.1800.0080.0080.0000.0000.0000.000
40A63MET0-0.0120.00521.1890.0180.0180.0000.0000.0000.000
41A64VAL0-0.013-0.01921.501-0.022-0.0220.0000.0000.0000.000
42A65LEU00.0000.01923.6600.0160.0160.0000.0000.0000.000
43A66ALA00.009-0.00425.841-0.004-0.0040.0000.0000.0000.000
44A67THR00.001-0.00127.651-0.007-0.0070.0000.0000.0000.000
45A68VAL00.0160.00131.3130.0120.0120.0000.0000.0000.000
46A69ALA00.0290.01434.009-0.012-0.0120.0000.0000.0000.000
47A70ASP-1-0.887-0.93837.1930.1250.1250.0000.0000.0000.000
48A71GLY00.0130.00636.9560.0000.0000.0000.0000.0000.000
49A72LYS10.8680.93834.094-0.134-0.1340.0000.0000.0000.000
50A73PRO00.0320.01729.117-0.009-0.0090.0000.0000.0000.000
51A74VAL0-0.025-0.01230.986-0.003-0.0030.0000.0000.0000.000
52A75THR00.0130.00425.8720.0050.0050.0000.0000.0000.000
53A76ARG10.7980.88627.736-0.172-0.1720.0000.0000.0000.000
54A77SER00.0330.01324.7910.0120.0120.0000.0000.0000.000
55A78VAL0-0.052-0.01726.162-0.017-0.0170.0000.0000.0000.000
56A79LEU00.0040.00325.9880.0060.0060.0000.0000.0000.000
57A80CYS0-0.0230.00324.597-0.008-0.0080.0000.0000.0000.000
58A81LYS10.8720.92826.738-0.039-0.0390.0000.0000.0000.000
59A82ILE00.0140.02528.890-0.011-0.0110.0000.0000.0000.000
60A83LEU00.0170.00721.8740.0150.0150.0000.0000.0000.000
61A84ASP-1-0.759-0.85526.6040.0320.0320.0000.0000.0000.000
62A85GLU-1-0.726-0.86227.8320.0230.0230.0000.0000.0000.000
63A86SER0-0.083-0.05229.3300.0080.0080.0000.0000.0000.000
64A87GLY0-0.009-0.01327.6880.0100.0100.0000.0000.0000.000
65A88VAL0-0.027-0.00323.627-0.011-0.0110.0000.0000.0000.000
66A89ALA00.0200.01327.0910.0080.0080.0000.0000.0000.000
67A90PHE00.0210.00228.961-0.004-0.0040.0000.0000.0000.000
68A91PHE00.0480.00730.820-0.002-0.0020.0000.0000.0000.000
69A92THR0-0.071-0.05633.7160.0070.0070.0000.0000.0000.000
70A93SER00.0010.00036.199-0.005-0.0050.0000.0000.0000.000
71A94TYR00.0260.00038.5710.0080.0080.0000.0000.0000.000
72A95THR00.0230.01040.6950.0020.0020.0000.0000.0000.000
73A96SER0-0.031-0.01137.7510.0040.0040.0000.0000.0000.000
74A97ALA00.1060.03137.5490.0010.0010.0000.0000.0000.000
75A98LYS10.9060.96332.271-0.099-0.0990.0000.0000.0000.000
76A99GLY00.0040.00035.6460.0030.0030.0000.0000.0000.000
77A100GLU-1-0.904-0.95038.2470.0930.0930.0000.0000.0000.000
78A101GLN00.0520.01534.7310.0090.0090.0000.0000.0000.000
79A102LEU0-0.014-0.00632.6340.0030.0030.0000.0000.0000.000
80A103ALA0-0.057-0.01636.705-0.003-0.0030.0000.0000.0000.000
81A104VAL0-0.021-0.00239.959-0.003-0.0030.0000.0000.0000.000
82A105THR0-0.017-0.01534.9220.0020.0020.0000.0000.0000.000
83A106PRO00.0020.02735.5660.0070.0070.0000.0000.0000.000
84A107TYR0-0.001-0.01931.959-0.003-0.0030.0000.0000.0000.000
85A108ALA0-0.038-0.01529.1850.0010.0010.0000.0000.0000.000
86A109SER00.006-0.01023.8370.0070.0070.0000.0000.0000.000
87A110ALA00.0060.00023.549-0.012-0.0120.0000.0000.0000.000
88A111THR00.0140.00817.4280.0040.0040.0000.0000.0000.000
89A112PHE00.0240.00217.331-0.033-0.0330.0000.0000.0000.000
90A113PRO00.0020.00415.9720.0630.0630.0000.0000.0000.000
91A114TRP0-0.013-0.01313.092-0.016-0.0160.0000.0000.0000.000
92A115TYR00.020-0.02111.642-0.029-0.0290.0000.0000.0000.000
93A116GLN0-0.046-0.01310.6050.1760.1760.0000.0000.0000.000
94A117LEU00.0360.0159.129-0.114-0.1140.0000.0000.0000.000
