FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 1VV8Z

Calculation Name: 2A2J-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: CME

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A2J

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIJ1

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2162676.535067
FMO2-HF: Nuclear repulsion 2083292.04247
FMO2-HF: Total energy -79384.492597
FMO2-MP2: Total energy -79617.580945


3D Structure Molmil
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.
-6.681-0.2198.318-5.029-9.752-0.041
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 : 1 / q_Mulliken : 0.824 / q_NPA : 0.894
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].
3A26LYS10.8660.9482.94545.40747.4720.001-0.891-1.175-0.002
4A27ASP-1-0.716-0.8304.918-40.159-39.899-0.001-0.022-0.2370.000
7A30GLY00.0470.0223.723-10.795-10.4610.003-0.128-0.209-0.001
181A204ARG10.7680.8682.32838.70142.8203.355-2.972-4.502-0.026
182A205GLU-1-0.885-0.9522.044-44.856-45.3614.952-1.182-3.266-0.012
183A206ASN00.007-0.0033.3245.3955.5490.0090.167-0.3300.000
184A207ARG10.8760.9245.38236.84336.878-0.001-0.001-0.0330.000
5A28GLY0-0.0110.0066.0354.6884.6880.0000.0000.0000.000
6A29CYS0-0.093-0.0355.2665.4225.4220.0000.0000.0000.000
8A31ASP-1-0.858-0.9375.202-50.248-50.2480.0000.0000.0000.000
9A32LEU0-0.036-0.0086.5653.3693.3690.0000.0000.0000.000
10A33ASP-1-0.818-0.9079.343-21.706-21.7060.0000.0000.0000.000
11A34PHE0-0.021-0.02712.5200.5600.5600.0000.0000.0000.000
12A35ASP-1-0.800-0.89014.324-19.901-19.9010.0000.0000.0000.000
13A36TRP0-0.066-0.0298.028-0.080-0.0800.0000.0000.0000.000
14A37LEU0-0.074-0.05415.1350.3050.3050.0000.0000.0000.000
15A38ASP-1-0.883-0.91818.366-14.056-14.0560.0000.0000.0000.000
16A39ASP-1-0.964-0.97020.452-13.322-13.3220.0000.0000.0000.000
17A40GLY00.005-0.00521.7230.4340.4340.0000.0000.0000.000
18A41TRP00.013-0.01819.899-0.750-0.7500.0000.0000.0000.000
19A42LEU0-0.0270.00020.411-0.556-0.5560.0000.0000.0000.000
20A43THR00.0180.00020.175-0.054-0.0540.0000.0000.0000.000
21A44LEU00.0220.02913.854-0.419-0.4190.0000.0000.0000.000
22A45LEU0-0.022-0.01216.999-0.823-0.8230.0000.0000.0000.000
23A46ARG10.8870.93118.96611.75011.7500.0000.0000.0000.000
24A47ARG10.8730.93214.27119.53819.5380.0000.0000.0000.000
25A48TRP00.007-0.01410.474-0.621-0.6210.0000.0000.0000.000
26A49LEU00.0080.02115.471-0.437-0.4370.0000.0000.0000.000
27A50ASN0-0.027-0.01318.5090.6940.6940.0000.0000.0000.000
28A51ASP-1-0.808-0.88713.279-21.486-21.4860.0000.0000.0000.000
29A52ALA00.000-0.00315.095-0.538-0.5380.0000.0000.0000.000
30A53GLN00.007-0.00515.9900.1020.1020.0000.0000.0000.000
31A54ARG10.9130.95916.20217.17317.1730.0000.0000.0000.000
32A55ALA0-0.027-0.00413.9960.0560.0560.0000.0000.0000.000
33A56GLY00.0050.01015.973-0.269-0.2690.0000.0000.0000.000
34A57VAL0-0.050-0.01514.9970.2060.2060.0000.0000.0000.000
35A58SER0-0.003-0.01717.8150.7510.7510.0000.0000.0000.000
36A59GLU-1-0.919-0.95820.569-12.350-12.3500.0000.0000.0000.000
37A60PRO00.0220.03619.382-0.222-0.2220.0000.0000.0000.000
38A61ASN0-0.001-0.01820.002-0.708-0.7080.0000.0000.0000.000
39A62ALA0-0.012-0.01622.0770.6440.6440.0000.0000.0000.000
