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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: LZ7L9

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240164.199975
FMO2-HF: Nuclear repulsion 2162523.283293
FMO2-HF: Total energy -77640.916682
FMO2-MP2: Total energy -77867.935244


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.
-4.726-1.780.123-1.447-1.6220.007
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 : -0.029 / q_NPA : -0.036
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].
3A19LYS10.9130.9463.336-7.065-4.1380.124-1.443-1.6080.007
4A20ASP-1-0.768-0.8795.344-0.723-0.704-0.001-0.004-0.0140.000
5A21GLY0-0.009-0.0018.2160.3630.3630.0000.0000.0000.000
6A22LYS10.8610.9608.874-0.201-0.2010.0000.0000.0000.000
7A23LYS10.9180.97912.585-0.534-0.5340.0000.0000.0000.000
8A24ALA00.0970.03314.863-0.074-0.0740.0000.0000.0000.000
9A25LYS10.8920.93818.369-0.325-0.3250.0000.0000.0000.000
10A26ASP-1-0.798-0.89915.1580.3860.3860.0000.0000.0000.000
11A27ARG10.7920.86413.416-0.572-0.5720.0000.0000.0000.000
12A28LYS10.9340.96318.831-0.227-0.2270.0000.0000.0000.000
13A29GLU-1-0.916-0.97121.7790.1730.1730.0000.0000.0000.000
14A30ALA00.0620.04419.703-0.024-0.0240.0000.0000.0000.000
15A31TRP00.0290.00221.730-0.028-0.0280.0000.0000.0000.000
16A32GLU-1-1.038-1.01423.6630.1010.1010.0000.0000.0000.000
17A33ARG10.8150.88821.5660.0010.0010.0000.0000.0000.000
18A34ILE00.0150.00020.711-0.014-0.0140.0000.0000.0000.000
19A35ARG10.8870.95525.107-0.109-0.1090.0000.0000.0000.000
20A36GLN0-0.028-0.01127.621-0.004-0.0040.0000.0000.0000.000
21A37ALA0-0.021-0.00726.741-0.009-0.0090.0000.0000.0000.000
22A38ILE0-0.021-0.00423.952-0.014-0.0140.0000.0000.0000.000
23A39PRO0-0.0190.00528.5240.0100.0100.0000.0000.0000.000
24A40ARG11.0091.01229.981-0.035-0.0350.0000.0000.0000.000
25A41GLU-1-0.914-0.96031.8780.0050.0050.0000.0000.0000.000
26A42LYS10.9771.00335.441-0.005-0.0050.0000.0000.0000.000
27A43THR0-0.017-0.01938.4210.0020.0020.0000.0000.0000.000
28A44ALA00.018-0.00739.976-0.004-0.0040.0000.0000.0000.000
29A45GLU-1-0.921-0.96938.767-0.018-0.0180.0000.0000.0000.000
30A46ALA00.0450.02335.526-0.004-0.0040.0000.0000.0000.000
31A47LYS10.9530.99236.2170.0260.0260.0000.0000.0000.000
32A48GLN0-0.017-0.00437.962-0.006-0.0060.0000.0000.0000.000
33A49ARG10.8600.92231.8530.0130.0130.0000.0000.0000.000
34A50ARG10.7850.86632.6810.0280.0280.0000.0000.0000.000
35A51ILE00.0340.03433.744-0.010-0.0100.0000.0000.0000.000
36A52GLU-1-0.982-0.99935.108-0.055-0.0550.0000.0000.0000.000
37A53LEU0-0.035-0.03228.884-0.008-0.0080.0000.0000.0000.000
38A54PHE00.0180.01230.596-0.011-0.0110.0000.0000.0000.000
39A55LYS10.9800.97931.7590.0660.0660.0000.0000.0000.000
40A56LYS10.8730.95129.6560.0790.0790.0000.0000.0000.000
41A57PHE0-0.038-0.01024.009-0.011-0.0110.0000.0000.0000.000
42A58ASP-1-0.805-0.88628.337-0.162-0.1620.0000.0000.0000.000
43A59LYS10.9510.97525.8860.2140.2140.0000.0000.0000.000
44A60ASN0-0.037-0.02429.7030.0120.0120.0000.0000.0000.000
