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: 98NZ2

Calculation Name: 2OI8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OI8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KXS8

Base Structure: X-ray

Registration Date: 2023-09-20

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2126141.293086
FMO2-HF: Nuclear repulsion 2047007.849087
FMO2-HF: Total energy -79133.443999
FMO2-MP2: Total energy -79366.049543


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:8:THR)


Summations of interaction energy for fragment #1(A:8:THR)
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.
-12.753-14.93810.526-4.246-4.0940.027
Interaction energy analysis for fragmet #1(A:8:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.012
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].
3A10ARG11.0551.0173.930-0.3280.889-0.013-0.683-0.5200.001
4A11GLU-1-0.848-0.8907.0560.3120.3120.0000.0000.0000.000
5A12ARG10.8690.9102.019-13.026-16.42810.539-3.563-3.5740.026
6A13TYR00.1150.0566.074-0.369-0.3690.0000.0000.0000.000
7A14ARG10.8530.9228.481-0.061-0.0610.0000.0000.0000.000
8A15THR0-0.020-0.0246.0530.3200.3200.0000.0000.0000.000
9A16GLN00.0520.0239.079-0.043-0.0430.0000.0000.0000.000
10A17VAL00.0250.03811.8830.0700.0700.0000.0000.0000.000
11A18ARG10.9210.9627.9510.1750.1750.0000.0000.0000.000
12A19ALA00.0050.00913.2600.0410.0410.0000.0000.0000.000
13A20GLU-1-0.750-0.85914.932-0.217-0.2170.0000.0000.0000.000
14A21ILE0-0.074-0.03916.6860.0400.0400.0000.0000.0000.000
15A22LYS10.8280.88013.7000.2300.2300.0000.0000.0000.000
16A23ASP-1-0.861-0.91718.877-0.263-0.2630.0000.0000.0000.000
17A24HIS10.7290.81020.8960.2090.2090.0000.0000.0000.000
18A25ALA0-0.023-0.01421.9630.0180.0180.0000.0000.0000.000
19A26TRP00.1010.05120.4730.0280.0280.0000.0000.0000.000
20A27GLU-1-0.803-0.86924.968-0.133-0.1330.0000.0000.0000.000
21A28GLN00.0080.00426.7150.0190.0190.0000.0000.0000.000
22A29ILE0-0.0210.00825.1360.0120.0120.0000.0000.0000.000
23A30ALA0-0.008-0.01028.8030.0060.0060.0000.0000.0000.000
24A31THR0-0.102-0.06730.7330.0070.0070.0000.0000.0000.000
25A32ALA0-0.028-0.02332.0510.0050.0050.0000.0000.0000.000
26A33GLY00.0370.03932.1550.0080.0080.0000.0000.0000.000
27A34ALA00.0510.00428.7680.0030.0030.0000.0000.0000.000
28A35SER0-0.047-0.02429.2290.0050.0050.0000.0000.0000.000
29A36ALA0-0.0270.00231.1350.0060.0060.0000.0000.0000.000
30A37LEU0-0.0370.00224.296-0.002-0.0020.0000.0000.0000.000
31A38SER00.013-0.01327.6440.0110.0110.0000.0000.0000.000
32A39LEU00.0530.02021.658-0.015-0.0150.0000.0000.0000.000
33A40ASN00.015-0.00324.969-0.004-0.0040.0000.0000.0000.000
34A41ALA00.0070.01827.692-0.006-0.0060.0000.0000.0000.000
35A42ILE00.0300.02521.811-0.010-0.0100.0000.0000.0000.000
36A43ALA0-0.010-0.00323.923-0.013-0.0130.0000.0000.0000.000
37A44LYS10.9580.97524.9010.0340.0340.0000.0000.0000.000
