Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 94MY2

Calculation Name: 3CS1-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-oxy cysteine

ligand 3-letter code: CSX

PDB ID: 3CS1

Chain ID: A

ChEMBL ID:

UniProt ID: P07749

Base Structure: X-ray

Registration Date: 2023-06-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243164.416839
FMO2-HF: Nuclear repulsion 2165521.611118
FMO2-HF: Total energy -77642.805721
FMO2-MP2: Total energy -77869.76469


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:17:SER)


Summations of interaction energy for fragment #1(A:17:SER)
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.
-4.348-1.4710.078-1.411-1.5430.006
Interaction energy analysis for fragmet #1(A:17:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.028
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].
3A19LYS10.9170.9583.363-6.812-3.9540.079-1.407-1.5290.006
4A20ASP-1-0.741-0.8565.344-0.806-0.787-0.001-0.004-0.0140.000
5A21GLY0-0.016-0.0038.2510.3670.3670.0000.0000.0000.000
6A22LYS10.7780.9158.903-0.145-0.1450.0000.0000.0000.000
7A23LYS10.9230.96812.616-0.496-0.4960.0000.0000.0000.000
8A24ALA00.0880.03614.889-0.076-0.0760.0000.0000.0000.000
9A25LYS10.8370.90218.396-0.278-0.2780.0000.0000.0000.000
10A26ASP-1-0.802-0.90614.9930.3900.3900.0000.0000.0000.000
11A27ARG10.8100.87613.410-0.583-0.5830.0000.0000.0000.000
12A28LYS10.8730.93318.865-0.209-0.2090.0000.0000.0000.000
13A29GLU-1-0.866-0.93921.7590.1620.1620.0000.0000.0000.000
14A30ALA00.0480.03519.713-0.023-0.0230.0000.0000.0000.000
15A31TRP00.0470.01821.766-0.028-0.0280.0000.0000.0000.000
16A32GLU-1-0.969-0.96523.7010.1090.1090.0000.0000.0000.000
17A33ARG10.8050.88021.6820.0180.0180.0000.0000.0000.000
18A34ILE00.016-0.00420.819-0.012-0.0120.0000.0000.0000.000
19A35ARG10.8840.94425.147-0.108-0.1080.0000.0000.0000.000
20A36GLN0-0.051-0.02327.661-0.006-0.0060.0000.0000.0000.000
21A37ALA0-0.043-0.02926.781-0.008-0.0080.0000.0000.0000.000
22A38ILE0-0.024-0.00323.921-0.014-0.0140.0000.0000.0000.000
23A39PRO0-0.0280.00728.5660.0100.0100.0000.0000.0000.000
24A40ARG10.9040.96229.821-0.039-0.0390.0000.0000.0000.000
25A41GLU-1-0.874-0.94231.8900.0030.0030.0000.0000.0000.000
26A42LYS10.9520.98835.469-0.006-0.0060.0000.0000.0000.000
27A43THR0-0.008-0.01438.4210.0020.0020.0000.0000.0000.000
28A44ALA00.017-0.00639.986-0.004-0.0040.0000.0000.0000.000
29A45GLU-1-0.859-0.93637.752-0.018-0.0180.0000.0000.0000.000
30A46ALA00.0360.01735.563-0.005-0.0050.0000.0000.0000.000
31A47LYS10.9000.96436.2560.0270.0270.0000.0000.0000.000
32A48GLN0-0.065-0.04137.962-0.007-0.0070.0000.0000.0000.000
33A49ARG10.8560.92232.3930.0130.0130.0000.0000.0000.000
34A50ARG10.7820.86832.6220.0260.0260.0000.0000.0000.000
35A51ILE00.0290.03133.831-0.011-0.0110.0000.0000.0000.000
36A52GLU-1-0.925-0.95535.243-0.061-0.0610.0000.0000.0000.000
37A53LEU0-0.055-0.03428.547-0.009-0.0090.0000.0000.0000.000
38A54PHE00.0320.01230.724-0.011-0.0110.0000.0000.0000.000
39A55LYS10.9920.98231.9060.0700.0700.0000.0000.0000.000
