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: V5QM1

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 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 268
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3651215.013235
FMO2-HF: Nuclear repulsion 3545318.394648
FMO2-HF: Total energy -105896.618587
FMO2-MP2: Total energy -106208.305385


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.
-5.5361.5213.025-3.229-6.853-0.01
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 : 0.028
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].
3A31THR0-0.051-0.0262.614-0.7822.1330.087-1.367-1.6350.004
4A32LEU0-0.054-0.0092.7140.1461.2290.294-0.410-0.9670.000
5A33LEU0-0.0120.0075.032-0.554-0.579-0.001-0.0040.0310.000
6A34PHE0-0.016-0.0234.5470.1160.244-0.001-0.009-0.1170.000
7A35VAL00.0240.0069.989-0.037-0.0370.0000.0000.0000.000
8A36SER00.0390.03113.5500.0550.0550.0000.0000.0000.000
9A37THR00.015-0.02216.0110.0010.0010.0000.0000.0000.000
10A38LEU00.0450.01719.3000.0000.0000.0000.0000.0000.000
11A39ASP-1-0.815-0.88520.9340.0320.0320.0000.0000.0000.000
12A40GLY00.0320.03420.3600.0120.0120.0000.0000.0000.000
13A41SER0-0.089-0.04917.1750.0130.0130.0000.0000.0000.000
14A42LEU0-0.031-0.00110.916-0.035-0.0350.0000.0000.0000.000
15A43HIS00.0190.00912.3180.0990.0990.0000.0000.0000.000
16A44ALA00.0120.0356.627-0.106-0.1060.0000.0000.0000.000
17A45VAL0-0.015-0.0088.5650.2160.2160.0000.0000.0000.000
18A46SER00.000-0.0058.100-0.094-0.0940.0000.0000.0000.000
19A47LYS10.8680.9256.1181.2851.2850.0000.0000.0000.000
20A48ARG10.8500.91610.0640.0990.0990.0000.0000.0000.000
21A49THR00.018-0.00612.3230.0190.0190.0000.0000.0000.000
22A50GLY00.0710.02812.931-0.004-0.0040.0000.0000.0000.000
23A51SER0-0.019-0.01312.960-0.001-0.0010.0000.0000.0000.000
24A52ILE00.0290.01811.4470.0660.0660.0000.0000.0000.000
25A53LYS10.8440.9237.785-1.249-1.2490.0000.0000.0000.000
26A54TRP00.0580.0246.471-0.075-0.0750.0000.0000.0000.000
27A55THR0-0.014-0.02611.013-0.040-0.0400.0000.0000.0000.000
28A56LEU00.0330.03511.6470.0160.0160.0000.0000.0000.000
29A57LYS10.7510.84514.290-0.072-0.0720.0000.0000.0000.000
30A58GLU-1-0.812-0.86616.9040.0290.0290.0000.0000.0000.000
31A59ASP-1-0.873-0.93819.825-0.021-0.0210.0000.0000.0000.000
32A60PRO0-0.039-0.01821.552-0.011-0.0110.0000.0000.0000.000
33A61VAL0-0.008-0.00320.481-0.006-0.0060.0000.0000.0000.000
34A62LEU0-0.020-0.01423.115-0.009-0.0090.0000.0000.0000.000
35A63GLN0-0.0030.00026.9340.0050.0050.0000.0000.0000.000
36A64VAL0-0.014-0.00429.647-0.004-0.0040.0000.0000.0000.000
37A65PRO00.0030.02332.9990.0040.0040.0000.0000.0000.000
38A66THR00.000-0.01935.5900.0000.0000.0000.0000.0000.000