38A45ARG10.8550.92325.9930.1310.1310.0000.0000.0000.000
39A46MET0-0.058-0.01518.993-0.005-0.0050.0000.0000.0000.000
40A47GLY0-0.0020.01924.181-0.008-0.0080.0000.0000.0000.000
41A48MET0-0.040-0.00918.634-0.005-0.0050.0000.0000.0000.000
42A49SER00.012-0.00624.1210.0100.0100.0000.0000.0000.000
43A50GLY00.0490.00823.7620.0010.0010.0000.0000.0000.000
44A51PRO00.039-0.00423.8370.0030.0030.0000.0000.0000.000
45A52ALA0-0.0020.01520.1840.0180.0180.0000.0000.0000.000
46A53LEU00.0290.00918.9640.0080.0080.0000.0000.0000.000
47A54TYR00.013-0.00819.2870.0050.0050.0000.0000.0000.000
48A55ARG10.7480.87717.082-0.149-0.1490.0000.0000.0000.000
49A56TYR0-0.095-0.05412.4910.0270.0270.0000.0000.0000.000
50A57PHE00.0370.01215.330-0.002-0.0020.0000.0000.0000.000
51A58ASP-1-0.809-0.86318.0380.1580.1580.0000.0000.0000.000
52A59GLY00.020-0.00420.4290.0010.0010.0000.0000.0000.000
53A60ARG10.8480.89822.061-0.036-0.0360.0000.0000.0000.000
54A61ASP-1-0.781-0.89023.6470.0540.0540.0000.0000.0000.000
55A62GLU-1-0.801-0.87517.9780.2140.2140.0000.0000.0000.000
56A63LEU0-0.049-0.01918.875-0.009-0.0090.0000.0000.0000.000
57A64ILE0-0.014-0.00720.130-0.021-0.0210.0000.0000.0000.000
58A65THR00.007-0.00119.061-0.013-0.0130.0000.0000.0000.000
59A66GLU-1-0.867-0.92014.7140.0680.0680.0000.0000.0000.000
60A67LEU0-0.048-0.01017.734-0.034-0.0340.0000.0000.0000.000
61A68ILE00.0450.01320.125-0.017-0.0170.0000.0000.0000.000
62A69ARG10.7720.85315.017-0.136-0.1360.0000.0000.0000.000
63A70ASP-1-0.804-0.87815.409-0.236-0.2360.0000.0000.0000.000
64A71ALA0-0.0150.00218.021-0.023-0.0230.0000.0000.0000.000
65A72TYR00.0450.00921.116-0.012-0.0120.0000.0000.0000.000
66A73ARG10.8870.94314.7010.1460.1460.0000.0000.0000.000
67A74SER00.0250.02219.140-0.012-0.0120.0000.0000.0000.000
68A75GLN00.0220.01020.7940.0010.0010.0000.0000.0000.000
69A76ALA0-0.018-0.01620.7220.0040.0040.0000.0000.0000.000
70A77ASP-1-0.837-0.90718.232-0.232-0.2320.0000.0000.0000.000
71A78SER0-0.047-0.01521.425-0.003-0.0030.0000.0000.0000.000
72A79LEU00.022-0.01324.8580.0030.0030.0000.0000.0000.000
73A80ARG10.7670.86718.5600.1340.1340.0000.0000.0000.000
74A81ALA0-0.023-0.00723.3590.0030.0030.0000.0000.0000.000
75A82ALA00.0170.01424.6680.0030.0030.0000.0000.0000.000
76A83ALA00.0210.00727.0880.0050.0050.0000.0000.0000.000
77A84ALA0-0.045-0.01724.1560.0050.0050.0000.0000.0000.000
78A85SER0-0.067-0.03026.163-0.005-0.0050.0000.0000.0000.000
79A86GLY0-0.035-0.01728.7480.0030.0030.0000.0000.0000.000
80A87ALA0-0.048-0.00531.0710.0060.0060.0000.0000.0000.000
81A88ASP-1-0.778-0.89932.897-0.047-0.0470.0000.0000.0000.000
82A89LEU00.000-0.02234.709-0.004-0.0040.0000.0000.0000.000
83A90ALA00.0050.00835.891-0.002-0.0020.0000.0000.0000.000
84A91GLY00.0450.02434.040-0.004-0.0040.0000.0000.0000.000
85A92LEU0-0.015-0.01730.444-0.008-0.0080.0000.0000.0000.000
86A93ALA0-0.004-0.00632.178-0.003-0.0030.0000.0000.0000.000
