FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: P7MZK

Calculation Name: 3D6I-A-Xray33

Preferred Name:

Target Type:

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

ligand 3-letter code: CME

PDB ID: 3D6I

Chain ID: A

ChEMBL ID:

UniProt ID: Q03835

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1059708.632193
FMO2-HF: Nuclear repulsion 1010476.668512
FMO2-HF: Total energy -49231.963681
FMO2-MP2: Total energy -49373.158198


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:37:PRO)


Summations of interaction energy for fragment #1(A:37: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.
-335.996-323.11511.305-10.774-13.412-0.091
Interaction energy analysis for fragmet #1(A:37:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.898
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].
3A39ILE0-0.031-0.0013.6100.0702.000-0.009-0.821-1.100-0.002
4A40GLU-1-0.877-0.9215.780-22.360-22.3600.0000.0000.0000.000
5A41ILE0-0.052-0.0208.9310.7780.7780.0000.0000.0000.000
6A42ASN0-0.041-0.03511.955-0.281-0.2810.0000.0000.0000.000
7A43ASP-1-0.744-0.83114.811-16.268-16.2680.0000.0000.0000.000
8A44GLN00.026-0.01816.279-0.942-0.9420.0000.0000.0000.000
9A45GLU-1-0.925-0.94918.312-14.028-14.0280.0000.0000.0000.000
10A46GLN0-0.0030.00410.4370.5130.5130.0000.0000.0000.000
11A47PHE00.0380.00413.974-1.410-1.4100.0000.0000.0000.000
12A48THR00.0270.02015.000-0.422-0.4220.0000.0000.0000.000
13A49TYR00.0070.04312.748-0.448-0.4480.0000.0000.0000.000
14A50LEU0-0.028-0.0189.406-0.417-0.4170.0000.0000.0000.000
15A51THR00.0090.02112.018-0.968-0.9680.0000.0000.0000.000
16A52THR0-0.056-0.04314.5091.1301.1300.0000.0000.0000.000
17A53THR0-0.044-0.03016.677-0.151-0.1510.0000.0000.0000.000
18A54ALA0-0.038-0.01512.4050.2930.2930.0000.0000.0000.000
19A55ALA0-0.0190.00712.148-1.694-1.6940.0000.0000.0000.000
20A56GLY0-0.023-0.00313.111-0.857-0.8570.0000.0000.0000.000
21A57ASP-1-0.957-0.98315.152-18.107-18.1070.0000.0000.0000.000
22A58LYS10.9630.9917.52431.19131.1910.0000.0000.0000.000
23A59LEU0-0.0110.01811.2791.2001.2000.0000.0000.0000.000
24A60ILE00.0040.00410.056-3.181-3.1810.0000.0000.0000.000
25A61VAL0-0.028-0.0138.7022.7112.7110.0000.0000.0000.000
26A62LEU00.0080.0099.567-3.024-3.0240.0000.0000.0000.000
27A63TYR0-0.017-0.01210.7431.6121.6120.0000.0000.0000.000
28A64PHE00.0740.03812.574-0.671-0.6710.0000.0000.0000.000
29A65HIS0-0.018-0.01512.963-0.777-0.7770.0000.0000.0000.000
30A66THR00.0670.04216.1810.2430.2430.0000.0000.0000.000
31A67SER0-0.071-0.01516.759-0.294-0.2940.0000.0000.0000.000
32A68TRP00.0990.06017.7490.2770.2770.0000.0000.0000.000
33A69ALA0-0.121-0.08921.1100.0990.0990.0000.0000.0000.000
34A70GLU-1-0.769-0.88019.311-15.541-15.5410.0000.0000.0000.000
35A71PRO0-0.063-0.01818.835-0.838-0.8380.0000.0000.0000.000
