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: YY2G2

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1764676.322885
FMO2-HF: Nuclear repulsion 1696990.578324
FMO2-HF: Total energy -67685.744561
FMO2-MP2: Total energy -67884.5983


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.
-35.784-34.85913.882-7.056-7.751-0.077
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 : -0.069 / q_NPA : -0.054
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].
3A60GLY00.0370.0093.000-2.458-0.0390.171-1.168-1.422-0.004
4A61ASP-1-0.855-0.9081.968-38.892-40.55313.712-5.859-6.192-0.073
5A62ILE0-0.040-0.0134.6092.4732.640-0.001-0.029-0.1370.000
6A63THR00.003-0.0038.2270.0380.0380.0000.0000.0000.000
7A64PRO0-0.028-0.01610.9070.2900.2900.0000.0000.0000.000
8A65ALA00.0450.02413.7540.1870.1870.0000.0000.0000.000
9A66LYS10.9200.95516.9330.5900.5900.0000.0000.0000.000
10A67ASN0-0.015-0.00419.3330.0750.0750.0000.0000.0000.000
11A68SER0-0.0060.00622.9050.0260.0260.0000.0000.0000.000
12A69GLY00.0220.01626.562-0.030-0.0300.0000.0000.0000.000
13A70SER00.0190.00129.4170.0280.0280.0000.0000.0000.000
14A71LEU0-0.0400.01228.8190.0000.0000.0000.0000.0000.000
15A72VAL00.0680.02932.6170.0020.0020.0000.0000.0000.000
16A73ARG10.8940.95136.3530.2400.2400.0000.0000.0000.000
17A74VAL00.0330.03239.6970.0020.0020.0000.0000.0000.000
18A75THR00.004-0.00842.2590.0060.0060.0000.0000.0000.000
19A76SER0-0.008-0.01446.002-0.005-0.0050.0000.0000.0000.000
20A77SER00.0580.03148.955-0.001-0.0010.0000.0000.0000.000
21A78ALA00.0220.00751.0720.0040.0040.0000.0000.0000.000
22A79THR0-0.015-0.00854.1390.0070.0070.0000.0000.0000.000
23A80ALA00.0320.00854.430-0.005-0.0050.0000.0000.0000.000
24A81GLY0-0.015-0.01553.5810.0030.0030.0000.0000.0000.000
25A82THR0-0.057-0.01951.717-0.001-0.0010.0000.0000.0000.000
26A83GLU-1-0.836-0.92346.662-0.184-0.1840.0000.0000.0000.000
27A84VAL0-0.032-0.00944.5270.0010.0010.0000.0000.0000.000
28A85SER0-0.051-0.04242.383-0.003-0.0030.0000.0000.0000.000
29A86GLY00.0250.01439.8310.0020.0020.0000.0000.0000.000
30A87THR0-0.017-0.01234.987-0.007-0.0070.0000.0000.0000.000
31A88VAL00.0070.01630.7070.0020.0020.0000.0000.0000.000
32A89LEU00.0440.02729.074-0.014-0.0140.0000.0000.0000.000
33A90PHE00.0060.00622.561-0.024-0.0240.0000.0000.0000.000
34A91ASN00.0620.01023.458-0.052-0.0520.0000.0000.0000.000
35A92VAL0-0.033-0.02118.5210.0330.0330.0000.0000.0000.000
36A93ARG10.8150.88320.8420.8270.8270.0000.0000.0000.000
37A94ASN0-0.025-0.01124.0770.0630.0630.0000.0000.0000.000
38A95ALA00.012-0.01227.4810.0070.0070.0000.0000.0000.000
39A96THR0-0.0230.00628.6070.0220.0220.0000.0000.0000.000
40A97GLU-1-0.827-0.91030.604-0.397-0.3970.0000.0000.0000.000
41A98LEU0-0.050-0.02225.174-0.001-0.0010.0000.0000.0000.000
