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: VK261

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2527946.038816
FMO2-HF: Nuclear repulsion 2442635.946102
FMO2-HF: Total energy -85310.092714
FMO2-MP2: Total energy -85563.155891


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.
-12.427-1.4310.682-8.045-13.634-0.022
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 : 0.013 / q_NPA : 0.006
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].
3A7LEU0-0.005-0.0173.496-1.0042.0170.042-1.626-1.4370.007
4A8GLY0-0.037-0.0205.9030.0260.0260.0000.0000.0000.000
5A9ASP-1-0.836-0.9002.035-7.062-5.0876.745-4.106-4.614-0.033
6A10VAL0-0.064-0.0443.479-0.0220.6990.030-0.301-0.451-0.002
7A11ALA00.0310.0192.831-0.4540.4150.204-0.334-0.7380.001
8A12PRO00.0560.0412.683-1.744-0.9350.245-0.194-0.8610.002
9A13ASN00.0140.0165.923-0.044-0.0440.0000.0000.0000.000
10A14PHE00.0410.0186.471-0.171-0.1710.0000.0000.0000.000
11A15GLU-1-0.895-0.94910.4060.3970.3970.0000.0000.0000.000
12A16ALA0-0.0100.00412.7870.0250.0250.0000.0000.0000.000
13A17ASN00.0180.00414.789-0.046-0.0460.0000.0000.0000.000
14A18THR00.004-0.00715.6150.0270.0270.0000.0000.0000.000
15A19THR00.0600.02018.213-0.012-0.0120.0000.0000.0000.000
16A20VAL0-0.043-0.01319.317-0.028-0.0280.0000.0000.0000.000
17A21GLY00.0280.03121.171-0.014-0.0140.0000.0000.0000.000
18A22ARG10.9390.96618.388-0.352-0.3520.0000.0000.0000.000
19A23ILE0-0.0060.01212.771-0.022-0.0220.0000.0000.0000.000
20A24ARG10.9690.98713.300-0.534-0.5340.0000.0000.0000.000
21A25PHE0-0.002-0.0145.877-0.050-0.0500.0000.0000.0000.000
22A26HIS0-0.038-0.0717.010-0.207-0.2070.0000.0000.0000.000
23A27ASP-1-0.898-0.93611.2910.3830.3830.0000.0000.0000.000
24A28PHE0-0.057-0.02512.051-0.053-0.0530.0000.0000.0000.000
25A29LEU0-0.026-0.0258.197-0.058-0.0580.0000.0000.0000.000
26A30GLY00.0220.01712.871-0.068-0.0680.0000.0000.0000.000
27A31ASP-1-0.939-0.96714.5220.2810.2810.0000.0000.0000.000
28A32SER0-0.039-0.02515.170-0.043-0.0430.0000.0000.0000.000
29A33TRP0-0.003-0.00611.5690.0500.0500.0000.0000.0000.000
30A34GLY0-0.004-0.00610.546-0.020-0.0200.0000.0000.0000.000
31A35ILE0-0.029-0.0079.2380.0660.0660.0000.0000.0000.000
32A36LEU0-0.0080.0036.322-0.017-0.0170.0000.0000.0000.000
33A37PHE0-0.019-0.0159.141-0.046-0.0460.0000.0000.0000.000
34A38SER00.0160.0109.0570.0890.0890.0000.0000.0000.000
35A39HIS0-0.022-0.04211.776-0.116-0.1160.0000.0000.0000.000
36A40PRO00.027-0.00215.0530.0440.0440.0000.0000.0000.000
37A41ARG10.9250.95716.412-0.185-0.1850.0000.0000.0000.000
38A42ASP-1-0.711-0.80919.4570.2620.2620.0000.0000.0000.000
39A43PHE00.009-0.00421.988-0.015-0.0150.0000.0000.0000.000
40A44THR0-0.037-0.01521.169-0.019-0.0190.0000.0000.0000.000
