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: YZV32

Calculation Name: 2HZ6-A-Xray372

Preferred Name: Serine/threonine-protein kinase/endoribonuclease IRE1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZ6

Chain ID: A

ChEMBL ID: CHEMBL1163101

UniProt ID: O75460

Base Structure: X-ray

Registration Date: 2023-06-22

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 268
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3654220.111402
FMO2-HF: Nuclear repulsion 3548325.527679
FMO2-HF: Total energy -105894.583723
FMO2-MP2: Total energy -106206.537498


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:29:PRO)


Summations of interaction energy for fragment #1(A:29:PRO)
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.
-6.664-0.1445.5-3.711-8.309-0.012
Interaction energy analysis for fragmet #1(A:29:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.025
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].
3A31THR0-0.026-0.0142.706-1.0321.9230.060-1.345-1.6710.004
4A32LEU0-0.061-0.0222.638-0.0551.0090.467-0.458-1.0730.000
5A33LEU0-0.0210.0084.930-0.517-0.541-0.001-0.0040.0300.000
6A34PHE0-0.015-0.0074.5150.1020.226-0.001-0.009-0.1140.000
7A35VAL00.007-0.0019.788-0.050-0.0500.0000.0000.0000.000
8A36SER00.0470.04313.3140.0540.0540.0000.0000.0000.000
9A37THR0-0.006-0.01315.8260.0010.0010.0000.0000.0000.000
10A38LEU00.0540.00819.010-0.001-0.0010.0000.0000.0000.000
11A39ASP-1-0.834-0.88220.8590.0620.0620.0000.0000.0000.000
12A40GLY00.0260.02619.8450.0090.0090.0000.0000.0000.000
13A41SER0-0.125-0.07116.9990.0130.0130.0000.0000.0000.000
14A42LEU00.0070.02510.524-0.031-0.0310.0000.0000.0000.000
15A43HIS00.008-0.00311.8450.1180.1180.0000.0000.0000.000
16A44ALA00.0410.0496.554-0.105-0.1050.0000.0000.0000.000
17A45VAL0-0.002-0.0068.2780.1950.1950.0000.0000.0000.000
18A46SER0-0.0200.0058.126-0.092-0.0920.0000.0000.0000.000
19A47LYS10.8690.9386.4930.9260.9260.0000.0000.0000.000
20A48ARG10.8870.93510.1320.0040.0040.0000.0000.0000.000
21A49THR00.020-0.02012.3100.0010.0010.0000.0000.0000.000
22A50GLY00.1240.04912.439-0.041-0.0410.0000.0000.0000.000
23A51SER0-0.044-0.02413.152-0.014-0.0140.0000.0000.0000.000
24A52ILE00.0110.00811.2970.0760.0760.0000.0000.0000.000
25A53LYS10.8350.9327.505-1.387-1.3870.0000.0000.0000.000
26A54TRP00.0740.0155.801-0.194-0.1940.0000.0000.0000.000
27A55THR0-0.008-0.01510.682-0.040-0.0400.0000.0000.0000.000
28A56LEU0-0.0160.00211.3670.0220.0220.0000.0000.0000.000
29A57LYS10.7860.88214.126-0.118-0.1180.0000.0000.0000.000
30A58GLU-1-0.820-0.89316.5710.0480.0480.0000.0000.0000.000
31A59ASP-1-0.881-0.93219.444-0.008-0.0080.0000.0000.0000.000
32A60PRO0-0.014-0.00321.057-0.012-0.0120.0000.0000.0000.000
