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: M993Z

Calculation Name: 3K94-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-hydroxycysteine

ligand 3-letter code: CSO

PDB ID: 3K94

Chain ID: A

ChEMBL ID:

UniProt ID: A4IM54

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2487029.090534
FMO2-HF: Nuclear repulsion 2400985.692403
FMO2-HF: Total energy -86043.398131
FMO2-MP2: Total energy -86289.221197


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.
-37.26-29.11721.071-12.038-17.176-0.103
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 : -0.037 / q_NPA : -0.022
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].
3A3ILE00.0240.0223.054-1.8590.4561.389-0.965-2.7390.003
4A4HIS0-0.013-0.0014.622-0.385-0.314-0.001-0.015-0.0550.000
5A5ILE00.0510.0268.0960.0340.0340.0000.0000.0000.000
6A6VAL0-0.023-0.00710.723-0.144-0.1440.0000.0000.0000.000
7A7GLY00.0350.01514.1330.0360.0360.0000.0000.0000.000
8A8GLY0-0.017-0.02117.330-0.043-0.0430.0000.0000.0000.000
9A9GLY0-0.0220.00120.637-0.014-0.0140.0000.0000.0000.000
10A10PRO0-0.029-0.01722.573-0.012-0.0120.0000.0000.0000.000
11A11ARG10.9940.99621.0860.0280.0280.0000.0000.0000.000
12A12GLU-1-0.888-0.95523.0970.0200.0200.0000.0000.0000.000
13A13LEU0-0.0010.01122.982-0.014-0.0140.0000.0000.0000.000
14A14LEU00.0080.01517.224-0.004-0.0040.0000.0000.0000.000
15A15PRO0-0.0130.00417.108-0.009-0.0090.0000.0000.0000.000
16A16ASP-1-0.831-0.90218.807-0.236-0.2360.0000.0000.0000.000
17A17LEU00.0390.01414.057-0.037-0.0370.0000.0000.0000.000
18A18ARG10.9050.92614.1730.1670.1670.0000.0000.0000.000
19A19PHE0-0.109-0.04915.010-0.069-0.0690.0000.0000.0000.000
20A20TYR0-0.036-0.02211.7300.0300.0300.0000.0000.0000.000
21A21ASP-1-0.810-0.89610.352-0.985-0.9850.0000.0000.0000.000
22A22GLY0-0.020-0.0238.914-0.010-0.0100.0000.0000.0000.000
23A23GLU-1-0.972-0.9837.660-1.684-1.6840.0000.0000.0000.000
24A24ASP-1-0.849-0.9211.922-21.232-22.65713.892-6.925-5.542-0.086
25A25VAL0-0.0410.0022.614-5.098-3.3201.082-1.387-1.473-0.015
26A26CSO0-0.044-0.0283.089-0.1720.7761.460-0.709-1.699-0.003
27A27TRP00.029-0.0104.9880.5850.628-0.001-0.003-0.0380.000
28A28VAL00.002-0.0037.5090.2140.2140.0000.0000.0000.000
29A29GLY00.0030.00510.200-0.138-0.1380.0000.0000.0000.000
30A30VAL00.0290.00413.9350.0750.0750.0000.0000.0000.000
31A31ASP-1-0.823-0.92116.4230.1330.1330.0000.0000.0000.000
32A32ARG10.8170.88819.548-0.108-0.1080.0000.0000.0000.000
33A33GLY0-0.0060.01317.261-0.036-0.0360.0000.0000.0000.000
34A34THR00.007-0.01616.195-0.005-0.0050.0000.0000.0000.000
35A35MET0-0.0400.00217.246-0.029-0.0290.0000.0000.0000.000
36A36THR0-0.030-0.01418.008-0.037-0.0370.0000.0000.0000.000