41A45PRO00.0330.01523.8320.0050.0050.0000.0000.0000.000
42A46VAL00.0370.02620.3320.0010.0010.0000.0000.0000.000
43A47CSO00.0210.03118.704-0.007-0.0070.0000.0000.0000.000
44A48THR00.0640.03620.3490.0190.0190.0000.0000.0000.000
45A49THR0-0.057-0.02523.194-0.004-0.0040.0000.0000.0000.000
46A50GLU-1-0.774-0.87318.0340.0850.0850.0000.0000.0000.000
47A51LEU00.0280.01117.1380.0090.0090.0000.0000.0000.000
48A52GLY00.0590.04120.4110.0050.0050.0000.0000.0000.000
49A53ARG10.9550.97021.680-0.055-0.0550.0000.0000.0000.000
50A54ALA00.0040.00218.214-0.005-0.0050.0000.0000.0000.000
51A55ALA0-0.030-0.01120.0700.0060.0060.0000.0000.0000.000
52A56LYS10.8840.93722.686-0.082-0.0820.0000.0000.0000.000
53A57LEU00.001-0.00420.735-0.009-0.0090.0000.0000.0000.000
54A58ALA00.0290.02620.223-0.001-0.0010.0000.0000.0000.000
55A59PRO00.005-0.00421.2210.0070.0070.0000.0000.0000.000
56A60GLU-1-0.884-0.95422.4860.0570.0570.0000.0000.0000.000
57A61PHE0-0.016-0.00716.385-0.007-0.0070.0000.0000.0000.000
58A62ALA00.0670.03519.2300.0070.0070.0000.0000.0000.000
59A63LYS10.8830.96320.794-0.062-0.0620.0000.0000.0000.000
60A64ARG10.8760.93819.329-0.063-0.0630.0000.0000.0000.000
61A65ASN0-0.0080.00217.8930.0160.0160.0000.0000.0000.000
62A66VAL0-0.0100.00013.8390.0290.0290.0000.0000.0000.000
63A67LYS10.8840.96114.318-0.386-0.3860.0000.0000.0000.000
64A68LEU0-0.003-0.01013.5660.0460.0460.0000.0000.0000.000
65A69ILE00.0010.00010.8980.0020.0020.0000.0000.0000.000
66A70ALA00.0110.02012.6000.0280.0280.0000.0000.0000.000
67A71LEU0-0.0040.0189.6730.0240.0240.0000.0000.0000.000
68A72SER0-0.029-0.03913.257-0.042-0.0420.0000.0000.0000.000
69A73ILE0-0.037-0.01313.4470.0140.0140.0000.0000.0000.000
70A74ASP-1-0.821-0.91816.8380.1990.1990.0000.0000.0000.000
71A75SER00.014-0.00219.4240.0400.0400.0000.0000.0000.000
72A76VAL0-0.022-0.00620.971-0.006-0.0060.0000.0000.0000.000
73A77GLU-1-0.924-0.96922.1010.1660.1660.0000.0000.0000.000
74A78ASP-1-0.875-0.92823.8350.1820.1820.0000.0000.0000.000
75A79HIS10.7240.84117.548-0.355-0.3550.0000.0000.0000.000
76A80LEU0-0.0010.01522.597-0.007-0.0070.0000.0000.0000.000
77A81ALA00.0310.01425.498-0.014-0.0140.0000.0000.0000.000
78A82TRP0-0.029-0.02519.321-0.004-0.0040.0000.0000.0000.000
79A83SER0-0.022-0.03223.725-0.004-0.0040.0000.0000.0000.000
80A84LYS10.9020.97325.522-0.132-0.1320.0000.0000.0000.000
81A85ASP-1-0.875-0.93527.7140.1060.1060.0000.0000.0000.000
82A86ILE0-0.024-0.01922.267-0.010-0.0100.0000.0000.0000.000
83A87ASN0-0.077-0.03926.390-0.012-0.0120.0000.0000.0000.000
84A88ALA00.0200.01828.799-0.009-0.0090.0000.0000.0000.000
85A89TYR0-0.058-0.02126.223-0.013-0.0130.0000.0000.0000.000
86A90ASN0-0.096-0.05225.634-0.015-0.0150.0000.0000.0000.000
