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: 9MMG2

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 OptHSide
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 -2485508.043425
FMO2-HF: Nuclear repulsion 2399464.909523
FMO2-HF: Total energy -86043.133902
FMO2-MP2: Total energy -86288.954568


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.
-34.034-25.54618.011-11.215-15.28-0.098
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 : -0.034 / q_NPA : -0.023
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].
3A3ILE00.0240.0282.979-2.2890.1532.019-1.317-3.1440.001
4A4HIS0-0.019-0.0024.756-0.401-0.345-0.001-0.012-0.0430.000
5A5ILE00.0550.0228.2140.1120.1120.0000.0000.0000.000
6A6VAL0-0.024-0.00710.931-0.137-0.1370.0000.0000.0000.000
7A7GLY00.0520.02314.2420.0340.0340.0000.0000.0000.000
8A8GLY0-0.004-0.01417.279-0.040-0.0400.0000.0000.0000.000
9A9GLY0-0.0310.00420.628-0.015-0.0150.0000.0000.0000.000
10A10PRO0-0.026-0.01922.627-0.011-0.0110.0000.0000.0000.000
11A11ARG11.0091.00021.4210.0280.0280.0000.0000.0000.000
12A12GLU-1-0.907-0.95823.0680.0110.0110.0000.0000.0000.000
13A13LEU0-0.0070.00323.175-0.016-0.0160.0000.0000.0000.000
14A14LEU0-0.0020.01517.854-0.003-0.0030.0000.0000.0000.000
15A15PRO0-0.0060.01717.024-0.009-0.0090.0000.0000.0000.000
16A16ASP-1-0.834-0.91118.940-0.224-0.2240.0000.0000.0000.000
17A17LEU00.0570.01614.373-0.038-0.0380.0000.0000.0000.000
18A18ARG10.9110.93714.3190.1630.1630.0000.0000.0000.000
19A19PHE0-0.110-0.04915.056-0.067-0.0670.0000.0000.0000.000
20A20TYR0-0.057-0.03911.912-0.007-0.0070.0000.0000.0000.000
21A21ASP-1-0.821-0.89710.420-0.980-0.9800.0000.0000.0000.000
22A22GLY0-0.003-0.0168.5990.0080.0080.0000.0000.0000.000
23A23GLU-1-0.963-0.9747.797-1.608-1.6080.0000.0000.0000.000
24A24ASP-1-0.868-0.9361.941-21.349-21.95512.913-6.804-5.502-0.084
25A25VAL0-0.045-0.0042.773-4.786-3.0660.617-1.146-1.190-0.011
26A26CSO0-0.034-0.0083.1770.0651.0831.357-0.683-1.692-0.002
27A27TRP00.018-0.0255.0530.2970.335-0.001-0.003-0.0330.000
28A28VAL00.008-0.0037.6220.2310.2310.0000.0000.0000.000
29A29GLY0-0.0050.00610.301-0.153-0.1530.0000.0000.0000.000
30A30VAL00.0290.00413.8940.0660.0660.0000.0000.0000.000
31A31ASP-1-0.794-0.89216.4040.1410.1410.0000.0000.0000.000
32A32ARG10.7910.86419.616-0.099-0.0990.0000.0000.0000.000
33A33GLY0-0.0180.00617.290-0.033-0.0330.0000.0000.0000.000
34A34THR0-0.011-0.02616.374-0.007-0.0070.0000.0000.0000.000
35A35MET0-0.040-0.00117.424-0.026-0.0260.0000.0000.0000.000
36A36THR0-0.026-0.00417.859-0.038-0.0380.0000.0000.0000.000
37A37LEU0-0.028-0.01012.616-0.042-0.0420.0000.0000.0000.000
