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

tag_button

FMODB ID: 37J1L

Calculation Name: 2ZB9-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 2ZB9

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q9RK47

Base Structure: X-ray

Registration Date: 2023-09-27

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1907192.09602
FMO2-HF: Nuclear repulsion 1835606.24766
FMO2-HF: Total energy -71585.84836
FMO2-MP2: Total energy -71799.240426


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:17:GLY)


Summations of interaction energy for fragment #1(A:17:GLY)
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.
-2.6921.58-0.026-2.336-1.9110.003
Interaction energy analysis for fragmet #1(A:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.020
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].
3A19ARG10.8460.9123.603-1.7042.354-0.025-2.287-1.7470.003
4A20PRO00.0930.0584.172-0.133-0.050-0.001-0.012-0.0700.000
5A21ALA0-0.028-0.0204.222-0.0950.0360.000-0.037-0.0940.000
6A22GLU-1-0.873-0.9335.916-1.403-1.4030.0000.0000.0000.000
7A23GLU-1-0.834-0.9167.974-0.190-0.1900.0000.0000.0000.000
8A24VAL00.0370.0189.2720.1120.1120.0000.0000.0000.000
9A25ARG10.7950.8979.5081.2781.2780.0000.0000.0000.000
10A26ALA00.0100.00611.4200.1400.1400.0000.0000.0000.000
11A27GLU-1-0.897-0.93713.813-0.295-0.2950.0000.0000.0000.000
12A28VAL0-0.033-0.02113.9750.0740.0740.0000.0000.0000.000
13A29LEU0-0.048-0.02214.9350.0610.0610.0000.0000.0000.000
14A30HIS00.0040.01417.3540.0360.0360.0000.0000.0000.000
15A31ALA00.0320.01119.2450.0420.0420.0000.0000.0000.000
16A32VAL0-0.090-0.05018.9410.0370.0370.0000.0000.0000.000
17A33GLY00.0260.01121.5220.0310.0310.0000.0000.0000.000
18A34GLU-1-0.892-0.94723.504-0.208-0.2080.0000.0000.0000.000
19A35LEU0-0.0060.01024.4230.0240.0240.0000.0000.0000.000
20A36LEU0-0.064-0.02924.7780.0200.0200.0000.0000.0000.000
21A37LEU0-0.014-0.02426.6840.0170.0170.0000.0000.0000.000
22A38THR0-0.067-0.03229.2120.0180.0180.0000.0000.0000.000
23A39GLU-1-0.762-0.83530.132-0.139-0.1390.0000.0000.0000.000
24A40GLY00.0160.02930.6060.0090.0090.0000.0000.0000.000
25A41THR00.035-0.01327.634-0.002-0.0020.0000.0000.0000.000
26A42ALA0-0.018-0.01128.759-0.008-0.0080.0000.0000.0000.000
27A43GLN00.0030.00130.2520.0070.0070.0000.0000.0000.000
28A44LEU0-0.0200.02822.5650.0000.0000.0000.0000.0000.000
29A45THR00.015-0.00624.9780.0000.0000.0000.0000.0000.000
30A46PHE00.0550.02117.9960.0030.0030.0000.0000.0000.000
31A47GLU-1-0.814-0.89521.073-0.174-0.1740.0000.0000.0000.000
32A48ARG10.7540.84923.4750.1750.1750.0000.0000.0000.000
33A49VAL00.0630.02418.5610.0040.0040.0000.0000.0000.000
34A50ALA0-0.0030.01318.651-0.011-0.0110.0000.0000.0000.000
35A51ARG10.9050.95819.6850.1430.1430.0000.0000.0000.000
36A52VAL0-0.038-0.02122.3700.0160.0160.0000.0000.0000.000
37A53SER00.018-0.00417.193-0.008-0.0080.0000.0000.0000.000
38A54GLY00.0170.02618.0990.0020.0020.0000.0000.0000.000
39A55VAL0-0.027-0.00112.8600.0170.0170.0000.0000.0000.000