87A91SER0-0.089-0.03729.825-0.007-0.0070.0000.0000.0000.000
88A92GLU-1-0.845-0.92729.5950.0870.0870.0000.0000.0000.000
89A93GLU-1-0.946-0.98232.8960.0830.0830.0000.0000.0000.000
90A94PRO00.0040.00931.6350.0080.0080.0000.0000.0000.000
91A95THR0-0.022-0.01030.2440.0060.0060.0000.0000.0000.000
92A96GLU-1-0.916-0.97126.9440.1610.1610.0000.0000.0000.000
93A97LYS10.9050.94525.917-0.140-0.1400.0000.0000.0000.000
94A98LEU00.0680.03721.282-0.012-0.0120.0000.0000.0000.000
95A99PRO0-0.111-0.04421.7640.0090.0090.0000.0000.0000.000
96A100PHE0-0.012-0.00917.2330.0070.0070.0000.0000.0000.000
97A101PRO0-0.0120.01015.797-0.015-0.0150.0000.0000.0000.000
98A102ILE00.034-0.00416.3040.0300.0300.0000.0000.0000.000
99A103ILE0-0.006-0.03011.148-0.021-0.0210.0000.0000.0000.000
100A104ASP-1-0.871-0.92015.1980.3620.3620.0000.0000.0000.000
101A105ASP-1-0.742-0.90812.2600.8410.8410.0000.0000.0000.000
102A106ARG10.9220.97515.182-0.314-0.3140.0000.0000.0000.000
103A107ASN0-0.066-0.05316.258-0.070-0.0700.0000.0000.0000.000
104A108ARG10.9080.96813.985-0.321-0.3210.0000.0000.0000.000
105A109GLU-1-0.892-0.93612.1960.6560.6560.0000.0000.0000.000
106A110LEU0-0.028-0.0278.7860.1640.1640.0000.0000.0000.000
107A111ALA00.0100.0087.5490.3750.3750.0000.0000.0000.000
108A112ILE0-0.0150.0128.2630.2540.2540.0000.0000.0000.000
109A113LEU0-0.050-0.0134.9280.2710.2710.0000.0000.0000.000
110A114LEU0-0.072-0.0582.989-0.1640.7400.090-0.166-0.8280.000
111A115GLY0-0.0030.0164.0051.2101.5460.002-0.083-0.2560.000
112A116MET0-0.075-0.0275.828-0.967-0.9670.0000.0000.0000.000
113A117LEU0-0.004-0.0287.998-0.238-0.2380.0000.0000.0000.000
114A118ASP-1-0.902-0.92710.8800.2460.2460.0000.0000.0000.000
115A119PRO00.0330.00311.3250.0150.0150.0000.0000.0000.000
116A120ALA0-0.0180.00713.970-0.021-0.0210.0000.0000.0000.000
117A121GLU-1-0.950-0.99714.9140.4730.4730.0000.0000.0000.000
118A122LYS10.9380.95916.990-0.208-0.2080.0000.0000.0000.000
119A123ASP-1-0.914-0.96020.3060.1290.1290.0000.0000.0000.000
120A124GLU-1-0.906-0.93521.7280.1760.1760.0000.0000.0000.000
121A125LYS10.9460.95022.859-0.174-0.1740.0000.0000.0000.000
122A126GLY00.0650.06421.4260.0200.0200.0000.0000.0000.000
123A127MET0-0.145-0.08119.940-0.006-0.0060.0000.0000.0000.000
124A128PRO00.0580.05115.561-0.027-0.0270.0000.0000.0000.000
125A129VAL0-0.026-0.04215.3960.0280.0280.0000.0000.0000.000
126A130THR0-0.016-0.01911.325-0.051-0.0510.0000.0000.0000.000
127A131ALA00.0250.03210.717-0.011-0.0110.0000.0000.0000.000
128A132ARG10.7200.81310.855-0.064-0.0640.0000.0000.0000.000
129A133VAL00.0090.0185.582-0.120-0.1200.0000.0000.0000.000
130A134VAL0-0.0220.0058.9260.2150.2150.0000.0000.0000.000
131A135PHE00.0290.0012.936-1.345-0.1760.145-0.316-0.998-0.002
