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: L77J9

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 OptH
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 -2484068.901566
FMO2-HF: Nuclear repulsion 2398026.615187
FMO2-HF: Total energy -86042.286379
FMO2-MP2: Total energy -86288.102864


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.
-26.664-14.89113.617-10.021-15.37-0.075
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 : 0.025 / q_NPA : 0.011
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].
3A3ILE00.0190.0242.980-2.1910.7512.299-1.592-3.6490.004
4A4HIS0-0.0110.0054.481-0.786-0.694-0.001-0.022-0.0700.000
5A5ILE00.0520.0207.9870.2180.2180.0000.0000.0000.000
6A6VAL0-0.020-0.00410.678-0.185-0.1850.0000.0000.0000.000
7A7GLY00.0520.02314.0190.0570.0570.0000.0000.0000.000
8A8GLY0-0.006-0.01317.030-0.037-0.0370.0000.0000.0000.000
9A9GLY0-0.0300.00220.376-0.015-0.0150.0000.0000.0000.000
10A10PRO0-0.024-0.01922.377-0.005-0.0050.0000.0000.0000.000
11A11ARG11.0201.00621.6060.0340.0340.0000.0000.0000.000
12A12GLU-1-0.928-0.97022.885-0.024-0.0240.0000.0000.0000.000
13A13LEU0-0.031-0.01722.877-0.020-0.0200.0000.0000.0000.000
14A14LEU0-0.0040.01417.788-0.017-0.0170.0000.0000.0000.000
15A15PRO0-0.0060.01916.902-0.003-0.0030.0000.0000.0000.000
16A16ASP-1-0.821-0.90718.798-0.236-0.2360.0000.0000.0000.000
17A17LEU00.0650.01814.004-0.055-0.0550.0000.0000.0000.000
18A18ARG10.9040.93914.2590.1730.1730.0000.0000.0000.000
19A19PHE0-0.122-0.05615.084-0.064-0.0640.0000.0000.0000.000
20A20TYR0-0.058-0.03611.751-0.028-0.0280.0000.0000.0000.000
21A21ASP-1-0.813-0.89510.415-0.878-0.8780.0000.0000.0000.000
22A22GLY0-0.019-0.0258.639-0.063-0.0630.0000.0000.0000.000
23A23GLU-1-0.962-0.9747.705-1.159-1.1590.0000.0000.0000.000
24A24ASP-1-0.881-0.9422.121-19.765-17.1537.461-5.309-4.765-0.068
25A25VAL0-0.050-0.0062.780-4.724-2.9970.570-1.112-1.184-0.011
26A26CSO0-0.035-0.0112.998-0.6550.1172.631-1.065-2.3380.000
27A27TRP00.018-0.0195.0380.0950.143-0.001-0.005-0.0420.000
28A28VAL00.010-0.0037.4260.2930.2930.0000.0000.0000.000
29A29GLY0-0.0100.00410.125-0.208-0.2080.0000.0000.0000.000
30A30VAL00.0330.01013.8150.0780.0780.0000.0000.0000.000
31A31ASP-1-0.857-0.91416.2190.1760.1760.0000.0000.0000.000
32A32ARG10.8680.88519.415-0.106-0.1060.0000.0000.0000.000
33A33GLY0-0.0170.00817.088-0.034-0.0340.0000.0000.0000.000
34A34THR00.015-0.01516.2380.0060.0060.0000.0000.0000.000
35A35MET0-0.047-0.00217.281-0.015-0.0150.0000.0000.0000.000
36A36THR0-0.033-0.00617.875-0.040-0.0400.0000.0000.0000.000
37A37LEU0-0.025-0.00912.529-0.048-0.0480.0000.0000.0000.000
38A38LEU00.0080.00816.139-0.042-0.0420.0000.0000.0000.000