42A99PRO00.0340.02625.825-0.058-0.0580.0000.0000.0000.000
43A100TRP00.0200.00019.226-0.057-0.0570.0000.0000.0000.000
44A101LEU00.0120.00719.614-0.059-0.0590.0000.0000.0000.000
45A102SER00.0540.03120.929-0.097-0.0970.0000.0000.0000.000
46A103GLY0-0.0130.01821.952-0.028-0.0280.0000.0000.0000.000
47A104GLN0-0.023-0.01016.989-0.124-0.1240.0000.0000.0000.000
48A105GLY00.0710.01517.026-0.141-0.1410.0000.0000.0000.000
49A106SER0-0.041-0.02218.081-0.081-0.0810.0000.0000.0000.000
50A107ARG10.8470.93114.7361.0901.0900.0000.0000.0000.000
51A108TYR00.0040.0199.695-0.077-0.0770.0000.0000.0000.000
52A109SER00.0370.02013.2840.3150.3150.0000.0000.0000.000
53A110LYS10.8010.88911.9432.5712.5710.0000.0000.0000.000
54A111TYR0-0.061-0.06214.001-0.207-0.2070.0000.0000.0000.000
55A112ARG10.8820.9269.5681.9251.9250.0000.0000.0000.000
56A113VAL00.0080.00516.360-0.063-0.0630.0000.0000.0000.000
57A114ARG10.8830.94711.5051.0621.0620.0000.0000.0000.000
58A115TYR00.012-0.01317.1360.1030.1030.0000.0000.0000.000
59A116ALA00.0170.01020.693-0.044-0.0440.0000.0000.0000.000
60A117HIS10.8240.91123.9210.4440.4440.0000.0000.0000.000
61A118PHE00.0670.02726.365-0.018-0.0180.0000.0000.0000.000
62A119THR00.0050.00230.7480.0130.0130.0000.0000.0000.000
63A120TRP00.005-0.00234.211-0.017-0.0170.0000.0000.0000.000
64A121GLU-1-0.929-0.96237.126-0.224-0.2240.0000.0000.0000.000
65A122PRO0-0.0150.00438.973-0.002-0.0020.0000.0000.0000.000
66A123ILE0-0.038-0.01941.315-0.003-0.0030.0000.0000.0000.000
67A124VAL0-0.0230.00344.7560.0080.0080.0000.0000.0000.000
68A125GLY00.0620.03247.574-0.001-0.0010.0000.0000.0000.000
69A126SER00.015-0.01350.006-0.002-0.0020.0000.0000.0000.000
70A127ASN0-0.016-0.00250.933-0.002-0.0020.0000.0000.0000.000
71A128THR0-0.035-0.01950.4080.0000.0000.0000.0000.0000.000
72A129ASN00.005-0.00351.388-0.001-0.0010.0000.0000.0000.000
73A130GLY00.0750.03649.790-0.003-0.0030.0000.0000.0000.000
74A131GLU-1-0.940-0.94646.036-0.154-0.1540.0000.0000.0000.000
75A132VAL00.0190.00440.873-0.004-0.0040.0000.0000.0000.000
76A133ALA00.012-0.00340.6130.0060.0060.0000.0000.0000.000
77A134MET0-0.035-0.01934.030-0.006-0.0060.0000.0000.0000.000
78A135ALA0-0.036-0.01234.6070.0100.0100.0000.0000.0000.000
79A136MET0-0.062-0.01826.723-0.014-0.0140.0000.0000.0000.000
80A137LEU00.0200.02031.8310.0190.0190.0000.0000.0000.000
81A138TYR0-0.001-0.05026.945-0.012-0.0120.0000.0000.0000.000
82A139ASP-1-0.776-0.87029.730-0.402-0.4020.0000.0000.0000.000
83A140VAL0-0.014-0.00529.8080.0180.0180.0000.0000.0000.000
84A141ALA0-0.041-0.01632.7750.0140.0140.0000.0000.0000.000
85A142ASP-1-0.935-0.95035.517-0.279-0.2790.0000.0000.0000.000
86A143VAL0-0.052-0.03436.515-0.009-0.0090.0000.0000.0000.000
87A144THR0-0.020-0.01938.9150.0110.0110.0000.0000.0000.000
