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: MV9MZ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2248521.48428
FMO2-HF: Nuclear repulsion 2170877.761145
FMO2-HF: Total energy -77643.723135
FMO2-MP2: Total energy -77870.604544


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.
-1.9120.369-0.007-1.152-1.1220.001
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 : -0.025 / q_NPA : -0.032
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].
3A19LYS10.8640.9373.618-4.774-2.493-0.007-1.152-1.1220.001
4A20ASP-1-0.703-0.8135.357-0.920-0.9200.0000.0000.0000.000
5A21GLY0-0.0140.0018.0840.3870.3870.0000.0000.0000.000
6A22LYS10.7500.8908.7520.0110.0110.0000.0000.0000.000
7A23LYS10.8610.90512.397-0.297-0.2970.0000.0000.0000.000
8A24ALA00.0930.04614.896-0.078-0.0780.0000.0000.0000.000
9A25LYS10.7680.86518.500-0.209-0.2090.0000.0000.0000.000
10A26ASP-1-0.787-0.88415.0580.2820.2820.0000.0000.0000.000
11A27ARG10.8100.86912.995-0.447-0.4470.0000.0000.0000.000
12A28LYS10.8710.93118.813-0.151-0.1510.0000.0000.0000.000
13A29GLU-1-0.810-0.88922.1050.1150.1150.0000.0000.0000.000
14A30ALA00.0310.02319.653-0.019-0.0190.0000.0000.0000.000
15A31TRP00.0430.01621.664-0.025-0.0250.0000.0000.0000.000
16A32GLU-1-0.849-0.89023.4610.0790.0790.0000.0000.0000.000
17A33ARG10.7720.86921.7550.0820.0820.0000.0000.0000.000
18A34ILE00.016-0.01020.685-0.008-0.0080.0000.0000.0000.000
19A35ARG10.8280.91124.973-0.065-0.0650.0000.0000.0000.000
20A36GLN0-0.050-0.02427.527-0.001-0.0010.0000.0000.0000.000
21A37ALA0-0.038-0.02426.453-0.006-0.0060.0000.0000.0000.000
22A38ILE0-0.0090.00923.442-0.015-0.0150.0000.0000.0000.000
23A39PRO0-0.0320.00028.1100.0120.0120.0000.0000.0000.000
24A40ARG10.8550.92528.985-0.008-0.0080.0000.0000.0000.000
25A41GLU-1-0.799-0.90331.305-0.029-0.0290.0000.0000.0000.000
26A42LYS10.9240.97234.8750.0150.0150.0000.0000.0000.000
27A43THR0-0.014-0.01737.7050.0020.0020.0000.0000.0000.000
28A44ALA00.0280.00339.437-0.005-0.0050.0000.0000.0000.000
29A45GLU-1-0.847-0.91637.708-0.041-0.0410.0000.0000.0000.000
30A46ALA00.0540.03235.255-0.006-0.0060.0000.0000.0000.000
31A47LYS10.8660.94535.7750.0440.0440.0000.0000.0000.000
32A48GLN0-0.075-0.04037.438-0.006-0.0060.0000.0000.0000.000
33A49ARG10.7960.87432.3080.0360.0360.0000.0000.0000.000
34A50ARG10.7890.86432.2080.0480.0480.0000.0000.0000.000
35A51ILE00.0030.00533.414-0.012-0.0120.0000.0000.0000.000
36A52GLU-1-0.913-0.95535.114-0.085-0.0850.0000.0000.0000.000
37A53LEU0-0.054-0.01027.938-0.009-0.0090.0000.0000.0000.000
38A54PHE00.0510.02330.144-0.013-0.0130.0000.0000.0000.000
39A55LYS10.9950.98330.9880.0900.0900.0000.0000.0000.000
40A56LYS10.8340.92529.1030.1130.1130.0000.0000.0000.000
41A57PHE0-0.0090.00323.537-0.014-0.0140.0000.0000.0000.000
42A58ASP-1-0.785-0.87727.840-0.187-0.1870.0000.0000.0000.000
43A59LYS10.8300.88124.8830.2820.2820.0000.0000.0000.000
44A60ASN0-0.064-0.03228.7420.0090.0090.0000.0000.0000.000
