FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G59Z1

Calculation Name: 4I2Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I2Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q18688

Base Structure: X-ray

Registration Date: 2023-09-24

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 899
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -24301079.313859
FMO2-HF: Nuclear repulsion 23944341.128822
FMO2-HF: Total energy -356738.185037
FMO2-MP2: Total energy -357768.227665


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:VAL)


Summations of interaction energy for fragment #1(A:5:VAL)
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.
-5.277-3.380.739-0.44-2.196-0.001
Interaction energy analysis for fragmet #1(A:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.016
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].
3A7THR0-0.060-0.0212.901-0.2311.6220.728-0.469-2.112-0.001
4A8ALA00.1090.0343.6820.3450.3890.0110.029-0.0840.000
5A9GLU-1-0.930-0.9856.835-0.728-0.7280.0000.0000.0000.000
6A10GLU-1-0.898-0.9455.371-3.226-3.2260.0000.0000.0000.000
7A11ILE00.0340.0607.3110.2020.2020.0000.0000.0000.000
8A12ARG10.9010.9339.1570.9560.9560.0000.0000.0000.000
9A13ASP-1-0.950-0.96112.163-0.807-0.8070.0000.0000.0000.000
10A14GLU-1-0.923-0.96210.382-1.372-1.3720.0000.0000.0000.000
11A15GLY00.0380.01613.5670.1070.1070.0000.0000.0000.000
12A16ASN0-0.083-0.04615.7130.0490.0490.0000.0000.0000.000
13A17ALA0-0.018-0.01017.2380.0720.0720.0000.0000.0000.000
14A18ALA00.1010.05317.7410.0510.0510.0000.0000.0000.000
15A19VAL0-0.105-0.05519.5980.0580.0580.0000.0000.0000.000
16A20LYS10.8620.92720.4080.4590.4590.0000.0000.0000.000
17A21ASP-1-0.883-0.91921.475-0.397-0.3970.0000.0000.0000.000
18A22GLN0-0.127-0.07423.9850.0320.0320.0000.0000.0000.000
19A23ASP-1-0.887-0.92722.441-0.270-0.2700.0000.0000.0000.000
20A24TYR00.018-0.03922.013-0.025-0.0250.0000.0000.0000.000
21A25ILE00.0240.01921.944-0.009-0.0090.0000.0000.0000.000
22A26LYS11.0311.01618.0090.4590.4590.0000.0000.0000.000
23A27ALA00.0180.02817.473-0.044-0.0440.0000.0000.0000.000
24A28ASP-1-0.821-0.89317.457-0.300-0.3000.0000.0000.0000.000
25A29GLU-1-0.908-0.96316.395-0.323-0.3230.0000.0000.0000.000
26A30LEU00.0110.01612.901-0.012-0.0120.0000.0000.0000.000
27A31TYR00.014-0.03012.896-0.058-0.0580.0000.0000.0000.000
28A32THR0-0.038-0.02514.0810.0050.0050.0000.0000.0000.000
29A33GLU-1-0.970-0.9939.545-0.793-0.7930.0000.0000.0000.000
30A34ALA00.001-0.0219.576-0.052-0.0520.0000.0000.0000.000
31A35LEU0-0.059-0.0519.938-0.018-0.0180.0000.0000.0000.000
32A36GLN0-0.073-0.02910.6270.0290.0290.0000.0000.0000.000
33A37LEU0-0.0170.0015.3790.1110.1110.0000.0000.0000.000
34A38THR0-0.102-0.0488.0790.0990.0990.0000.0000.0000.000
