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: P59VZ

Calculation Name: 4HI7-A-Xray13

Preferred Name:

Target Type:

Ligand Name: glutathione

ligand 3-letter code: GSH

PDB ID: 4HI7

Chain ID: A

ChEMBL ID:

UniProt ID: B4KM86

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 223
LigandCharge GTT=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2736051.282505
FMO2-HF: Nuclear repulsion 2649800.013207
FMO2-HF: Total energy -86251.269298
FMO2-MP2: Total energy -86506.241131


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:2:ACE)


Summations of interaction energy for fragment #1(A:2:ACE)
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.
-0.8150.15-0.014-0.418-0.533-0.001
Interaction energy analysis for fragmet #1(A:2:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.010
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].
3A4PRO00.0510.0513.8340.5921.557-0.014-0.418-0.533-0.001
4A5ILE0-0.0070.0037.017-0.081-0.0810.0000.0000.0000.000
5A6LEU0-0.019-0.0029.4490.1080.1080.0000.0000.0000.000
6A7TYR0-0.045-0.04012.2920.0250.0250.0000.0000.0000.000
7A8GLY00.026-0.02915.9300.0100.0100.0000.0000.0000.000
8A9ILE00.0170.02419.0970.0070.0070.0000.0000.0000.000
9A10ASP-1-0.723-0.83820.580-0.214-0.2140.0000.0000.0000.000
10A11ALA00.0350.01522.8470.0050.0050.0000.0000.0000.000
11A12SER0-0.024-0.00523.5350.0100.0100.0000.0000.0000.000
12A13PRO00.0460.01024.383-0.012-0.0120.0000.0000.0000.000
13A14PRO00.0420.02123.322-0.012-0.0120.0000.0000.0000.000
14A15VAL0-0.019-0.00918.951-0.018-0.0180.0000.0000.0000.000
15A16ARG10.8230.92019.8920.1090.1090.0000.0000.0000.000
16A17ALA0-0.0210.00621.468-0.014-0.0140.0000.0000.0000.000
17A18VAL00.0160.00016.029-0.012-0.0120.0000.0000.0000.000
18A19LYS10.8310.91116.8910.2400.2400.0000.0000.0000.000
19A20LEU0-0.0160.00017.781-0.019-0.0190.0000.0000.0000.000
20A21THR0-0.013-0.01616.8820.0050.0050.0000.0000.0000.000
21A22LEU00.0040.00011.726-0.010-0.0100.0000.0000.0000.000
22A23ALA0-0.015-0.00514.697-0.037-0.0370.0000.0000.0000.000
23A24ALA0-0.050-0.02016.9890.0070.0070.0000.0000.0000.000
24A25LEU0-0.042-0.02014.4290.0200.0200.0000.0000.0000.000
25A26GLN0-0.057-0.01414.411-0.012-0.0120.0000.0000.0000.000
26A27LEU00.0060.0198.211-0.055-0.0550.0000.0000.0000.000
27A28PRO0-0.040-0.0347.542-0.001-0.0010.0000.0000.0000.000
28A29TYR0-0.018-0.0207.618-0.358-0.3580.0000.0000.0000.000
29A30ASP-1-0.892-0.9366.494-0.884-0.8840.0000.0000.0000.000
30A31TYR0-0.058-0.0599.3160.0690.0690.0000.0000.0000.000
31A32LYS10.9300.96910.0650.2960.2960.0000.0000.0000.000
32A33ILE00.025-0.00514.7990.0070.0070.0000.0000.0000.000
33A34VAL00.0160.01918.3030.0180.0180.0000.0000.0000.000
34A35ASN0-0.003-0.01620.7720.0030.0030.0000.0000.0000.000
35A36LEU00.012-0.00924.0580.0100.0100.0000.0000.0000.000
