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: GYQ41

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535181.305873
FMO2-HF: Nuclear repulsion 2449869.562031
FMO2-HF: Total energy -85311.743842
FMO2-MP2: Total energy -85564.906015


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.
-11.794-0.5387.044-6.413-11.885-0.025
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 : 0.013
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].
3A7LEU0-0.025-0.0263.599-0.8441.5370.004-1.308-1.0760.005
4A8GLY00.0020.0045.9740.1230.1230.0000.0000.0000.000
5A9ASP-1-0.823-0.8982.349-6.981-3.5513.120-2.842-3.708-0.026
6A10VAL0-0.061-0.0394.4050.2300.461-0.001-0.029-0.2020.000
7A11ALA00.0360.0272.949-0.2500.5170.119-0.260-0.6260.001
8A12PRO00.0470.0362.829-1.525-0.7380.330-0.218-0.8980.001
9A13ASN00.0130.0185.731-0.005-0.0050.0000.0000.0000.000
10A14PHE00.018-0.0026.348-0.183-0.1830.0000.0000.0000.000
11A15GLU-1-0.839-0.9049.6370.3370.3370.0000.0000.0000.000
12A16ALA00.0130.01412.2350.0290.0290.0000.0000.0000.000
13A17ASN00.0220.00514.174-0.043-0.0430.0000.0000.0000.000
14A18THR00.013-0.00815.3190.0210.0210.0000.0000.0000.000
15A19THR00.0500.01818.053-0.009-0.0090.0000.0000.0000.000
16A20VAL0-0.034-0.00819.421-0.023-0.0230.0000.0000.0000.000
17A21GLY00.0280.02920.970-0.012-0.0120.0000.0000.0000.000
18A22ARG10.8720.92617.927-0.323-0.3230.0000.0000.0000.000
19A23ILE0-0.0180.00412.778-0.021-0.0210.0000.0000.0000.000
20A24ARG10.8690.92312.494-0.519-0.5190.0000.0000.0000.000
21A25PHE00.0280.0216.295-0.032-0.0320.0000.0000.0000.000
22A26HIS0-0.019-0.0507.464-0.175-0.1750.0000.0000.0000.000
23A27ASP-1-0.844-0.92711.5020.3700.3700.0000.0000.0000.000
24A28PHE0-0.020-0.00512.333-0.051-0.0510.0000.0000.0000.000
25A29LEU00.0130.0078.421-0.054-0.0540.0000.0000.0000.000
26A30GLY00.0210.02713.135-0.066-0.0660.0000.0000.0000.000
27A31ASP-1-0.935-0.97814.5150.2330.2330.0000.0000.0000.000
28A32SER0-0.040-0.02815.418-0.039-0.0390.0000.0000.0000.000
29A33TRP0-0.012-0.00812.6100.0320.0320.0000.0000.0000.000
30A34GLY0-0.007-0.00611.3820.0050.0050.0000.0000.0000.000
31A35ILE0-0.046-0.0159.8910.0110.0110.0000.0000.0000.000
32A36LEU0-0.0070.0086.0340.0110.0110.0000.0000.0000.000
33A37PHE0-0.001-0.0078.641-0.052-0.0520.0000.0000.0000.000
34A38SER00.0230.0098.4370.1230.1230.0000.0000.0000.000
35A39HIS00.005-0.01511.073-0.111-0.1110.0000.0000.0000.000
36A40PRO0-0.006-0.01414.5990.0360.0360.0000.0000.0000.000
37A41ARG10.8670.89816.411-0.183-0.1830.0000.0000.0000.000
38A42ASP-1-0.718-0.80419.4040.2050.2050.0000.0000.0000.000
39A43PHE0-0.001-0.00921.310-0.012-0.0120.0000.0000.0000.000