38A38LEU00.0010.00316.232-0.048-0.0480.0000.0000.0000.000
39A39GLU-1-0.867-0.92718.599-0.021-0.0210.0000.0000.0000.000
40A40ALA0-0.106-0.04116.763-0.022-0.0220.0000.0000.0000.000
41A41GLY0-0.026-0.00117.971-0.044-0.0440.0000.0000.0000.000
42A42PHE0-0.029-0.01412.345-0.051-0.0510.0000.0000.0000.000
43A43ARG10.8800.92313.5120.0140.0140.0000.0000.0000.000
44A44PRO0-0.022-0.00310.854-0.028-0.0280.0000.0000.0000.000
45A45VAL0-0.020-0.0116.313-0.099-0.0990.0000.0000.0000.000
46A46ARG10.8420.9209.629-0.854-0.8540.0000.0000.0000.000
47A47ALA0-0.016-0.00911.2910.0130.0130.0000.0000.0000.000
48A48PHE00.0170.00910.6280.0290.0290.0000.0000.0000.000
49A49GLY00.0670.03016.005-0.030-0.0300.0000.0000.0000.000
50A50ASP-1-0.897-0.95019.7790.2310.2310.0000.0000.0000.000
51A51PHE00.008-0.02821.450-0.008-0.0080.0000.0000.0000.000
52A52ASP-1-0.912-0.95224.8100.1150.1150.0000.0000.0000.000
53A53SER0-0.050-0.01924.126-0.015-0.0150.0000.0000.0000.000
54A54LEU0-0.052-0.01422.110-0.008-0.0080.0000.0000.0000.000
55A55PRO0-0.002-0.00926.211-0.007-0.0070.0000.0000.0000.000
56A56ALA00.0480.02328.6340.0010.0010.0000.0000.0000.000
57A57GLU-1-0.897-0.97130.2950.0480.0480.0000.0000.0000.000
58A58ASP-1-0.709-0.85225.3200.0520.0520.0000.0000.0000.000
59A59VAL00.0230.03125.5370.0050.0050.0000.0000.0000.000
60A60VAL0-0.028-0.01126.5590.0000.0000.0000.0000.0000.000
61A61LYS10.7570.84924.404-0.026-0.0260.0000.0000.0000.000
62A62LEU0-0.015-0.00519.889-0.009-0.0090.0000.0000.0000.000
63A63GLN0-0.023-0.01923.033-0.011-0.0110.0000.0000.0000.000
64A64GLN0-0.072-0.02224.961-0.010-0.0100.0000.0000.0000.000
65A65ALA0-0.041-0.01523.482-0.011-0.0110.0000.0000.0000.000
66A66PHE0-0.053-0.03518.309-0.017-0.0170.0000.0000.0000.000
67A67PRO00.0460.02420.5670.0290.0290.0000.0000.0000.000
68A68ASP-1-0.896-0.94418.5090.0650.0650.0000.0000.0000.000
69A69LEU0-0.072-0.02214.5100.0210.0210.0000.0000.0000.000
70A70ASP-1-0.775-0.86312.3640.5460.5460.0000.0000.0000.000
71A71VAL0-0.027-0.01814.5950.0840.0840.0000.0000.0000.000
72A72TRP0-0.086-0.05513.231-0.007-0.0070.0000.0000.0000.000
73A73PRO00.0200.01416.9160.0140.0140.0000.0000.0000.000
74A74ALA00.0480.02819.3640.0370.0370.0000.0000.0000.000
75A75GLU-1-0.817-0.90118.1170.3960.3960.0000.0000.0000.000
76A76LYS10.8070.88121.305-0.315-0.3150.0000.0000.0000.000
77A77ASP-1-0.946-0.97724.0060.2160.2160.0000.0000.0000.000
78A78LYS10.8360.93017.330-0.455-0.4550.0000.0000.0000.000
79A79THR0-0.0120.00019.980-0.002-0.0020.0000.0000.0000.000
80A80ASP-1-0.816-0.92618.3500.3430.3430.0000.0000.0000.000
81A81MET0-0.026-0.01615.0350.0990.0990.0000.0000.0000.000