36A37MET0-0.043-0.01026.7280.0090.0090.0000.0000.0000.000
37A38ASN0-0.018-0.00226.9750.0100.0100.0000.0000.0000.000
38A39LYS10.9100.95328.3060.0430.0430.0000.0000.0000.000
39A40GLU-1-0.802-0.89722.743-0.080-0.0800.0000.0000.0000.000
40A41GLN0-0.027-0.01323.078-0.001-0.0010.0000.0000.0000.000
41A42HIS0-0.051-0.05024.1550.0050.0050.0000.0000.0000.000
42A43SER00.0020.02922.5430.0090.0090.0000.0000.0000.000
43A44GLU-1-0.859-0.94924.171-0.010-0.0100.0000.0000.0000.000
44A45GLU-1-0.973-0.98417.8450.0160.0160.0000.0000.0000.000
45A46TYR0-0.049-0.04417.735-0.009-0.0090.0000.0000.0000.000
46A47LEU00.009-0.00220.695-0.006-0.0060.0000.0000.0000.000
47A48LYS10.9460.97120.134-0.035-0.0350.0000.0000.0000.000
48A49LYS10.8310.93113.8240.0390.0390.0000.0000.0000.000
49A50ASN0-0.001-0.00318.7910.0020.0020.0000.0000.0000.000
50A51PRO00.0710.04021.291-0.003-0.0030.0000.0000.0000.000
51A52GLN0-0.060-0.02524.3870.0010.0010.0000.0000.0000.000
52A53HIS10.8510.93324.0720.0520.0520.0000.0000.0000.000
53A54THR0-0.010-0.00223.588-0.003-0.0030.0000.0000.0000.000
54A55VAL00.0000.03619.884-0.006-0.0060.0000.0000.0000.000
55A56PRO0-0.011-0.02818.0110.0130.0130.0000.0000.0000.000
56A57LEU0-0.012-0.00115.4010.0210.0210.0000.0000.0000.000
57A58LEU0-0.020-0.01210.981-0.037-0.0370.0000.0000.0000.000
58A59GLU-1-0.779-0.86710.271-0.045-0.0450.0000.0000.0000.000
59A60ASP-1-0.803-0.8846.911-0.872-0.8720.0000.0000.0000.000
60A61GLY00.0190.0236.3320.1180.1180.0000.0000.0000.000
61A62ASP-1-0.918-0.9627.0760.3320.3320.0000.0000.0000.000
62A63ALA0-0.076-0.02510.297-0.024-0.0240.0000.0000.0000.000
63A64ASN0-0.016-0.01511.789-0.050-0.0500.0000.0000.0000.000
64A65ILE00.0070.00813.3790.0130.0130.0000.0000.0000.000
65A66ALA00.0530.02016.402-0.027-0.0270.0000.0000.0000.000
66A67ASP-1-0.776-0.86719.203-0.106-0.1060.0000.0000.0000.000
67A68SER00.007-0.02220.159-0.013-0.0130.0000.0000.0000.000
68A69HIS10.8360.88420.5220.1020.1020.0000.0000.0000.000
69A70ALA00.0010.01620.369-0.004-0.0040.0000.0000.0000.000
70A71ILE0-0.017-0.01815.179-0.011-0.0110.0000.0000.0000.000
71A72MET0-0.043-0.01716.557-0.028-0.0280.0000.0000.0000.000
72A73ALA00.0460.02918.337-0.011-0.0110.0000.0000.0000.000
73A74TYR0-0.077-0.05210.4320.0460.0460.0000.0000.0000.000
74A75LEU00.013-0.00712.071-0.016-0.0160.0000.0000.0000.000
75A76VAL00.0320.01714.673-0.018-0.0180.0000.0000.0000.000
76A77SER0-0.076-0.04317.2000.0150.0150.0000.0000.0000.000
77A78LYS10.8770.96110.8470.1690.1690.0000.0000.0000.000
78A79TYR0-0.073-0.0817.862-0.047-0.0470.0000.0000.0000.000
79A80GLY00.0000.02213.254-0.018-0.0180.0000.0000.0000.000
80A81LYS10.9140.94514.3760.2260.2260.0000.0000.0000.000
81A82ASP-1-0.882-0.93118.186-0.124-0.1240.0000.0000.0000.000
82A83ASP-1-0.884-0.95420.550-0.119-0.1190.0000.0000.0000.000