39A39GLU-1-0.971-0.99818.5490.0250.0250.0000.0000.0000.000
40A40ALA0-0.095-0.03516.694-0.027-0.0270.0000.0000.0000.000
41A41GLY0-0.031-0.00417.865-0.044-0.0440.0000.0000.0000.000
42A42PHE0-0.028-0.01412.299-0.051-0.0510.0000.0000.0000.000
43A43ARG10.9490.96713.353-0.171-0.1710.0000.0000.0000.000
44A44PRO0-0.0050.00810.8060.0090.0090.0000.0000.0000.000
45A45VAL0-0.019-0.0126.158-0.123-0.1230.0000.0000.0000.000
46A46ARG10.9210.9688.624-1.190-1.1900.0000.0000.0000.000
47A47ALA0-0.016-0.00211.0690.0100.0100.0000.0000.0000.000
48A48PHE00.0180.00710.5570.0430.0430.0000.0000.0000.000
49A49GLY00.0670.03115.811-0.043-0.0430.0000.0000.0000.000
50A50ASP-1-0.902-0.94519.5870.2830.2830.0000.0000.0000.000
51A51PHE0-0.010-0.04521.015-0.014-0.0140.0000.0000.0000.000
52A52ASP-1-0.908-0.94724.5970.1450.1450.0000.0000.0000.000
53A53SER0-0.049-0.01923.935-0.019-0.0190.0000.0000.0000.000
54A54LEU0-0.072-0.02721.894-0.011-0.0110.0000.0000.0000.000
55A55PRO0-0.002-0.00626.004-0.007-0.0070.0000.0000.0000.000
56A56ALA00.0540.02928.4350.0060.0060.0000.0000.0000.000
57A57GLU-1-0.903-0.97730.0750.0790.0790.0000.0000.0000.000
58A58ASP-1-0.777-0.88225.0890.0940.0940.0000.0000.0000.000
59A59VAL00.0140.02325.3840.0140.0140.0000.0000.0000.000
60A60VAL0-0.017-0.00326.3340.0050.0050.0000.0000.0000.000
61A61LYS10.9090.94025.302-0.047-0.0470.0000.0000.0000.000
62A62LEU0-0.008-0.00619.410-0.004-0.0040.0000.0000.0000.000
63A63GLN0-0.021-0.01322.808-0.004-0.0040.0000.0000.0000.000
64A64GLN0-0.071-0.01924.735-0.005-0.0050.0000.0000.0000.000
65A65ALA0-0.033-0.01323.196-0.009-0.0090.0000.0000.0000.000
66A66PHE0-0.088-0.05617.796-0.005-0.0050.0000.0000.0000.000
67A67PRO00.0430.01820.2940.0310.0310.0000.0000.0000.000
68A68ASP-1-0.947-0.97117.9080.2290.2290.0000.0000.0000.000
69A69LEU0-0.100-0.03514.5470.0360.0360.0000.0000.0000.000
70A70ASP-1-0.862-0.93312.2600.6790.6790.0000.0000.0000.000
71A71VAL0-0.036-0.02314.2490.0940.0940.0000.0000.0000.000
72A72TRP0-0.055-0.03012.406-0.012-0.0120.0000.0000.0000.000
73A73PRO00.0120.01616.6330.0040.0040.0000.0000.0000.000
74A74ALA00.0820.04019.2140.0370.0370.0000.0000.0000.000
75A75GLU-1-0.920-0.96317.6210.4680.4680.0000.0000.0000.000
76A76LYS10.8090.89220.951-0.369-0.3690.0000.0000.0000.000
77A77ASP-1-0.941-0.97124.0270.2110.2110.0000.0000.0000.000
78A78LYS10.9190.97718.634-0.424-0.4240.0000.0000.0000.000
79A79THR0-0.0060.00319.9590.0050.0050.0000.0000.0000.000
80A80ASP-1-0.782-0.91318.0050.3800.3800.0000.0000.0000.000
81A81MET0-0.061-0.03514.8950.1050.1050.0000.0000.0000.000
82A82GLU-1-0.911-0.96014.8870.4290.4290.0000.0000.0000.000