45A61GLU-1-0.981-0.97232.739-0.106-0.1060.0000.0000.0000.000
46A62THR0-0.038-0.00732.1670.0070.0070.0000.0000.0000.000
47A63GLY0-0.035-0.03834.1710.0060.0060.0000.0000.0000.000
48A64LYS10.8360.92231.4890.1340.1340.0000.0000.0000.000
49A65LEU0-0.0020.01226.824-0.008-0.0080.0000.0000.0000.000
50A66CSO00.0250.00724.782-0.009-0.0090.0000.0000.0000.000
51A67TYR0-0.048-0.03416.110-0.035-0.0350.0000.0000.0000.000
52A68ASP-1-0.899-0.96819.931-0.424-0.4240.0000.0000.0000.000
53A69GLU-1-0.822-0.91220.982-0.224-0.2240.0000.0000.0000.000
54A70VAL00.0100.00121.5500.0140.0140.0000.0000.0000.000
55A71TYR0-0.009-0.01013.962-0.007-0.0070.0000.0000.0000.000
56A72SER00.0330.02019.3060.0010.0010.0000.0000.0000.000
57A73GLY00.0080.01721.0830.0190.0190.0000.0000.0000.000
58A74CYS0-0.038-0.02619.7010.0370.0370.0000.0000.0000.000
59A75LEU00.002-0.00515.7740.0320.0320.0000.0000.0000.000
60A76GLU-1-0.943-0.97419.362-0.231-0.2310.0000.0000.0000.000
61A77VAL0-0.100-0.05622.4890.0290.0290.0000.0000.0000.000
62A78LEU0-0.030-0.02022.5910.0210.0210.0000.0000.0000.000
63A79LYS10.9100.98920.4480.1500.1500.0000.0000.0000.000
64A80LEU00.019-0.00418.0650.0330.0330.0000.0000.0000.000
65A81ASP-1-0.878-0.94714.829-0.154-0.1540.0000.0000.0000.000
66A82GLU-1-0.877-0.91015.1140.0880.0880.0000.0000.0000.000
67A83PHE0-0.059-0.02916.6190.0660.0660.0000.0000.0000.000
68A84THR00.021-0.01112.1730.0220.0220.0000.0000.0000.000
69A85SER0-0.0020.0097.7880.0460.0460.0000.0000.0000.000
70A86ARG10.7860.8587.996-0.347-0.3470.0000.0000.0000.000
71A87VAL00.0870.04610.7660.0440.0440.0000.0000.0000.000
72A88ARG10.9861.0056.6811.8421.8420.0000.0000.0000.000
73A89ASP-1-0.886-0.93611.438-0.231-0.2310.0000.0000.0000.000
74A90ILE00.0390.03713.5130.0540.0540.0000.0000.0000.000
75A91THR00.003-0.00116.3010.0420.0420.0000.0000.0000.000
76A92LYS10.9410.97114.9430.5630.5630.0000.0000.0000.000
77A93ARG10.8690.95213.7910.1070.1070.0000.0000.0000.000
78A94ALA00.0430.01719.3580.0240.0240.0000.0000.0000.000
79A95PHE0-0.0240.00021.3810.0120.0120.0000.0000.0000.000
80A96ASP-1-0.858-0.92620.809-0.256-0.2560.0000.0000.0000.000
81A97LYS10.9280.97423.4150.0780.0780.0000.0000.0000.000
82A98SER0-0.030-0.01725.2830.0120.0120.0000.0000.0000.000
83A99ARG10.9310.96523.7600.2330.2330.0000.0000.0000.000
84A100THR0-0.104-0.03627.0380.0080.0080.0000.0000.0000.000
85A101LEU0-0.060-0.02729.5030.0080.0080.0000.0000.0000.000
86A102GLY00.0420.01631.3390.0080.0080.0000.0000.0000.000
87A103SER0-0.021-0.01632.8570.0070.0070.0000.0000.0000.000
88A104LYS10.9430.97933.4810.0450.0450.0000.0000.0000.000
89A105LEU0-0.029-0.02234.8950.0050.0050.0000.0000.0000.000
90A106GLU-1-0.921-0.95236.666-0.080-0.0800.0000.0000.0000.000
91A107ASN0-0.106-0.03838.8620.0030.0030.0000.0000.0000.000
92A108LYS10.9130.95738.4840.0780.0780.0000.0000.0000.000
93A109GLY0-0.006-0.00336.3540.0010.0010.0000.0000.0000.000
94A110SER0-0.006-0.02030.9930.0010.0010.0000.0000.0000.000