83A84SER00.0050.02122.7120.0040.0040.0000.0000.0000.000
84A85LEU00.020-0.00119.8770.0060.0060.0000.0000.0000.000
85A86TYR0-0.087-0.09021.519-0.001-0.0010.0000.0000.0000.000
86A87PRO00.0620.04423.5660.0030.0030.0000.0000.0000.000
87A88LYS10.9480.95922.2460.0940.0940.0000.0000.0000.000
88A89ASP-1-0.898-0.93626.199-0.052-0.0520.0000.0000.0000.000
89A90LEU00.0660.02329.089-0.004-0.0040.0000.0000.0000.000
90A91VAL00.0080.01831.182-0.001-0.0010.0000.0000.0000.000
91A92LYS10.9420.95230.4650.0680.0680.0000.0000.0000.000
92A93ARG10.8780.94822.5860.0970.0970.0000.0000.0000.000
93A94ALA00.0470.02828.937-0.003-0.0030.0000.0000.0000.000
94A95LEU0-0.044-0.00931.6400.0010.0010.0000.0000.0000.000
95A96VAL00.0450.00526.073-0.002-0.0020.0000.0000.0000.000
96A97ASP-1-0.820-0.89426.872-0.093-0.0930.0000.0000.0000.000
97A98ASN0-0.041-0.00828.988-0.001-0.0010.0000.0000.0000.000
98A99ARG10.8750.92730.7200.0690.0690.0000.0000.0000.000
99A100MET00.0180.01923.902-0.006-0.0060.0000.0000.0000.000
100A101TYR0-0.011-0.00327.759-0.001-0.0010.0000.0000.0000.000
101A102PHE00.0060.02630.8540.0030.0030.0000.0000.0000.000
102A103GLU-1-0.807-0.88128.540-0.103-0.1030.0000.0000.0000.000
103A104SER0-0.041-0.02528.7320.0030.0030.0000.0000.0000.000
104A105GLY00.0090.00130.2960.0020.0020.0000.0000.0000.000
105A106VAL00.0090.00533.8870.0020.0020.0000.0000.0000.000
106A107VAL00.0130.01632.8910.0020.0020.0000.0000.0000.000
107A108PHE00.008-0.01128.7140.0020.0020.0000.0000.0000.000
108A109ALA0-0.037-0.01532.2250.0030.0030.0000.0000.0000.000
109A110ASN0-0.011-0.01033.8330.0050.0050.0000.0000.0000.000
110A111ALA00.0300.03836.4260.0030.0030.0000.0000.0000.000
111A112LEU0-0.0230.01230.9800.0000.0000.0000.0000.0000.000
112A113ARG10.8110.88729.1060.0720.0720.0000.0000.0000.000
113A114SER0-0.035-0.03233.6510.0020.0020.0000.0000.0000.000
114A115LEU00.0680.03737.2110.0030.0030.0000.0000.0000.000
115A116ALA00.0430.01033.6260.0020.0020.0000.0000.0000.000
116A117LYS10.9440.97534.1560.0490.0490.0000.0000.0000.000
117A118MET0-0.040-0.02335.4970.0030.0030.0000.0000.0000.000
118A119ILE00.0280.02638.0250.0020.0020.0000.0000.0000.000
119A120LEU0-0.042-0.02532.8790.0010.0010.0000.0000.0000.000
120A121PHE0-0.057-0.03029.8480.0000.0000.0000.0000.0000.000
121A122LEU0-0.085-0.04535.6920.0030.0030.0000.0000.0000.000
122A123GLY0-0.0050.01239.1290.0030.0030.0000.0000.0000.000
123A124LYS10.9190.96941.4510.0360.0360.0000.0000.0000.000
124A125THR00.0460.01342.949-0.002-0.0020.0000.0000.0000.000
125A126GLU-1-0.930-0.94945.588-0.029-0.0290.0000.0000.0000.000
126A127VAL0-0.036-0.02543.247-0.001-0.0010.0000.0000.0000.000
127A128PRO00.0150.00545.3230.0010.0010.0000.0000.0000.000
128A129GLN00.0390.00946.497-0.002-0.0020.0000.0000.0000.000
129A130GLU-1-0.837-0.91846.389-0.034-0.0340.0000.0000.0000.000