83A83ILE00.0090.02114.8980.0810.0810.0000.0000.0000.000
84A84ALA00.0070.01011.7630.1270.1270.0000.0000.0000.000
85A85LEU0-0.019-0.01510.3800.3180.3180.0000.0000.0000.000
86A86ASP-1-0.850-0.89910.8490.7490.7490.0000.0000.0000.000
87A87TRP00.0180.0165.4060.2590.382-0.001-0.011-0.1110.000
88A88ALA0-0.005-0.0166.3630.3890.3890.0000.0000.0000.000
89A89VAL0-0.020-0.0156.4450.6670.6670.0000.0000.0000.000
90A90GLU-1-1.004-1.0008.5770.8740.8740.0000.0000.0000.000
91A91GLN0-0.070-0.0312.867-1.562-0.7600.336-0.214-0.924-0.001
92A92THR0-0.127-0.0593.799-0.4190.1400.024-0.151-0.432-0.001
93A93ALA00.0440.0382.651-0.7530.4800.286-0.425-1.0940.002
94A94ARG10.9160.9573.2611.6322.3080.014-0.098-0.5920.000
95A95CSO0-0.051-0.0394.8650.5070.694-0.001-0.017-0.1690.000
96A96ILE00.0530.0435.810-0.265-0.2650.0000.0000.0000.000
97A97ARG10.8300.9187.9641.1581.1580.0000.0000.0000.000
98A98LEU00.0200.01210.4110.1490.1490.0000.0000.0000.000
99A99PHE00.024-0.00210.718-0.090-0.0900.0000.0000.0000.000
100A100GLY00.004-0.00615.2060.0670.0670.0000.0000.0000.000
101A101ALA00.0270.01617.0500.0310.0310.0000.0000.0000.000
102A102THR0-0.041-0.03918.9580.0070.0070.0000.0000.0000.000
103A103GLY00.025-0.00222.1790.0010.0010.0000.0000.0000.000
104A104GLY0-0.011-0.01225.5340.0150.0150.0000.0000.0000.000
105A105ARG10.8460.91927.052-0.131-0.1310.0000.0000.0000.000
106A106LEU00.0610.01726.3870.0070.0070.0000.0000.0000.000
107A107ASP-1-0.816-0.89526.8290.1140.1140.0000.0000.0000.000
108A108HIS00.0440.02222.6160.0180.0180.0000.0000.0000.000
109A109LEU00.0060.01621.8840.0120.0120.0000.0000.0000.000
110A110PHE0-0.027-0.03422.5690.0010.0010.0000.0000.0000.000
111A111GLY00.0470.03323.4490.0030.0030.0000.0000.0000.000
112A112ASN00.019-0.00918.5660.0560.0560.0000.0000.0000.000
113A113VAL0-0.024-0.01018.9690.0100.0100.0000.0000.0000.000
114A114GLU-1-0.929-0.97020.9730.1200.1200.0000.0000.0000.000
115A115LEU0-0.0260.00516.4720.0160.0160.0000.0000.0000.000
116A116LEU0-0.018-0.01915.5090.0230.0230.0000.0000.0000.000
117A117LEU0-0.041-0.01417.685-0.015-0.0150.0000.0000.0000.000
118A118LYS10.9300.97318.114-0.394-0.3940.0000.0000.0000.000
119A119TYR0-0.105-0.09614.2920.0270.0270.0000.0000.0000.000
120A120ALA00.0600.03115.337-0.014-0.0140.0000.0000.0000.000
121A121ASP-1-0.981-0.98916.0350.2330.2330.0000.0000.0000.000
122A122ARG10.8720.94610.554-0.637-0.6370.0000.0000.0000.000
123A123PRO0-0.014-0.0028.817-0.029-0.0290.0000.0000.0000.000
124A124ILE00.0230.00710.172-0.028-0.0280.0000.0000.0000.000
125A125GLU-1-0.917-0.96412.096-0.626-0.6260.0000.0000.0000.000
126A126ILE00.0070.00913.5140.0580.0580.0000.0000.0000.000
127A127VAL0-0.025-0.01114.271-0.050-0.0500.0000.0000.0000.000