35A39THR0-0.034-0.03110.1250.0880.0880.0000.0000.0000.000
36A40ASP-1-1.063-1.04613.333-0.080-0.0800.0000.0000.0000.000
37A41GLU-1-0.812-0.91111.199-0.191-0.1910.0000.0000.0000.000
38A42ASP-1-0.771-0.83810.321-0.517-0.5170.0000.0000.0000.000
39A43LYS10.8550.90413.6430.1190.1190.0000.0000.0000.000
40A44ALA00.0420.01616.885-0.013-0.0130.0000.0000.0000.000
41A45LEU00.0310.01910.3310.0260.0260.0000.0000.0000.000
42A46ARG11.0161.00914.7650.1930.1930.0000.0000.0000.000
43A47PRO0-0.027-0.00516.149-0.007-0.0070.0000.0000.0000.000
44A48VAL0-0.052-0.01316.1180.0200.0200.0000.0000.0000.000
45A49LEU00.1070.05012.4280.0130.0130.0000.0000.0000.000
46A50TYR0-0.106-0.04717.0030.0060.0060.0000.0000.0000.000
47A51ARG10.8390.91320.0150.2840.2840.0000.0000.0000.000
48A52ASN0-0.077-0.04318.396-0.010-0.0100.0000.0000.0000.000
49A53ARG10.8900.94218.0140.3020.3020.0000.0000.0000.000
50A54ALA00.0320.01420.3890.0200.0200.0000.0000.0000.000
51A55MET0-0.071-0.04723.5830.0200.0200.0000.0000.0000.000
52A56ALA00.0310.02321.6950.0120.0120.0000.0000.0000.000
53A57ARG10.8100.90322.0460.2470.2470.0000.0000.0000.000
54A58LEU0-0.043-0.01925.4420.0150.0150.0000.0000.0000.000
55A59LYS10.8970.94926.7490.2060.2060.0000.0000.0000.000
56A60ARG10.8140.93023.2240.2250.2250.0000.0000.0000.000
57A61ASP-1-0.900-0.95928.490-0.133-0.1330.0000.0000.0000.000
58A62ASP-1-0.807-0.87125.971-0.151-0.1510.0000.0000.0000.000
59A63PHE00.0660.00428.339-0.011-0.0110.0000.0000.0000.000
60A64GLU-1-0.819-0.92430.071-0.093-0.0930.0000.0000.0000.000
61A65GLY0-0.021-0.01326.3650.0020.0020.0000.0000.0000.000
62A66ALA0-0.018-0.01025.940-0.009-0.0090.0000.0000.0000.000
63A67GLN00.012-0.01426.879-0.005-0.0050.0000.0000.0000.000
64A68SER0-0.010-0.01324.6920.0050.0050.0000.0000.0000.000
65A69ASP-1-0.752-0.88921.830-0.233-0.2330.0000.0000.0000.000
66A70CYS0-0.052-0.00424.032-0.009-0.0090.0000.0000.0000.000
67A71THR0-0.083-0.04426.3370.0030.0030.0000.0000.0000.000
68A72LYS10.9650.99521.8430.1620.1620.0000.0000.0000.000
69A73ALA0-0.012-0.00222.962-0.005-0.0050.0000.0000.0000.000
70A74LEU0-0.094-0.05123.9630.0040.0040.0000.0000.0000.000
71A75GLU-1-0.966-0.95924.846-0.103-0.1030.0000.0000.0000.000
72A76PHE0-0.081-0.02421.0990.0050.0050.0000.0000.0000.000
73A77ASP-1-0.855-0.93624.886-0.151-0.1510.0000.0000.0000.000
74A78GLY0-0.006-0.00727.034-0.005-0.0050.0000.0000.0000.000
75A79ALA00.0140.00429.7480.0040.0040.0000.0000.0000.000
76A80ASP-1-0.778-0.90324.497-0.229-0.2290.0000.0000.0000.000
77A81VAL00.0560.03127.940-0.002-0.0020.0000.0000.0000.000
78A82LYS10.8960.94125.3470.2360.2360.0000.0000.0000.000
79A83ALA0-0.0120.01426.4090.0000.0000.0000.0000.0000.000
80A84LEU00.0280.00127.7440.0060.0060.0000.0000.0000.000