40A56SER00.015-0.00514.538-0.016-0.0160.0000.0000.0000.000
41A57LYS10.9380.92615.3400.1160.1160.0000.0000.0000.000
42A58THR0-0.043-0.01114.007-0.041-0.0410.0000.0000.0000.000
43A59THR0-0.018-0.0099.700-0.013-0.0130.0000.0000.0000.000
44A60LEU00.0340.02112.201-0.114-0.1140.0000.0000.0000.000
45A61TYR0-0.003-0.01514.714-0.024-0.0240.0000.0000.0000.000
46A62LYS10.9060.9669.8730.3150.3150.0000.0000.0000.000
47A63TRP0-0.019-0.0046.9600.0500.0500.0000.0000.0000.000
48A64TRP0-0.028-0.02812.369-0.010-0.0100.0000.0000.0000.000
49A65PRO00.0420.02015.9660.0570.0570.0000.0000.0000.000
50A66SER00.0280.00618.2780.0450.0450.0000.0000.0000.000
51A67LYS10.8930.93820.8500.1850.1850.0000.0000.0000.000
52A68GLY00.0380.02123.257-0.008-0.0080.0000.0000.0000.000
53A69ALA00.0380.00818.864-0.008-0.0080.0000.0000.0000.000
54A70LEU0-0.016-0.00317.919-0.034-0.0340.0000.0000.0000.000
55A71ALA00.003-0.01019.972-0.012-0.0120.0000.0000.0000.000
56A72LEU00.0100.00522.5480.0020.0020.0000.0000.0000.000
57A73ASP-1-0.710-0.83815.823-0.757-0.7570.0000.0000.0000.000
58A74GLY00.0340.01219.536-0.019-0.0190.0000.0000.0000.000
59A75TYR00.001-0.00720.6180.0190.0190.0000.0000.0000.000
60A76PHE0-0.022-0.01820.3650.0260.0260.0000.0000.0000.000
61A77HIS10.8450.91217.3400.6140.6140.0000.0000.0000.000
62A78ALA0-0.0070.02420.8920.0100.0100.0000.0000.0000.000
63A79VAL0-0.032-0.01723.8980.0250.0250.0000.0000.0000.000
64A80GLU-1-0.911-0.96219.969-0.471-0.4710.0000.0000.0000.000
65A81ASP-1-0.893-0.94922.968-0.306-0.3060.0000.0000.0000.000
66A82THR0-0.049-0.02725.5510.0250.0250.0000.0000.0000.000
67A83LEU0-0.052-0.01527.8140.0180.0180.0000.0000.0000.000
68A84ALA00.0300.04226.1440.0000.0000.0000.0000.0000.000
69A85PHE0-0.005-0.01227.8330.0170.0170.0000.0000.0000.000
70A86PRO0-0.0320.00830.029-0.004-0.0040.0000.0000.0000.000
71A87ASP-1-0.844-0.93230.946-0.164-0.1640.0000.0000.0000.000
72A88THR0-0.057-0.05932.8660.0050.0050.0000.0000.0000.000
73A89GLY00.0300.02735.9590.0070.0070.0000.0000.0000.000
74A90ASP-1-0.869-0.92437.872-0.094-0.0940.0000.0000.0000.000
75A91VAL00.0240.00137.484-0.005-0.0050.0000.0000.0000.000
76A92ARG10.8170.87439.1370.0840.0840.0000.0000.0000.000
77A93ALA00.0000.00240.572-0.002-0.0020.0000.0000.0000.000
78A94ASP-1-0.729-0.83235.324-0.141-0.1410.0000.0000.0000.000
79A95LEU00.003-0.00535.952-0.009-0.0090.0000.0000.0000.000
80A96LEU0-0.023-0.00337.719-0.003-0.0030.0000.0000.0000.000
81A97ALA0-0.027-0.01236.658-0.001-0.0010.0000.0000.0000.000
82A98GLN00.011-0.00130.8180.0050.0050.0000.0000.0000.000
83A99LEU00.0420.01434.780-0.006-0.0060.0000.0000.0000.000
84A100ARG10.8210.88637.0890.1070.1070.0000.0000.0000.000
85A101ALA00.0190.02633.3190.0020.0020.0000.0000.0000.000
86A102PHE0-0.016-0.02432.379-0.005-0.0050.0000.0000.0000.000
87A103THR00.034-0.00334.4750.0000.0000.0000.0000.0000.000
88A104HIS0-0.0230.00135.2290.0080.0080.0000.0000.0000.000
89A105VAL0-0.008-0.01231.0100.0020.0020.0000.0000.0000.000