130A131ARG10.7880.88440.6480.0430.0430.0000.0000.0000.000
131A132ILE0-0.004-0.00542.356-0.003-0.0030.0000.0000.0000.000
132A133ASP-1-0.800-0.89344.083-0.039-0.0390.0000.0000.0000.000
133A134ALA0-0.021-0.00740.775-0.001-0.0010.0000.0000.0000.000
134A135ILE0-0.054-0.02839.041-0.004-0.0040.0000.0000.0000.000
135A136THR00.0140.00040.837-0.002-0.0020.0000.0000.0000.000
136A137GLU-1-0.917-0.94542.746-0.043-0.0430.0000.0000.0000.000
137A138ALA0-0.035-0.01537.515-0.001-0.0010.0000.0000.0000.000
138A139TYR0-0.031-0.04937.380-0.004-0.0040.0000.0000.0000.000
139A140ASP-1-0.854-0.90940.404-0.047-0.0470.0000.0000.0000.000
140A141PHE0-0.029-0.02539.4450.0000.0000.0000.0000.0000.000
141A142VAL0-0.031-0.01635.756-0.001-0.0010.0000.0000.0000.000
142A143GLU-1-0.783-0.89438.315-0.058-0.0580.0000.0000.0000.000
143A144ALA0-0.027-0.02141.0820.0010.0010.0000.0000.0000.000
144A145PHE0-0.077-0.02935.0640.0010.0010.0000.0000.0000.000
145A146PHE0-0.0100.00635.0960.0000.0000.0000.0000.0000.000
146A147LYS10.9280.97239.3290.0530.0530.0000.0000.0000.000
147A148ASP-1-0.857-0.93342.123-0.051-0.0510.0000.0000.0000.000
148A149GLN0-0.044-0.00736.854-0.004-0.0040.0000.0000.0000.000
149A150THR0-0.004-0.01134.7410.0010.0010.0000.0000.0000.000
150A151TYR0-0.019-0.01230.391-0.006-0.0060.0000.0000.0000.000
151A152VAL00.0160.01530.9330.0060.0060.0000.0000.0000.000
152A153ALA0-0.028-0.01030.2380.0060.0060.0000.0000.0000.000
153A154GLY00.0340.02131.718-0.002-0.0020.0000.0000.0000.000
154A155ASN0-0.048-0.04033.651-0.005-0.0050.0000.0000.0000.000
155A156GLN00.0040.00128.549-0.006-0.0060.0000.0000.0000.000
156A157LEU00.0020.01924.9770.0020.0020.0000.0000.0000.000
157A158THR00.0130.00225.266-0.003-0.0030.0000.0000.0000.000
158A159ILE00.0310.00120.781-0.001-0.0010.0000.0000.0000.000
159A160ALA0-0.009-0.00323.9460.0010.0010.0000.0000.0000.000
160A161ASP-1-0.740-0.87227.369-0.104-0.1040.0000.0000.0000.000
161A162PHE00.0350.01421.2800.0030.0030.0000.0000.0000.000
162A163SER00.0350.01025.3340.0010.0010.0000.0000.0000.000
163A164LEU00.0200.02326.3260.0040.0040.0000.0000.0000.000
164A165ILE00.0060.01927.1670.0050.0050.0000.0000.0000.000
165A166SER0-0.046-0.01025.5730.0040.0040.0000.0000.0000.000
166A167SER0-0.018-0.04927.5590.0050.0050.0000.0000.0000.000
167A168ILE00.0590.03130.5300.0060.0060.0000.0000.0000.000
168A169SER0-0.038-0.03129.6750.0030.0030.0000.0000.0000.000
169A170SER00.000-0.01130.033-0.001-0.0010.0000.0000.0000.000
170A171LEU00.013-0.00432.5530.0050.0050.0000.0000.0000.000
171A172VAL00.0250.03335.1090.0050.0050.0000.0000.0000.000
172A173ALA0-0.080-0.03235.6060.0030.0030.0000.0000.0000.000
173A174PHE0-0.081-0.05235.8680.0030.0030.0000.0000.0000.000
174A175VAL00.0410.02139.9520.0040.0040.0000.0000.0000.000
175A176PRO00.0060.02140.281-0.003-0.0030.0000.0000.0000.000
