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

tag_button

FMODB ID: 16J3Z

Calculation Name: 1PRX-A-Xray372

Preferred Name: Peroxiredoxin-6

Target Type: SINGLE PROTEIN

Ligand Name: s-hydroxycysteine

ligand 3-letter code: CSO

PDB ID: 1PRX

Chain ID: A

ChEMBL ID: CHEMBL4295741

UniProt ID: P30041

Base Structure: X-ray

Registration Date: 2023-09-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2529110.043531
FMO2-HF: Nuclear repulsion 2443798.75226
FMO2-HF: Total energy -85311.291271
FMO2-MP2: Total energy -85564.409438


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:5:LEU)


Summations of interaction energy for fragment #1(A:5:LEU)
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.
-11.9-0.1178.137-7.21-12.71-0.023
Interaction energy analysis for fragmet #1(A:5:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.008
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].
3A7LEU0-0.003-0.0183.334-1.1931.8170.040-1.638-1.4120.007
4A8GLY0-0.036-0.0205.9590.0230.0230.0000.0000.0000.000
5A9ASP-1-0.829-0.9002.078-6.560-3.8284.764-3.287-4.209-0.029
6A10VAL0-0.058-0.0423.9100.1430.5610.004-0.116-0.3060.000
7A11ALA00.0270.0203.027-0.4050.4820.136-0.321-0.7020.000
8A12PRO00.0570.0412.782-1.455-0.7620.216-0.169-0.7390.001
9A13ASN00.0170.0165.802-0.027-0.0270.0000.0000.0000.000
10A14PHE00.0290.0066.414-0.169-0.1690.0000.0000.0000.000
11A15GLU-1-0.830-0.89910.2470.3690.3690.0000.0000.0000.000
12A16ALA00.0020.00612.4970.0240.0240.0000.0000.0000.000
13A17ASN00.0100.00514.493-0.046-0.0460.0000.0000.0000.000
14A18THR00.013-0.01015.3380.0260.0260.0000.0000.0000.000
15A19THR00.0640.02018.033-0.012-0.0120.0000.0000.0000.000
16A20VAL0-0.050-0.01619.327-0.026-0.0260.0000.0000.0000.000
17A21GLY00.0360.03621.051-0.013-0.0130.0000.0000.0000.000
18A22ARG10.8760.92618.247-0.329-0.3290.0000.0000.0000.000
19A23ILE0-0.0170.00613.145-0.021-0.0210.0000.0000.0000.000
20A24ARG10.9080.95813.293-0.498-0.4980.0000.0000.0000.000
21A25PHE00.007-0.0086.284-0.027-0.0270.0000.0000.0000.000
22A26HIS0-0.025-0.0577.399-0.181-0.1810.0000.0000.0000.000
23A27ASP-1-0.880-0.93811.5160.3800.3800.0000.0000.0000.000
24A28PHE0-0.030-0.01112.319-0.048-0.0480.0000.0000.0000.000
25A29LEU00.0150.0108.564-0.055-0.0550.0000.0000.0000.000
26A30GLY00.0240.02613.242-0.068-0.0680.0000.0000.0000.000
27A31ASP-1-0.927-0.96314.5600.2670.2670.0000.0000.0000.000
28A32SER0-0.045-0.03515.250-0.043-0.0430.0000.0000.0000.000
29A33TRP0-0.020-0.01512.3360.0420.0420.0000.0000.0000.000
30A34GLY00.002-0.00410.931-0.016-0.0160.0000.0000.0000.000
31A35ILE0-0.030-0.0079.5500.0570.0570.0000.0000.0000.000
32A36LEU0-0.016-0.0036.463-0.017-0.0170.0000.0000.0000.000
33A37PHE0-0.023-0.0148.975-0.042-0.0420.0000.0000.0000.000
34A38SER00.0210.0048.9780.0920.0920.0000.0000.0000.000