95A118GLY0-0.024-0.0106.7650.0110.0110.0000.0000.0000.000
96A119ARG10.7630.8677.3400.7640.7640.0000.0000.0000.000
97A120GLN0-0.056-0.0339.766-0.161-0.1610.0000.0000.0000.000
98A121ALA00.0260.02013.1240.0220.0220.0000.0000.0000.000
99A122HIS00.0310.03515.650-0.078-0.0780.0000.0000.0000.000
100A123VAL00.0060.00519.149-0.014-0.0140.0000.0000.0000.000
101A124GLN0-0.0110.00122.6090.0150.0150.0000.0000.0000.000
102A125GLY00.0740.04725.700-0.002-0.0020.0000.0000.0000.000
103A126PRO00.0120.01529.2380.0020.0020.0000.0000.0000.000
104A127VAL0-0.061-0.02631.381-0.001-0.0010.0000.0000.0000.000
105A128SER0-0.0020.01133.720-0.008-0.0080.0000.0000.0000.000
106A129LYS10.8820.94635.485-0.065-0.0650.0000.0000.0000.000
107A130VAL0-0.0320.00134.592-0.002-0.0020.0000.0000.0000.000
108A131SER00.014-0.02637.568-0.002-0.0020.0000.0000.0000.000
109A132THR00.007-0.02940.5940.0000.0000.0000.0000.0000.000
110A133GLU-1-0.862-0.91041.6260.0110.0110.0000.0000.0000.000
111A134GLU-1-0.754-0.83035.6120.0380.0380.0000.0000.0000.000
112A135ILE0-0.040-0.02138.454-0.001-0.0010.0000.0000.0000.000
113A136PHE00.0340.01440.0730.0000.0000.0000.0000.0000.000
114A137THR00.0110.01137.668-0.004-0.0040.0000.0000.0000.000
115A138TYR00.031-0.01332.291-0.004-0.0040.0000.0000.0000.000
116A139TRP0-0.061-0.04537.0930.0030.0030.0000.0000.0000.000
117A140SER0-0.021-0.02539.701-0.002-0.0020.0000.0000.0000.000
118A141MET0-0.0310.00533.532-0.003-0.0030.0000.0000.0000.000
119A142ARG10.7810.91235.800-0.033-0.0330.0000.0000.0000.000
120A143PRO00.0730.03736.201-0.001-0.0010.0000.0000.0000.000
121A144ARG10.9330.93339.1340.0030.0030.0000.0000.0000.000
122A145GLY00.0180.01340.7970.0030.0030.0000.0000.0000.000
123A146ALA00.0320.00736.9880.0050.0050.0000.0000.0000.000
124A147GLN0-0.055-0.00938.8950.0050.0050.0000.0000.0000.000
125A148LEU00.0560.02741.7420.0040.0040.0000.0000.0000.000
126A149GLY00.0150.00540.4110.0030.0030.0000.0000.0000.000
127A150ALA0-0.060-0.03339.4990.0050.0050.0000.0000.0000.000
128A151TRP0-0.011-0.01341.0730.0050.0050.0000.0000.0000.000
129A152ALA0-0.0190.00143.6470.0010.0010.0000.0000.0000.000
130A153SER0-0.030-0.01040.9120.0040.0040.0000.0000.0000.000
131A154GLN00.000-0.00443.0010.0030.0030.0000.0000.0000.000
132A155GLN00.0280.01441.0880.0070.0070.0000.0000.0000.000
133A156SER00.0010.00343.681-0.001-0.0010.0000.0000.0000.000
134A157ARG10.9100.98045.139-0.044-0.0440.0000.0000.0000.000
135A158PRO00.0130.00846.7200.0020.0020.0000.0000.0000.000
136A159VAL00.000-0.00744.575-0.004-0.0040.0000.0000.0000.000
137A160GLY00.0220.02846.5830.0030.0030.0000.0000.0000.000
138A161SER0-0.008-0.01446.2990.0000.0000.0000.0000.0000.000
139A162ARG10.8710.89639.828-0.040-0.0400.0000.0000.0000.000
140A163ALA00.0870.03944.659-0.001-0.0010.0000.0000.0000.000
141A164GLN0-0.043-0.02047.805-0.002-0.0020.0000.0000.0000.000
142A165LEU00.0210.00641.804-0.001-0.0010.0000.0000.0000.000
143A166ASP-1-0.776-0.85244.7250.0320.0320.0000.0000.0000.000
144A167ASN0-0.039-0.03246.803-0.005-0.0050.0000.0000.0000.000
145A168GLN0-0.0140.00145.898-0.001-0.0010.0000.0000.0000.000
146A169LEU00.0390.01443.313-0.001-0.0010.0000.0000.0000.000
147A170ALA00.0050.01446.963-0.003-0.0030.0000.0000.0000.000
148A171GLU-1-0.924-0.94950.2810.0270.0270.0000.0000.0000.000
149A172VAL00.026-0.00146.530-0.002-0.0020.0000.0000.0000.000