128A128ASP-1-0.784-0.88516.849-0.050-0.0500.0000.0000.0000.000
129A129ARG10.8610.92719.6830.0430.0430.0000.0000.0000.000
130A130GLN0-0.105-0.05322.0710.0000.0000.0000.0000.0000.000
131A131ASN0-0.034-0.03021.7080.0030.0030.0000.0000.0000.000
132A132VAL00.0210.02016.562-0.012-0.0120.0000.0000.0000.000
133A133LEU0-0.047-0.01618.4730.0070.0070.0000.0000.0000.000
134A134THR00.015-0.03916.049-0.003-0.0030.0000.0000.0000.000
135A135VAL0-0.005-0.00818.2160.0090.0090.0000.0000.0000.000
136A136HIS00.0350.06517.527-0.008-0.0080.0000.0000.0000.000
137A137LEU00.0740.03319.3940.0120.0120.0000.0000.0000.000
138A138PRO0-0.0020.03021.945-0.025-0.0250.0000.0000.0000.000
139A139GLY00.0340.02621.7240.0050.0050.0000.0000.0000.000
140A140THR0-0.036-0.03521.7710.0030.0030.0000.0000.0000.000
141A141TYR0-0.052-0.04417.510-0.027-0.0270.0000.0000.0000.000
142A142THR0-0.007-0.01218.4470.0160.0160.0000.0000.0000.000
143A143VAL0-0.023-0.00218.651-0.033-0.0330.0000.0000.0000.000
144A144MET00.0160.00517.6110.0280.0280.0000.0000.0000.000
145A145TYR00.023-0.00120.305-0.001-0.0010.0000.0000.0000.000
146A146ASP-1-0.868-0.94118.920-0.465-0.4650.0000.0000.0000.000
147A147ALA0-0.012-0.00721.7780.0290.0290.0000.0000.0000.000
148A148ARG10.8980.96119.1220.4160.4160.0000.0000.0000.000
149A149TYR0-0.031-0.01719.3010.0060.0060.0000.0000.0000.000
150A150CYS0-0.0790.01024.703-0.004-0.0040.0000.0000.0000.000
151A151TYR0-0.029-0.04327.2860.0120.0120.0000.0000.0000.000
152A152VAL0-0.032-0.02424.651-0.018-0.0180.0000.0000.0000.000
153A153SER0-0.039-0.02326.3140.0160.0160.0000.0000.0000.000
154A154TYR00.001-0.00423.767-0.006-0.0060.0000.0000.0000.000
155A155ILE00.004-0.01327.2170.0060.0060.0000.0000.0000.000
156A156PRO0-0.0040.02127.6140.0020.0020.0000.0000.0000.000
157A157VAL00.0110.00324.8690.0040.0040.0000.0000.0000.000
158A158SER0-0.040-0.02928.1220.0080.0080.0000.0000.0000.000
159A159GLU-1-0.929-0.97629.8370.0280.0280.0000.0000.0000.000
160A160THR0-0.030-0.02032.756-0.007-0.0070.0000.0000.0000.000
161A161VAL00.0040.02528.8250.0050.0050.0000.0000.0000.000
162A162ALA00.0300.02330.934-0.005-0.0050.0000.0000.0000.000
163A163GLU-1-0.885-0.95530.787-0.032-0.0320.0000.0000.0000.000
164A164PHE0-0.006-0.00326.901-0.008-0.0080.0000.0000.0000.000
165A165THR0-0.015-0.00429.3510.0040.0040.0000.0000.0000.000
166A166LEU0-0.045-0.00527.637-0.010-0.0100.0000.0000.0000.000
167A167THR00.0020.01227.5960.0050.0050.0000.0000.0000.000
168A168GLY00.007-0.02027.800-0.015-0.0150.0000.0000.0000.000
169A169PHE00.0140.00025.131-0.009-0.0090.0000.0000.0000.000
170A170LYS10.9490.98830.7520.1040.1040.0000.0000.0000.000