81A85PHE00.0210.02430.8080.0060.0060.0000.0000.0000.000
82A86ARG10.9140.97724.2160.2510.2510.0000.0000.0000.000
83A87ARG10.8870.92930.0550.1250.1250.0000.0000.0000.000
84A88SER0-0.045-0.04931.2290.0100.0100.0000.0000.0000.000
85A89LEU00.0300.00632.8010.0060.0060.0000.0000.0000.000
86A90ALA0-0.0220.00330.9990.0030.0030.0000.0000.0000.000
87A91ARG10.8940.94333.0790.1090.1090.0000.0000.0000.000
88A92GLU-1-0.922-0.97935.928-0.094-0.0940.0000.0000.0000.000
89A93GLN0-0.0040.01334.8960.0090.0090.0000.0000.0000.000
90A94LEU0-0.065-0.00333.4590.0050.0050.0000.0000.0000.000
91A95GLY00.0320.01637.6330.0060.0060.0000.0000.0000.000
92A96ASN0-0.070-0.04038.6370.0050.0050.0000.0000.0000.000
93A97VAL00.0940.01540.112-0.002-0.0020.0000.0000.0000.000
94A98GLY00.0070.00242.0000.0000.0000.0000.0000.0000.000
95A99PRO0-0.058-0.02838.639-0.002-0.0020.0000.0000.0000.000
96A100ALA00.0530.04237.665-0.005-0.0050.0000.0000.0000.000
97A101PHE00.0440.01538.315-0.006-0.0060.0000.0000.0000.000
98A102GLN0-0.094-0.06840.117-0.004-0.0040.0000.0000.0000.000
99A103ASP-1-0.757-0.86934.599-0.110-0.1100.0000.0000.0000.000
100A104ALA00.0330.00336.267-0.006-0.0060.0000.0000.0000.000
101A105LYS10.9100.96637.6350.0800.0800.0000.0000.0000.000
102A106GLU-1-0.968-1.01336.249-0.100-0.1000.0000.0000.0000.000
103A107ALA00.0690.06134.794-0.003-0.0030.0000.0000.0000.000
104A108LEU00.0550.03735.888-0.004-0.0040.0000.0000.0000.000
105A109ARG10.8710.93538.0330.0950.0950.0000.0000.0000.000
106A110LEU0-0.046-0.02233.4790.0030.0030.0000.0000.0000.000
107A111SER0-0.084-0.03734.276-0.008-0.0080.0000.0000.0000.000
108A112PRO0-0.035-0.02236.4110.0000.0000.0000.0000.0000.000
109A113ASN0-0.015-0.00239.0710.0050.0050.0000.0000.0000.000
110A114ASP-1-0.818-0.92834.189-0.160-0.1600.0000.0000.0000.000
111A115LYS10.9400.95737.6320.1260.1260.0000.0000.0000.000
112A116GLY00.0570.05435.7450.0040.0040.0000.0000.0000.000
113A117ILE00.0090.00634.5500.0050.0050.0000.0000.0000.000
114A118VAL00.001-0.01137.3750.0060.0060.0000.0000.0000.000
115A119GLU-1-0.953-0.96439.429-0.113-0.1130.0000.0000.0000.000
116A120VAL0-0.036-0.00536.6030.0030.0030.0000.0000.0000.000
117A121LEU0-0.015-0.00839.9230.0060.0060.0000.0000.0000.000
118A122GLN0-0.004-0.00142.3130.0070.0070.0000.0000.0000.000
119A123ARG10.9520.97237.7630.1150.1150.0000.0000.0000.000
120A124LEU0-0.010-0.02539.1170.0040.0040.0000.0000.0000.000
121A125VAL00.0140.01443.5380.0040.0040.0000.0000.0000.000
122A126LYS10.8910.96146.9760.0670.0670.0000.0000.0000.000
123A127ALA00.0630.04245.0710.0020.0020.0000.0000.0000.000
124A128ASN0-0.013-0.04244.8930.0020.0020.0000.0000.0000.000
125A129ASN0-0.027-0.00747.9930.0030.0030.0000.0000.0000.000
126A130ASP-1-0.876-0.93650.625-0.054-0.0540.0000.0000.0000.000