40A56LYS10.8570.94429.7600.0830.0830.0000.0000.0000.000
41A57PHE0-0.017-0.00424.272-0.012-0.0120.0000.0000.0000.000
42A58ASP-1-0.809-0.89428.483-0.163-0.1630.0000.0000.0000.000
43A59LYS10.8790.93125.6030.2330.2330.0000.0000.0000.000
44A60ASN0-0.069-0.04129.2110.0100.0100.0000.0000.0000.000
45A61GLU-1-0.984-0.97632.894-0.106-0.1060.0000.0000.0000.000
46A62THR0-0.019-0.00232.4160.0070.0070.0000.0000.0000.000
47A63GLY0-0.026-0.02534.3460.0070.0070.0000.0000.0000.000
48A64LYS10.7640.89131.6730.1310.1310.0000.0000.0000.000
49A65LEU0-0.0060.00926.888-0.008-0.0080.0000.0000.0000.000
50A66CSO00.0330.00024.911-0.008-0.0080.0000.0000.0000.000
51A67TYR0-0.049-0.03016.023-0.032-0.0320.0000.0000.0000.000
52A68ASP-1-0.894-0.96219.738-0.460-0.4600.0000.0000.0000.000
53A69GLU-1-0.806-0.88921.169-0.233-0.2330.0000.0000.0000.000
54A70VAL0-0.002-0.00922.0420.0140.0140.0000.0000.0000.000
55A71TYR0-0.011-0.01013.911-0.012-0.0120.0000.0000.0000.000
56A72SER00.0060.00019.440-0.005-0.0050.0000.0000.0000.000
57A73GLY00.0360.02821.2110.0170.0170.0000.0000.0000.000
58A74CYS0-0.037-0.02319.7680.0400.0400.0000.0000.0000.000
59A75LEU00.0120.00316.1060.0290.0290.0000.0000.0000.000
60A76GLU-1-0.881-0.93019.449-0.229-0.2290.0000.0000.0000.000
61A77VAL0-0.083-0.03922.5530.0280.0280.0000.0000.0000.000
62A78LEU0-0.015-0.01222.5310.0210.0210.0000.0000.0000.000
63A79LYS10.8880.96120.4500.1770.1770.0000.0000.0000.000
64A80LEU00.009-0.00518.0520.0330.0330.0000.0000.0000.000
65A81ASP-1-0.861-0.93315.035-0.165-0.1650.0000.0000.0000.000
66A82GLU-1-0.872-0.91115.1510.0650.0650.0000.0000.0000.000
67A83PHE0-0.030-0.01216.7300.0660.0660.0000.0000.0000.000
68A84THR00.003-0.03512.2290.0290.0290.0000.0000.0000.000
69A85SER0-0.0010.0057.8990.0570.0570.0000.0000.0000.000
70A86ARG10.7710.8578.102-0.455-0.4550.0000.0000.0000.000
71A87VAL00.0940.04510.7660.0530.0530.0000.0000.0000.000
72A88ARG10.8740.9416.8472.0062.0060.0000.0000.0000.000
73A89ASP-1-0.857-0.91211.438-0.175-0.1750.0000.0000.0000.000
74A90ILE00.0460.03613.5130.0570.0570.0000.0000.0000.000
75A91THR0-0.010-0.01916.3010.0440.0440.0000.0000.0000.000
76A92LYS10.8500.91916.3290.3720.3720.0000.0000.0000.000
77A93ARG10.8720.92913.8060.0900.0900.0000.0000.0000.000
78A94ALA00.0460.01719.3220.0240.0240.0000.0000.0000.000
79A95PHE0-0.0070.00621.3760.0120.0120.0000.0000.0000.000
80A96ASP-1-0.823-0.89920.564-0.247-0.2470.0000.0000.0000.000
81A97LYS10.8810.94723.3720.0500.0500.0000.0000.0000.000
82A98SER0-0.036-0.02225.2400.0110.0110.0000.0000.0000.000
83A99ARG10.9130.95623.5110.2270.2270.0000.0000.0000.000
84A100THR0-0.081-0.02626.9450.0080.0080.0000.0000.0000.000
85A101LEU0-0.068-0.02929.4500.0080.0080.0000.0000.0000.000
86A102GLY00.0520.02131.3160.0080.0080.0000.0000.0000.000
87A103SER0-0.049-0.03132.7760.0060.0060.0000.0000.0000.000
88A104LYS10.8540.91433.1850.0320.0320.0000.0000.0000.000
89A105LEU0-0.042-0.02734.9810.0040.0040.0000.0000.0000.000
90A106GLU-1-0.905-0.94537.249-0.074-0.0740.0000.0000.0000.000
91A107ASN0-0.126-0.05438.8260.0050.0050.0000.0000.0000.000
92A108LYS10.9160.96938.2930.0760.0760.0000.0000.0000.000