37A37LEU0-0.023-0.00412.479-0.045-0.0450.0000.0000.0000.000
38A38LEU0-0.019-0.00416.248-0.049-0.0490.0000.0000.0000.000
39A39GLU-1-0.854-0.92118.676-0.035-0.0350.0000.0000.0000.000
40A40ALA0-0.102-0.03716.567-0.019-0.0190.0000.0000.0000.000
41A41GLY0-0.022-0.00217.798-0.047-0.0470.0000.0000.0000.000
42A42PHE0-0.046-0.02512.566-0.047-0.0470.0000.0000.0000.000
43A43ARG10.8380.89814.1450.0320.0320.0000.0000.0000.000
44A44PRO0-0.031-0.00110.912-0.050-0.0500.0000.0000.0000.000
45A45VAL0-0.010-0.0146.343-0.063-0.0630.0000.0000.0000.000
46A46ARG10.8130.9079.765-0.772-0.7720.0000.0000.0000.000
47A47ALA0-0.026-0.01711.342-0.011-0.0110.0000.0000.0000.000
48A48PHE00.0250.01510.5980.0340.0340.0000.0000.0000.000
49A49GLY00.0590.03316.051-0.034-0.0340.0000.0000.0000.000
50A50ASP-1-0.857-0.93419.8290.2320.2320.0000.0000.0000.000
51A51PHE00.014-0.01822.000-0.010-0.0100.0000.0000.0000.000
52A52ASP-1-0.931-0.96224.8480.1140.1140.0000.0000.0000.000
53A53SER0-0.031-0.00424.113-0.013-0.0130.0000.0000.0000.000
54A54LEU0-0.052-0.02222.161-0.009-0.0090.0000.0000.0000.000
55A55PRO0-0.014-0.00626.331-0.006-0.0060.0000.0000.0000.000
56A56ALA00.0440.02828.6570.0010.0010.0000.0000.0000.000
57A57GLU-1-0.894-0.97530.4100.0430.0430.0000.0000.0000.000
58A58ASP-1-0.706-0.84425.2840.0480.0480.0000.0000.0000.000
59A59VAL0-0.0080.01225.5770.0030.0030.0000.0000.0000.000
60A60VAL0-0.019-0.00826.550-0.001-0.0010.0000.0000.0000.000
61A61LYS10.7400.85024.076-0.020-0.0200.0000.0000.0000.000
62A62LEU0-0.0050.00220.359-0.010-0.0100.0000.0000.0000.000
63A63GLN00.000-0.01923.473-0.017-0.0170.0000.0000.0000.000
64A64GLN0-0.062-0.02825.302-0.011-0.0110.0000.0000.0000.000
65A65ALA0-0.044-0.01923.637-0.011-0.0110.0000.0000.0000.000
66A66PHE0-0.024-0.01518.429-0.019-0.0190.0000.0000.0000.000
67A67PRO00.0040.00620.8740.0280.0280.0000.0000.0000.000
68A68ASP-1-0.840-0.90019.6060.0290.0290.0000.0000.0000.000
69A69LEU0-0.041-0.02214.6190.0040.0040.0000.0000.0000.000
70A70ASP-1-0.766-0.85312.4340.5110.5110.0000.0000.0000.000
71A71VAL0-0.026-0.01214.5330.0900.0900.0000.0000.0000.000
72A72TRP0-0.089-0.05313.8790.0020.0020.0000.0000.0000.000
73A73PRO00.0150.01117.1660.0180.0180.0000.0000.0000.000
74A74ALA00.0230.00219.4280.0410.0410.0000.0000.0000.000
75A75GLU-1-0.842-0.90318.2440.3950.3950.0000.0000.0000.000
76A76LYS10.8140.89021.547-0.312-0.3120.0000.0000.0000.000
77A77ASP-1-0.949-0.98823.6760.2320.2320.0000.0000.0000.000
78A78LYS10.8370.93917.099-0.482-0.4820.0000.0000.0000.000
79A79THR0-0.007-0.00519.649-0.007-0.0070.0000.0000.0000.000
80A80ASP-1-0.850-0.94518.5570.3420.3420.0000.0000.0000.000