82A82GLU-1-0.861-0.93014.9810.4890.4890.0000.0000.0000.000
83A83ILE0-0.0130.00614.9900.0860.0860.0000.0000.0000.000
84A84ALA00.0110.01011.9920.1010.1010.0000.0000.0000.000
85A85LEU0-0.016-0.01110.4970.2880.2880.0000.0000.0000.000
86A86ASP-1-0.799-0.88010.8970.7630.7630.0000.0000.0000.000
87A87TRP00.0220.0215.8460.2280.321-0.001-0.005-0.0860.000
88A88ALA00.007-0.0066.4470.2770.2770.0000.0000.0000.000
89A89VAL0-0.020-0.0186.4400.6840.6840.0000.0000.0000.000
90A90GLU-1-0.988-0.9908.0930.8140.8140.0000.0000.0000.000
91A91GLN0-0.091-0.0452.447-1.644-0.8820.600-0.256-1.106-0.001
92A92THR0-0.108-0.0473.216-1.647-0.6530.140-0.410-0.724-0.003
93A93ALA00.0430.0332.621-0.7340.6120.360-0.486-1.2200.002
94A94ARG10.9140.9563.615-2.323-1.6980.008-0.093-0.5400.000
95A95CSO0-0.104-0.0815.410-0.477-0.4770.0000.0000.0000.000
96A96ILE00.0550.0396.072-0.204-0.2040.0000.0000.0000.000
97A97ARG10.7830.8728.2610.3710.3710.0000.0000.0000.000
98A98LEU00.0070.00410.6860.0710.0710.0000.0000.0000.000
99A99PHE00.025-0.00311.038-0.077-0.0770.0000.0000.0000.000
100A100GLY00.007-0.00415.4520.0480.0480.0000.0000.0000.000
101A101ALA00.0220.01517.2210.0200.0200.0000.0000.0000.000
102A102THR0-0.049-0.04719.2400.0060.0060.0000.0000.0000.000
103A103GLY00.0320.00322.456-0.008-0.0080.0000.0000.0000.000
104A104GLY0-0.006-0.01125.8110.0120.0120.0000.0000.0000.000
105A105ARG10.8420.89227.567-0.157-0.1570.0000.0000.0000.000
106A106LEU00.0500.01626.6800.0110.0110.0000.0000.0000.000
107A107ASP-1-0.820-0.87827.1370.1600.1600.0000.0000.0000.000
108A108HIS00.0500.02722.8880.0240.0240.0000.0000.0000.000
109A109LEU00.0020.01322.3870.0200.0200.0000.0000.0000.000
110A110PHE0-0.013-0.02722.8820.0120.0120.0000.0000.0000.000
111A111GLY00.0460.03223.5630.0090.0090.0000.0000.0000.000
112A112ASN00.008-0.01518.8690.0590.0590.0000.0000.0000.000
113A113VAL0-0.025-0.01419.2790.0310.0310.0000.0000.0000.000
114A114GLU-1-0.923-0.96521.2530.2400.2400.0000.0000.0000.000
115A115LEU0-0.0380.00316.7420.0250.0250.0000.0000.0000.000
116A116LEU0-0.009-0.01715.5840.0400.0400.0000.0000.0000.000
117A117LEU0-0.043-0.01717.9270.0100.0100.0000.0000.0000.000
118A118LYS10.8010.91217.175-0.505-0.5050.0000.0000.0000.000
119A119TYR0-0.076-0.07514.3560.0220.0220.0000.0000.0000.000
120A120ALA00.0660.03515.3690.0400.0400.0000.0000.0000.000
121A121ASP-1-0.914-0.94515.5110.6000.6000.0000.0000.0000.000
122A122ARG10.8070.90011.030-0.785-0.7850.0000.0000.0000.000
123A123PRO0-0.026-0.0048.797-0.113-0.1130.0000.0000.0000.000
124A124ILE00.0300.00610.1870.0830.0830.0000.0000.0000.000
125A125GLU-1-0.810-0.85612.374-0.222-0.2220.0000.0000.0000.000
126A126ILE00.0110.01313.8010.0320.0320.0000.0000.0000.000