33A61VAL0-0.005-0.00520.201-0.007-0.0070.0000.0000.0000.000
34A62LEU00.0060.02122.799-0.010-0.0100.0000.0000.0000.000
35A63GLN0-0.002-0.01326.5930.0040.0040.0000.0000.0000.000
36A64VAL0-0.031-0.01429.504-0.001-0.0010.0000.0000.0000.000
37A65PRO00.0370.04732.5820.0040.0040.0000.0000.0000.000
38A66THR0-0.037-0.04335.1970.0020.0020.0000.0000.0000.000
39A67HIS0-0.031-0.01136.8180.0000.0000.0000.0000.0000.000
40A68VAL00.0230.02741.239-0.001-0.0010.0000.0000.0000.000
41A69GLU-1-1.006-0.99843.482-0.015-0.0150.0000.0000.0000.000
42A70GLU-1-0.924-0.96539.784-0.011-0.0110.0000.0000.0000.000
43A71PRO0-0.038-0.00339.212-0.002-0.0020.0000.0000.0000.000
44A72ALA00.017-0.01938.640-0.001-0.0010.0000.0000.0000.000
45A73PHE0-0.037-0.03235.481-0.002-0.0020.0000.0000.0000.000
46A74LEU0-0.053-0.02834.1040.0020.0020.0000.0000.0000.000
47A75PRO00.0290.00729.013-0.005-0.0050.0000.0000.0000.000
48A76ASP-1-0.719-0.88827.024-0.078-0.0780.0000.0000.0000.000
49A77PRO0-0.031-0.04124.271-0.010-0.0100.0000.0000.0000.000
50A78ASN0-0.005-0.01122.0300.0000.0000.0000.0000.0000.000
51A79ASP-1-0.811-0.87922.470-0.143-0.1430.0000.0000.0000.000
52A80GLY0-0.0020.00823.7580.0020.0020.0000.0000.0000.000
53A81SER0-0.059-0.04526.6750.0080.0080.0000.0000.0000.000
54A82LEU0-0.016-0.00529.2410.0070.0070.0000.0000.0000.000
55A83TYR0-0.005-0.01230.348-0.001-0.0010.0000.0000.0000.000
56A84THR0-0.0030.01335.6090.0020.0020.0000.0000.0000.000
57A85LEU00.0570.01039.0740.0000.0000.0000.0000.0000.000
58A86GLY00.0060.02041.8150.0010.0010.0000.0000.0000.000
59A87SER00.002-0.01541.5880.0010.0010.0000.0000.0000.000
60A88LYS10.8160.91640.6240.0470.0470.0000.0000.0000.000
61A89ASN00.034-0.00942.7940.0000.0000.0000.0000.0000.000
62A90ASN0-0.046-0.01246.5890.0000.0000.0000.0000.0000.000
63A91GLH00.0110.00745.0080.0010.0010.0000.0000.0000.000
64A92GLY00.0260.03544.5940.0010.0010.0000.0000.0000.000
65A93LEU00.0230.02136.8260.0000.0000.0000.0000.0000.000
66A94THR00.0170.01039.524-0.001-0.0010.0000.0000.0000.000
67A95LYS10.9010.94129.7050.0920.0920.0000.0000.0000.000
68A96LEU0-0.062-0.02435.5450.0000.0000.0000.0000.0000.000
69A97PRO0-0.011-0.02235.140-0.003-0.0030.0000.0000.0000.000
70A98PHE00.0090.02232.645-0.003-0.0030.0000.0000.0000.000
71A99THR0-0.022-0.03727.3760.0070.0070.0000.0000.0000.000
72A100ILE0-0.0030.00027.6060.0050.0050.0000.0000.0000.000
73A101PRO00.0500.01124.6430.0060.0060.0000.0000.0000.000
74A102GLU-1-0.826-0.87027.399-0.112-0.1120.0000.0000.0000.000
75A103LEU0-0.032-0.00730.0010.0050.0050.0000.0000.0000.000
76A104VAL00.0110.01028.6260.0060.0060.0000.0000.0000.000
77A105GLN0-0.101-0.04725.757-0.001-0.0010.0000.0000.0000.000
78A106ALA0-0.046-0.03930.500-0.003-0.0030.0000.0000.0000.000