45A61GLU-1-0.996-0.98932.497-0.120-0.1200.0000.0000.0000.000
46A62THR0-0.018-0.00232.1990.0070.0070.0000.0000.0000.000
47A63GLY0-0.016-0.02933.4920.0090.0090.0000.0000.0000.000
48A64LYS10.7500.88031.4470.1490.1490.0000.0000.0000.000
49A65LEU00.0120.02926.537-0.012-0.0120.0000.0000.0000.000
50A66CSO00.049-0.00324.429-0.005-0.0050.0000.0000.0000.000
51A67TYR0-0.068-0.04115.039-0.038-0.0380.0000.0000.0000.000
52A68ASP-1-0.871-0.95018.889-0.539-0.5390.0000.0000.0000.000
53A69GLU-1-0.811-0.88020.555-0.265-0.2650.0000.0000.0000.000
54A70VAL0-0.029-0.01921.6360.0180.0180.0000.0000.0000.000
55A71TYR0-0.026-0.01313.085-0.026-0.0260.0000.0000.0000.000
56A72SER00.011-0.00118.820-0.008-0.0080.0000.0000.0000.000
57A73GLY00.0540.02820.6520.0160.0160.0000.0000.0000.000
58A74CYS0-0.049-0.03718.9690.0440.0440.0000.0000.0000.000
59A75LEU00.0070.01515.5200.0230.0230.0000.0000.0000.000
60A76GLU-1-0.839-0.91919.045-0.261-0.2610.0000.0000.0000.000
61A77VAL0-0.063-0.01822.3420.0330.0330.0000.0000.0000.000
62A78LEU0-0.008-0.00422.0700.0230.0230.0000.0000.0000.000
63A79LYS10.8820.95320.1490.2380.2380.0000.0000.0000.000
64A80LEU00.0160.00817.5410.0310.0310.0000.0000.0000.000
65A81ASP-1-0.849-0.92614.722-0.263-0.2630.0000.0000.0000.000
66A82GLU-1-0.846-0.89815.180-0.012-0.0120.0000.0000.0000.000
67A83PHE0-0.011-0.00116.5630.0590.0590.0000.0000.0000.000
68A84THR0-0.026-0.03811.9890.0270.0270.0000.0000.0000.000
69A85SER0-0.058-0.0638.541-0.101-0.1010.0000.0000.0000.000
70A86ARG10.8020.8717.920-0.293-0.2930.0000.0000.0000.000
71A87VAL00.0780.03610.4670.0260.0260.0000.0000.0000.000
72A88ARG10.8790.9416.4642.3262.3260.0000.0000.0000.000
73A89ASP-1-0.880-0.90910.962-0.300-0.3000.0000.0000.0000.000
74A90ILE00.0380.02313.0070.0790.0790.0000.0000.0000.000
75A91THR00.010-0.00815.8990.0600.0600.0000.0000.0000.000
76A92LYS10.8280.90315.5990.4130.4130.0000.0000.0000.000
77A93ARG10.8520.91013.1870.1890.1890.0000.0000.0000.000
78A94ALA00.0420.01918.6550.0350.0350.0000.0000.0000.000
79A95PHE00.0250.01620.7340.0180.0180.0000.0000.0000.000
80A96ASP-1-0.796-0.85620.087-0.274-0.2740.0000.0000.0000.000
81A97LYS10.7920.90722.9210.0700.0700.0000.0000.0000.000
82A98SER0-0.034-0.03124.8760.0130.0130.0000.0000.0000.000
83A99ARG10.8790.92122.8220.2590.2590.0000.0000.0000.000
84A100THR0-0.063-0.03226.2120.0120.0120.0000.0000.0000.000
85A101LEU0-0.058-0.02028.8630.0100.0100.0000.0000.0000.000
86A102GLY00.0590.01730.7730.0090.0090.0000.0000.0000.000
87A103SER0-0.049-0.02332.2000.0080.0080.0000.0000.0000.000
88A104LYS10.8460.91032.4050.0480.0480.0000.0000.0000.000
89A105LEU0-0.045-0.02634.4420.0060.0060.0000.0000.0000.000
90A106GLU-1-0.890-0.95336.283-0.082-0.0820.0000.0000.0000.000
91A107ASN0-0.120-0.05338.5460.0060.0060.0000.0000.0000.000
92A108LYS10.8770.95237.1800.0830.0830.0000.0000.0000.000
93A109GLY00.0240.01335.3830.0020.0020.0000.0000.0000.000
94A110SER0-0.031-0.03229.8700.0030.0030.0000.0000.0000.000
95A111GLU-1-0.893-0.93131.292-0.144-0.1440.0000.0000.0000.000