35A39HIS00.004-0.01611.636-0.106-0.1060.0000.0000.0000.000
36A40PRO00.026-0.00115.1730.0390.0390.0000.0000.0000.000
37A41ARG10.8640.90116.561-0.204-0.2040.0000.0000.0000.000
38A42ASP-1-0.733-0.80619.6150.2460.2460.0000.0000.0000.000
39A43PHE00.009-0.00222.030-0.013-0.0130.0000.0000.0000.000
40A44THR0-0.0100.01021.342-0.017-0.0170.0000.0000.0000.000
41A45PRO00.0350.02523.8140.0050.0050.0000.0000.0000.000
42A46VAL00.0310.02320.3370.0010.0010.0000.0000.0000.000
43A47CSO0-0.0090.00418.947-0.002-0.0020.0000.0000.0000.000
44A48THR00.0470.01920.1960.0170.0170.0000.0000.0000.000
45A49THR0-0.055-0.02422.966-0.004-0.0040.0000.0000.0000.000
46A50GLU-1-0.775-0.86717.9580.0810.0810.0000.0000.0000.000
47A51LEU00.0310.00916.8360.0080.0080.0000.0000.0000.000
48A52GLY00.0610.03920.2030.0050.0050.0000.0000.0000.000
49A53ARG10.8990.94821.736-0.044-0.0440.0000.0000.0000.000
50A54ALA0-0.001-0.00518.145-0.005-0.0050.0000.0000.0000.000
51A55ALA0-0.031-0.01620.0420.0060.0060.0000.0000.0000.000
52A56LYS10.7780.87422.635-0.079-0.0790.0000.0000.0000.000
53A57LEU0-0.021-0.00720.551-0.009-0.0090.0000.0000.0000.000
54A58ALA00.0370.02620.353-0.001-0.0010.0000.0000.0000.000
55A59PRO00.0240.00521.4070.0060.0060.0000.0000.0000.000
56A60GLU-1-0.776-0.87523.0140.0500.0500.0000.0000.0000.000
57A61PHE00.0180.01316.841-0.008-0.0080.0000.0000.0000.000
58A62ALA00.0630.03219.5770.0060.0060.0000.0000.0000.000
59A63LYS10.7750.90021.080-0.055-0.0550.0000.0000.0000.000
60A64ARG10.8420.90419.899-0.059-0.0590.0000.0000.0000.000
61A65ASN0-0.0100.01018.3540.0200.0200.0000.0000.0000.000
62A66VAL0-0.007-0.00114.0700.0270.0270.0000.0000.0000.000
63A67LYS10.8300.91914.467-0.361-0.3610.0000.0000.0000.000
64A68LEU0-0.006-0.01013.7360.0430.0430.0000.0000.0000.000
65A69ILE00.005-0.00110.9180.0030.0030.0000.0000.0000.000
66A70ALA00.0070.01912.4280.0290.0290.0000.0000.0000.000
67A71LEU0-0.0110.0139.2290.0250.0250.0000.0000.0000.000
68A72SER0-0.022-0.04613.048-0.037-0.0370.0000.0000.0000.000
69A73ILE0-0.039-0.00813.1620.0140.0140.0000.0000.0000.000
70A74ASP-1-0.785-0.88016.7780.1840.1840.0000.0000.0000.000
71A75SER00.000-0.01519.1540.0360.0360.0000.0000.0000.000
72A76VAL0-0.029-0.01220.788-0.005-0.0050.0000.0000.0000.000
73A77GLU-1-0.923-0.96321.8040.1570.1570.0000.0000.0000.000
74A78ASP-1-0.843-0.90523.2680.1810.1810.0000.0000.0000.000
75A79HIS10.7640.85917.181-0.330-0.3300.0000.0000.0000.000
76A80LEU0-0.0160.01322.368-0.007-0.0070.0000.0000.0000.000
77A81ALA00.003-0.00525.321-0.013-0.0130.0000.0000.0000.000
78A82TRP0-0.003-0.01219.018-0.004-0.0040.0000.0000.0000.000
79A83SER0-0.036-0.03823.628-0.003-0.0030.0000.0000.0000.000
80A84LYS10.8300.92825.373-0.137-0.1370.0000.0000.0000.000
81A85ASP-1-0.867-0.93627.3020.1030.1030.0000.0000.0000.000