176A177VAL00.0120.00838.2790.0020.0020.0000.0000.0000.000
177A178ASP-1-0.844-0.92041.350-0.045-0.0450.0000.0000.0000.000
178A179ALA00.010-0.01343.1440.0000.0000.0000.0000.0000.000
179A180ALA0-0.025-0.00644.3330.0000.0000.0000.0000.0000.000
180A181LYS10.9030.97446.4340.0430.0430.0000.0000.0000.000
181A182TYR0-0.081-0.06941.9380.0000.0000.0000.0000.0000.000
182A183PRO00.0550.04042.316-0.004-0.0040.0000.0000.0000.000
183A184LYS10.8550.91040.5080.0480.0480.0000.0000.0000.000
184A185LEU0-0.0010.00336.403-0.005-0.0050.0000.0000.0000.000
185A186SER0-0.004-0.01937.262-0.005-0.0050.0000.0000.0000.000
186A187ALA0-0.047-0.02437.896-0.003-0.0030.0000.0000.0000.000
187A188TRP0-0.070-0.04630.810-0.003-0.0030.0000.0000.0000.000
188A189ILE00.0270.01633.233-0.007-0.0070.0000.0000.0000.000
189A190LYS10.9340.96533.0310.0700.0700.0000.0000.0000.000
190A191ARG10.9130.97532.2160.0780.0780.0000.0000.0000.000
191A192LEU0-0.016-0.02428.259-0.007-0.0070.0000.0000.0000.000
192A193GLU-1-0.950-0.97928.707-0.102-0.1020.0000.0000.0000.000
193A194GLN0-0.057-0.02330.2040.0010.0010.0000.0000.0000.000
194A195LEU0-0.047-0.00825.093-0.003-0.0030.0000.0000.0000.000
195A196PRO00.0180.01123.324-0.001-0.0010.0000.0000.0000.000
196A197TYR00.0340.00820.646-0.002-0.0020.0000.0000.0000.000
197A198TYR00.0630.02922.587-0.008-0.0080.0000.0000.0000.000
198A199ALA00.0390.02024.1170.0030.0030.0000.0000.0000.000
199A200GLU-1-0.876-0.95318.875-0.271-0.2710.0000.0000.0000.000
200A201ASN0-0.045-0.02122.082-0.004-0.0040.0000.0000.0000.000
201A202SER0-0.008-0.01924.9650.0060.0060.0000.0000.0000.000
202A203THR00.0550.03224.7500.0150.0150.0000.0000.0000.000
203A204GLY00.0250.00025.4860.0090.0090.0000.0000.0000.000
204A205ALA0-0.0120.00326.3900.0090.0090.0000.0000.0000.000
205A206GLN00.007-0.00329.3730.0070.0070.0000.0000.0000.000
206A207GLN0-0.0020.00125.6800.0030.0030.0000.0000.0000.000
207A208PHE0-0.0140.00329.7930.0070.0070.0000.0000.0000.000
208A209VAL00.022-0.00631.3370.0080.0080.0000.0000.0000.000
209A210ALA0-0.009-0.00933.4570.0060.0060.0000.0000.0000.000
210A211ALA0-0.015-0.00332.4930.0050.0050.0000.0000.0000.000
211A212VAL00.0150.01334.5940.0050.0050.0000.0000.0000.000
212A213LYS10.8780.94937.1790.0610.0610.0000.0000.0000.000
213A214SER0-0.083-0.04037.2230.0040.0040.0000.0000.0000.000
214A215LYS10.8890.94737.6640.0510.0510.0000.0000.0000.000
215A216PRO00.0210.02140.793-0.001-0.0010.0000.0000.0000.000
216A217PHE0-0.011-0.01841.2810.0010.0010.0000.0000.0000.000
217A218THR0-0.019-0.00245.5160.0000.0000.0000.0000.0000.000
218A219VAL00.010-0.00146.353-0.001-0.0010.0000.0000.0000.000
219A220VAL0-0.0160.00048.9590.0020.0020.0000.0000.0000.000
220A221GLY00.0390.00651.050-0.001-0.0010.0000.0000.0000.000
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