81A81MET0-0.024-0.00614.9990.0850.0850.0000.0000.0000.000
82A82GLU-1-0.829-0.90914.6800.5360.5360.0000.0000.0000.000
83A83ILE0-0.022-0.00514.7460.0880.0880.0000.0000.0000.000
84A84ALA00.0130.01511.7790.0940.0940.0000.0000.0000.000
85A85LEU0-0.010-0.01410.1990.3140.3140.0000.0000.0000.000
86A86ASP-1-0.775-0.86110.6370.8380.8380.0000.0000.0000.000
87A87TRP00.0290.0226.6400.3490.3490.0000.0000.0000.000
88A88ALA00.013-0.0066.2810.2920.2920.0000.0000.0000.000
89A89VAL0-0.028-0.0186.2260.7530.801-0.0010.000-0.0470.000
90A90GLU-1-0.966-0.9807.8800.8120.8120.0000.0000.0000.000
91A91GLN0-0.085-0.0382.350-1.581-0.8560.807-0.314-1.219-0.001
92A92THR0-0.113-0.0592.858-2.687-1.3640.576-0.722-1.177-0.008
93A93ALA00.0300.0272.260-0.5770.5381.714-0.949-1.8800.003
94A94ARG10.9200.9662.949-4.703-3.5010.154-0.049-1.3070.004
95A95CSO0-0.117-0.0924.915-1.141-1.1410.0000.0000.0000.000
96A96ILE00.0560.0415.624-0.062-0.0620.0000.0000.0000.000
97A97ARG10.7580.8487.9940.1800.1800.0000.0000.0000.000
98A98LEU00.0180.00910.5540.0780.0780.0000.0000.0000.000
99A99PHE00.0310.00910.961-0.069-0.0690.0000.0000.0000.000
100A100GLY00.008-0.00315.4000.0430.0430.0000.0000.0000.000
101A101ALA00.0170.01516.9410.0220.0220.0000.0000.0000.000
102A102THR0-0.023-0.03019.0650.0110.0110.0000.0000.0000.000
103A103GLY00.0230.00522.325-0.010-0.0100.0000.0000.0000.000
104A104GLY00.017-0.00425.7740.0120.0120.0000.0000.0000.000
105A105ARG10.8470.89426.709-0.173-0.1730.0000.0000.0000.000
106A106LEU00.0370.01326.4210.0140.0140.0000.0000.0000.000
107A107ASP-1-0.812-0.87126.9090.1770.1770.0000.0000.0000.000
108A108HIS00.0530.02922.5520.0280.0280.0000.0000.0000.000
109A109LEU0-0.0230.01022.3920.0210.0210.0000.0000.0000.000
110A110PHE0-0.008-0.02622.6730.0150.0150.0000.0000.0000.000
111A111GLY00.0430.03023.0610.0130.0130.0000.0000.0000.000
112A112ASN0-0.002-0.02118.5290.0640.0640.0000.0000.0000.000
113A113VAL0-0.010-0.00618.9550.0340.0340.0000.0000.0000.000
114A114GLU-1-0.922-0.97020.9360.2790.2790.0000.0000.0000.000
115A115LEU0-0.042-0.00916.8540.0290.0290.0000.0000.0000.000
116A116LEU0-0.008-0.00815.2890.0630.0630.0000.0000.0000.000
117A117LEU0-0.047-0.02617.6000.0250.0250.0000.0000.0000.000
118A118LYS10.7370.86216.873-0.555-0.5550.0000.0000.0000.000
119A119TYR0-0.044-0.05514.1000.0290.0290.0000.0000.0000.000
120A120ALA00.0440.02115.0550.0610.0610.0000.0000.0000.000
121A121ASP-1-0.873-0.91315.5180.6710.6710.0000.0000.0000.000
122A122ARG10.8050.88710.721-0.837-0.8370.0000.0000.0000.000
123A123PRO0-0.027-0.0058.226-0.170-0.1700.0000.0000.0000.000
124A124ILE00.0220.0099.7210.1270.1270.0000.0000.0000.000
125A125GLU-1-0.804-0.84711.820-0.099-0.0990.0000.0000.0000.000