40A63MET0-0.0140.00321.257-0.762-0.7620.0000.0000.0000.000
41A64VAL0-0.023-0.02221.5530.7390.7390.0000.0000.0000.000
42A65LEU00.0030.01423.790-0.152-0.1520.0000.0000.0000.000
43A66ALA00.003-0.00826.1640.3240.3240.0000.0000.0000.000
44A67THR00.000-0.00127.950-0.007-0.0070.0000.0000.0000.000
45A68VAL00.0220.00331.634-0.163-0.1630.0000.0000.0000.000
46A69ALA00.0100.00134.2300.2000.2000.0000.0000.0000.000
47A70ASP-1-0.895-0.94237.329-7.827-7.8270.0000.0000.0000.000
48A71GLY0-0.011-0.00536.9130.0360.0360.0000.0000.0000.000
49A72LYS10.9260.96734.1348.1028.1020.0000.0000.0000.000
50A73PRO00.0290.01929.2410.0770.0770.0000.0000.0000.000
51A74VAL0-0.020-0.01331.2630.0800.0800.0000.0000.0000.000
52A75THR00.0160.00925.746-0.149-0.1490.0000.0000.0000.000
53A76ARG10.8000.88727.83310.41010.4100.0000.0000.0000.000
54A77SER00.0270.01324.535-0.215-0.2150.0000.0000.0000.000
55A78VAL0-0.047-0.01426.2620.6090.6090.0000.0000.0000.000
56A79LEU0-0.0100.00025.808-0.399-0.3990.0000.0000.0000.000
57A80CYS0-0.0270.00025.0100.5900.5900.0000.0000.0000.000
58A81LYS10.8820.93227.03710.35410.3540.0000.0000.0000.000
59A82ILE00.0210.02429.5300.1580.1580.0000.0000.0000.000
60A83LEU00.0210.01222.319-0.178-0.1780.0000.0000.0000.000
61A84ASP-1-0.772-0.85827.061-10.158-10.1580.0000.0000.0000.000
62A85GLU-1-0.821-0.92127.968-10.786-10.7860.0000.0000.0000.000
63A86SER0-0.108-0.07229.4660.0800.0800.0000.0000.0000.000
64A87GLY0-0.004-0.00127.4630.1140.1140.0000.0000.0000.000
65A88VAL0-0.007-0.01124.291-0.210-0.2100.0000.0000.0000.000
66A89ALA00.0140.01527.7240.3040.3040.0000.0000.0000.000
67A90PHE00.0160.00229.432-0.229-0.2290.0000.0000.0000.000
68A91PHE00.0440.00231.3510.2960.2960.0000.0000.0000.000
69A92THR0-0.041-0.02933.979-0.230-0.2300.0000.0000.0000.000
70A93SER00.0030.01236.4200.2460.2460.0000.0000.0000.000
71A94TYR00.007-0.02639.016-0.054-0.0540.0000.0000.0000.000
72A95THR0-0.002-0.00741.2350.0470.0470.0000.0000.0000.000
73A96SER0-0.034-0.01637.965-0.051-0.0510.0000.0000.0000.000
74A97ALA00.0970.03537.632-0.041-0.0410.0000.0000.0000.000
75A98LYS10.9230.96932.9159.3249.3240.0000.0000.0000.000
76A99GLY00.0020.00035.828-0.107-0.1070.0000.0000.0000.000
77A100GLU-1-0.920-0.96438.472-7.436-7.4360.0000.0000.0000.000
78A101GLN00.0500.01334.998-0.243-0.2430.0000.0000.0000.000
79A102LEU0-0.014-0.00332.959-0.068-0.0680.0000.0000.0000.000
80A103ALA0-0.070-0.02437.0210.0460.0460.0000.0000.0000.000
81A104VAL0-0.0160.00340.1540.1430.1430.0000.0000.0000.000
82A105THR0-0.008-0.01135.2160.0660.0660.0000.0000.0000.000
83A106PRO0-0.0010.02435.815-0.282-0.2820.0000.0000.0000.000
84A107TYR00.005-0.01632.151-0.008-0.0080.0000.0000.0000.000
85A108ALA0-0.031-0.01129.3810.0580.0580.0000.0000.0000.000
86A109SER00.002-0.00223.855-0.274-0.2740.0000.0000.0000.000
87A110ALA00.002-0.00423.9290.3190.3190.0000.0000.0000.000
88A111THR00.0160.00617.759-0.173-0.1730.0000.0000.0000.000
89A112PHE00.0130.00117.8870.6690.6690.0000.0000.0000.000
90A113PRO00.0070.00515.936-1.294-1.2940.0000.0000.0000.000
91A114TRP00.000-0.00313.193-0.467-0.4670.0000.0000.0000.000
92A115TYR00.039-0.01011.265-2.302-2.3020.0000.0000.0000.000
93A116GLN0-0.052-0.01610.130-1.736-1.7360.0000.0000.0000.000