39A67HIS0-0.015-0.00637.365-0.001-0.0010.0000.0000.0000.000
40A68VAL00.0090.02341.418-0.001-0.0010.0000.0000.0000.000
41A69GLU-1-0.996-0.99543.619-0.018-0.0180.0000.0000.0000.000
42A70GLU-1-0.905-0.96039.667-0.017-0.0170.0000.0000.0000.000
43A71PRO0-0.0010.00439.483-0.003-0.0030.0000.0000.0000.000
44A72ALA00.009-0.00939.1160.0000.0000.0000.0000.0000.000
45A73PHE0-0.044-0.04035.978-0.002-0.0020.0000.0000.0000.000
46A74LEU0-0.022-0.00134.1130.0020.0020.0000.0000.0000.000
47A75PRO00.0440.00729.161-0.004-0.0040.0000.0000.0000.000
48A76ASP-1-0.753-0.87327.058-0.087-0.0870.0000.0000.0000.000
49A77PRO0-0.023-0.02324.497-0.008-0.0080.0000.0000.0000.000
50A78ASN00.0170.01422.2540.0000.0000.0000.0000.0000.000
51A79ASP-1-0.838-0.88621.749-0.149-0.1490.0000.0000.0000.000
52A80GLY00.0560.04423.745-0.001-0.0010.0000.0000.0000.000
53A81SER0-0.060-0.05426.4900.0080.0080.0000.0000.0000.000
54A82LEU0-0.0170.00329.3140.0060.0060.0000.0000.0000.000
55A83TYR0-0.010-0.02330.2170.0000.0000.0000.0000.0000.000
56A84THR0-0.003-0.00135.6990.0020.0020.0000.0000.0000.000
57A85LEU00.022-0.00139.147-0.001-0.0010.0000.0000.0000.000
58A86GLY00.0180.01441.8740.0020.0020.0000.0000.0000.000
59A87SER00.0090.00942.1400.0010.0010.0000.0000.0000.000
60A88LYS10.8180.92440.5160.0490.0490.0000.0000.0000.000
61A89ASN00.046-0.00342.8690.0010.0010.0000.0000.0000.000
62A90ASN0-0.038-0.00546.7340.0000.0000.0000.0000.0000.000
63A91GLH00.0460.02045.6680.0000.0000.0000.0000.0000.000
64A92GLY00.0290.02844.5130.0020.0020.0000.0000.0000.000
65A93LEU0-0.010-0.00236.670-0.001-0.0010.0000.0000.0000.000
66A94THR00.0020.01139.7220.0000.0000.0000.0000.0000.000
67A95LYS10.8900.93329.6360.0980.0980.0000.0000.0000.000
68A96LEU0-0.047-0.02735.4890.0030.0030.0000.0000.0000.000
69A97PRO0-0.041-0.03934.772-0.004-0.0040.0000.0000.0000.000
70A98PHE00.0080.01732.461-0.001-0.0010.0000.0000.0000.000
71A99THR0-0.016-0.03627.2180.0070.0070.0000.0000.0000.000
72A100ILE0-0.019-0.01927.7440.0050.0050.0000.0000.0000.000
73A101PRO00.0230.00224.7330.0050.0050.0000.0000.0000.000
74A102GLU-1-0.822-0.87527.287-0.115-0.1150.0000.0000.0000.000
75A103LEU0-0.016-0.00830.2050.0050.0050.0000.0000.0000.000
76A104VAL0-0.033-0.00928.6780.0060.0060.0000.0000.0000.000
77A105GLN0-0.072-0.04125.957-0.002-0.0020.0000.0000.0000.000
78A106ALA00.0080.01330.836-0.002-0.0020.0000.0000.0000.000
79A107SER0-0.046-0.01734.2880.0080.0080.0000.0000.0000.000
80A108PRO0-0.004-0.01635.388-0.002-0.0020.0000.0000.0000.000
81A109CYS0-0.0380.01038.5510.0000.0000.0000.0000.0000.000
82A110ARG10.9510.96240.6610.0410.0410.0000.0000.0000.000
83A111SER00.0250.01543.317-0.001-0.0010.0000.0000.0000.000