82A86ILE0-0.022-0.01722.055-0.009-0.0090.0000.0000.0000.000
83A87ASN0-0.075-0.04826.108-0.009-0.0090.0000.0000.0000.000
84A88ALA00.0300.02328.577-0.009-0.0090.0000.0000.0000.000
85A89TYR0-0.048-0.01325.820-0.013-0.0130.0000.0000.0000.000
86A90ASN0-0.100-0.06025.532-0.014-0.0140.0000.0000.0000.000
87A91SER0-0.069-0.03329.678-0.006-0.0060.0000.0000.0000.000
88A92GLU-1-0.779-0.87329.7290.0800.0800.0000.0000.0000.000
89A93GLU-1-0.926-0.97032.7490.0790.0790.0000.0000.0000.000
90A94PRO0-0.0020.00631.4060.0080.0080.0000.0000.0000.000
91A95THR0-0.033-0.01630.3240.0060.0060.0000.0000.0000.000
92A96GLU-1-0.824-0.91126.9700.1500.1500.0000.0000.0000.000
93A97LYS10.9160.95025.880-0.133-0.1330.0000.0000.0000.000
94A98LEU00.0670.04321.112-0.010-0.0100.0000.0000.0000.000
95A99PRO0-0.109-0.04321.7660.0070.0070.0000.0000.0000.000
96A100PHE0-0.007-0.00517.2050.0070.0070.0000.0000.0000.000
97A101PRO0-0.0060.00915.771-0.015-0.0150.0000.0000.0000.000
98A102ILE00.030-0.00116.2080.0300.0300.0000.0000.0000.000
99A103ILE0-0.009-0.03410.836-0.019-0.0190.0000.0000.0000.000
100A104ASP-1-0.846-0.91614.9780.3310.3310.0000.0000.0000.000
101A105ASP-1-0.755-0.91212.4020.7690.7690.0000.0000.0000.000
102A106ARG10.8930.95515.120-0.295-0.2950.0000.0000.0000.000
103A107ASN0-0.071-0.06616.809-0.065-0.0650.0000.0000.0000.000
104A108ARG10.8070.91714.270-0.287-0.2870.0000.0000.0000.000
105A109GLU-1-0.825-0.89112.5200.5750.5750.0000.0000.0000.000
106A110LEU0-0.032-0.0259.0410.1410.1410.0000.0000.0000.000
107A111ALA00.0110.0057.9670.3370.3370.0000.0000.0000.000
108A112ILE0-0.0070.0208.1000.2370.2370.0000.0000.0000.000
109A113LEU0-0.059-0.0214.8970.2650.2650.0000.0000.0000.000
110A114LEU0-0.066-0.0503.101-0.0990.6270.064-0.125-0.665-0.001
111A115GLY00.0010.0163.7450.9831.4690.006-0.190-0.302-0.001
112A116MET0-0.077-0.0235.843-0.874-0.8740.0000.0000.0000.000
113A117LEU00.005-0.0097.983-0.223-0.2230.0000.0000.0000.000
114A118ASP-1-0.884-0.92310.8940.2430.2430.0000.0000.0000.000
115A119PRO00.028-0.00311.4970.0210.0210.0000.0000.0000.000
116A120ALA0-0.0250.00614.145-0.021-0.0210.0000.0000.0000.000
117A121GLU-1-0.954-0.99615.4450.4050.4050.0000.0000.0000.000
118A122LYS10.9390.95817.149-0.199-0.1990.0000.0000.0000.000
119A123ASP-1-0.834-0.90820.1280.1470.1470.0000.0000.0000.000
120A124GLU-1-0.851-0.91121.6160.1630.1630.0000.0000.0000.000
121A125LYS10.8380.89222.712-0.155-0.1550.0000.0000.0000.000
122A126GLY00.0740.06621.2730.0160.0160.0000.0000.0000.000
123A127MET0-0.093-0.05019.437-0.006-0.0060.0000.0000.0000.000
124A128PRO00.0580.04915.359-0.025-0.0250.0000.0000.0000.000
125A129VAL0-0.025-0.04515.3810.0260.0260.0000.0000.0000.000
126A130THR0-0.032-0.03411.291-0.050-0.0500.0000.0000.0000.000
127A131ALA00.0180.02110.694-0.010-0.0100.0000.0000.0000.000
128A132ARG10.7170.80910.820-0.064-0.0640.0000.0000.0000.000