171A171TYR0-0.043-0.02233.4060.0080.0080.0000.0000.0000.000
172A172PRO00.0180.01833.451-0.002-0.0020.0000.0000.0000.000
173A173LEU00.0300.00832.2490.0080.0080.0000.0000.0000.000
174A174THR0-0.012-0.02433.101-0.007-0.0070.0000.0000.0000.000
175A175ASN00.0020.00233.5730.0070.0070.0000.0000.0000.000
176A176CSO0-0.0270.00034.1340.0050.0050.0000.0000.0000.000
177A177HIS00.0400.02434.215-0.002-0.0020.0000.0000.0000.000
178A178ILE0-0.0060.00632.135-0.001-0.0010.0000.0000.0000.000
179A179SER00.018-0.00534.7530.0070.0070.0000.0000.0000.000
180A180ARG11.0221.01530.659-0.040-0.0400.0000.0000.0000.000
181A181GLY0-0.028-0.00935.1830.0030.0030.0000.0000.0000.000
182A182SER0-0.060-0.03237.960-0.003-0.0030.0000.0000.0000.000
183A183THR0-0.023-0.01534.272-0.006-0.0060.0000.0000.0000.000
184A184LEU0-0.042-0.02435.0280.0020.0020.0000.0000.0000.000
185A185CSO00.013-0.00631.4980.0020.0020.0000.0000.0000.000
186A186ILE0-0.0090.01931.017-0.001-0.0010.0000.0000.0000.000
187A187SER00.0340.01630.799-0.010-0.0100.0000.0000.0000.000
188A188ASN0-0.019-0.03329.623-0.002-0.0020.0000.0000.0000.000
189A189GLU-1-0.888-0.94029.278-0.135-0.1350.0000.0000.0000.000
190A190LEU0-0.0410.01223.8310.0070.0070.0000.0000.0000.000
191A191ILE0-0.019-0.01527.991-0.005-0.0050.0000.0000.0000.000
192A192GLN0-0.0090.01327.6550.0040.0040.0000.0000.0000.000
193A193SER0-0.010-0.01124.739-0.009-0.0090.0000.0000.0000.000
194A194SER0-0.010-0.00522.227-0.030-0.0300.0000.0000.0000.000
195A195GLY00.0330.00923.3470.0240.0240.0000.0000.0000.000
196A196THR0-0.069-0.04423.135-0.018-0.0180.0000.0000.0000.000
197A197PHE00.0530.01720.5460.0140.0140.0000.0000.0000.000
198A198SER0-0.0030.00723.811-0.009-0.0090.0000.0000.0000.000
199A199PHE0-0.004-0.00323.2360.0010.0010.0000.0000.0000.000
200A200SER0-0.0040.00126.5390.0000.0000.0000.0000.0000.000
201A201GLU-1-0.928-0.95928.7020.0220.0220.0000.0000.0000.000
202A202GLY00.0160.00328.395-0.008-0.0080.0000.0000.0000.000
203A203ILE0-0.011-0.02023.0400.0010.0010.0000.0000.0000.000
204A204LEU0-0.0170.00224.208-0.001-0.0010.0000.0000.0000.000
205A205MET00.0190.01522.6450.0000.0000.0000.0000.0000.000
206A206MET0-0.034-0.01419.497-0.008-0.0080.0000.0000.0000.000
207A207ILE00.0200.00721.9260.0000.0000.0000.0000.0000.000
208A208ARG10.8620.93619.3240.3100.3100.0000.0000.0000.000
209A209SER00.0410.01022.800-0.006-0.0060.0000.0000.0000.000
210A210SER00.009-0.00325.170-0.002-0.0020.0000.0000.0000.000
211A211ASP-1-0.754-0.85827.302-0.093-0.0930.0000.0000.0000.000
212A212SER0-0.044-0.03430.246-0.008-0.0080.0000.0000.0000.000
213A213SER0-0.047-0.01532.9500.0030.0030.0000.0000.0000.000
214A215LEU0-0.0090.00030.545-0.004-0.0040.0000.0000.0000.000