94A117LEU00.0530.0168.680-1.695-1.6950.0000.0000.0000.000
95A118GLY0-0.038-0.0056.689-4.640-4.6400.0000.0000.0000.000
96A119ARG10.8000.8867.76227.96927.9690.0000.0000.0000.000
97A120GLN0-0.050-0.03210.2832.9782.9780.0000.0000.0000.000
98A121ALA00.0250.01913.598-0.688-0.6880.0000.0000.0000.000
99A122HIS00.0350.04215.6871.3181.3180.0000.0000.0000.000
100A123VAL00.0070.00119.453-0.023-0.0230.0000.0000.0000.000
101A124GLN0-0.010-0.00522.963-0.063-0.0630.0000.0000.0000.000
102A125GLY00.0760.04725.956-0.077-0.0770.0000.0000.0000.000
103A126PRO00.0120.01529.5050.0630.0630.0000.0000.0000.000
104A127VAL0-0.058-0.02731.802-0.222-0.2220.0000.0000.0000.000
105A128SER00.0000.01134.1480.3360.3360.0000.0000.0000.000
106A129LYS10.8830.94536.0807.4897.4890.0000.0000.0000.000
107A130VAL0-0.0360.00035.1140.0040.0040.0000.0000.0000.000
108A131SER00.023-0.00438.1070.2580.2580.0000.0000.0000.000
109A132THR00.010-0.02241.013-0.131-0.1310.0000.0000.0000.000
110A133GLU-1-0.874-0.91941.682-7.292-7.2920.0000.0000.0000.000
111A134GLU-1-0.752-0.84235.957-8.881-8.8810.0000.0000.0000.000
112A135ILE0-0.051-0.02138.890-0.147-0.1470.0000.0000.0000.000
113A136PHE00.0280.01240.529-0.071-0.0710.0000.0000.0000.000
114A137THR00.0180.01538.0000.0160.0160.0000.0000.0000.000
115A138TYR00.022-0.01632.922-0.132-0.1320.0000.0000.0000.000
116A139TRP0-0.069-0.04437.316-0.269-0.2690.0000.0000.0000.000
117A140SER0-0.016-0.01939.9540.0690.0690.0000.0000.0000.000
118A141MET0-0.0240.00333.6420.0130.0130.0000.0000.0000.000
119A142ARG10.8040.92535.0358.4488.4480.0000.0000.0000.000
120A143PRO00.0760.04135.7970.2300.2300.0000.0000.0000.000
121A144ARG10.9260.93238.9046.7736.7730.0000.0000.0000.000
122A145GLY00.0080.01540.2230.1050.1050.0000.0000.0000.000
123A146ALA00.013-0.00336.6890.0070.0070.0000.0000.0000.000
124A147GLN0-0.052-0.01238.6550.1150.1150.0000.0000.0000.000
125A148LEU00.0550.02341.6360.0850.0850.0000.0000.0000.000
126A149GLY00.0220.00840.2340.0790.0790.0000.0000.0000.000
127A150ALA0-0.064-0.03639.440-0.011-0.0110.0000.0000.0000.000
128A151TRP0-0.027-0.02341.0290.1300.1300.0000.0000.0000.000
129A152ALA0-0.0240.00243.4960.1390.1390.0000.0000.0000.000
130A153SER0-0.045-0.02540.839-0.008-0.0080.0000.0000.0000.000
131A154GLN00.0150.02042.8410.0740.0740.0000.0000.0000.000
132A155GLN00.0390.01441.324-0.061-0.0610.0000.0000.0000.000
133A156SER0-0.016-0.01043.6420.0810.0810.0000.0000.0000.000
134A157ARG10.9120.97445.1706.4976.4970.0000.0000.0000.000
135A158PRO00.0050.00546.333-0.141-0.1410.0000.0000.0000.000
136A159VAL0-0.005-0.00944.3800.1050.1050.0000.0000.0000.000
137A160GLY00.0260.02845.946-0.072-0.0720.0000.0000.0000.000
138A161SER0-0.012-0.01746.232-0.024-0.0240.0000.0000.0000.000
139A162ARG10.8840.91139.6297.6587.6580.0000.0000.0000.000
140A163ALA00.0760.03144.606-0.037-0.0370.0000.0000.0000.000
141A164GLN0-0.035-0.01547.4550.1240.1240.0000.0000.0000.000
142A165LEU00.0100.00241.2950.0220.0220.0000.0000.0000.000
143A166ASP-1-0.792-0.86844.309-7.278-7.2780.0000.0000.0000.000
144A167ASN0-0.006-0.00946.4130.0750.0750.0000.0000.0000.000
145A168GLN0-0.017-0.00545.5070.1600.1600.0000.0000.0000.000
146A169LEU00.0350.01342.9460.0190.0190.0000.0000.0000.000