84A112SER0-0.026-0.02145.3120.0020.0020.0000.0000.0000.000
85A113ASP-1-0.772-0.87541.330-0.045-0.0450.0000.0000.0000.000
86A114GLY00.0930.05142.7060.0020.0020.0000.0000.0000.000
87A115ILE0-0.124-0.04643.748-0.001-0.0010.0000.0000.0000.000
88A116LEU0-0.012-0.01942.6950.0000.0000.0000.0000.0000.000
89A117TYR0-0.0150.00737.6210.0010.0010.0000.0000.0000.000
90A118MET0-0.012-0.02137.207-0.001-0.0010.0000.0000.0000.000
91A119GLY00.0590.02333.1410.0000.0000.0000.0000.0000.000
92A120LYS10.7850.88428.3410.0570.0570.0000.0000.0000.000
93A121LYS10.8560.93421.9330.1480.1480.0000.0000.0000.000
94A122GLN0-0.082-0.03723.517-0.003-0.0030.0000.0000.0000.000
95A123ASP-1-0.789-0.87919.900-0.161-0.1610.0000.0000.0000.000
96A124ILE00.0200.02318.0910.0080.0080.0000.0000.0000.000
97A125TRP0-0.013-0.01811.921-0.041-0.0410.0000.0000.0000.000
98A126TYR0-0.063-0.04812.6880.0240.0240.0000.0000.0000.000
99A127VAL00.003-0.01711.031-0.069-0.0690.0000.0000.0000.000
100A128ILE00.0110.0108.4290.0410.0410.0000.0000.0000.000
101A129ASP-1-0.919-0.9457.4490.5130.5130.0000.0000.0000.000
102A130LEU0-0.050-0.0192.451-0.5890.1280.663-0.291-1.089-0.002
103A153LEU0-0.033-0.0337.1140.0990.0990.0000.0000.0000.000
104A154LEU0-0.0120.0023.113-0.597-0.2440.041-0.082-0.3130.000
105A155TYR00.0140.0056.3600.1990.1990.0000.0000.0000.000
106A156LEU0-0.027-0.0188.716-0.156-0.1560.0000.0000.0000.000
107A157GLY00.0480.03510.6650.0780.0780.0000.0000.0000.000
108A158ARG10.8460.91514.3320.0570.0570.0000.0000.0000.000
109A159THR0-0.045-0.02716.9920.0080.0080.0000.0000.0000.000
110A160GLU-1-0.761-0.83520.603-0.057-0.0570.0000.0000.0000.000
111A161TYR00.032-0.00321.9340.0010.0010.0000.0000.0000.000
112A162THR00.008-0.01226.5810.0060.0060.0000.0000.0000.000
113A163ILE0-0.013-0.00729.983-0.003-0.0030.0000.0000.0000.000
114A164THR0-0.033-0.02232.9510.0070.0070.0000.0000.0000.000
115A165MET0-0.0180.02536.682-0.003-0.0030.0000.0000.0000.000
116A166TYR00.008-0.00139.8120.0030.0030.0000.0000.0000.000
117A167ASP-1-0.728-0.84443.180-0.030-0.0300.0000.0000.0000.000
118A168THR00.009-0.00146.8930.0010.0010.0000.0000.0000.000
119A169LYS10.8150.90449.6370.0300.0300.0000.0000.0000.000
120A170THR0-0.019-0.02049.2240.0010.0010.0000.0000.0000.000
121A171ARG10.8560.89449.0750.0220.0220.0000.0000.0000.000
122A172GLU-1-0.806-0.88744.534-0.020-0.0200.0000.0000.0000.000
123A173LEU0-0.045-0.04038.906-0.002-0.0020.0000.0000.0000.000
124A174ARG10.7850.86742.1250.0370.0370.0000.0000.0000.000
125A175TRP00.0440.00833.379-0.002-0.0020.0000.0000.0000.000
126A176ASN0-0.031-0.02634.388-0.001-0.0010.0000.0000.0000.000
127A177ALA00.0160.01531.2020.0020.0020.0000.0000.0000.000