127A131LYS10.8880.94346.4000.0640.0640.0000.0000.0000.000
128A132ILE00.0030.01249.7420.0010.0010.0000.0000.0000.000
129A133LYS10.9500.96152.2370.0470.0470.0000.0000.0000.000
130A134GLN00.0470.04949.2880.0020.0020.0000.0000.0000.000
131A135THR0-0.021-0.01148.6570.0010.0010.0000.0000.0000.000
132A136THR0-0.032-0.02951.2090.0020.0020.0000.0000.0000.000
133A137SER00.0720.03954.3520.0020.0020.0000.0000.0000.000
134A138LEU0-0.0120.01048.4890.0010.0010.0000.0000.0000.000
135A139ALA0-0.019-0.00953.0450.0010.0010.0000.0000.0000.000
136A140ASN00.0170.00153.8180.0010.0010.0000.0000.0000.000
137A141LYS11.0061.01652.5470.0470.0470.0000.0000.0000.000
138A142VAL0-0.017-0.02951.2510.0010.0010.0000.0000.0000.000
139A143THR00.0240.01554.1720.0020.0020.0000.0000.0000.000
140A144ASP-1-0.898-0.94556.984-0.028-0.0280.0000.0000.0000.000
141A145MET0-0.062-0.03353.6140.0010.0010.0000.0000.0000.000
142A146GLU-1-0.968-0.98554.196-0.028-0.0280.0000.0000.0000.000
143A147LYS10.8800.93856.4900.0270.0270.0000.0000.0000.000
144A148LEU0-0.021-0.00560.1730.0010.0010.0000.0000.0000.000
145A149ALA00.0080.00756.0520.0010.0010.0000.0000.0000.000
146A150PHE00.0510.01551.9860.0010.0010.0000.0000.0000.000
147A151ARG10.9220.97857.4070.0230.0230.0000.0000.0000.000
148A152GLY0-0.007-0.02660.4250.0010.0010.0000.0000.0000.000
149A153GLU-1-0.959-0.94962.809-0.021-0.0210.0000.0000.0000.000
150A154ALA00.0120.00063.307-0.001-0.0010.0000.0000.0000.000
151A155LYS10.8940.94665.1930.0160.0160.0000.0000.0000.000
152A156ASP-1-0.825-0.93266.661-0.020-0.0200.0000.0000.0000.000
153A157THR0-0.0140.00062.247-0.001-0.0010.0000.0000.0000.000
154A158GLU-1-0.897-0.94861.818-0.024-0.0240.0000.0000.0000.000
155A159GLN0-0.0040.00761.201-0.002-0.0020.0000.0000.0000.000
156A160LYS10.8910.96058.7930.0170.0170.0000.0000.0000.000
157A161MET0-0.013-0.00454.886-0.001-0.0010.0000.0000.0000.000
158A162THR00.028-0.00356.560-0.002-0.0020.0000.0000.0000.000
159A163ALA0-0.0410.02356.653-0.002-0.0020.0000.0000.0000.000
160A164LEU00.029-0.00252.802-0.002-0.0020.0000.0000.0000.000
161A165ASN0-0.004-0.00452.484-0.004-0.0040.0000.0000.0000.000
162A166ASN00.0120.00652.090-0.003-0.0030.0000.0000.0000.000
163A167LEU0-0.004-0.00851.389-0.003-0.0030.0000.0000.0000.000
164A168LEU0-0.029-0.00446.510-0.002-0.0020.0000.0000.0000.000
165A169VAL0-0.027-0.02247.639-0.003-0.0030.0000.0000.0000.000
166A170LEU0-0.0260.00348.033-0.003-0.0030.0000.0000.0000.000
167A171CYS0-0.096-0.03045.442-0.003-0.0030.0000.0000.0000.000
168A172ARG10.9670.97942.9250.0470.0470.0000.0000.0000.000
169A173GLU-1-1.019-0.97843.262-0.058-0.0580.0000.0000.0000.000
170A174SER00.0260.01643.054-0.004-0.0040.0000.0000.0000.000
171A175GLU-1-0.856-0.93437.135-0.085-0.0850.0000.0000.0000.000