147A170ALA00.0050.01346.6320.0450.0450.0000.0000.0000.000
148A171GLU-1-0.998-1.00249.960-6.059-6.0590.0000.0000.0000.000
149A172VAL0-0.006-0.01246.4650.0950.0950.0000.0000.0000.000
150A173THR0-0.031-0.04047.431-0.027-0.0270.0000.0000.0000.000
151A174ARG10.9380.97749.4095.9245.9240.0000.0000.0000.000
152A175ARG10.9340.97251.6466.2246.2240.0000.0000.0000.000
153A176PHE0-0.030-0.02048.6370.0470.0470.0000.0000.0000.000
154A177ALA00.0000.01351.199-0.087-0.0870.0000.0000.0000.000
155A178ASP-1-0.915-0.94652.928-5.712-5.7120.0000.0000.0000.000
156A179GLN0-0.022-0.02151.1930.0310.0310.0000.0000.0000.000
157A180ASP-1-0.822-0.89649.610-6.532-6.5320.0000.0000.0000.000
158A181GLN0-0.064-0.03747.305-0.205-0.2050.0000.0000.0000.000
159A182ILE00.0020.00745.1550.0930.0930.0000.0000.0000.000
160A183PRO00.0140.02646.280-0.132-0.1320.0000.0000.0000.000
161A184VAL00.0530.01843.108-0.104-0.1040.0000.0000.0000.000
162A185PRO0-0.007-0.00143.0230.1590.1590.0000.0000.0000.000
163A186PRO00.0130.00445.328-0.106-0.1060.0000.0000.0000.000
164A187GLY00.0410.02945.1370.0190.0190.0000.0000.0000.000
165A188TRP0-0.046-0.02736.877-0.206-0.2060.0000.0000.0000.000
166A189GLY00.0800.02639.7260.1730.1730.0000.0000.0000.000
167A190GLY00.0170.00936.218-0.208-0.2080.0000.0000.0000.000
168A191TYR0-0.029-0.00833.9860.3770.3770.0000.0000.0000.000
169A192ARG10.8470.90231.5939.2049.2040.0000.0000.0000.000
170A193ILE0-0.0110.00027.1700.2910.2910.0000.0000.0000.000
171A194ALA00.0530.02729.241-0.225-0.2250.0000.0000.0000.000
172A195PRO0-0.024-0.01225.875-0.237-0.2370.0000.0000.0000.000
173A196GLU-1-0.968-0.98126.943-10.207-10.2070.0000.0000.0000.000
174A197ILE0-0.023-0.02522.463-0.121-0.1210.0000.0000.0000.000
175A198VAL0-0.021-0.00319.551-0.010-0.0100.0000.0000.0000.000
176A199GLU-1-0.794-0.88215.823-18.060-18.0600.0000.0000.0000.000
177A200PHE00.0130.01413.5760.0350.0350.0000.0000.0000.000
178A201TRP00.0210.0069.332-1.647-1.6470.0000.0000.0000.000
179A202GLN00.027-0.0165.6960.0410.0410.0000.0000.0000.000
180A203GLY00.0310.0226.060-1.343-1.3430.0000.0000.0000.000
185A208MET00.0210.0276.7213.8103.8100.0000.0000.0000.000
186A209HIS0-0.0090.0006.552-6.494-6.4940.0000.0000.0000.000
187A210ASN0-0.0020.0156.2716.9316.9310.0000.0000.0000.000
188A211ARG10.7880.8818.95620.08820.0880.0000.0000.0000.000
189A212ILE00.0430.02712.4830.8810.8810.0000.0000.0000.000
190A213ARG10.8680.93115.28215.37615.3760.0000.0000.0000.000
191A214VAL00.0130.00018.7610.2110.2110.0000.0000.0000.000
192A215ALA00.0490.01821.7150.1920.1920.0000.0000.0000.000
193A216ASN0-0.032-0.02425.303-0.153-0.1530.0000.0000.0000.000
194A217GLY00.0100.01426.1930.2620.2620.0000.0000.0000.000
195A218ARG10.8690.93723.66712.31112.3110.0000.0000.0000.000
196A219LEU00.0340.01618.922-0.284-0.2840.0000.0000.0000.000
197A220GLU-1-0.888-0.93819.761-13.326-13.3260.0000.0000.0000.000
198A221ARG10.8050.88010.37124.12524.1250.0000.0000.0000.000
199A222LEU0-0.057-0.01415.4170.8270.8270.0000.0000.0000.000
200A223GLN00.0490.02614.447-2.232-2.2320.0000.0000.0000.000
201A224PRO0-0.002-0.00810.4980.1350.1350.0000.0000.0000.000
202A225GLY0-0.056-0.03812.436-0.005-0.0050.0000.0000.0000.000
203A226SER-1-0.925-0.94715.523-15.414-15.4140.0000.0000.0000.000