95A111GLU-1-0.858-0.90731.955-0.135-0.1350.0000.0000.0000.000
96A112ASP-1-0.980-1.01127.157-0.216-0.2160.0000.0000.0000.000
97A113PHE00.019-0.00727.032-0.026-0.0260.0000.0000.0000.000
98A114VAL0-0.041-0.01626.6670.0130.0130.0000.0000.0000.000
99A115GLU-1-0.840-0.91729.188-0.113-0.1130.0000.0000.0000.000
100A116PHE0-0.026-0.03131.8120.0030.0030.0000.0000.0000.000
101A117LEU00.0180.02332.9710.0040.0040.0000.0000.0000.000
102A118GLU-1-0.728-0.88829.220-0.102-0.1020.0000.0000.0000.000
103A119PHE00.000-0.00127.4190.0030.0030.0000.0000.0000.000
104A120ARG10.7820.86528.8220.0670.0670.0000.0000.0000.000
105A121LEU00.0120.01029.7790.0100.0100.0000.0000.0000.000
106A122MET0-0.050-0.02824.405-0.003-0.0030.0000.0000.0000.000
107A123LEU0-0.047-0.01725.1300.0070.0070.0000.0000.0000.000
108A124CYS0-0.008-0.00626.4080.0130.0130.0000.0000.0000.000
109A125TYR00.0800.04920.5110.0110.0110.0000.0000.0000.000
110A126ILE0-0.024-0.01720.9410.0160.0160.0000.0000.0000.000
111A127TYR0-0.051-0.02622.5920.0280.0280.0000.0000.0000.000
112A128ASP-1-0.855-0.93824.8370.0390.0390.0000.0000.0000.000
113A129PHE0-0.001-0.00616.4210.0180.0180.0000.0000.0000.000
114A130PHE00.002-0.02517.5260.0310.0310.0000.0000.0000.000
115A131GLU-1-0.854-0.92321.1560.1120.1120.0000.0000.0000.000
116A132LEU0-0.053-0.02122.3310.0230.0230.0000.0000.0000.000
117A133THR0-0.043-0.02916.7940.0400.0400.0000.0000.0000.000
118A134VAL0-0.024-0.00820.0370.0420.0420.0000.0000.0000.000
119A135MET00.0070.01121.9500.0180.0180.0000.0000.0000.000
120A136PHE0-0.008-0.01219.5500.0050.0050.0000.0000.0000.000
121A137ASP-1-0.730-0.85217.9950.4840.4840.0000.0000.0000.000
122A138GLU-1-1.081-1.02620.5320.2290.2290.0000.0000.0000.000
123A139ILE0-0.120-0.06822.493-0.016-0.0160.0000.0000.0000.000
124A140ASP-1-0.751-0.88016.5150.7180.7180.0000.0000.0000.000
125A141ALA00.0070.01319.8480.0170.0170.0000.0000.0000.000
126A142SER0-0.110-0.05116.1070.0330.0330.0000.0000.0000.000
127A143GLY0-0.0130.00316.1160.0790.0790.0000.0000.0000.000
128A144ASN0-0.083-0.05012.0790.0860.0860.0000.0000.0000.000
129A145MET0-0.050-0.03112.0970.1840.1840.0000.0000.0000.000
130A146LEU0-0.049-0.01712.630-0.010-0.0100.0000.0000.0000.000
131A147VAL00.0040.01515.540-0.026-0.0260.0000.0000.0000.000
132A148ASP-1-0.775-0.88819.3000.3680.3680.0000.0000.0000.000
133A149GLU-1-0.947-0.98321.2400.1900.1900.0000.0000.0000.000
134A150GLU-1-0.952-0.98224.6340.2410.2410.0000.0000.0000.000
135A151GLU-1-0.869-0.94720.7600.4420.4420.0000.0000.0000.000
136A152PHE00.0200.00122.494-0.026-0.0260.0000.0000.0000.000
137A153LYS10.8930.94324.576-0.211-0.2110.0000.0000.0000.000
138A154ARG10.9070.97124.930-0.306-0.3060.0000.0000.0000.000
139A155ALA00.016-0.00325.236-0.011-0.0110.0000.0000.0000.000
140A156VAL0-0.0130.00427.161-0.018-0.0180.0000.0000.0000.000
141A157PRO00.0300.02029.569-0.011-0.0110.0000.0000.0000.000
142A158LYS10.8850.94827.964-0.193-0.1930.0000.0000.0000.000
143A159LEU00.0520.02425.625-0.009-0.0090.0000.0000.0000.000