127A127VAL0-0.028-0.01614.644-0.046-0.0460.0000.0000.0000.000
128A128ASP-1-0.782-0.86617.0940.0440.0440.0000.0000.0000.000
129A129ARG10.8280.90119.909-0.008-0.0080.0000.0000.0000.000
130A130GLN0-0.080-0.04122.262-0.011-0.0110.0000.0000.0000.000
131A131ASN0-0.043-0.03821.9060.0060.0060.0000.0000.0000.000
132A132VAL00.0170.01616.819-0.011-0.0110.0000.0000.0000.000
133A133LEU0-0.042-0.01818.7400.0010.0010.0000.0000.0000.000
134A134THR00.021-0.01816.3020.0130.0130.0000.0000.0000.000
135A135VAL0-0.004-0.00618.233-0.030-0.0300.0000.0000.0000.000
136A136HIS00.0310.04718.0110.0110.0110.0000.0000.0000.000
137A137LEU00.0680.03119.387-0.025-0.0250.0000.0000.0000.000
138A138PRO0-0.0060.01722.016-0.006-0.0060.0000.0000.0000.000
139A139GLY00.0270.02422.4540.0220.0220.0000.0000.0000.000
140A140THR0-0.033-0.03722.566-0.019-0.0190.0000.0000.0000.000
141A141TYR0-0.029-0.02118.0000.0220.0220.0000.0000.0000.000
142A142THR0-0.003-0.01118.666-0.013-0.0130.0000.0000.0000.000
143A143VAL0-0.0160.00118.9030.0020.0020.0000.0000.0000.000
144A144MET00.0120.00617.3620.0050.0050.0000.0000.0000.000
145A145TYR00.023-0.00320.192-0.003-0.0030.0000.0000.0000.000
146A146ASP-1-0.855-0.94118.871-0.208-0.2080.0000.0000.0000.000
147A147ALA0-0.012-0.00621.4010.0180.0180.0000.0000.0000.000
148A148ARG10.9070.97018.6050.2480.2480.0000.0000.0000.000
149A149TYR0-0.041-0.01819.1030.0030.0030.0000.0000.0000.000
150A150CYS0-0.097-0.00124.4400.0050.0050.0000.0000.0000.000
151A151TYR0-0.012-0.01827.1540.0060.0060.0000.0000.0000.000
152A152VAL0-0.032-0.02824.550-0.003-0.0030.0000.0000.0000.000
153A153SER0-0.032-0.01626.5250.0000.0000.0000.0000.0000.000
154A154TYR00.004-0.00523.9800.0010.0010.0000.0000.0000.000
155A155ILE0-0.003-0.01127.394-0.009-0.0090.0000.0000.0000.000
156A156PRO00.0000.02327.6280.0130.0130.0000.0000.0000.000
157A157VAL00.0270.00924.861-0.004-0.0040.0000.0000.0000.000
158A158SER0-0.024-0.01328.1490.0020.0020.0000.0000.0000.000
159A159GLU-1-0.902-0.96229.8580.1030.1030.0000.0000.0000.000
160A160THR0-0.003-0.01132.848-0.010-0.0100.0000.0000.0000.000
161A161VAL0-0.053-0.00328.8750.0110.0110.0000.0000.0000.000
162A162ALA00.0340.02531.141-0.011-0.0110.0000.0000.0000.000
163A163GLU-1-0.816-0.88431.2820.0950.0950.0000.0000.0000.000
164A164PHE0-0.002-0.00127.4760.0010.0010.0000.0000.0000.000
165A165THR0-0.022-0.00729.938-0.012-0.0120.0000.0000.0000.000
166A166LEU0-0.038-0.00628.0480.0040.0040.0000.0000.0000.000
167A167THR0-0.033-0.01728.051-0.007-0.0070.0000.0000.0000.000
168A168GLY00.0400.00427.993-0.002-0.0020.0000.0000.0000.000
169A169PHE0-0.005-0.01025.238-0.008-0.0080.0000.0000.0000.000