126A126ILE00.0060.01113.5890.0230.0230.0000.0000.0000.000
127A127VAL0-0.048-0.02714.475-0.048-0.0480.0000.0000.0000.000
128A128ASP-1-0.793-0.88416.8600.0590.0590.0000.0000.0000.000
129A129ARG10.7940.87919.644-0.023-0.0230.0000.0000.0000.000
130A130GLN0-0.038-0.01522.029-0.014-0.0140.0000.0000.0000.000
131A131ASN0-0.047-0.03821.7640.0070.0070.0000.0000.0000.000
132A132VAL00.0250.01916.666-0.013-0.0130.0000.0000.0000.000
133A133LEU0-0.031-0.00818.367-0.002-0.0020.0000.0000.0000.000
134A134THR00.014-0.01116.0990.0180.0180.0000.0000.0000.000
135A135VAL0-0.003-0.00617.973-0.040-0.0400.0000.0000.0000.000
136A136HIS00.0230.03717.8250.0170.0170.0000.0000.0000.000
137A137LEU00.0780.03919.100-0.034-0.0340.0000.0000.0000.000
138A138PRO0-0.0080.00621.808-0.004-0.0040.0000.0000.0000.000
139A139GLY00.0080.01822.5480.0250.0250.0000.0000.0000.000
140A140THR0-0.028-0.03822.200-0.024-0.0240.0000.0000.0000.000
141A141TYR0-0.016-0.00717.7550.0370.0370.0000.0000.0000.000
142A142THR0-0.010-0.01618.148-0.020-0.0200.0000.0000.0000.000
143A143VAL0-0.017-0.00418.5420.0100.0100.0000.0000.0000.000
144A144MET00.0160.01117.1170.0010.0010.0000.0000.0000.000
145A145TYR00.020-0.00619.8750.0010.0010.0000.0000.0000.000
146A146ASP-1-0.843-0.93618.743-0.171-0.1710.0000.0000.0000.000
147A147ALA0-0.013-0.00621.1610.0180.0180.0000.0000.0000.000
148A148ARG10.8740.96217.7570.2260.2260.0000.0000.0000.000
149A149TYR0-0.033-0.00618.5180.0010.0010.0000.0000.0000.000
150A150CYS0-0.078-0.00723.7640.0100.0100.0000.0000.0000.000
151A151TYR0-0.034-0.03926.8220.0040.0040.0000.0000.0000.000
152A152VAL0-0.026-0.03023.662-0.001-0.0010.0000.0000.0000.000
153A153SER0-0.024-0.01025.847-0.004-0.0040.0000.0000.0000.000
154A154TYR00.0140.00123.5510.0030.0030.0000.0000.0000.000
155A155ILE00.011-0.00527.157-0.013-0.0130.0000.0000.0000.000
156A156PRO0-0.0060.02127.4570.0170.0170.0000.0000.0000.000
157A157VAL00.0100.00424.907-0.006-0.0060.0000.0000.0000.000
158A158SER0-0.009-0.01428.1440.0020.0020.0000.0000.0000.000
159A159GLU-1-0.881-0.96029.8340.1240.1240.0000.0000.0000.000
160A160THR0-0.027-0.00932.715-0.009-0.0090.0000.0000.0000.000
161A161VAL0-0.0300.00728.6420.0130.0130.0000.0000.0000.000
162A162ALA00.0380.02931.084-0.013-0.0130.0000.0000.0000.000
163A163GLU-1-0.804-0.86831.1670.1200.1200.0000.0000.0000.000
164A164PHE0-0.0060.01127.092-0.002-0.0020.0000.0000.0000.000
165A165THR0-0.012-0.00929.532-0.016-0.0160.0000.0000.0000.000
166A166LEU0-0.034-0.00927.6340.0080.0080.0000.0000.0000.000
167A167THR0-0.021-0.01327.514-0.010-0.0100.0000.0000.0000.000
168A168GLY00.0440.00527.4040.0010.0010.0000.0000.0000.000