40A44THR0-0.0090.02220.809-0.021-0.0210.0000.0000.0000.000
41A45PRO00.0270.01822.9180.0030.0030.0000.0000.0000.000
42A46VAL00.0250.01719.8100.0020.0020.0000.0000.0000.000
43A47CSO0-0.009-0.00318.470-0.005-0.0050.0000.0000.0000.000
44A48THR00.0540.03619.7000.0150.0150.0000.0000.0000.000
45A49THR0-0.054-0.03222.645-0.004-0.0040.0000.0000.0000.000
46A50GLU-1-0.764-0.85317.2150.0130.0130.0000.0000.0000.000
47A51LEU00.0240.00916.6160.0030.0030.0000.0000.0000.000
48A52GLY00.0810.04619.9050.0050.0050.0000.0000.0000.000
49A53ARG10.8550.90621.6050.0030.0030.0000.0000.0000.000
50A54ALA00.004-0.00918.149-0.004-0.0040.0000.0000.0000.000
51A55ALA0-0.038-0.01620.0360.0040.0040.0000.0000.0000.000
52A56LYS10.7610.85922.629-0.050-0.0500.0000.0000.0000.000
53A57LEU0-0.032-0.01020.591-0.009-0.0090.0000.0000.0000.000
54A58ALA00.0310.01920.147-0.003-0.0030.0000.0000.0000.000
55A59PRO00.0350.01121.1760.0040.0040.0000.0000.0000.000
56A60GLU-1-0.779-0.87522.9080.0120.0120.0000.0000.0000.000
57A61PHE00.0240.01916.998-0.010-0.0100.0000.0000.0000.000
58A62ALA00.0560.02619.6260.0030.0030.0000.0000.0000.000
59A63LYS10.7810.89221.090-0.018-0.0180.0000.0000.0000.000
60A64ARG10.8240.90120.169-0.008-0.0080.0000.0000.0000.000
61A65ASN00.0010.01418.5570.0140.0140.0000.0000.0000.000
62A66VAL0-0.015-0.00514.2760.0170.0170.0000.0000.0000.000
63A67LYS10.8250.90814.320-0.291-0.2910.0000.0000.0000.000
64A68LEU00.005-0.00713.8710.0140.0140.0000.0000.0000.000
65A69ILE0-0.0050.00010.7890.0130.0130.0000.0000.0000.000
66A70ALA00.0080.01812.3690.0010.0010.0000.0000.0000.000
67A71LEU0-0.0100.0048.9710.0360.0360.0000.0000.0000.000
68A72SER0-0.017-0.04712.697-0.044-0.0440.0000.0000.0000.000
69A73ILE0-0.0240.00612.8580.0150.0150.0000.0000.0000.000
70A74ASP-1-0.813-0.87816.4180.1650.1650.0000.0000.0000.000
71A75SER0-0.019-0.03118.8280.0330.0330.0000.0000.0000.000
72A76VAL0-0.041-0.02820.542-0.007-0.0070.0000.0000.0000.000
73A77GLU-1-0.920-0.96121.4650.1480.1480.0000.0000.0000.000
74A78ASP-1-0.814-0.88122.5970.1650.1650.0000.0000.0000.000
75A79HIS10.7750.86316.944-0.293-0.2930.0000.0000.0000.000
76A80LEU0-0.0330.00921.969-0.007-0.0070.0000.0000.0000.000
77A81ALA00.004-0.01324.996-0.014-0.0140.0000.0000.0000.000
78A82TRP00.014-0.00418.529-0.004-0.0040.0000.0000.0000.000
79A83SER0-0.047-0.04123.069-0.007-0.0070.0000.0000.0000.000
80A84LYS10.8110.91824.843-0.119-0.1190.0000.0000.0000.000
81A85ASP-1-0.837-0.92826.8600.0830.0830.0000.0000.0000.000
82A86ILE0-0.033-0.01521.674-0.010-0.0100.0000.0000.0000.000
83A87ASN0-0.058-0.03625.750-0.011-0.0110.0000.0000.0000.000