90A106MET0-0.047-0.01933.583-0.005-0.0050.0000.0000.0000.000
91A107THR0-0.020-0.01535.8610.0070.0070.0000.0000.0000.000
92A108ARG10.8760.94538.0940.1160.1160.0000.0000.0000.000
93A109THR00.0020.00932.485-0.003-0.0030.0000.0000.0000.000
94A110PRO00.0310.01532.6810.0010.0010.0000.0000.0000.000
95A111GLY00.020-0.00231.076-0.004-0.0040.0000.0000.0000.000
96A112GLY00.0640.03831.929-0.007-0.0070.0000.0000.0000.000
97A113ARG10.7850.87231.8220.1610.1610.0000.0000.0000.000
98A114ILE0-0.052-0.03028.686-0.001-0.0010.0000.0000.0000.000
99A115LEU0-0.0120.00028.452-0.005-0.0050.0000.0000.0000.000
100A116THR00.020-0.00831.3060.0000.0000.0000.0000.0000.000
101A117GLU-1-0.765-0.84733.853-0.141-0.1410.0000.0000.0000.000
102A118LEU0-0.073-0.02727.370-0.002-0.0020.0000.0000.0000.000
103A119ILE0-0.0160.00031.142-0.002-0.0020.0000.0000.0000.000
104A120GLY00.0340.01632.8910.0050.0050.0000.0000.0000.000
105A121ALA0-0.006-0.00931.9620.0050.0050.0000.0000.0000.000
106A122ALA0-0.028-0.02030.4370.0020.0020.0000.0000.0000.000
107A123GLN0-0.070-0.03532.0120.0060.0060.0000.0000.0000.000
108A124THR0-0.033-0.01334.8380.0090.0090.0000.0000.0000.000
109A125ASP-1-0.874-0.92429.483-0.192-0.1920.0000.0000.0000.000
110A126ALA00.0340.00530.437-0.012-0.0120.0000.0000.0000.000
111A127ASP-1-0.898-0.94925.576-0.230-0.2300.0000.0000.0000.000
112A128LEU0-0.040-0.01325.615-0.030-0.0300.0000.0000.0000.000
113A129ALA00.013-0.00126.751-0.018-0.0180.0000.0000.0000.000
114A130THR0-0.063-0.04623.521-0.006-0.0060.0000.0000.0000.000
115A131ALA00.0260.01522.470-0.025-0.0250.0000.0000.0000.000
116A132TYR00.0200.00723.125-0.029-0.0290.0000.0000.0000.000
117A133ARG10.8960.95825.3570.2260.2260.0000.0000.0000.000
118A134GLN0-0.037-0.03320.038-0.019-0.0190.0000.0000.0000.000
119A135LEU0-0.0210.00417.615-0.039-0.0390.0000.0000.0000.000
120A136TYR00.0430.02120.969-0.006-0.0060.0000.0000.0000.000
121A137SER00.0280.00824.1280.0030.0030.0000.0000.0000.000
122A138ALA0-0.0210.00023.5590.0140.0140.0000.0000.0000.000
123A139GLN00.0390.01218.8370.0050.0050.0000.0000.0000.000
124A140ARG10.8970.95123.6210.2950.2950.0000.0000.0000.000
125A141ARG10.8040.87026.7330.2020.2020.0000.0000.0000.000
126A142ALA0-0.0190.00424.6300.0160.0160.0000.0000.0000.000
127A143LEU00.0260.01223.0300.0110.0110.0000.0000.0000.000
128A144ALA00.0280.01626.9170.0160.0160.0000.0000.0000.000
129A145ALA0-0.029-0.03229.7820.0140.0140.0000.0000.0000.000
130A146GLU-1-0.847-0.90225.235-0.250-0.2500.0000.0000.0000.000
131A147ARG10.8410.92429.5490.1660.1660.0000.0000.0000.000
132A148LEU0-0.012-0.02231.7440.0140.0140.0000.0000.0000.000
133A149ARG10.8100.88927.8610.2160.2160.0000.0000.0000.000
134A150HIS0-0.014-0.00431.7040.0160.0160.0000.0000.0000.000
135A151ALA00.0250.00433.6890.0100.0100.0000.0000.0000.000
136A152ARG10.8270.92335.6630.1360.1360.0000.0000.0000.000
137A153GLU-1-0.964-0.98132.867-0.144-0.1440.0000.0000.0000.000
138A154LEU0-0.056-0.01935.9390.0080.0080.0000.0000.0000.000
139A155GLY0-0.029-0.00939.0130.0060.0060.0000.0000.0000.000