170A170LYS10.8010.90130.8580.0150.0150.0000.0000.0000.000
171A171TYR0-0.032-0.01533.549-0.002-0.0020.0000.0000.0000.000
172A172PRO00.0010.00833.7150.0050.0050.0000.0000.0000.000
173A173LEU00.0360.01632.7010.0020.0020.0000.0000.0000.000
174A174THR0-0.010-0.02733.536-0.001-0.0010.0000.0000.0000.000
175A175ASN0-0.039-0.01834.1490.0000.0000.0000.0000.0000.000
176A176CSO0-0.046-0.01034.743-0.004-0.0040.0000.0000.0000.000
177A177HIS00.0430.02734.7990.0070.0070.0000.0000.0000.000
178A178ILE0-0.014-0.00232.469-0.006-0.0060.0000.0000.0000.000
179A179SER00.0320.00634.8260.0070.0070.0000.0000.0000.000
180A180ARG10.9800.99330.672-0.139-0.1390.0000.0000.0000.000
181A181GLY0-0.020-0.00635.203-0.002-0.0020.0000.0000.0000.000
182A182SER0-0.073-0.03338.081-0.005-0.0050.0000.0000.0000.000
183A183THR0-0.029-0.02834.872-0.006-0.0060.0000.0000.0000.000
184A184LEU0-0.032-0.01535.0920.0060.0060.0000.0000.0000.000
185A185CSO00.0310.00431.8770.0080.0080.0000.0000.0000.000
186A186ILE0-0.0220.01231.401-0.008-0.0080.0000.0000.0000.000
187A187SER00.0270.01531.1140.0000.0000.0000.0000.0000.000
188A188ASN00.009-0.02229.766-0.007-0.0070.0000.0000.0000.000
189A189GLU-1-0.769-0.86829.280-0.024-0.0240.0000.0000.0000.000
190A190LEU0-0.0200.01723.8200.0040.0040.0000.0000.0000.000
191A191ILE0-0.032-0.02027.959-0.009-0.0090.0000.0000.0000.000
192A192GLN0-0.0010.00727.739-0.007-0.0070.0000.0000.0000.000
193A193SER00.012-0.00124.3530.0000.0000.0000.0000.0000.000
194A194SER00.009-0.00422.222-0.014-0.0140.0000.0000.0000.000
195A195GLY00.0050.00123.4170.0020.0020.0000.0000.0000.000
196A196THR0-0.063-0.03323.2080.0050.0050.0000.0000.0000.000
197A197PHE00.0460.01921.134-0.010-0.0100.0000.0000.0000.000
198A198SER00.0130.01424.3600.0090.0090.0000.0000.0000.000
199A199PHE0-0.009-0.00623.431-0.013-0.0130.0000.0000.0000.000
200A200SER0-0.035-0.04727.1340.0140.0140.0000.0000.0000.000
201A201GLU-1-0.924-0.95928.8720.1280.1280.0000.0000.0000.000
202A202GLY00.010-0.00128.357-0.009-0.0090.0000.0000.0000.000
203A203ILE0-0.013-0.02223.0440.0130.0130.0000.0000.0000.000
204A204LEU0-0.0200.00324.197-0.017-0.0170.0000.0000.0000.000
205A205MET00.0260.01722.9390.0210.0210.0000.0000.0000.000
206A206MET0-0.042-0.01519.716-0.028-0.0280.0000.0000.0000.000
207A207ILE00.0160.00422.2050.0100.0100.0000.0000.0000.000
208A208ARG10.8650.94719.4010.0450.0450.0000.0000.0000.000
209A209SER00.0440.00823.023-0.002-0.0020.0000.0000.0000.000
210A210SER00.000-0.01725.031-0.004-0.0040.0000.0000.0000.000
211A211ASP-1-0.785-0.88227.492-0.009-0.0090.0000.0000.0000.000
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