96A112ASP-1-0.920-0.97126.525-0.232-0.2320.0000.0000.0000.000
97A113PHE0-0.0130.00126.217-0.030-0.0300.0000.0000.0000.000
98A114VAL0-0.046-0.03126.0150.0110.0110.0000.0000.0000.000
99A115GLU-1-0.806-0.89629.036-0.135-0.1350.0000.0000.0000.000
100A116PHE0-0.043-0.04231.4990.0000.0000.0000.0000.0000.000
101A117LEU0-0.0020.00733.0140.0040.0040.0000.0000.0000.000
102A118GLU-1-0.755-0.90228.484-0.121-0.1210.0000.0000.0000.000
103A119PHE00.0070.00926.837-0.001-0.0010.0000.0000.0000.000
104A120ARG10.7850.87228.5400.0840.0840.0000.0000.0000.000
105A121LEU0-0.0040.00529.1170.0070.0070.0000.0000.0000.000
106A122MET0-0.032-0.01224.331-0.005-0.0050.0000.0000.0000.000
107A123LEU0-0.0170.00424.7830.0050.0050.0000.0000.0000.000
108A124CYS0-0.0030.00426.2480.0100.0100.0000.0000.0000.000
109A125TYR00.0410.02620.2490.0090.0090.0000.0000.0000.000
110A126ILE0-0.007-0.01320.5650.0110.0110.0000.0000.0000.000
111A127TYR0-0.050-0.02722.2690.0210.0210.0000.0000.0000.000
112A128ASP-1-0.790-0.89424.5250.0190.0190.0000.0000.0000.000
113A129PHE00.0580.02515.9130.0170.0170.0000.0000.0000.000
114A130PHE0-0.023-0.01417.7690.0270.0270.0000.0000.0000.000
115A131GLU-1-0.808-0.90721.0150.0730.0730.0000.0000.0000.000
116A132LEU0-0.026-0.00922.2320.0250.0250.0000.0000.0000.000
117A133THR0-0.061-0.03716.6270.0360.0360.0000.0000.0000.000
118A134VAL0-0.027-0.02119.5830.0420.0420.0000.0000.0000.000
119A135MET0-0.0210.00221.5750.0200.0200.0000.0000.0000.000
120A136PHE00.005-0.00619.2310.0090.0090.0000.0000.0000.000
121A137ASP-1-0.755-0.86817.4620.4220.4220.0000.0000.0000.000
122A138GLU-1-0.905-0.92220.1960.1810.1810.0000.0000.0000.000
123A139ILE0-0.093-0.04422.336-0.011-0.0110.0000.0000.0000.000
124A140ASP-1-0.697-0.82616.3750.7080.7080.0000.0000.0000.000
125A141ALA0-0.032-0.02020.0670.0070.0070.0000.0000.0000.000
126A142SER0-0.115-0.07916.8290.0390.0390.0000.0000.0000.000
127A143GLY0-0.032-0.00516.1460.0810.0810.0000.0000.0000.000
128A144ASN0-0.043-0.02112.1730.1010.1010.0000.0000.0000.000
129A145MET0-0.038-0.02011.4890.3090.3090.0000.0000.0000.000
130A146LEU0-0.043-0.01012.156-0.002-0.0020.0000.0000.0000.000
131A147VAL00.0000.00715.410-0.043-0.0430.0000.0000.0000.000
132A148ASP-1-0.734-0.88619.1940.3560.3560.0000.0000.0000.000
133A149GLU-1-0.864-0.90921.1990.1980.1980.0000.0000.0000.000
134A150GLU-1-0.868-0.92324.5550.2360.2360.0000.0000.0000.000
135A151GLU-1-0.835-0.91720.5260.4480.4480.0000.0000.0000.000
136A152PHE00.0190.00622.056-0.027-0.0270.0000.0000.0000.000
137A153LYS10.7680.86024.421-0.233-0.2330.0000.0000.0000.000
138A154ARG10.7780.87024.635-0.313-0.3130.0000.0000.0000.000
139A155ALA00.0040.01124.663-0.013-0.0130.0000.0000.0000.000
140A156VAL0-0.0040.00826.781-0.018-0.0180.0000.0000.0000.000
141A157PRO00.0150.01129.530-0.013-0.0130.0000.0000.0000.000
142A158LYS10.7880.87827.742-0.178-0.1780.0000.0000.0000.000
143A159LEU00.0480.01725.253-0.013-0.0130.0000.0000.0000.000