132A136VAL00.0370.0236.1870.0440.0440.0000.0000.0000.000
133A137PHE00.0340.0032.426-1.069-0.6070.982-0.265-1.1780.001
134A138GLY00.0040.0037.386-0.173-0.1730.0000.0000.0000.000
135A139PRO00.0650.03010.2460.1120.1120.0000.0000.0000.000
136A140ASP-1-0.830-0.9119.9920.2640.2640.0000.0000.0000.000
137A141LYS10.8430.9227.664-0.532-0.5320.0000.0000.0000.000
138A142LYS10.9070.9795.4500.2160.2160.0000.0000.0000.000
139A143LEU0-0.020-0.0072.107-1.122-0.4262.198-0.650-2.2440.004
140A144LYS10.8270.9104.907-0.726-0.691-0.001-0.004-0.0290.000
141A145LEU0-0.011-0.0037.126-0.201-0.2010.0000.0000.0000.000
142A146SER0-0.006-0.0025.6590.0450.0450.0000.0000.0000.000
143A147ILE00.0140.0147.799-0.102-0.1020.0000.0000.0000.000
144A148LEU00.0270.0058.2430.1080.1080.0000.0000.0000.000
145A149TYR00.0030.01410.572-0.003-0.0030.0000.0000.0000.000
146A150PRO00.0830.04214.1770.0580.0580.0000.0000.0000.000
147A151ALA00.0410.00016.0280.0130.0130.0000.0000.0000.000
148A152THR0-0.007-0.00718.2560.0090.0090.0000.0000.0000.000
149A153THR0-0.046-0.01418.493-0.014-0.0140.0000.0000.0000.000
150A154GLY00.0260.00918.544-0.001-0.0010.0000.0000.0000.000
151A155ARG10.8000.89112.912-0.174-0.1740.0000.0000.0000.000
152A156ASN00.0710.04618.5630.0300.0300.0000.0000.0000.000
153A157PHE00.039-0.02417.144-0.010-0.0100.0000.0000.0000.000
154A158ASP-1-0.892-0.91919.795-0.007-0.0070.0000.0000.0000.000
155A159GLU-1-0.910-0.96717.413-0.180-0.1800.0000.0000.0000.000
156A160ILE0-0.003-0.01014.168-0.012-0.0120.0000.0000.0000.000
157A161LEU00.012-0.00116.1150.0130.0130.0000.0000.0000.000
158A162ARG10.8510.93118.7010.1760.1760.0000.0000.0000.000
159A163VAL00.0040.00014.054-0.008-0.0080.0000.0000.0000.000
160A164VAL0-0.0020.00713.827-0.003-0.0030.0000.0000.0000.000
161A165ILE00.0090.00815.7450.0070.0070.0000.0000.0000.000
162A166SER0-0.030-0.01917.263-0.011-0.0110.0000.0000.0000.000
163A167LEU0-0.033-0.01011.326-0.007-0.0070.0000.0000.0000.000
164A168GLN0-0.021-0.02215.540-0.015-0.0150.0000.0000.0000.000
165A169LEU00.0220.01517.6830.0030.0030.0000.0000.0000.000
166A170THR0-0.087-0.05617.112-0.006-0.0060.0000.0000.0000.000
167A171ALA0-0.064-0.03216.099-0.004-0.0040.0000.0000.0000.000
168A172GLU-1-0.949-0.97118.0480.0400.0400.0000.0000.0000.000
169A173LYS10.8690.92821.5350.0150.0150.0000.0000.0000.000
170A174ARG10.8830.94221.6580.0890.0890.0000.0000.0000.000
171A175VAL0-0.0050.00522.035-0.007-0.0070.0000.0000.0000.000
172A176ALA00.0430.02820.180-0.009-0.0090.0000.0000.0000.000
173A177THR00.0160.00919.7650.0090.0090.0000.0000.0000.000
174A178PRO0-0.009-0.00120.848-0.027-0.0270.0000.0000.0000.000
175A179VAL00.0380.00922.079-0.004-0.0040.0000.0000.0000.000
