Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 53L6Z

Calculation Name: 2IZW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IZW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9E962

Base Structure: X-ray

Registration Date: 2023-06-21

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1764114.058279
FMO2-HF: Nuclear repulsion 1696428.875114
FMO2-HF: Total energy -67685.183165
FMO2-MP2: Total energy -67884.078867


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:58:GLN)


Summations of interaction energy for fragment #1(A:58:GLN)
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.
-43.825-38.34510.792-8.015-8.257-0.09
Interaction energy analysis for fragmet #1(A:58:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.050
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].
3A60GLY00.0230.0122.658-5.863-3.0140.615-1.504-1.960-0.007
4A61ASP-1-0.828-0.8911.878-43.192-40.72210.178-6.495-6.153-0.083
5A62ILE0-0.045-0.0184.7792.6002.761-0.001-0.016-0.1440.000
6A63THR0-0.0230.0047.8320.4570.4570.0000.0000.0000.000
7A64PRO0-0.0200.00810.5820.2510.2510.0000.0000.0000.000
8A65ALA00.0150.00213.5620.0810.0810.0000.0000.0000.000
9A66LYS10.9290.95516.9130.4930.4930.0000.0000.0000.000
10A67ASN0-0.0070.00719.5750.0730.0730.0000.0000.0000.000
11A68SER0-0.004-0.00223.1030.0180.0180.0000.0000.0000.000
12A69GLY00.0320.01726.607-0.026-0.0260.0000.0000.0000.000
13A70SER00.005-0.00329.5210.0220.0220.0000.0000.0000.000
14A71LEU0-0.0290.00228.806-0.014-0.0140.0000.0000.0000.000
15A72VAL00.0590.02232.5360.0000.0000.0000.0000.0000.000
16A73ARG10.8930.95336.1960.2410.2410.0000.0000.0000.000
17A74VAL00.0330.01639.5900.0000.0000.0000.0000.0000.000
18A75THR0-0.015-0.01742.0530.0080.0080.0000.0000.0000.000
19A76SER0-0.031-0.02445.669-0.003-0.0030.0000.0000.0000.000
20A77SER00.0610.03648.713-0.003-0.0030.0000.0000.0000.000
21A78ALA00.0190.00350.6600.0050.0050.0000.0000.0000.000
22A79THR0-0.022-0.00453.7880.0060.0060.0000.0000.0000.000
23A80ALA00.0450.01354.168-0.004-0.0040.0000.0000.0000.000
24A81GLY0-0.023-0.02053.4830.0030.0030.0000.0000.0000.000
25A82THR0-0.045-0.02051.376-0.001-0.0010.0000.0000.0000.000
26A83GLU-1-0.852-0.94146.527-0.172-0.1720.0000.0000.0000.000
27A84VAL0-0.060-0.01344.284-0.001-0.0010.0000.0000.0000.000
28A85SER0-0.016-0.01642.225-0.004-0.0040.0000.0000.0000.000
29A86GLY00.0200.00339.5690.0000.0000.0000.0000.0000.000
30A87THR0-0.030-0.02135.004-0.005-0.0050.0000.0000.0000.000
31A88VAL0-0.0100.00630.542-0.003-0.0030.0000.0000.0000.000
32A89LEU00.0390.02829.035-0.009-0.0090.0000.0000.0000.000
33A90PHE00.0030.00222.099-0.014-0.0140.0000.0000.0000.000
34A91ASN00.044-0.00323.250-0.052-0.0520.0000.0000.0000.000
35A92VAL0-0.018-0.00818.6620.0290.0290.0000.0000.0000.000
36A93ARG10.8120.90421.2200.8740.8740.0000.0000.0000.000