93A109GLY00.003-0.00136.1960.0010.0010.0000.0000.0000.000
94A110SER0-0.005-0.01630.7260.0010.0010.0000.0000.0000.000
95A111GLU-1-0.894-0.93131.777-0.130-0.1300.0000.0000.0000.000
96A112ASP-1-0.942-0.98927.028-0.212-0.2120.0000.0000.0000.000
97A113PHE0-0.014-0.01827.021-0.027-0.0270.0000.0000.0000.000
98A114VAL0-0.045-0.02526.4040.0130.0130.0000.0000.0000.000
99A115GLU-1-0.774-0.87629.362-0.118-0.1180.0000.0000.0000.000
100A116PHE0-0.017-0.02732.0160.0040.0040.0000.0000.0000.000
101A117LEU0-0.0030.00833.0310.0040.0040.0000.0000.0000.000
102A118GLU-1-0.730-0.88929.220-0.097-0.0970.0000.0000.0000.000
103A119PHE00.010-0.00127.6600.0030.0030.0000.0000.0000.000
104A120ARG10.7880.87328.8220.0650.0650.0000.0000.0000.000
105A121LEU0-0.0020.00529.7160.0100.0100.0000.0000.0000.000
106A122MET0-0.064-0.02424.825-0.001-0.0010.0000.0000.0000.000
107A123LEU0-0.029-0.00525.1300.0070.0070.0000.0000.0000.000
108A124CYS00.0070.00426.4080.0110.0110.0000.0000.0000.000
109A125TYR00.0630.04020.6460.0120.0120.0000.0000.0000.000
110A126ILE0-0.022-0.01720.7880.0170.0170.0000.0000.0000.000
111A127TYR0-0.041-0.01722.5920.0280.0280.0000.0000.0000.000
112A128ASP-1-0.817-0.92324.8760.0510.0510.0000.0000.0000.000
113A129PHE00.0340.01316.3340.0190.0190.0000.0000.0000.000
114A130PHE0-0.010-0.01817.5570.0330.0330.0000.0000.0000.000
115A131GLU-1-0.830-0.91321.1940.1110.1110.0000.0000.0000.000
116A132LEU0-0.040-0.01622.3840.0230.0230.0000.0000.0000.000
117A133THR0-0.061-0.04216.9590.0390.0390.0000.0000.0000.000
118A134VAL0-0.017-0.00820.0370.0410.0410.0000.0000.0000.000
119A135MET0-0.0010.00721.9830.0190.0190.0000.0000.0000.000
120A136PHE00.000-0.01319.5860.0070.0070.0000.0000.0000.000
121A137ASP-1-0.748-0.85817.8440.5050.5050.0000.0000.0000.000
122A138GLU-1-0.990-0.97320.5320.2270.2270.0000.0000.0000.000
123A139ILE0-0.095-0.05522.209-0.015-0.0150.0000.0000.0000.000
124A140ASP-1-0.750-0.86816.4450.7680.7680.0000.0000.0000.000
125A141ALA00.0010.00619.8480.0160.0160.0000.0000.0000.000
126A142SER0-0.097-0.05015.8900.0090.0090.0000.0000.0000.000
127A143GLY0-0.023-0.00216.1160.0810.0810.0000.0000.0000.000
128A144ASN0-0.107-0.06412.0180.0960.0960.0000.0000.0000.000
129A145MET0-0.046-0.02712.0970.1980.1980.0000.0000.0000.000
130A146LEU0-0.058-0.01812.0860.0020.0020.0000.0000.0000.000
131A147VAL00.0000.01315.540-0.030-0.0300.0000.0000.0000.000
132A148ASP-1-0.779-0.89119.3000.3870.3870.0000.0000.0000.000
133A149GLU-1-0.865-0.92121.2400.1990.1990.0000.0000.0000.000
134A150GLU-1-0.864-0.92824.5970.2560.2560.0000.0000.0000.000
135A151GLU-1-0.809-0.91420.7320.4700.4700.0000.0000.0000.000
136A152PHE00.017-0.00422.270-0.028-0.0280.0000.0000.0000.000
137A153LYS10.7910.87424.576-0.237-0.2370.0000.0000.0000.000
138A154ARG10.8070.91025.056-0.328-0.3280.0000.0000.0000.000
139A155ALA00.0180.00625.111-0.013-0.0130.0000.0000.0000.000
140A156VAL0-0.018-0.00427.161-0.019-0.0190.0000.0000.0000.000
141A157PRO00.0180.01329.569-0.013-0.0130.0000.0000.0000.000
142A158LYS10.8500.92527.897-0.212-0.2120.0000.0000.0000.000