176A180ASP-1-0.952-0.98022.842-0.161-0.1610.0000.0000.0000.000
177A181TRP0-0.0320.00221.4270.0120.0120.0000.0000.0000.000
178A182LYS10.9080.96223.8450.1090.1090.0000.0000.0000.000
179A183ASP-1-0.885-0.96324.717-0.031-0.0310.0000.0000.0000.000
180A184GLY0-0.0010.00425.9930.0060.0060.0000.0000.0000.000
181A185ASP-1-0.892-0.93827.594-0.088-0.0880.0000.0000.0000.000
182A186SER0-0.077-0.05728.2880.0030.0030.0000.0000.0000.000
183A187VAL0-0.0020.01124.725-0.009-0.0090.0000.0000.0000.000
184A188MET0-0.018-0.02024.217-0.002-0.0020.0000.0000.0000.000
185A189VAL0-0.0160.00724.6920.0010.0010.0000.0000.0000.000
186A190LEU00.020-0.00120.103-0.016-0.0160.0000.0000.0000.000
187A191PRO0-0.026-0.02021.6650.0170.0170.0000.0000.0000.000
188A192THR00.010-0.00520.9830.0030.0030.0000.0000.0000.000
189A193ILE0-0.0280.01024.0650.0120.0120.0000.0000.0000.000
190A194PRO00.0800.04826.895-0.003-0.0030.0000.0000.0000.000
191A195GLU-1-0.929-0.97430.308-0.087-0.0870.0000.0000.0000.000
192A196GLU-1-0.917-0.97933.279-0.087-0.0870.0000.0000.0000.000
193A197GLU-1-0.821-0.90328.413-0.087-0.0870.0000.0000.0000.000
194A198ALA00.0280.01130.3260.0060.0060.0000.0000.0000.000
195A199LYS10.9280.97731.6080.0760.0760.0000.0000.0000.000
196A200LYS10.8810.94234.2330.0510.0510.0000.0000.0000.000
197A201LEU00.0270.01327.2270.0060.0060.0000.0000.0000.000
198A202PHE0-0.032-0.01326.4850.0050.0050.0000.0000.0000.000
199A203PRO00.0210.01232.502-0.002-0.0020.0000.0000.0000.000
200A204LYS10.8820.94432.3110.0430.0430.0000.0000.0000.000
201A205GLY00.0110.02335.4980.0000.0000.0000.0000.0000.000
202A206VAL0-0.014-0.00931.863-0.004-0.0040.0000.0000.0000.000
203A207PHE0-0.015-0.00433.5290.0030.0030.0000.0000.0000.000
204A208THR00.019-0.00233.135-0.011-0.0110.0000.0000.0000.000
205A209LYS10.9560.98532.9470.1220.1220.0000.0000.0000.000
206A210GLU-1-0.883-0.94634.212-0.117-0.1170.0000.0000.0000.000
207A211LEU0-0.033-0.01931.621-0.002-0.0020.0000.0000.0000.000
208A212PRO00.0230.00034.9420.0030.0030.0000.0000.0000.000
209A213SER0-0.027-0.01532.3770.0040.0040.0000.0000.0000.000
210A214GLY00.0490.04135.4410.0000.0000.0000.0000.0000.000
211A215LYS10.9010.95129.6740.1950.1950.0000.0000.0000.000
212A216LYS10.9850.99432.5000.1100.1100.0000.0000.0000.000
213A217TYR00.0230.00126.8370.0000.0000.0000.0000.0000.000
214A218LEU0-0.0130.00627.350-0.008-0.0080.0000.0000.0000.000
215A219ARG10.8510.92727.1710.1560.1560.0000.0000.0000.000
216A220TYR00.0220.00828.378-0.010-0.0100.0000.0000.0000.000
217A221THR0-0.018-0.01628.6380.0090.0090.0000.0000.0000.000
218A222PRO00.0390.01829.731-0.004-0.0040.0000.0000.0000.000
219A223GLN00.0970.06826.163-0.009-0.0090.0000.0000.0000.000
220A224PRO0-0.029-0.01426.8600.0120.0120.0000.0000.0000.000