37A94ASN0-0.014-0.00624.1910.0560.0560.0000.0000.0000.000
38A95ALA00.018-0.01427.4960.0130.0130.0000.0000.0000.000
39A96THR0-0.024-0.00328.7280.0170.0170.0000.0000.0000.000
40A97GLU-1-0.830-0.90330.860-0.381-0.3810.0000.0000.0000.000
41A98LEU0-0.051-0.01625.4150.0060.0060.0000.0000.0000.000
42A99PRO00.0380.02625.953-0.059-0.0590.0000.0000.0000.000
43A100TRP00.012-0.00419.295-0.063-0.0630.0000.0000.0000.000
44A101LEU00.0170.00620.024-0.061-0.0610.0000.0000.0000.000
45A102SER00.0780.03821.143-0.094-0.0940.0000.0000.0000.000
46A103GLY0-0.0540.00721.940-0.042-0.0420.0000.0000.0000.000
47A104GLN0-0.013-0.00817.139-0.126-0.1260.0000.0000.0000.000
48A105GLY00.0750.01617.372-0.134-0.1340.0000.0000.0000.000
49A106SER0-0.058-0.03418.425-0.082-0.0820.0000.0000.0000.000
50A107ARG10.8590.93414.9541.1161.1160.0000.0000.0000.000
51A108TYR0-0.023-0.0149.975-0.060-0.0600.0000.0000.0000.000
52A109SER00.0220.00813.3410.3020.3020.0000.0000.0000.000
53A110LYS10.8230.89612.5322.5342.5340.0000.0000.0000.000
54A111TYR0-0.044-0.05014.231-0.193-0.1930.0000.0000.0000.000
55A112ARG10.8960.9479.8741.6071.6070.0000.0000.0000.000
56A113VAL0-0.014-0.00416.109-0.062-0.0620.0000.0000.0000.000
57A114ARG10.8860.95811.8960.7770.7770.0000.0000.0000.000
58A115TYR00.018-0.01717.3480.0960.0960.0000.0000.0000.000
59A116ALA00.0150.00620.952-0.041-0.0410.0000.0000.0000.000
60A117HIS10.8150.89924.1010.3760.3760.0000.0000.0000.000
61A118PHE00.0600.02126.311-0.012-0.0120.0000.0000.0000.000
62A119THR0-0.007-0.01430.6940.0140.0140.0000.0000.0000.000
63A120TRP00.004-0.00434.061-0.019-0.0190.0000.0000.0000.000
64A121GLU-1-0.925-0.96336.871-0.198-0.1980.0000.0000.0000.000
65A122PRO0-0.0260.00538.740-0.003-0.0030.0000.0000.0000.000
66A123ILE0-0.024-0.00841.401-0.002-0.0020.0000.0000.0000.000
67A124VAL0-0.029-0.00444.6950.0080.0080.0000.0000.0000.000
68A125GLY00.0550.03547.6480.0010.0010.0000.0000.0000.000
69A126SER00.017-0.02249.783-0.002-0.0020.0000.0000.0000.000
70A127ASN0-0.029-0.01250.654-0.002-0.0020.0000.0000.0000.000
71A128THR0-0.032-0.01350.188-0.001-0.0010.0000.0000.0000.000
72A129ASN00.0200.00851.6270.0010.0010.0000.0000.0000.000
73A130GLY00.0490.02249.819-0.004-0.0040.0000.0000.0000.000
74A131GLU-1-0.998-0.99646.168-0.141-0.1410.0000.0000.0000.000
75A132VAL00.0220.00640.993-0.005-0.0050.0000.0000.0000.000
76A133ALA00.0300.00540.4130.0060.0060.0000.0000.0000.000
77A134MET0-0.057-0.02533.735-0.008-0.0080.0000.0000.0000.000
78A135ALA00.0090.01934.7340.0130.0130.0000.0000.0000.000
79A136MET0-0.066-0.02026.605-0.013-0.0130.0000.0000.0000.000
80A137LEU00.0050.01431.6600.0170.0170.0000.0000.0000.000
81A138TYR0-0.031-0.06826.889-0.013-0.0130.0000.0000.0000.000
82A139ASP-1-0.756-0.87029.945-0.377-0.3770.0000.0000.0000.000
83A140VAL0-0.043-0.01129.6070.0150.0150.0000.0000.0000.000
84A141ALA0-0.053-0.01932.3780.0140.0140.0000.0000.0000.000