84A88ALA00.0220.01328.229-0.008-0.0080.0000.0000.0000.000
85A89TYR0-0.049-0.01825.578-0.011-0.0110.0000.0000.0000.000
86A90ASN0-0.055-0.03925.400-0.012-0.0120.0000.0000.0000.000
87A91SER0-0.079-0.02329.164-0.006-0.0060.0000.0000.0000.000
88A92GLU-1-0.793-0.87429.0610.0550.0550.0000.0000.0000.000
89A93GLU-1-0.908-0.95832.1240.0610.0610.0000.0000.0000.000
90A94PRO0-0.0100.01131.0720.0070.0070.0000.0000.0000.000
91A95THR0-0.038-0.03029.7240.0070.0070.0000.0000.0000.000
92A96GLU-1-0.802-0.90426.8110.1310.1310.0000.0000.0000.000
93A97LYS10.8730.94025.448-0.108-0.1080.0000.0000.0000.000
94A98LEU00.0700.03920.570-0.010-0.0100.0000.0000.0000.000
95A99PRO0-0.076-0.03121.7760.0070.0070.0000.0000.0000.000
96A100PHE0-0.022-0.01417.0650.0030.0030.0000.0000.0000.000
97A101PRO0-0.0080.00815.659-0.011-0.0110.0000.0000.0000.000
98A102ILE00.0300.00215.8620.0230.0230.0000.0000.0000.000
99A103ILE0-0.003-0.02510.632-0.012-0.0120.0000.0000.0000.000
100A104ASP-1-0.859-0.92714.7420.3070.3070.0000.0000.0000.000
101A105ASP-1-0.750-0.89812.1400.7300.7300.0000.0000.0000.000
102A106ARG10.8890.94914.732-0.284-0.2840.0000.0000.0000.000
103A107ASN0-0.039-0.03516.561-0.070-0.0700.0000.0000.0000.000
104A108ARG10.7990.90113.955-0.272-0.2720.0000.0000.0000.000
105A109GLU-1-0.844-0.90412.3060.5850.5850.0000.0000.0000.000
106A110LEU0-0.036-0.0268.6280.1640.1640.0000.0000.0000.000
107A111ALA0-0.002-0.0137.6790.3150.3150.0000.0000.0000.000
108A112ILE0-0.0220.0068.0870.1720.1720.0000.0000.0000.000
109A113LEU0-0.046-0.0155.1930.3450.3450.0000.0000.0000.000
110A114LEU0-0.062-0.0433.000-0.2360.6290.168-0.169-0.864-0.001
111A115GLY00.0000.0053.8050.2500.7750.008-0.192-0.340-0.001
112A116MET0-0.059-0.0085.329-1.248-1.202-0.001-0.002-0.0430.000
113A117LEU0-0.015-0.0077.358-0.278-0.2780.0000.0000.0000.000
114A118ASP-1-0.832-0.91410.3290.3370.3370.0000.0000.0000.000
115A119PRO00.005-0.01711.5940.0310.0310.0000.0000.0000.000
116A120ALA0-0.0080.02514.236-0.016-0.0160.0000.0000.0000.000
117A121GLU-1-0.874-0.95715.5930.3420.3420.0000.0000.0000.000
118A122LYS10.8130.89516.967-0.268-0.2680.0000.0000.0000.000
119A123ASP-1-0.792-0.87219.7190.1360.1360.0000.0000.0000.000
120A124GLU-1-0.825-0.87921.4490.1570.1570.0000.0000.0000.000
121A125LYS10.7960.85322.489-0.148-0.1480.0000.0000.0000.000
122A126GLY00.0710.04321.1860.0140.0140.0000.0000.0000.000
123A127MET0-0.055-0.02719.194-0.011-0.0110.0000.0000.0000.000
124A128PRO00.0370.04515.084-0.023-0.0230.0000.0000.0000.000
125A129VAL0-0.038-0.04214.5650.0180.0180.0000.0000.0000.000
126A130THR0-0.021-0.03210.700-0.050-0.0500.0000.0000.0000.000
127A131ALA00.0300.02910.284-0.038-0.0380.0000.0000.0000.000