144A160GLU-1-0.900-0.94129.7560.0880.0880.0000.0000.0000.000
145A161ALA0-0.049-0.01733.327-0.010-0.0100.0000.0000.0000.000
146A162TRP0-0.052-0.02427.128-0.005-0.0050.0000.0000.0000.000
147A163GLY0-0.022-0.01332.040-0.011-0.0110.0000.0000.0000.000
148A164ALA00.0120.00929.074-0.009-0.0090.0000.0000.0000.000
149A165LYS10.9010.93630.584-0.068-0.0680.0000.0000.0000.000
150A166VAL00.0170.02328.300-0.004-0.0040.0000.0000.0000.000
151A167GLU-1-0.994-1.00131.3290.0710.0710.0000.0000.0000.000
152A168ASP-1-0.849-0.92532.2670.1000.1000.0000.0000.0000.000
153A169PRO00.004-0.01429.3470.0060.0060.0000.0000.0000.000
154A170ALA0-0.022-0.01528.0370.0150.0150.0000.0000.0000.000
155A171ALA00.0030.01027.9060.0100.0100.0000.0000.0000.000
156A172LEU00.0360.02125.0850.0010.0010.0000.0000.0000.000
157A173PHE0-0.052-0.01721.6510.0000.0000.0000.0000.0000.000
158A174LYS10.9670.97022.860-0.097-0.0970.0000.0000.0000.000
159A175GLU-1-0.995-0.98123.2550.0660.0660.0000.0000.0000.000
160A176LEU0-0.018-0.02820.315-0.011-0.0110.0000.0000.0000.000
161A177ASP-1-0.792-0.86018.5630.3570.3570.0000.0000.0000.000
162A178LYS10.8750.93616.618-0.065-0.0650.0000.0000.0000.000
163A179ASN0-0.085-0.04713.909-0.090-0.0900.0000.0000.0000.000
164A180GLY0-0.0100.01317.5190.0030.0030.0000.0000.0000.000
165A181THR0-0.126-0.07414.4360.0350.0350.0000.0000.0000.000
166A182GLY00.015-0.00117.8310.0330.0330.0000.0000.0000.000
167A183SER0-0.045-0.02316.2640.0410.0410.0000.0000.0000.000
168A184VAL0-0.030-0.00617.722-0.016-0.0160.0000.0000.0000.000
169A185THR00.0250.00512.5320.0270.0270.0000.0000.0000.000
170A186PHE00.0680.01914.660-0.083-0.0830.0000.0000.0000.000
171A187ASP-1-0.828-0.90112.4490.0870.0870.0000.0000.0000.000
172A188GLU-1-0.922-0.97915.5630.0200.0200.0000.0000.0000.000
173A189PHE00.0120.00817.837-0.046-0.0460.0000.0000.0000.000
174A190ALA00.0390.01118.843-0.033-0.0330.0000.0000.0000.000
175A191ALA0-0.0040.02118.974-0.040-0.0400.0000.0000.0000.000
176A192TRP0-0.007-0.00120.881-0.022-0.0220.0000.0000.0000.000
177A193ALA00.0230.01123.650-0.016-0.0160.0000.0000.0000.000
178A194SER00.011-0.04222.815-0.011-0.0110.0000.0000.0000.000
179A195ALA0-0.084-0.03024.903-0.017-0.0170.0000.0000.0000.000
180A196VAL0-0.012-0.00226.496-0.009-0.0090.0000.0000.0000.000
181A197LYS10.8860.95128.567-0.051-0.0510.0000.0000.0000.000
182A198LEU00.0060.00427.221-0.008-0.0080.0000.0000.0000.000
183A199ASP-1-1.022-1.02130.024-0.024-0.0240.0000.0000.0000.000
184A200ALA0-0.0230.00532.300-0.001-0.0010.0000.0000.0000.000
185A201ASP-1-0.953-0.98032.6660.0140.0140.0000.0000.0000.000
186A202GLY0-0.047-0.01133.816-0.003-0.0030.0000.0000.0000.000
187A203ASP-1-0.744-0.86234.045-0.054-0.0540.0000.0000.0000.000
188A204PRO00.0260.02533.2810.0050.0050.0000.0000.0000.000
189A205ASP-1-0.801-0.92736.316-0.043-0.0430.0000.0000.0000.000
190A206ASN0-0.061-0.02138.8660.0000.0000.0000.0000.0000.000
191A207VAL0-0.040-0.03541.0510.0050.0050.0000.0000.0000.000
192A208PRO0-0.0090.01142.8490.0000.0000.0000.0000.0000.000