129A133VAL00.0040.0195.477-0.123-0.1230.0000.0000.0000.000
130A134VAL0-0.0180.0148.9110.2060.2060.0000.0000.0000.000
131A135PHE00.0240.0002.917-1.822-0.3610.430-0.427-1.464-0.003
132A136VAL00.0350.0246.2670.0350.0350.0000.0000.0000.000
133A137PHE00.0300.0032.735-1.143-0.3660.400-0.215-0.9620.003
134A138GLY00.0290.0177.924-0.142-0.1420.0000.0000.0000.000
135A139PRO00.0560.02510.3730.0980.0980.0000.0000.0000.000
136A140ASP-1-0.788-0.86810.3370.2270.2270.0000.0000.0000.000
137A141LYS10.8480.9207.804-0.478-0.4780.0000.0000.0000.000
138A142LYS10.8350.9385.7460.1550.1550.0000.0000.0000.000
139A143LEU0-0.015-0.0042.286-1.074-0.4812.077-0.722-1.9490.000
140A144LYS10.7970.8865.414-0.570-0.5700.0000.0000.0000.000
141A145LEU0-0.005-0.0017.602-0.174-0.1740.0000.0000.0000.000
142A146SER00.0250.0045.2810.3530.3530.0000.0000.0000.000
143A147ILE0-0.0090.0087.707-0.100-0.1000.0000.0000.0000.000
144A148LEU00.0250.0057.8720.0990.0990.0000.0000.0000.000
145A149TYR00.0070.01510.571-0.008-0.0080.0000.0000.0000.000
146A150PRO00.0870.04314.1710.0520.0520.0000.0000.0000.000
147A151ALA00.032-0.00716.0240.0130.0130.0000.0000.0000.000
148A152THR0-0.010-0.00518.2460.0090.0090.0000.0000.0000.000
149A153THR0-0.035-0.01218.494-0.010-0.0100.0000.0000.0000.000
150A154GLY00.0280.01218.5380.0000.0000.0000.0000.0000.000
151A155ARG10.7770.86812.977-0.172-0.1720.0000.0000.0000.000
152A156ASN00.0620.03618.5160.0270.0270.0000.0000.0000.000
153A157PHE00.037-0.02117.300-0.010-0.0100.0000.0000.0000.000
154A158ASP-1-0.847-0.90319.9510.0020.0020.0000.0000.0000.000
155A159GLU-1-0.848-0.91617.555-0.159-0.1590.0000.0000.0000.000
156A160ILE00.002-0.00714.418-0.011-0.0110.0000.0000.0000.000
157A161LEU00.009-0.00116.4550.0120.0120.0000.0000.0000.000
158A162ARG10.7990.89119.0360.1610.1610.0000.0000.0000.000
159A163VAL00.003-0.00914.261-0.007-0.0070.0000.0000.0000.000
160A164VAL00.0020.00914.332-0.003-0.0030.0000.0000.0000.000
161A165ILE00.0040.00616.2340.0050.0050.0000.0000.0000.000
162A166SER0-0.0190.00317.686-0.010-0.0100.0000.0000.0000.000
163A167LEU0-0.013-0.00211.730-0.006-0.0060.0000.0000.0000.000
164A168GLN0-0.013-0.02516.182-0.012-0.0120.0000.0000.0000.000
165A169LEU00.0190.01718.3280.0030.0030.0000.0000.0000.000
166A170THR0-0.085-0.05017.350-0.006-0.0060.0000.0000.0000.000
167A171ALA0-0.069-0.03716.493-0.003-0.0030.0000.0000.0000.000
168A172GLU-1-0.890-0.93018.4220.0310.0310.0000.0000.0000.000
169A173LYS10.8090.88521.9100.0110.0110.0000.0000.0000.000
170A174ARG10.8540.92521.5490.0780.0780.0000.0000.0000.000
171A175VAL0-0.0060.00222.198-0.006-0.0060.0000.0000.0000.000
172A176ALA00.0330.02120.541-0.008-0.0080.0000.0000.0000.000
173A177THR00.0170.00520.0490.0080.0080.0000.0000.0000.000
174A178PRO0-0.0130.00021.117-0.025-0.0250.0000.0000.0000.000