150A173THR0-0.033-0.04147.658-0.002-0.0020.0000.0000.0000.000
151A174ARG10.9380.97449.542-0.018-0.0180.0000.0000.0000.000
152A175ARG10.8550.92051.638-0.028-0.0280.0000.0000.0000.000
153A176PHE0-0.007-0.00248.7220.0000.0000.0000.0000.0000.000
154A177ALA00.0170.02750.962-0.002-0.0020.0000.0000.0000.000
155A178ASP-1-0.912-0.95552.3130.0020.0020.0000.0000.0000.000
156A179GLN0-0.055-0.04450.792-0.002-0.0020.0000.0000.0000.000
157A180ASP-1-0.830-0.90448.873-0.003-0.0030.0000.0000.0000.000
158A181GLN0-0.058-0.02347.247-0.002-0.0020.0000.0000.0000.000
159A182ILE00.0080.01745.2950.0020.0020.0000.0000.0000.000
160A183PRO00.0080.02546.1620.0000.0000.0000.0000.0000.000
161A184VAL00.0520.01842.6850.0010.0010.0000.0000.0000.000
162A185PRO0-0.0040.00042.9010.0000.0000.0000.0000.0000.000
163A186PRO00.006-0.00245.0510.0020.0020.0000.0000.0000.000
164A187GLY00.0200.02144.8730.0010.0010.0000.0000.0000.000
165A188TRP0-0.056-0.03436.6970.0050.0050.0000.0000.0000.000
166A189GLY00.0560.01039.346-0.004-0.0040.0000.0000.0000.000
167A190GLY00.0120.00835.6200.0020.0020.0000.0000.0000.000
168A191TYR0-0.050-0.01833.405-0.005-0.0050.0000.0000.0000.000
169A192ARG10.8110.88430.575-0.053-0.0530.0000.0000.0000.000
170A193ILE0-0.014-0.00226.594-0.001-0.0010.0000.0000.0000.000
171A194ALA00.0520.02728.608-0.005-0.0050.0000.0000.0000.000
172A195PRO0-0.014-0.00925.5510.0160.0160.0000.0000.0000.000
173A196GLU-1-0.955-0.98226.3070.1510.1510.0000.0000.0000.000
174A197ILE0-0.024-0.02422.3960.0070.0070.0000.0000.0000.000
175A198VAL0-0.0160.00119.2490.0010.0010.0000.0000.0000.000
176A199GLU-1-0.796-0.88515.7710.6050.6050.0000.0000.0000.000
177A200PHE00.0170.01413.097-0.023-0.0230.0000.0000.0000.000
178A201TRP00.003-0.0049.3520.1920.1920.0000.0000.0000.000
179A202GLN00.033-0.0095.0990.3000.3000.0000.0000.0000.000
180A203GLY00.0170.0115.8500.2390.2390.0000.0000.0000.000
181A204ARG10.8440.9112.371-5.041-1.6655.812-3.485-5.703-0.003
182A205GLU-1-0.789-0.9051.910-9.936-13.84814.125-4.444-5.7690.022
183A206ASN00.0210.0122.993-3.379-2.7010.051-0.050-0.6780.002
184A207ARG10.8100.8854.902-4.588-4.528-0.001-0.006-0.0520.000
185A208MET0-0.0120.0066.304-0.701-0.7010.0000.0000.0000.000
186A209HIS0-0.009-0.0036.6730.7970.7970.0000.0000.0000.000
187A210ASN00.0130.0196.070-0.658-0.6580.0000.0000.0000.000
188A211ARG10.7460.8528.861-0.928-0.9280.0000.0000.0000.000
189A212ILE00.0480.03012.329-0.058-0.0580.0000.0000.0000.000
190A213ARG10.7970.88615.048-0.427-0.4270.0000.0000.0000.000
191A214VAL00.0100.00118.534-0.030-0.0300.0000.0000.0000.000
192A215ALA00.0460.02121.4840.0060.0060.0000.0000.0000.000
193A216ASN0-0.020-0.01725.0370.0070.0070.0000.0000.0000.000
194A217GLY00.0230.02226.249-0.010-0.0100.0000.0000.0000.000
195A218ARG10.8120.90423.851-0.223-0.2230.0000.0000.0000.000
196A219LEU00.0470.02419.2150.0160.0160.0000.0000.0000.000
197A220GLU-1-0.810-0.90219.5640.3020.3020.0000.0000.0000.000
198A221ARG10.8420.9079.958-0.590-0.5900.0000.0000.0000.000
199A222LEU0-0.082-0.02715.136-0.030-0.0300.0000.0000.0000.000
200A223GLN00.0450.01514.0010.1780.1780.0000.0000.0000.000
201A224PRO00.0390.02210.271-0.050-0.0500.0000.0000.0000.000
202A225GLY0-0.023-0.00712.4870.0000.0000.0000.0000.0000.000
203A226SER0-0.0060.01515.689-0.113-0.1130.0000.0000.0000.000