85A142ASP-1-0.912-0.94035.537-0.264-0.2640.0000.0000.0000.000
86A143VAL0-0.035-0.03036.335-0.008-0.0080.0000.0000.0000.000
87A144THR0-0.019-0.01238.7880.0080.0080.0000.0000.0000.000
88A145SER0-0.023-0.02342.0340.0010.0010.0000.0000.0000.000
89A146ILE00.0320.03738.7550.0060.0060.0000.0000.0000.000
90A147THR00.019-0.00442.6480.0030.0030.0000.0000.0000.000
91A148ILE00.0340.01043.547-0.006-0.0060.0000.0000.0000.000
92A149GLU-1-0.913-0.96243.568-0.141-0.1410.0000.0000.0000.000
93A150ARG10.8980.94742.8280.1760.1760.0000.0000.0000.000
94A151LEU0-0.0310.00137.957-0.007-0.0070.0000.0000.0000.000
95A152MET0-0.044-0.02739.242-0.005-0.0050.0000.0000.0000.000
96A153GLN0-0.087-0.01941.0360.0050.0050.0000.0000.0000.000
97A154THR00.0130.01235.516-0.006-0.0060.0000.0000.0000.000
98A155ARG10.8660.90928.4840.3190.3190.0000.0000.0000.000
99A156GLY00.000-0.01132.833-0.015-0.0150.0000.0000.0000.000
100A157GLY00.0750.03833.720-0.003-0.0030.0000.0000.0000.000
101A158THR0-0.092-0.02235.2840.0120.0120.0000.0000.0000.000
102A159TRP00.0610.02037.862-0.007-0.0070.0000.0000.0000.000
103A160GLY0-0.0080.00241.2030.0030.0030.0000.0000.0000.000
104A161PRO00.0340.01143.933-0.005-0.0050.0000.0000.0000.000
105A162ILE00.0300.02944.764-0.005-0.0050.0000.0000.0000.000
106A163TRP00.0100.03244.614-0.007-0.0070.0000.0000.0000.000
107A164SER0-0.018-0.00642.9280.0050.0050.0000.0000.0000.000
108A165PRO00.0210.00939.117-0.007-0.0070.0000.0000.0000.000
109A166THR0-0.0180.00236.3760.0030.0030.0000.0000.0000.000
110A167ARG10.9540.98337.4080.1230.1230.0000.0000.0000.000
111A168LYS10.8340.92134.6980.2040.2040.0000.0000.0000.000
112A169ARG10.9070.91928.5730.2510.2510.0000.0000.0000.000
113A170LEU00.0040.02930.5040.0070.0070.0000.0000.0000.000
114A171SER0-0.005-0.01626.472-0.019-0.0190.0000.0000.0000.000
115A172TYR00.0540.02120.2890.0010.0010.0000.0000.0000.000
116A173ASP-1-0.780-0.83224.368-0.354-0.3540.0000.0000.0000.000
117A174PRO00.0110.00119.131-0.012-0.0120.0000.0000.0000.000
118A175GLU-1-0.903-0.96220.554-0.354-0.3540.0000.0000.0000.000
119A176HIS10.7860.87521.9730.3360.3360.0000.0000.0000.000
120A177ALA0-0.0070.02219.9410.0040.0040.0000.0000.0000.000
121A178SER00.0100.00122.0350.0110.0110.0000.0000.0000.000
122A179LEU0-0.013-0.01319.7600.0080.0080.0000.0000.0000.000
123A180PRO0-0.032-0.00814.825-0.031-0.0310.0000.0000.0000.000
124A181TRP0-0.037-0.0299.460-0.146-0.1460.0000.0000.0000.000
125A182TYR00.0590.04216.0360.0610.0610.0000.0000.0000.000
126A183LEU00.008-0.00817.905-0.165-0.1650.0000.0000.0000.000
127A184SER0-0.014-0.01617.8610.1570.1570.0000.0000.0000.000
128A185GLY00.0120.00019.721-0.015-0.0150.0000.0000.0000.000
129A186VAL0-0.002-0.01722.8690.0190.0190.0000.0000.0000.000
130A187SER0-0.0280.00626.3550.0490.0490.0000.0000.0000.000
131A188SER00.0330.02128.388-0.005-0.0050.0000.0000.0000.000