175A179VAL00.015-0.00921.958-0.002-0.0020.0000.0000.0000.000
176A180ASP-1-0.921-0.96122.941-0.148-0.1480.0000.0000.0000.000
177A181TRP0-0.0300.01121.8000.0120.0120.0000.0000.0000.000
178A182LYS10.9020.94823.9710.1020.1020.0000.0000.0000.000
179A183ASP-1-0.856-0.93925.109-0.029-0.0290.0000.0000.0000.000
180A184GLY0-0.012-0.00526.5020.0060.0060.0000.0000.0000.000
181A185ASP-1-0.876-0.92427.741-0.084-0.0840.0000.0000.0000.000
182A186SER0-0.078-0.05828.5420.0030.0030.0000.0000.0000.000
183A187VAL00.0050.01525.169-0.009-0.0090.0000.0000.0000.000
184A188MET0-0.027-0.02324.571-0.001-0.0010.0000.0000.0000.000
185A189VAL0-0.0160.00624.9840.0000.0000.0000.0000.0000.000
186A190LEU00.0340.01119.923-0.015-0.0150.0000.0000.0000.000
187A191PRO0-0.025-0.02721.7990.0150.0150.0000.0000.0000.000
188A192THR00.004-0.00221.1700.0060.0060.0000.0000.0000.000
189A193ILE0-0.0140.02123.9310.0110.0110.0000.0000.0000.000
190A194PRO00.0760.04526.741-0.002-0.0020.0000.0000.0000.000
191A195GLU-1-0.813-0.90030.174-0.081-0.0810.0000.0000.0000.000
192A196GLU-1-0.831-0.92133.183-0.077-0.0770.0000.0000.0000.000
193A197GLU-1-0.798-0.88327.977-0.084-0.0840.0000.0000.0000.000
194A198ALA00.0300.01030.3390.0060.0060.0000.0000.0000.000
195A199LYS10.7620.87231.5510.0770.0770.0000.0000.0000.000
196A200LYS10.8970.94934.2500.0470.0470.0000.0000.0000.000
197A201LEU0-0.0080.00627.0450.0060.0060.0000.0000.0000.000
198A202PHE0-0.003-0.00926.4880.0040.0040.0000.0000.0000.000
199A203PRO00.0290.01332.580-0.002-0.0020.0000.0000.0000.000
200A204LYS10.8460.91932.6360.0420.0420.0000.0000.0000.000
201A205GLY00.0150.02235.6790.0000.0000.0000.0000.0000.000
202A206VAL0-0.020-0.00731.945-0.004-0.0040.0000.0000.0000.000
203A207PHE0-0.006-0.00133.8430.0020.0020.0000.0000.0000.000
204A208THR00.019-0.00333.493-0.009-0.0090.0000.0000.0000.000
205A209LYS10.9530.99033.1760.1160.1160.0000.0000.0000.000
206A210GLU-1-0.877-0.94734.573-0.109-0.1090.0000.0000.0000.000
207A211LEU0-0.034-0.01532.030-0.002-0.0020.0000.0000.0000.000
208A212PRO00.020-0.00735.3060.0030.0030.0000.0000.0000.000
209A213SER0-0.021-0.00832.6890.0040.0040.0000.0000.0000.000
210A214GLY00.0390.03235.6090.0000.0000.0000.0000.0000.000
211A215LYS10.9010.95229.9310.1780.1780.0000.0000.0000.000
212A216LYS10.9420.96332.6550.0990.0990.0000.0000.0000.000
213A217TYR00.0260.00026.8670.0050.0050.0000.0000.0000.000
214A218LEU0-0.0210.00327.653-0.008-0.0080.0000.0000.0000.000
215A219ARG10.8460.92127.2190.1450.1450.0000.0000.0000.000
216A220TYR00.0170.00428.411-0.008-0.0080.0000.0000.0000.000
217A221THR0-0.010-0.01728.8990.0080.0080.0000.0000.0000.000
218A222PRO00.0350.01430.069-0.004-0.0040.0000.0000.0000.000
219A223GLN00.0760.05026.681-0.009-0.0090.0000.0000.0000.000
220A224PRO0-0.0090.00827.3750.0100.0100.0000.0000.0000.000