143A159LEU00.0390.01425.689-0.011-0.0110.0000.0000.0000.000
144A160GLU-1-0.916-0.95129.7560.0930.0930.0000.0000.0000.000
145A161ALA0-0.048-0.01733.327-0.011-0.0110.0000.0000.0000.000
146A162TRP0-0.067-0.04027.049-0.005-0.0050.0000.0000.0000.000
147A163GLY0-0.012-0.00432.040-0.011-0.0110.0000.0000.0000.000
148A164ALA0-0.016-0.01329.035-0.009-0.0090.0000.0000.0000.000
149A165LYS10.8580.91530.536-0.077-0.0770.0000.0000.0000.000
150A166VAL00.0080.01728.261-0.003-0.0030.0000.0000.0000.000
151A167GLU-1-0.898-0.94331.2820.0810.0810.0000.0000.0000.000
152A168ASP-1-0.877-0.94132.2810.1180.1180.0000.0000.0000.000
153A169PRO00.008-0.01229.3030.0070.0070.0000.0000.0000.000
154A170ALA0-0.011-0.00527.9950.0160.0160.0000.0000.0000.000
155A171ALA0-0.0060.00027.8660.0110.0110.0000.0000.0000.000
156A172LEU00.0320.01625.1190.0030.0030.0000.0000.0000.000
157A173PHE0-0.047-0.01021.6900.0040.0040.0000.0000.0000.000
158A174LYS10.9580.96822.820-0.118-0.1180.0000.0000.0000.000
159A175GLU-1-0.998-0.98523.2170.0890.0890.0000.0000.0000.000
160A176LEU0-0.023-0.02920.318-0.009-0.0090.0000.0000.0000.000
161A177ASP-1-0.769-0.85118.2020.4220.4220.0000.0000.0000.000
162A178LYS10.7920.88016.579-0.128-0.1280.0000.0000.0000.000
163A179ASN0-0.075-0.04413.906-0.094-0.0940.0000.0000.0000.000
164A180GLY0-0.0180.01117.4910.0050.0050.0000.0000.0000.000
165A181THR0-0.123-0.08014.4280.0390.0390.0000.0000.0000.000
166A182GLY0-0.007-0.01017.8040.0330.0330.0000.0000.0000.000
167A183SER0-0.056-0.03416.3070.0370.0370.0000.0000.0000.000
168A184VAL0-0.0240.00117.684-0.014-0.0140.0000.0000.0000.000
169A185THR00.0280.00812.4690.0250.0250.0000.0000.0000.000
170A186PHE00.0810.02114.744-0.084-0.0840.0000.0000.0000.000
171A187ASP-1-0.831-0.88512.5580.1320.1320.0000.0000.0000.000
172A188GLU-1-0.841-0.91415.5140.0570.0570.0000.0000.0000.000
173A189PHE00.0220.01317.790-0.051-0.0510.0000.0000.0000.000
174A190ALA00.0260.01118.807-0.036-0.0360.0000.0000.0000.000
175A191ALA00.0000.00518.887-0.043-0.0430.0000.0000.0000.000
176A192TRP00.0070.00120.832-0.024-0.0240.0000.0000.0000.000
177A193ALA00.0250.01723.602-0.018-0.0180.0000.0000.0000.000
178A194SER00.019-0.02122.825-0.015-0.0150.0000.0000.0000.000
179A195ALA0-0.066-0.02424.825-0.019-0.0190.0000.0000.0000.000
180A196VAL0-0.012-0.00226.448-0.011-0.0110.0000.0000.0000.000
181A197LYS10.8640.94728.457-0.057-0.0570.0000.0000.0000.000
182A198LEU00.0150.00327.241-0.009-0.0090.0000.0000.0000.000
183A199ASP-1-0.833-0.90129.976-0.029-0.0290.0000.0000.0000.000
184A200ALA0-0.051-0.01032.253-0.002-0.0020.0000.0000.0000.000
185A201ASP-1-0.904-0.95532.7200.0200.0200.0000.0000.0000.000
186A202GLY0-0.042-0.00733.812-0.003-0.0030.0000.0000.0000.000
187A203ASP-1-0.743-0.86534.045-0.050-0.0500.0000.0000.0000.000
188A204PRO00.0190.01933.2400.0050.0050.0000.0000.0000.000
189A205ASP-1-0.790-0.93536.316-0.042-0.0420.0000.0000.0000.000
190A206ASN0-0.0300.00238.8660.0000.0000.0000.0000.0000.000
191A207VAL0-0.065-0.02541.1840.0050.0050.0000.0000.0000.000
192A208PRO00.0290.01442.8490.0020.0020.0000.0000.0000.000