128A178THR00.0100.01426.734-0.003-0.0030.0000.0000.0000.000
129A179TYR0-0.051-0.03421.7170.0090.0090.0000.0000.0000.000
130A180PHE00.0290.01020.709-0.004-0.0040.0000.0000.0000.000
131A181ASP-1-0.788-0.86518.194-0.210-0.2100.0000.0000.0000.000
132A182TYR00.003-0.01113.5080.0070.0070.0000.0000.0000.000
133A183ALA0-0.018-0.00814.826-0.015-0.0150.0000.0000.0000.000
134A184ALA0-0.026-0.01713.041-0.066-0.0660.0000.0000.0000.000
135A185SER0-0.032-0.02412.5050.0360.0360.0000.0000.0000.000
136A186LEU00.0350.00115.028-0.016-0.0160.0000.0000.0000.000
137A187PRO0-0.041-0.00216.656-0.041-0.0410.0000.0000.0000.000
138A188GLU-1-0.917-0.96417.782-0.278-0.2780.0000.0000.0000.000
139A189ASP-1-0.909-0.93918.398-0.268-0.2680.0000.0000.0000.000
140A190ASP-1-0.797-0.89714.877-0.476-0.4760.0000.0000.0000.000
141A191DVA0-0.034-0.01917.237-0.011-0.0110.0000.0000.0000.000
142A192ASP-1-0.896-0.95212.622-0.587-0.5870.0000.0000.0000.000
143A193TYR0-0.016-0.02411.392-0.034-0.0340.0000.0000.0000.000
144A194LYS10.7950.88815.1180.2840.2840.0000.0000.0000.000
145A195MET0-0.047-0.01012.5540.0370.0370.0000.0000.0000.000
146A196SER00.0280.00717.207-0.020-0.0200.0000.0000.0000.000
147A197HIS00.0190.00814.352-0.036-0.0360.0000.0000.0000.000
148A198PHE00.0150.01019.541-0.005-0.0050.0000.0000.0000.000
149A199VAL00.006-0.00720.1920.0080.0080.0000.0000.0000.000
150A200SER00.0050.00222.8920.0000.0000.0000.0000.0000.000
151A201ASN00.0170.01225.574-0.002-0.0020.0000.0000.0000.000
152A202GLY00.0040.00426.9760.0040.0040.0000.0000.0000.000
153A203ASP-1-0.828-0.90826.4260.0220.0220.0000.0000.0000.000
154A204GLY00.0220.02422.430-0.012-0.0120.0000.0000.0000.000
155A205LEU0-0.040-0.00721.3690.0060.0060.0000.0000.0000.000
156A206VAL0-0.012-0.01217.545-0.016-0.0160.0000.0000.0000.000
157A207VAL0-0.011-0.00520.9050.0190.0190.0000.0000.0000.000
158A208THR00.0180.02315.483-0.034-0.0340.0000.0000.0000.000
159A209VAL0-0.023-0.00518.7850.0270.0270.0000.0000.0000.000
160A210ASP-1-0.787-0.89819.318-0.158-0.1580.0000.0000.0000.000
161A211SER0-0.0080.01019.6310.0190.0190.0000.0000.0000.000
162A212GLU-1-0.847-0.92021.056-0.170-0.1700.0000.0000.0000.000
163A213SER0-0.125-0.08123.3970.0100.0100.0000.0000.0000.000
164A214GLY00.0550.02424.0780.0030.0030.0000.0000.0000.000
165A215ASP-1-0.814-0.87123.815-0.034-0.0340.0000.0000.0000.000
166A216VAL0-0.007-0.01222.271-0.012-0.0120.0000.0000.0000.000
167A217LEU0-0.048-0.03016.0240.0080.0080.0000.0000.0000.000
168A218TRP0-0.032-0.02112.9490.0400.0400.0000.0000.0000.000
169A219ILE00.0020.01918.895-0.020-0.0200.0000.0000.0000.000
170A220GLN0-0.063-0.02716.3820.0310.0310.0000.0000.0000.000