132A189GLY00.0340.00731.633-0.004-0.0040.0000.0000.0000.000
133A190ALA00.0400.01831.937-0.020-0.0200.0000.0000.0000.000
134A191ALA00.0440.01730.194-0.023-0.0230.0000.0000.0000.000
135A192ALA00.009-0.00327.674-0.033-0.0330.0000.0000.0000.000
136A193GLY00.0370.02426.912-0.048-0.0480.0000.0000.0000.000
137A194ASN00.019-0.01427.147-0.040-0.0400.0000.0000.0000.000
138A195ILE0-0.031-0.00922.896-0.030-0.0300.0000.0000.0000.000
139A196GLN0-0.023-0.00522.499-0.106-0.1060.0000.0000.0000.000
140A197THR0-0.0400.00423.263-0.049-0.0490.0000.0000.0000.000
141A198PRO0-0.026-0.00321.5350.0380.0380.0000.0000.0000.000
142A199PHE0-0.011-0.00823.1770.0370.0370.0000.0000.0000.000
143A200GLN0-0.012-0.03127.234-0.045-0.0450.0000.0000.0000.000
144A201ILE0-0.062-0.02129.0960.0190.0190.0000.0000.0000.000
145A202ALA00.0410.03932.4550.0030.0030.0000.0000.0000.000
146A203TRP0-0.002-0.02436.0710.0110.0110.0000.0000.0000.000
147A204ALA00.0440.01038.6470.0000.0000.0000.0000.0000.000
148A205ALA0-0.029-0.01242.4240.0020.0020.0000.0000.0000.000
149A206GLN00.0530.04244.8850.0020.0020.0000.0000.0000.000
150A207SER00.049-0.00748.6080.0030.0030.0000.0000.0000.000
151A208SER00.0340.02750.8580.0010.0010.0000.0000.0000.000
152A209LEU0-0.052-0.01951.1480.0040.0040.0000.0000.0000.000
153A210VAL00.0440.02553.102-0.004-0.0040.0000.0000.0000.000
154A211SER0-0.026-0.00250.6910.0000.0000.0000.0000.0000.000
155A212THR00.0260.02750.059-0.003-0.0030.0000.0000.0000.000
156A213THR0-0.030-0.04443.661-0.006-0.0060.0000.0000.0000.000
157A214LEU0-0.0010.00344.7850.0040.0040.0000.0000.0000.000
158A215GLY00.0680.01141.8390.0070.0070.0000.0000.0000.000
159A216ARG10.8700.93336.5930.2460.2460.0000.0000.0000.000
160A217ILE00.0400.03633.2990.0080.0080.0000.0000.0000.000
161A218MET0-0.026-0.00832.072-0.028-0.0280.0000.0000.0000.000
162A219ALA00.0430.01727.433-0.002-0.0020.0000.0000.0000.000
163A220GLU-1-0.862-0.91025.920-0.310-0.3100.0000.0000.0000.000
164A221TYR0-0.016-0.02121.058-0.009-0.0090.0000.0000.0000.000
165A222LEU0-0.030-0.01215.0340.0070.0070.0000.0000.0000.000
166A223VAL0-0.006-0.01116.6900.0320.0320.0000.0000.0000.000
167A224GLU-1-0.774-0.86011.026-1.382-1.3820.0000.0000.0000.000
168A225LEU00.015-0.00612.7600.1350.1350.0000.0000.0000.000
169A226THR00.000-0.0207.984-0.371-0.3710.0000.0000.0000.000
170A227ASP-1-0.791-0.8748.684-2.752-2.7520.0000.0000.0000.000
171A228PRO00.0380.0228.4120.5910.5910.0000.0000.0000.000
172A229VAL0-0.029-0.01911.4860.0580.0580.0000.0000.0000.000
173A230ASP-1-0.822-0.90914.821-0.775-0.7750.0000.0000.0000.000
174A231VAL0-0.021-0.02817.6470.0250.0250.0000.0000.0000.000
175A232THR0-0.007-0.00620.1960.0490.0490.0000.0000.0000.000
176A233ILE0-0.039-0.00419.1000.0400.0400.0000.0000.0000.000
177A234ASN0-0.027-0.00918.1640.0760.0760.0000.0000.0000.000
178A235GLN0-0.0190.01220.5560.0460.0460.0000.0000.0000.000