36A72CYS00.0570.02717.244-0.472-0.4720.0000.0000.0000.000
37A73LYS10.9450.99514.36617.48617.4860.0000.0000.0000.000
38A74ALA00.0100.00213.563-1.820-1.8200.0000.0000.0000.000
39A75LEU00.0190.01013.556-1.390-1.3900.0000.0000.0000.000
40A76LYS10.9691.0058.56926.30126.3010.0000.0000.0000.000
41A77GLN0-0.038-0.0169.032-2.483-2.4830.0000.0000.0000.000
42A78VAL00.0150.0138.879-2.673-2.6730.0000.0000.0000.000
43A79PHE00.0330.0257.685-2.804-2.8040.0000.0000.0000.000
44A80GLU-1-0.863-0.9333.866-44.881-44.7720.000-0.025-0.0850.000
45A81ALA00.0080.0174.561-9.749-9.619-0.001-0.010-0.1180.000
46A82ILE00.0250.0205.933-2.866-2.8660.0000.0000.0000.000
47A83SER0-0.017-0.0122.817-14.623-12.2661.194-1.510-2.041-0.017
48A84ASN0-0.035-0.0042.090-52.840-50.7239.258-5.301-6.073-0.044
49A85GLU-1-0.791-0.8662.918-23.282-23.4730.0460.424-0.2790.000
50A86PRO00.0390.0285.611-4.358-4.3580.0000.0000.0000.000
51A87SER0-0.026-0.0146.961-0.594-0.5940.0000.0000.0000.000
52A88ASN0-0.001-0.0015.7976.9676.9670.0000.0000.0000.000
53A89SER0-0.021-0.0013.963-3.215-3.161-0.001-0.022-0.0320.000
54A90ASN0-0.020-0.0095.042-1.900-1.876-0.0010.000-0.0230.000
55A91VAL0-0.0030.0166.5064.3574.3570.0000.0000.0000.000
56A92SER0-0.054-0.0245.480-9.091-9.0910.0000.0000.0000.000
57A93PHE00.010-0.0043.5014.1114.5720.000-0.121-0.3400.000
58A94LEU00.0270.0136.190-3.944-3.9440.0000.0000.0000.000
59A95SER0-0.050-0.0308.7050.3970.3970.0000.0000.0000.000
60A96ILE00.0280.00910.1760.2000.2000.0000.0000.0000.000
61A97ASP-1-0.750-0.84713.788-16.437-16.4370.0000.0000.0000.000
62A98ALA00.026-0.01216.0300.4970.4970.0000.0000.0000.000
63A99ASP-1-0.952-0.98319.165-12.574-12.5740.0000.0000.0000.000
64A100GLU-1-0.898-0.93216.863-16.795-16.7950.0000.0000.0000.000
65A101ASN0-0.034-0.01015.5560.1210.1210.0000.0000.0000.000
66A102SER00.0380.01519.401-0.287-0.2870.0000.0000.0000.000
67A103GLU-1-0.876-0.93922.524-11.757-11.7570.0000.0000.0000.000
68A104ILE0-0.0010.00216.4990.0380.0380.0000.0000.0000.000
69A105SER0-0.033-0.03820.451-0.408-0.4080.0000.0000.0000.000
70A106GLU-1-0.967-0.97021.603-10.980-10.9800.0000.0000.0000.000
71A107LEU0-0.038-0.00820.9590.2670.2670.0000.0000.0000.000
72A108PHE0-0.062-0.04818.680-0.133-0.1330.0000.0000.0000.000
73A109GLU-1-0.961-0.96622.355-11.513-11.5130.0000.0000.0000.000
74A110ILE0-0.070-0.02319.681-0.019-0.0190.0000.0000.0000.000
75A111SER0-0.018-0.01623.1730.4410.4410.0000.0000.0000.000
76A112ALA0-0.057-0.03423.4570.4120.4120.0000.0000.0000.000
77A113VAL0-0.0110.03618.507-0.658-0.6580.0000.0000.0000.000
78A114PRO0-0.033-0.03816.2670.6340.6340.0000.0000.0000.000
79A115TYR0-0.038-0.04116.8310.7290.7290.0000.0000.0000.000
80A116PHE0-0.017-0.00811.272-1.263-1.2630.0000.0000.0000.000
81A117ILE00.0280.02314.5931.2921.2920.0000.0000.0000.000