171A221ASN0-0.015-0.02019.859-0.024-0.0240.0000.0000.0000.000
172A222TYR0-0.018-0.00714.6560.0000.0000.0000.0000.0000.000
173A223ALA00.013-0.00620.138-0.009-0.0090.0000.0000.0000.000
174A224SER00.0020.00721.636-0.009-0.0090.0000.0000.0000.000
175A225PRO00.0020.00721.5200.0000.0000.0000.0000.0000.000
176A226VAL00.005-0.00317.4920.0010.0010.0000.0000.0000.000
177A227VAL0-0.024-0.00719.226-0.001-0.0010.0000.0000.0000.000
178A228ALA00.0140.01217.122-0.011-0.0110.0000.0000.0000.000
179A229PHE00.0230.01713.5300.0260.0260.0000.0000.0000.000
180A230TYR0-0.001-0.02010.799-0.002-0.0020.0000.0000.0000.000
181A231VAL00.0180.0077.690-0.011-0.0110.0000.0000.0000.000
182A232TRP00.0230.0232.635-2.587-0.7011.942-1.066-2.763-0.012
183A233GLN00.000-0.0085.395-0.400-0.4000.0000.0000.0000.000
184A234ARG10.8350.8937.2690.9090.9090.0000.0000.0000.000
185A235GLU-1-0.913-0.9595.252-0.995-0.9950.0000.0000.0000.000
186A236GLY00.0280.0146.6300.2210.2210.0000.0000.0000.000
187A237LEU0-0.040-0.0087.598-0.148-0.1480.0000.0000.0000.000
188A238ARG10.8010.9229.4860.6230.6230.0000.0000.0000.000
189A239LYS10.8790.93211.9360.1870.1870.0000.0000.0000.000
190A240VAL0-0.027-0.01812.852-0.011-0.0110.0000.0000.0000.000
191A241MET00.0040.00815.6580.0420.0420.0000.0000.0000.000
192A242HIS0-0.035-0.02518.939-0.029-0.0290.0000.0000.0000.000
193A243ILE0-0.045-0.02320.7890.0080.0080.0000.0000.0000.000
194A244ASN0-0.018-0.00924.1790.0050.0050.0000.0000.0000.000
195A245VAL0-0.050-0.02425.9810.0010.0010.0000.0000.0000.000
196A246ALA00.0780.04028.3670.0040.0040.0000.0000.0000.000
197A247VAL0-0.011-0.00628.1140.0000.0000.0000.0000.0000.000
198A248GLU-1-0.880-0.93830.096-0.009-0.0090.0000.0000.0000.000
199A249THR00.037-0.01231.3080.0020.0020.0000.0000.0000.000
200A250LEU0-0.0200.00524.3040.0010.0010.0000.0000.0000.000
201A251ARG10.8840.93428.7680.0010.0010.0000.0000.0000.000
202A252TYR0-0.0100.00230.3980.0050.0050.0000.0000.0000.000
203A253LEU00.0200.00229.6560.0020.0020.0000.0000.0000.000
204A254THR0-0.021-0.02126.7300.0000.0000.0000.0000.0000.000
205A255PHE0-0.031-0.01328.9730.0050.0050.0000.0000.0000.000
206A256MET0-0.002-0.00132.3340.0020.0020.0000.0000.0000.000
207A257SER0-0.022-0.01628.2810.0030.0030.0000.0000.0000.000
208A258GLY00.0280.00730.5720.0030.0030.0000.0000.0000.000
209A259GLU-1-0.826-0.87331.2680.0170.0170.0000.0000.0000.000
210A260VAL00.0240.00833.2330.0020.0020.0000.0000.0000.000
211A261GLY00.0310.03530.9610.0000.0000.0000.0000.0000.000
212A262ARG10.7810.85631.906-0.016-0.0160.0000.0000.0000.000
213A263ILE0-0.016-0.00434.2390.0020.0020.0000.0000.0000.000
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