144A160GLU-1-0.930-0.96229.4330.0800.0800.0000.0000.0000.000
145A161ALA0-0.049-0.01933.042-0.010-0.0100.0000.0000.0000.000
146A162TRP0-0.075-0.04426.548-0.005-0.0050.0000.0000.0000.000
147A163GLY0-0.014-0.01032.096-0.011-0.0110.0000.0000.0000.000
148A164ALA0-0.042-0.02128.423-0.009-0.0090.0000.0000.0000.000
149A165LYS10.8480.89629.986-0.065-0.0650.0000.0000.0000.000
150A166VAL00.0090.01027.772-0.004-0.0040.0000.0000.0000.000
151A167GLU-1-0.886-0.92830.7310.0750.0750.0000.0000.0000.000
152A168ASP-1-0.836-0.91531.8750.1180.1180.0000.0000.0000.000
153A169PRO0-0.010-0.02328.8990.0080.0080.0000.0000.0000.000
154A170ALA0-0.0180.00027.8570.0200.0200.0000.0000.0000.000
155A171ALA0-0.020-0.01627.6910.0120.0120.0000.0000.0000.000
156A172LEU00.0430.02024.8660.0070.0070.0000.0000.0000.000
157A173PHE0-0.0260.00021.6270.0060.0060.0000.0000.0000.000
158A174LYS10.9420.96022.569-0.126-0.1260.0000.0000.0000.000
159A175GLU-1-0.998-0.98623.2730.0850.0850.0000.0000.0000.000
160A176LEU0-0.010-0.01920.015-0.010-0.0100.0000.0000.0000.000
161A177ASP-1-0.761-0.84717.9560.4560.4560.0000.0000.0000.000
162A178LYS10.7620.86016.457-0.127-0.1270.0000.0000.0000.000
163A179ASN0-0.082-0.04014.137-0.067-0.0670.0000.0000.0000.000
164A180GLY0-0.0250.00517.4620.0100.0100.0000.0000.0000.000
165A181THR0-0.101-0.07714.3690.0330.0330.0000.0000.0000.000
166A182GLY00.0070.00817.7000.0290.0290.0000.0000.0000.000
167A183SER0-0.060-0.04816.7030.0300.0300.0000.0000.0000.000
168A184VAL0-0.0210.01817.596-0.001-0.0010.0000.0000.0000.000
169A185THR00.021-0.00212.4400.0250.0250.0000.0000.0000.000
170A186PHE00.0570.01014.418-0.077-0.0770.0000.0000.0000.000
171A187ASP-1-0.816-0.88412.1190.0470.0470.0000.0000.0000.000
172A188GLU-1-0.815-0.89215.2580.0520.0520.0000.0000.0000.000
173A189PHE00.0330.01717.600-0.048-0.0480.0000.0000.0000.000
174A190ALA00.0390.02818.457-0.032-0.0320.0000.0000.0000.000
175A191ALA0-0.0080.00018.394-0.042-0.0420.0000.0000.0000.000
176A192TRP00.0270.00920.343-0.023-0.0230.0000.0000.0000.000
177A193ALA00.0400.02023.292-0.018-0.0180.0000.0000.0000.000
178A194SER00.013-0.02722.475-0.015-0.0150.0000.0000.0000.000
179A195ALA0-0.070-0.03024.108-0.019-0.0190.0000.0000.0000.000
180A196VAL00.0120.01425.823-0.011-0.0110.0000.0000.0000.000
181A197LYS10.8480.92927.898-0.026-0.0260.0000.0000.0000.000
182A198LEU0-0.014-0.01126.875-0.006-0.0060.0000.0000.0000.000
183A199ASP-1-0.813-0.89129.699-0.045-0.0450.0000.0000.0000.000
184A200ALA0-0.0330.00632.0800.0000.0000.0000.0000.0000.000
185A201ASP-1-0.846-0.91732.1940.0000.0000.0000.0000.0000.000
186A202GLY0-0.035-0.00733.453-0.003-0.0030.0000.0000.0000.000
187A203ASP-1-0.740-0.84833.450-0.071-0.0710.0000.0000.0000.000
188A204PRO00.0050.00832.7460.0060.0060.0000.0000.0000.000
189A205ASP-1-0.764-0.92035.815-0.063-0.0630.0000.0000.0000.000
190A206ASN0-0.0380.00238.3930.0030.0030.0000.0000.0000.000
191A207VAL00.0080.00140.6070.0050.0050.0000.0000.0000.000
192A208PRO00.0020.01142.4380.0010.0010.0000.0000.0000.000