88A145SER0-0.004-0.01042.1830.0000.0000.0000.0000.0000.000
89A146ILE00.0190.03638.6270.0080.0080.0000.0000.0000.000
90A147THR00.0120.01142.5470.0020.0020.0000.0000.0000.000
91A148ILE00.012-0.01043.433-0.008-0.0080.0000.0000.0000.000
92A149GLU-1-0.906-0.95843.653-0.156-0.1560.0000.0000.0000.000
93A150ARG10.9000.95342.7670.1840.1840.0000.0000.0000.000
94A151LEU0-0.0200.00337.861-0.009-0.0090.0000.0000.0000.000
95A152MET0-0.048-0.02839.308-0.006-0.0060.0000.0000.0000.000
96A153GLN0-0.076-0.02340.8860.0060.0060.0000.0000.0000.000
97A154THR00.0090.01235.512-0.006-0.0060.0000.0000.0000.000
98A155ARG10.8590.90428.6000.3630.3630.0000.0000.0000.000
99A156GLY00.017-0.00332.630-0.017-0.0170.0000.0000.0000.000
100A157GLY00.0400.02433.4070.0010.0010.0000.0000.0000.000
101A158THR0-0.064-0.02335.2260.0080.0080.0000.0000.0000.000
102A159TRP00.0490.02737.756-0.008-0.0080.0000.0000.0000.000
103A160GLY0-0.027-0.00941.1380.0030.0030.0000.0000.0000.000
104A161PRO00.0420.01643.705-0.004-0.0040.0000.0000.0000.000
105A162ILE00.0280.02044.985-0.005-0.0050.0000.0000.0000.000
106A163TRP00.0150.03744.946-0.007-0.0070.0000.0000.0000.000
107A164SER0-0.037-0.02342.6280.0060.0060.0000.0000.0000.000
108A165PRO00.0300.01438.719-0.007-0.0070.0000.0000.0000.000
109A166THR0-0.0110.00236.3310.0050.0050.0000.0000.0000.000
110A167ARG10.9310.95837.0350.1400.1400.0000.0000.0000.000
111A168LYS10.8490.93834.6360.2390.2390.0000.0000.0000.000
112A169ARG10.8620.90328.8490.2970.2970.0000.0000.0000.000
113A170LEU00.0450.05430.7800.0050.0050.0000.0000.0000.000
114A171SER0-0.043-0.04826.599-0.015-0.0150.0000.0000.0000.000
115A172TYR00.0370.03220.5110.0070.0070.0000.0000.0000.000
116A173ASP-1-0.784-0.84824.517-0.400-0.4000.0000.0000.0000.000
117A174PRO00.0340.00519.162-0.003-0.0030.0000.0000.0000.000
118A175GLU-1-0.879-0.93920.625-0.426-0.4260.0000.0000.0000.000
119A176HIS10.7680.86021.9240.4080.4080.0000.0000.0000.000
120A177ALA0-0.0210.00820.3160.0120.0120.0000.0000.0000.000
121A178SER00.0380.01222.402-0.002-0.0020.0000.0000.0000.000
122A179LEU0-0.0140.00519.9380.0150.0150.0000.0000.0000.000
123A180PRO0-0.018-0.00815.064-0.017-0.0170.0000.0000.0000.000
124A181TRP0-0.050-0.0399.801-0.203-0.2030.0000.0000.0000.000
125A182TYR00.0440.04216.3630.0390.0390.0000.0000.0000.000
126A183LEU00.009-0.00317.847-0.158-0.1580.0000.0000.0000.000
127A184SER0-0.017-0.02617.5000.1420.1420.0000.0000.0000.000
128A185GLY00.0150.01819.4710.0070.0070.0000.0000.0000.000
129A186VAL0-0.009-0.01722.7490.0140.0140.0000.0000.0000.000
130A187SER0-0.029-0.00325.6420.0550.0550.0000.0000.0000.000
131A188SER00.0230.01228.188-0.008-0.0080.0000.0000.0000.000
132A189GLY00.0420.01731.6490.0000.0000.0000.0000.0000.000
133A190ALA00.0250.01431.508-0.027-0.0270.0000.0000.0000.000