79A107SER0-0.032-0.00634.1820.0080.0080.0000.0000.0000.000
80A108PRO0-0.009-0.02135.458-0.002-0.0020.0000.0000.0000.000
81A109CYS0-0.0260.02038.552-0.001-0.0010.0000.0000.0000.000
82A110ARG10.9720.97740.6230.0420.0420.0000.0000.0000.000
83A111SER00.004-0.00543.317-0.001-0.0010.0000.0000.0000.000
84A112SER0-0.026-0.02245.3720.0020.0020.0000.0000.0000.000
85A113ASP-1-0.765-0.85941.059-0.042-0.0420.0000.0000.0000.000
86A114GLY00.0710.03742.3260.0020.0020.0000.0000.0000.000
87A115ILE0-0.121-0.05343.337-0.001-0.0010.0000.0000.0000.000
88A116LEU0-0.026-0.02842.634-0.001-0.0010.0000.0000.0000.000
89A117TYR00.0020.01537.0070.0020.0020.0000.0000.0000.000
90A118MET0-0.030-0.01636.609-0.002-0.0020.0000.0000.0000.000
91A119GLY00.0660.03032.738-0.001-0.0010.0000.0000.0000.000
92A120LYS10.8010.87828.0740.0560.0560.0000.0000.0000.000
93A121LYS10.8490.92021.8340.1530.1530.0000.0000.0000.000
94A122GLN0-0.0430.00223.148-0.014-0.0140.0000.0000.0000.000
95A123ASP-1-0.781-0.87819.679-0.166-0.1660.0000.0000.0000.000
96A124ILE00.0090.01217.6640.0130.0130.0000.0000.0000.000
97A125TRP0-0.012-0.02111.893-0.040-0.0400.0000.0000.0000.000
98A126TYR0-0.063-0.05712.5420.0280.0280.0000.0000.0000.000
99A127VAL0-0.019-0.01111.064-0.070-0.0700.0000.0000.0000.000
100A128ILE00.0220.0008.3210.0530.0530.0000.0000.0000.000
101A129ASP-1-0.902-0.9357.3570.4820.4820.0000.0000.0000.000
102A130LEU0-0.046-0.0092.287-0.4700.0081.962-0.604-1.835-0.003
103A153LEU0-0.044-0.0316.5330.1410.1410.0000.0000.0000.000
104A154LEU0-0.056-0.0263.060-0.735-0.3500.054-0.092-0.3480.000
105A155TYR00.0360.0086.4540.2260.2260.0000.0000.0000.000
106A156LEU0-0.008-0.0058.749-0.111-0.1110.0000.0000.0000.000
107A157GLY00.0680.04110.3380.0880.0880.0000.0000.0000.000
108A158ARG10.8240.92713.9510.0460.0460.0000.0000.0000.000
109A159THR0-0.024-0.03116.6890.0030.0030.0000.0000.0000.000
110A160GLU-1-0.773-0.85120.366-0.051-0.0510.0000.0000.0000.000
111A161TYR00.0160.00421.6640.0040.0040.0000.0000.0000.000
112A162THR0-0.027-0.02326.1410.0070.0070.0000.0000.0000.000
113A163ILE0-0.0140.00329.643-0.002-0.0020.0000.0000.0000.000
114A164THR0-0.043-0.04032.6700.0070.0070.0000.0000.0000.000
115A165MET0-0.0200.03136.378-0.002-0.0020.0000.0000.0000.000
116A166TYR00.0630.02039.5400.0030.0030.0000.0000.0000.000
117A167ASP-1-0.764-0.87042.930-0.029-0.0290.0000.0000.0000.000
118A168THR00.019-0.00246.5950.0010.0010.0000.0000.0000.000
119A169LYS10.8080.89648.9490.0290.0290.0000.0000.0000.000
120A170THR0-0.0030.00948.5720.0010.0010.0000.0000.0000.000
121A171ARG10.8600.90548.6210.0220.0220.0000.0000.0000.000
122A172GLU-1-0.820-0.89044.368-0.016-0.0160.0000.0000.0000.000
123A173LEU0-0.039-0.03338.850-0.003-0.0030.0000.0000.0000.000