169A169PHE0-0.013-0.00924.481-0.008-0.0080.0000.0000.0000.000
170A170LYS10.7960.88730.141-0.002-0.0020.0000.0000.0000.000
171A171TYR0-0.027-0.01232.937-0.004-0.0040.0000.0000.0000.000
172A172PRO00.0040.00633.0040.0070.0070.0000.0000.0000.000
173A173LEU00.0420.02332.2740.0010.0010.0000.0000.0000.000
174A174THR0-0.041-0.04732.922-0.001-0.0010.0000.0000.0000.000
175A175ASN0-0.054-0.02533.738-0.003-0.0030.0000.0000.0000.000
176A176CSO0-0.042-0.00534.334-0.006-0.0060.0000.0000.0000.000
177A177HIS00.0120.01134.4890.0090.0090.0000.0000.0000.000
178A178ILE0-0.0030.00532.290-0.007-0.0070.0000.0000.0000.000
179A179SER00.009-0.01734.7490.0050.0050.0000.0000.0000.000
180A180ARG10.9470.98230.053-0.168-0.1680.0000.0000.0000.000
181A181GLY0-0.0030.00534.813-0.005-0.0050.0000.0000.0000.000
182A182SER0-0.076-0.03837.623-0.006-0.0060.0000.0000.0000.000
183A183THR0-0.029-0.02734.742-0.005-0.0050.0000.0000.0000.000
184A184LEU0-0.017-0.00334.3820.0070.0070.0000.0000.0000.000
185A185CSO00.0230.00931.3250.0090.0090.0000.0000.0000.000
186A186ILE0-0.0180.00830.819-0.008-0.0080.0000.0000.0000.000
187A187SER00.005-0.00230.4060.0010.0010.0000.0000.0000.000
188A188ASN00.002-0.02029.121-0.010-0.0100.0000.0000.0000.000
189A189GLU-1-0.755-0.85228.792-0.004-0.0040.0000.0000.0000.000
190A190LEU0-0.0300.00723.3950.0040.0040.0000.0000.0000.000
191A191ILE0-0.035-0.02027.514-0.010-0.0100.0000.0000.0000.000
192A192GLN00.0060.00127.168-0.006-0.0060.0000.0000.0000.000
193A193SER00.0140.00524.0060.0010.0010.0000.0000.0000.000
194A194SER0-0.002-0.01121.898-0.013-0.0130.0000.0000.0000.000
195A195GLY00.0100.01323.152-0.001-0.0010.0000.0000.0000.000
196A196THR0-0.055-0.02522.5370.0090.0090.0000.0000.0000.000
197A197PHE00.0390.01520.769-0.015-0.0150.0000.0000.0000.000
198A198SER00.0090.00423.9870.0140.0140.0000.0000.0000.000
199A199PHE00.000-0.00523.388-0.015-0.0150.0000.0000.0000.000
200A200SER0-0.027-0.04026.8950.0180.0180.0000.0000.0000.000
201A201GLU-1-0.916-0.95928.8140.1510.1510.0000.0000.0000.000
202A202GLY00.021-0.00128.285-0.010-0.0100.0000.0000.0000.000
203A203ILE0-0.017-0.01722.8610.0170.0170.0000.0000.0000.000
204A204LEU0-0.026-0.00123.999-0.021-0.0210.0000.0000.0000.000
205A205MET00.0280.01622.6310.0280.0280.0000.0000.0000.000
206A206MET0-0.048-0.02119.335-0.033-0.0330.0000.0000.0000.000
207A207ILE00.0190.00321.9740.0140.0140.0000.0000.0000.000
208A208ARG10.8400.92819.501-0.001-0.0010.0000.0000.0000.000
209A209SER00.0340.00822.633-0.001-0.0010.0000.0000.0000.000
210A210SER0-0.007-0.02624.830-0.005-0.0050.0000.0000.0000.000
211A211ASP-1-0.751-0.84227.2440.0040.0040.0000.0000.0000.000
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