134A191ALA00.0500.02230.385-0.024-0.0240.0000.0000.0000.000
135A192ALA00.0280.01427.458-0.038-0.0380.0000.0000.0000.000
136A193GLY00.0160.00426.634-0.050-0.0500.0000.0000.0000.000
137A194ASN00.036-0.00326.942-0.045-0.0450.0000.0000.0000.000
138A195ILE0-0.010-0.00322.723-0.041-0.0410.0000.0000.0000.000
139A196GLN0-0.0090.00522.388-0.110-0.1100.0000.0000.0000.000
140A197THR0-0.0400.00323.345-0.043-0.0430.0000.0000.0000.000
141A198PRO0-0.0270.00321.9680.0350.0350.0000.0000.0000.000
142A199PHE0-0.016-0.01823.4110.0350.0350.0000.0000.0000.000
143A200GLN0-0.027-0.02827.595-0.041-0.0410.0000.0000.0000.000
144A201ILE0-0.050-0.02229.0180.0180.0180.0000.0000.0000.000
145A202ALA00.0310.02432.4070.0080.0080.0000.0000.0000.000
146A203TRP0-0.018-0.02935.9890.0130.0130.0000.0000.0000.000
147A204ALA00.0480.00938.6200.0030.0030.0000.0000.0000.000
148A205ALA0-0.024-0.00842.4120.0000.0000.0000.0000.0000.000
149A206GLN00.0040.00144.9680.0040.0040.0000.0000.0000.000
150A207SER00.049-0.01048.7970.0010.0010.0000.0000.0000.000
151A208SER00.0230.02051.1740.0010.0010.0000.0000.0000.000
152A209LEU0-0.034-0.00651.0260.0050.0050.0000.0000.0000.000
153A210VAL00.0240.02453.011-0.004-0.0040.0000.0000.0000.000
154A211SER0-0.023-0.01150.8810.0020.0020.0000.0000.0000.000
155A212THR00.0180.02149.927-0.002-0.0020.0000.0000.0000.000
156A213THR0-0.049-0.04743.771-0.006-0.0060.0000.0000.0000.000
157A214LEU0-0.002-0.00245.2940.0070.0070.0000.0000.0000.000
158A215GLY00.0550.01042.1040.0060.0060.0000.0000.0000.000
159A216ARG10.8660.91836.5040.2560.2560.0000.0000.0000.000
160A217ILE00.0340.02933.5320.0080.0080.0000.0000.0000.000
161A218MET0-0.026-0.00832.377-0.029-0.0290.0000.0000.0000.000
162A219ALA00.0280.00227.629-0.005-0.0050.0000.0000.0000.000
163A220GLU-1-0.835-0.90726.134-0.341-0.3410.0000.0000.0000.000
164A221TYR0-0.064-0.05221.290-0.012-0.0120.0000.0000.0000.000
165A222LEU0-0.022-0.01215.1920.0040.0040.0000.0000.0000.000
166A223VAL0-0.0030.00317.1430.0270.0270.0000.0000.0000.000
167A224GLU-1-0.786-0.85110.802-1.718-1.7180.0000.0000.0000.000
168A225LEU00.0100.00012.9090.1570.1570.0000.0000.0000.000
169A226THR00.008-0.0157.713-0.361-0.3610.0000.0000.0000.000
170A227ASP-1-0.765-0.8708.748-2.322-2.3220.0000.0000.0000.000
171A228PRO00.0270.0128.3170.5040.5040.0000.0000.0000.000
172A229VAL0-0.032-0.01211.2070.0820.0820.0000.0000.0000.000
173A230ASP-1-0.792-0.88814.592-0.679-0.6790.0000.0000.0000.000
174A231VAL0-0.011-0.01717.735-0.011-0.0110.0000.0000.0000.000
175A232THR0-0.055-0.03220.3490.0500.0500.0000.0000.0000.000
176A233ILE0-0.001-0.00119.3550.0380.0380.0000.0000.0000.000
177A234ASN0-0.039-0.00317.6240.0530.0530.0000.0000.0000.000
178A235GLN0-0.041-0.01420.2510.0330.0330.0000.0000.0000.000