124A174ARG10.7820.87741.7640.0350.0350.0000.0000.0000.000
125A175TRP00.0410.01232.960-0.001-0.0010.0000.0000.0000.000
126A176ASN0-0.004-0.01834.0060.0000.0000.0000.0000.0000.000
127A177ALA00.0390.01630.7920.0010.0010.0000.0000.0000.000
128A178THR0-0.009-0.02326.8570.0000.0000.0000.0000.0000.000
129A179TYR0-0.084-0.04421.5840.0120.0120.0000.0000.0000.000
130A180PHE00.0580.02720.463-0.011-0.0110.0000.0000.0000.000
131A181ASP-1-0.832-0.91618.491-0.191-0.1910.0000.0000.0000.000
132A182TYR0-0.018-0.00913.326-0.001-0.0010.0000.0000.0000.000
133A183ALA00.0030.00714.790-0.008-0.0080.0000.0000.0000.000
134A184ALA0-0.032-0.02812.969-0.065-0.0650.0000.0000.0000.000
135A185SER0-0.039-0.02412.5900.0390.0390.0000.0000.0000.000
136A186LEU00.029-0.00615.119-0.009-0.0090.0000.0000.0000.000
137A187PRO0-0.0470.00116.788-0.038-0.0380.0000.0000.0000.000
138A188GLU-1-0.935-0.97417.386-0.286-0.2860.0000.0000.0000.000
139A189ASP-1-0.900-0.95118.172-0.265-0.2650.0000.0000.0000.000
140A190ASP-1-0.799-0.87914.907-0.486-0.4860.0000.0000.0000.000
141A191DVA0-0.036-0.02617.754-0.002-0.0020.0000.0000.0000.000
142A192ASP-1-0.934-0.97713.081-0.556-0.5560.0000.0000.0000.000
143A193TYR0-0.039-0.03311.619-0.043-0.0430.0000.0000.0000.000
144A194LYS10.8250.89115.7220.2570.2570.0000.0000.0000.000
145A195MET0-0.0230.01812.3480.0440.0440.0000.0000.0000.000
146A196SER00.0560.03017.304-0.015-0.0150.0000.0000.0000.000
147A197HIS00.0070.01614.114-0.030-0.0300.0000.0000.0000.000
148A198PHE00.0130.00919.183-0.007-0.0070.0000.0000.0000.000
149A199VAL00.0230.01020.0530.0140.0140.0000.0000.0000.000
150A200SER00.0240.03322.7770.0000.0000.0000.0000.0000.000
151A201ASN00.0030.01425.163-0.002-0.0020.0000.0000.0000.000
152A202GLY0-0.001-0.00227.2260.0050.0050.0000.0000.0000.000
153A203ASP-1-0.786-0.92726.0300.0380.0380.0000.0000.0000.000
154A204GLY00.0020.02222.109-0.011-0.0110.0000.0000.0000.000
155A205LEU0-0.0350.01021.3240.0140.0140.0000.0000.0000.000
156A206VAL0-0.010-0.01717.200-0.017-0.0170.0000.0000.0000.000
157A207VAL0-0.023-0.02020.5340.0190.0190.0000.0000.0000.000
158A208THR00.0080.00515.538-0.036-0.0360.0000.0000.0000.000
159A209VAL0-0.046-0.01018.7590.0220.0220.0000.0000.0000.000
160A210ASP-1-0.850-0.92519.339-0.126-0.1260.0000.0000.0000.000
161A211SER00.011-0.00119.7340.0150.0150.0000.0000.0000.000
162A212GLU-1-0.926-0.94021.125-0.156-0.1560.0000.0000.0000.000
163A213SER0-0.057-0.06023.2830.0120.0120.0000.0000.0000.000
164A214GLY00.0530.03924.5180.0010.0010.0000.0000.0000.000
165A215ASP-1-0.837-0.88423.988-0.020-0.0200.0000.0000.0000.000
166A216VAL00.001-0.01722.403-0.007-0.0070.0000.0000.0000.000
167A217LEU0-0.062-0.04116.3180.0100.0100.0000.0000.0000.000
168A218TRP0-0.024-0.01613.0630.0350.0350.0000.0000.0000.000