128A132ARG10.7350.81410.5870.0190.0190.0000.0000.0000.000
129A133VAL0-0.0030.0205.224-0.087-0.0870.0000.0000.0000.000
130A134VAL0-0.0260.0028.5560.2240.2240.0000.0000.0000.000
131A135PHE00.017-0.0022.708-1.970-0.4350.747-0.543-1.739-0.005
132A136VAL00.0140.0086.4240.0930.0930.0000.0000.0000.000
133A137PHE00.0570.0112.885-0.923-0.2500.136-0.153-0.6560.002
134A138GLY00.0510.0258.208-0.096-0.0960.0000.0000.0000.000
135A139PRO00.0520.02910.5890.0880.0880.0000.0000.0000.000
136A140ASP-1-0.811-0.88410.6230.1060.1060.0000.0000.0000.000
137A141LYS10.8580.9468.501-0.378-0.3780.0000.0000.0000.000
138A142LYS10.8410.9225.8940.1730.1730.0000.0000.0000.000
139A143LEU0-0.018-0.0082.304-0.477-0.4612.414-0.697-1.733-0.001
140A144LYS10.7460.8635.651-0.193-0.1930.0000.0000.0000.000
141A145LEU00.0090.0118.209-0.118-0.1180.0000.0000.0000.000
142A146SER00.0240.0065.4000.3040.3040.0000.0000.0000.000
143A147ILE00.0000.0037.719-0.034-0.0340.0000.0000.0000.000
144A148LEU00.0160.0117.6840.0790.0790.0000.0000.0000.000
145A149TYR00.0240.02210.6440.0150.0150.0000.0000.0000.000
146A150PRO00.0760.03614.2470.0430.0430.0000.0000.0000.000
147A151ALA00.0410.00515.7840.0150.0150.0000.0000.0000.000
148A152THR0-0.020-0.00117.9970.0100.0100.0000.0000.0000.000
149A153THR0-0.045-0.03118.226-0.014-0.0140.0000.0000.0000.000
150A154GLY00.0370.02618.348-0.001-0.0010.0000.0000.0000.000
151A155ARG10.7480.84012.303-0.072-0.0720.0000.0000.0000.000
152A156ASN00.0460.02618.1050.0360.0360.0000.0000.0000.000
153A157PHE00.0600.00317.095-0.016-0.0160.0000.0000.0000.000
154A158ASP-1-0.836-0.88619.551-0.034-0.0340.0000.0000.0000.000
155A159GLU-1-0.847-0.91017.423-0.209-0.2090.0000.0000.0000.000
156A160ILE0-0.009-0.00714.421-0.015-0.0150.0000.0000.0000.000
157A161LEU00.0160.00116.7270.0060.0060.0000.0000.0000.000
158A162ARG10.7870.89219.3520.1990.1990.0000.0000.0000.000
159A163VAL00.008-0.00814.137-0.007-0.0070.0000.0000.0000.000
160A164VAL00.0110.01014.764-0.005-0.0050.0000.0000.0000.000
161A165ILE00.0000.00616.6290.0040.0040.0000.0000.0000.000
162A166SER0-0.0300.00117.786-0.006-0.0060.0000.0000.0000.000
163A167LEU0-0.004-0.00211.826-0.006-0.0060.0000.0000.0000.000
164A168GLN0-0.012-0.01616.310-0.003-0.0030.0000.0000.0000.000
165A169LEU0-0.015-0.00318.7600.0070.0070.0000.0000.0000.000
166A170THR0-0.060-0.04817.304-0.005-0.0050.0000.0000.0000.000
167A171ALA0-0.055-0.03116.5870.0010.0010.0000.0000.0000.000
168A172GLU-1-0.897-0.93518.484-0.008-0.0080.0000.0000.0000.000
169A173LYS10.8180.89922.0120.0510.0510.0000.0000.0000.000
170A174ARG10.8340.90121.6630.0990.0990.0000.0000.0000.000