140A156GLN0-0.073-0.05639.922-0.001-0.0010.0000.0000.0000.000
141A157ILE0-0.012-0.00438.3470.0000.0000.0000.0000.0000.000
142A158ARG10.8710.92542.0090.0870.0870.0000.0000.0000.000
143A159PRO00.0700.00941.107-0.005-0.0050.0000.0000.0000.000
144A160ASP-1-0.871-0.92141.001-0.091-0.0910.0000.0000.0000.000
145A161VAL00.0020.01140.1880.0000.0000.0000.0000.0000.000
146A162ASP-1-0.849-0.92436.378-0.146-0.1460.0000.0000.0000.000
147A163VAL00.013-0.01633.4570.0000.0000.0000.0000.0000.000
148A164GLN00.0280.00230.127-0.004-0.0040.0000.0000.0000.000
149A165VAL0-0.0030.01134.873-0.002-0.0020.0000.0000.0000.000
150A166LEU00.0110.00337.5310.0010.0010.0000.0000.0000.000
151A167VAL0-0.008-0.00732.3640.0000.0000.0000.0000.0000.000
152A168ASP-1-0.828-0.89635.691-0.162-0.1620.0000.0000.0000.000
153A169GLN0-0.029-0.01537.6970.0040.0040.0000.0000.0000.000
154A170LEU00.0110.02137.7340.0050.0050.0000.0000.0000.000
155A171TRP00.003-0.01634.0010.0020.0020.0000.0000.0000.000
156A172GLY0-0.0120.00636.5730.0000.0000.0000.0000.0000.000
157A173ALA00.0400.02437.6470.0040.0040.0000.0000.0000.000
158A174VAL00.003-0.00138.1860.0050.0050.0000.0000.0000.000
159A175TYR0-0.017-0.02231.402-0.003-0.0030.0000.0000.0000.000
160A176HIS00.0090.01437.939-0.001-0.0010.0000.0000.0000.000
161A177ARG10.8290.90641.1020.0980.0980.0000.0000.0000.000
162A178LEU0-0.052-0.02637.4010.0020.0020.0000.0000.0000.000
163A179LEU0-0.060-0.04136.423-0.001-0.0010.0000.0000.0000.000
164A180ILE0-0.041-0.00840.4820.0030.0030.0000.0000.0000.000
165A181PRO0-0.025-0.00343.6790.0020.0020.0000.0000.0000.000
166A182ASP-1-0.917-0.94646.039-0.083-0.0830.0000.0000.0000.000
167A183GLU-1-0.925-0.96348.011-0.077-0.0770.0000.0000.0000.000
168A184PRO0-0.0050.00347.003-0.005-0.0050.0000.0000.0000.000
169A185VAL00.0140.00341.026-0.001-0.0010.0000.0000.0000.000
170A186ASP-1-0.862-0.93744.018-0.093-0.0930.0000.0000.0000.000
171A187ASP-1-0.760-0.86443.828-0.105-0.1050.0000.0000.0000.000
172A188ALA00.0050.01845.3240.0000.0000.0000.0000.0000.000
173A189PHE0-0.004-0.00242.6160.0000.0000.0000.0000.0000.000
174A190VAL00.0170.00240.930-0.001-0.0010.0000.0000.0000.000
175A191THR0-0.031-0.04143.436-0.002-0.0020.0000.0000.0000.000
176A192ALA0-0.0060.00745.5490.0010.0010.0000.0000.0000.000
177A193LEU0-0.058-0.01441.6150.0010.0010.0000.0000.0000.000
178A194VAL00.006-0.00341.105-0.001-0.0010.0000.0000.0000.000
179A195THR00.0180.00943.7680.0010.0010.0000.0000.0000.000
180A196ASN0-0.026-0.01047.3470.0050.0050.0000.0000.0000.000
181A197LEU0-0.038-0.00841.6290.0020.0020.0000.0000.0000.000
182A198LEU0-0.056-0.02841.8540.0010.0010.0000.0000.0000.000
183A199ASP-1-0.826-0.87345.848-0.081-0.0810.0000.0000.0000.000
184A200GLY0-0.0100.01749.0450.0040.0040.0000.0000.0000.000
185A201VAL00.003-0.01850.5740.0010.0010.0000.0000.0000.000
186A202CYS0-0.059-0.01853.1530.0030.0030.0000.0000.0000.000
187A203PRO00.0430.01556.1130.0000.0000.0000.0000.0000.000
188A204ARG10.9410.97856.3690.0520.0520.0000.0000.0000.000