169A219ILE0-0.0020.01419.243-0.021-0.0210.0000.0000.0000.000
170A220GLN0-0.058-0.02816.2750.0340.0340.0000.0000.0000.000
171A221ASN00.0290.00819.711-0.028-0.0280.0000.0000.0000.000
172A222TYR0-0.056-0.04414.5560.0040.0040.0000.0000.0000.000
173A223ALA00.001-0.00619.792-0.013-0.0130.0000.0000.0000.000
174A224SER00.0080.01021.062-0.014-0.0140.0000.0000.0000.000
175A225PRO00.017-0.00221.1170.0020.0020.0000.0000.0000.000
176A226VAL0-0.008-0.00217.1690.0000.0000.0000.0000.0000.000
177A227VAL0-0.035-0.02219.127-0.006-0.0060.0000.0000.0000.000
178A228ALA00.0100.00817.008-0.016-0.0160.0000.0000.0000.000
179A229PHE00.0420.01813.6890.0300.0300.0000.0000.0000.000
180A230TYR0-0.013-0.01010.552-0.021-0.0210.0000.0000.0000.000
181A231VAL00.0450.0168.113-0.015-0.0150.0000.0000.0000.000
182A232TRP00.0120.0122.349-2.565-1.0272.959-1.199-3.298-0.013
183A233GLN00.0220.0205.299-0.626-0.6260.0000.0000.0000.000
184A234ARG10.8470.9107.4520.9190.9190.0000.0000.0000.000
185A235GLU-1-0.930-0.9615.290-1.131-1.1310.0000.0000.0000.000
186A236GLY00.0650.0185.9350.3620.3620.0000.0000.0000.000
187A237LEU0-0.066-0.0307.259-0.096-0.0960.0000.0000.0000.000
188A238ARG10.8490.9369.1900.6520.6520.0000.0000.0000.000
189A239LYS10.9440.97711.7500.1980.1980.0000.0000.0000.000
190A240VAL0-0.018-0.01112.678-0.001-0.0010.0000.0000.0000.000
191A241MET0-0.0070.00415.4540.0400.0400.0000.0000.0000.000
192A242HIS0-0.049-0.02518.632-0.024-0.0240.0000.0000.0000.000
193A243ILE0-0.011-0.01220.5150.0070.0070.0000.0000.0000.000
194A244ASN0-0.0100.00823.8000.0030.0030.0000.0000.0000.000
195A245VAL0-0.035-0.01125.9650.0010.0010.0000.0000.0000.000
196A246ALA00.0960.05427.8350.0030.0030.0000.0000.0000.000
197A247VAL00.0170.00627.7940.0020.0020.0000.0000.0000.000
198A248GLU-1-0.885-0.93629.795-0.002-0.0020.0000.0000.0000.000
199A249THR00.036-0.01431.3620.0020.0020.0000.0000.0000.000
200A250LEU0-0.010-0.00124.2360.0000.0000.0000.0000.0000.000
201A251ARG10.8920.95328.571-0.015-0.0150.0000.0000.0000.000
202A252TYR0-0.010-0.01730.2250.0040.0040.0000.0000.0000.000
203A253LEU0-0.001-0.00129.2640.0010.0010.0000.0000.0000.000
204A254THR0-0.011-0.02326.4160.0010.0010.0000.0000.0000.000
205A255PHE0-0.041-0.01828.7420.0050.0050.0000.0000.0000.000
206A256MET00.0200.01532.1400.0020.0020.0000.0000.0000.000
207A257SER0-0.053-0.02628.0920.0040.0040.0000.0000.0000.000
208A258GLY00.0650.01630.4680.0020.0020.0000.0000.0000.000
209A259GLU-1-0.827-0.86631.1710.0270.0270.0000.0000.0000.000
210A260VAL0-0.007-0.01533.3620.0010.0010.0000.0000.0000.000
211A261GLY00.0440.03331.167-0.001-0.0010.0000.0000.0000.000
212A262ARG10.7700.85731.994-0.026-0.0260.0000.0000.0000.000
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