82A118ILE0-0.024-0.00413.206-1.712-1.7120.0000.0000.0000.000
83A119ILE00.0310.00914.0901.5861.5860.0000.0000.0000.000
84A120HIS0-0.019-0.02814.571-0.424-0.4240.0000.0000.0000.000
85A121LYS10.9300.96116.78516.30816.3080.0000.0000.0000.000
86A122GLY00.0250.01018.3180.9590.9590.0000.0000.0000.000
87A123THR0-0.069-0.01819.9040.8010.8010.0000.0000.0000.000
88A124ILE00.0330.00918.984-1.072-1.0720.0000.0000.0000.000
89A125LEU0-0.058-0.01616.8510.7240.7240.0000.0000.0000.000
90A126LYS10.9330.94517.89615.09115.0910.0000.0000.0000.000
91A127GLU-1-0.775-0.84118.008-15.255-15.2550.0000.0000.0000.000
92A128LEU0-0.029-0.02216.8150.5990.5990.0000.0000.0000.000
93A129SER00.0420.04018.626-0.848-0.8480.0000.0000.0000.000
94A130GLY0-0.038-0.04917.4180.2590.2590.0000.0000.0000.000
95A131ALA00.0350.01218.0220.6040.6040.0000.0000.0000.000
96A132ASP-1-0.844-0.90718.937-15.834-15.8340.0000.0000.0000.000
97A133PRO00.017-0.00214.266-0.553-0.5530.0000.0000.0000.000
98A134LYS10.9270.97515.31013.38713.3870.0000.0000.0000.000
99A135GLU-1-0.917-0.96617.742-15.054-15.0540.0000.0000.0000.000
100A136TYR00.029-0.0098.6500.5550.5550.0000.0000.0000.000
101A137VAL00.0080.00411.917-0.684-0.6840.0000.0000.0000.000
102A138SER0-0.032-0.00814.082-0.021-0.0210.0000.0000.0000.000
103A139LEU00.0620.05016.4070.2760.2760.0000.0000.0000.000
104A140LEU0-0.0010.0018.9570.1700.1700.0000.0000.0000.000
105A141GLU-1-0.820-0.91312.145-25.042-25.0420.0000.0000.0000.000
106A142ASP-1-0.683-0.80314.936-14.769-14.7690.0000.0000.0000.000
107A143CME0-0.082-0.02315.0000.8090.8090.0000.0000.0000.000
108A144LYS10.8540.89410.06328.12728.1270.0000.0000.0000.000
109A145ASN0-0.078-0.03014.6651.0511.0510.0000.0000.0000.000
110A146SER0-0.027-0.01418.0200.8950.8950.0000.0000.0000.000
111A147VAL0-0.039-0.01915.3580.7130.7130.0000.0000.0000.000
112A148ASN-1-0.984-0.97014.763-15.689-15.6890.0000.0000.0000.000
113A616SO4-2-1.709-1.83420.105-28.778-28.7780.0000.0000.0000.000
114A617HOH0-0.0050.0126.5302.7442.7440.0000.0000.0000.000
115A622HOH00.0250.02022.159-0.035-0.0350.0000.0000.0000.000
116A623HOH0-0.027-0.02612.0470.3900.3900.0000.0000.0000.000
117A625HOH0-0.011-0.0217.650-0.063-0.0630.0000.0000.0000.000
118A626HOH0-0.028-0.02014.859-0.321-0.3210.0000.0000.0000.000
119A628HOH00.0010.00417.187-0.242-0.2420.0000.0000.0000.000
120A629HOH0-0.030-0.01722.9230.2440.2440.0000.0000.0000.000
121A630HOH0-0.024-0.02119.2170.1870.1870.0000.0000.0000.000
122A631HOH0-0.033-0.01721.9620.1780.1780.0000.0000.0000.000
123A632HOH0-0.029-0.04118.524-0.145-0.1450.0000.0000.0000.000
124A633HOH0-0.056-0.0406.486-0.819-0.8190.0000.0000.0000.000
125A634HOH0-0.044-0.03218.146-0.106-0.1060.0000.0000.0000.000
126A635HOH0-0.072-0.0462.9440.1100.6530.037-0.263-0.317-0.002
127A637HOH0-0.052-0.02824.0190.2180.2180.0000.0000.0000.000