172A176SER0-0.050-0.03041.2190.0020.0020.0000.0000.0000.000
173A177GLY00.003-0.02144.2370.0040.0040.0000.0000.0000.000
174A178ALA00.1040.05642.0350.0040.0040.0000.0000.0000.000
175A179THR0-0.093-0.06842.3760.0030.0030.0000.0000.0000.000
176A180GLY0-0.042-0.00843.9990.0030.0030.0000.0000.0000.000
177A181VAL00.0510.02447.0850.0030.0030.0000.0000.0000.000
178A182TRP0-0.013-0.01142.5050.0020.0020.0000.0000.0000.000
179A183ASN00.0180.01246.1760.0020.0020.0000.0000.0000.000
180A184GLN0-0.067-0.05345.6940.0040.0040.0000.0000.0000.000
181A185GLY00.0280.02145.9400.0010.0010.0000.0000.0000.000
182A186ALA0-0.053-0.02846.5380.0030.0030.0000.0000.0000.000
183A187LEU00.0230.03645.9320.0010.0010.0000.0000.0000.000
184A188VAL00.0190.00145.0720.0010.0010.0000.0000.0000.000
185A189PRO0-0.0040.00647.9960.0020.0020.0000.0000.0000.000
186A190PHE00.019-0.00351.2100.0020.0020.0000.0000.0000.000
187A191VAL00.0560.04547.9760.0010.0010.0000.0000.0000.000
188A192LEU0-0.016-0.02047.3710.0020.0020.0000.0000.0000.000
189A193ASN0-0.126-0.06750.9130.0030.0030.0000.0000.0000.000
190A194LEU00.0470.02853.2720.0010.0010.0000.0000.0000.000
191A195ILE0-0.047-0.01248.0500.0010.0010.0000.0000.0000.000
192A196ASN0-0.023-0.02452.4070.0030.0030.0000.0000.0000.000
193A197ASP-1-0.796-0.83554.682-0.009-0.0090.0000.0000.0000.000
194A198ALA0-0.039-0.04057.5150.0000.0000.0000.0000.0000.000
195A199SER0-0.102-0.07959.0720.0000.0000.0000.0000.0000.000
196A200GLU-1-0.844-0.91757.287-0.017-0.0170.0000.0000.0000.000
197A201ASN00.0520.01957.003-0.001-0.0010.0000.0000.0000.000
198A202GLU-1-0.780-0.91251.911-0.015-0.0150.0000.0000.0000.000
199A203GLU-1-0.854-0.94253.081-0.025-0.0250.0000.0000.0000.000
200A204VAL00.0030.02853.333-0.002-0.0020.0000.0000.0000.000
201A205THR0-0.040-0.01250.708-0.001-0.0010.0000.0000.0000.000
202A206VAL00.0230.00848.128-0.002-0.0020.0000.0000.0000.000
203A207THR0-0.045-0.05948.495-0.003-0.0030.0000.0000.0000.000
204A208ALA00.0270.00248.964-0.002-0.0020.0000.0000.0000.000
205A209ILE0-0.020-0.01244.878-0.001-0.0010.0000.0000.0000.000
206A210ARG10.9480.96444.5850.0290.0290.0000.0000.0000.000
207A211ILE00.0060.00744.633-0.004-0.0040.0000.0000.0000.000
208A212LEU0-0.003-0.01943.734-0.003-0.0030.0000.0000.0000.000
209A213ASP-1-0.887-0.89640.272-0.048-0.0480.0000.0000.0000.000
210A214GLU-1-0.845-0.94140.311-0.067-0.0670.0000.0000.0000.000
211A215THR0-0.057-0.04540.061-0.003-0.0030.0000.0000.0000.000
212A216ILE0-0.035-0.03138.288-0.002-0.0020.0000.0000.0000.000
213A217LYS10.9170.97235.5470.0690.0690.0000.0000.0000.000
214A218ASN0-0.0030.00934.2400.0010.0010.0000.0000.0000.000
215A219SER00.0760.03430.7570.0070.0070.0000.0000.0000.000
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