171A175VAL00.002-0.00722.265-0.004-0.0040.0000.0000.0000.000
172A176ALA00.0240.02320.564-0.011-0.0110.0000.0000.0000.000
173A177THR00.0210.00020.2100.0110.0110.0000.0000.0000.000
174A178PRO0-0.018-0.00321.486-0.025-0.0250.0000.0000.0000.000
175A179VAL00.025-0.00522.206-0.004-0.0040.0000.0000.0000.000
176A180ASP-1-0.905-0.95623.432-0.162-0.1620.0000.0000.0000.000
177A181TRP0-0.0520.00421.7110.0100.0100.0000.0000.0000.000
178A182LYS10.9030.94124.1690.1140.1140.0000.0000.0000.000
179A183ASP-1-0.838-0.93325.176-0.061-0.0610.0000.0000.0000.000
180A184GLY0-0.008-0.00126.5120.0090.0090.0000.0000.0000.000
181A185ASP-1-0.879-0.92727.759-0.102-0.1020.0000.0000.0000.000
182A186SER0-0.080-0.05828.5160.0010.0010.0000.0000.0000.000
183A187VAL00.0160.02125.295-0.011-0.0110.0000.0000.0000.000
184A188MET0-0.028-0.01724.9100.0020.0020.0000.0000.0000.000
185A189VAL0-0.0060.01124.912-0.006-0.0060.0000.0000.0000.000
186A190LEU00.0350.02019.845-0.012-0.0120.0000.0000.0000.000
187A191PRO0-0.018-0.02021.8360.0160.0160.0000.0000.0000.000
188A192THR0-0.002-0.01121.1590.0070.0070.0000.0000.0000.000
189A193ILE0-0.0210.02824.3010.0130.0130.0000.0000.0000.000
190A194PRO00.0740.03427.049-0.001-0.0010.0000.0000.0000.000
191A195GLU-1-0.790-0.87230.561-0.088-0.0880.0000.0000.0000.000
192A196GLU-1-0.835-0.91933.321-0.080-0.0800.0000.0000.0000.000
193A197GLU-1-0.784-0.85827.834-0.095-0.0950.0000.0000.0000.000
194A198ALA00.0270.01230.5120.0050.0050.0000.0000.0000.000
195A199LYS10.7680.85231.6880.0820.0820.0000.0000.0000.000
196A200LYS10.8710.93234.1100.0570.0570.0000.0000.0000.000
197A201LEU0-0.0020.00727.0400.0050.0050.0000.0000.0000.000
198A202PHE00.0110.00426.5460.0020.0020.0000.0000.0000.000
199A203PRO00.0070.00132.585-0.001-0.0010.0000.0000.0000.000
200A204LYS10.8530.92132.2970.0600.0600.0000.0000.0000.000
201A205GLY00.0170.02635.7650.0010.0010.0000.0000.0000.000
202A206VAL0-0.025-0.01331.986-0.005-0.0050.0000.0000.0000.000
203A207PHE0-0.006-0.00333.7930.0030.0030.0000.0000.0000.000
204A208THR00.002-0.00533.575-0.010-0.0100.0000.0000.0000.000
205A209LYS10.9180.97533.4000.1250.1250.0000.0000.0000.000
206A210GLU-1-0.830-0.92734.347-0.113-0.1130.0000.0000.0000.000
207A211LEU0-0.054-0.03032.197-0.001-0.0010.0000.0000.0000.000
208A212PRO00.013-0.00635.9030.0040.0040.0000.0000.0000.000
209A213SER0-0.0040.00333.1250.0030.0030.0000.0000.0000.000
210A214GLY00.0420.02636.163-0.001-0.0010.0000.0000.0000.000
211A215LYS10.9200.96630.5560.1670.1670.0000.0000.0000.000
212A216LYS10.9350.95832.6540.0930.0930.0000.0000.0000.000
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