128A640HOH0-0.014-0.01514.398-0.645-0.6450.0000.0000.0000.000
129A641HOH0-0.046-0.03320.9970.3050.3050.0000.0000.0000.000
130A642HOH0-0.001-0.05018.4640.2230.2230.0000.0000.0000.000
131A644HOH0-0.088-0.05316.6290.0700.0700.0000.0000.0000.000
132A646HOH00.001-0.00414.7250.5240.5240.0000.0000.0000.000
133A647HOH0-0.003-0.00413.342-0.390-0.3900.0000.0000.0000.000
134A648HOH0-0.029-0.02320.618-0.106-0.1060.0000.0000.0000.000
135A649HOH0-0.055-0.0357.6500.2770.2770.0000.0000.0000.000
136A650HOH0-0.004-0.0027.117-2.044-2.0440.0000.0000.0000.000
137A651HOH0-0.006-0.0068.966-1.147-1.1470.0000.0000.0000.000
138A652HOH0-0.013-0.0209.652-0.022-0.0220.0000.0000.0000.000
139A654HOH0-0.038-0.0362.857-0.5940.3310.191-0.520-0.596-0.004
140A655HOH00.0050.0053.2706.6507.3640.022-0.386-0.349-0.001
141A656HOH0-0.0060.00010.990-0.092-0.0920.0000.0000.0000.000
142A657HOH00.0030.00110.433-1.246-1.2460.0000.0000.0000.000
143A658HOH00.0330.01923.314-0.216-0.2160.0000.0000.0000.000
144A659HOH0-0.012-0.02211.688-1.059-1.0590.0000.0000.0000.000
145A660HOH00.0020.0002.966-11.257-9.6340.192-0.952-0.864-0.010
146A661HOH0-0.031-0.0262.604-1.623-0.1100.328-0.957-0.884-0.008
147A662HOH0-0.035-0.02317.4160.2230.2230.0000.0000.0000.000
148A663HOH0-0.009-0.00712.518-0.647-0.6470.0000.0000.0000.000
149A664HOH00.0270.0229.0270.2530.2530.0000.0000.0000.000
150A666HOH0-0.0060.00015.9320.3610.3610.0000.0000.0000.000
151A667HOH0-0.072-0.05518.315-0.001-0.0010.0000.0000.0000.000
152A668HOH0-0.058-0.03522.1830.2140.2140.0000.0000.0000.000
153A669HOH0-0.066-0.05817.9940.0070.0070.0000.0000.0000.000
154A670HOH0-0.050-0.0289.531-0.302-0.3020.0000.0000.0000.000
155A671HOH0-0.007-0.0089.592-1.246-1.2460.0000.0000.0000.000
156A672HOH0-0.051-0.02515.0440.0840.0840.0000.0000.0000.000
157A673HOH0-0.044-0.0273.250-5.377-4.8050.049-0.310-0.311-0.003
158A674HOH0-0.032-0.0177.4750.3490.3490.0000.0000.0000.000
159A675HOH0-0.062-0.04813.821-0.374-0.3740.0000.0000.0000.000
160A680HOH0-0.033-0.01522.8200.1010.1010.0000.0000.0000.000
161A681HOH0-0.028-0.02717.7180.1820.1820.0000.0000.0000.000
162A682HOH0-0.050-0.03920.0890.0490.0490.0000.0000.0000.000
163A684HOH0-0.027-0.01821.5450.1750.1750.0000.0000.0000.000
164A685HOH0-0.048-0.02720.8920.3240.3240.0000.0000.0000.000
165A687HOH0-0.009-0.0129.709-0.675-0.6750.0000.0000.0000.000
166A688HOH0-0.029-0.02024.7990.0340.0340.0000.0000.0000.000
167A689HOH0-0.075-0.05018.573-0.026-0.0260.0000.0000.0000.000
168A690HOH00.0310.01921.7720.0470.0470.0000.0000.0000.000
169A692HOH0-0.051-0.03023.038-0.005-0.0050.0000.0000.0000.000
170B622HOH0-0.020-0.03312.546-0.682-0.6820.0000.0000.0000.000
171B653HOH00.0000.0007.042-1.702-1.7020.0000.0000.0000.000
172B661HOH00.004-0.00713.902-0.368-0.3680.0000.0000.0000.000