87A94HIS0-0.062-0.05434.402-0.005-0.0050.0000.0000.0000.000
88A95ALA0-0.0010.01328.900-0.007-0.0070.0000.0000.0000.000
89A96LEU0-0.038-0.02129.695-0.007-0.0070.0000.0000.0000.000
90A97ARG10.8170.88631.0600.0640.0640.0000.0000.0000.000
91A98ALA00.0220.01530.6850.0000.0000.0000.0000.0000.000
92A99TRP00.0430.01323.6500.0030.0030.0000.0000.0000.000
93A100ALA0-0.009-0.01628.399-0.003-0.0030.0000.0000.0000.000
94A101LEU0-0.057-0.04630.7780.0000.0000.0000.0000.0000.000
95A102ASP-1-0.908-0.92226.273-0.175-0.1750.0000.0000.0000.000
96A103ASP-1-0.835-0.92925.218-0.145-0.1450.0000.0000.0000.000
97A104PRO00.0480.01628.6170.0080.0080.0000.0000.0000.000
98A105GLN0-0.024-0.01628.3070.0140.0140.0000.0000.0000.000
99A106ARG10.7600.88422.9270.1610.1610.0000.0000.0000.000
100A107TYR0-0.0030.00826.5030.0130.0130.0000.0000.0000.000
101A108PHE0-0.015-0.02929.1380.0120.0120.0000.0000.0000.000
102A109LEU0-0.0410.00723.8970.0090.0090.0000.0000.0000.000
103A110ILE0-0.072-0.02524.0230.0110.0110.0000.0000.0000.000
104A111PHE0-0.063-0.04528.0250.0100.0100.0000.0000.0000.000
105A112GLY00.0140.02331.5570.0010.0010.0000.0000.0000.000
106A113THR0-0.059-0.03333.5750.0060.0060.0000.0000.0000.000
107A114PRO00.0450.03131.821-0.001-0.0010.0000.0000.0000.000
108A115VAL00.004-0.00228.236-0.002-0.0020.0000.0000.0000.000
109A116PRO00.0340.00831.3700.0090.0090.0000.0000.0000.000
110A117GLY0-0.020-0.01632.460-0.001-0.0010.0000.0000.0000.000
111A118TYR0-0.072-0.04823.1150.0040.0040.0000.0000.0000.000
112A119ARG10.9270.96228.425-0.099-0.0990.0000.0000.0000.000
113A120ALA00.0300.01224.7760.0060.0060.0000.0000.0000.000
114A121PRO00.0050.00920.9590.0030.0030.0000.0000.0000.000
115A122ASP-1-0.867-0.94423.8110.1330.1330.0000.0000.0000.000
116A123ASP-1-0.849-0.91919.3030.1730.1730.0000.0000.0000.000
117A124ILE0-0.022-0.01720.735-0.015-0.0150.0000.0000.0000.000
118A125THR00.0230.00322.847-0.021-0.0210.0000.0000.0000.000
119A126GLU-1-0.940-0.95421.6660.1230.1230.0000.0000.0000.000
120A127ILE0-0.082-0.03117.1660.0000.0000.0000.0000.0000.000
121A128ALA0-0.017-0.01321.363-0.024-0.0240.0000.0000.0000.000
122A129ALA0-0.010-0.01624.862-0.013-0.0130.0000.0000.0000.000
123A130GLU-1-0.815-0.88619.719-0.040-0.0400.0000.0000.0000.000
124A131THR00.004-0.01823.438-0.005-0.0050.0000.0000.0000.000
125A132MET0-0.008-0.00625.592-0.006-0.0060.0000.0000.0000.000
126A133ALA0-0.0100.00625.8800.0000.0000.0000.0000.0000.000
127A134VAL00.0250.01925.570-0.001-0.0010.0000.0000.0000.000
128A135ILE00.0040.00528.363-0.002-0.0020.0000.0000.0000.000
129A136VAL0-0.0060.00031.3720.0010.0010.0000.0000.0000.000
130A137ASP-1-0.871-0.92328.4970.0020.0020.0000.0000.0000.000
131A138ALA00.0100.00732.0300.0000.0000.0000.0000.0000.000
132A139CYS0-0.129-0.06534.2430.0000.0000.0000.0000.0000.000
133A140ALA0-0.0380.00435.6360.0040.0040.0000.0000.0000.000
134A141ALA00.0060.00837.246-0.003-0.0030.0000.0000.0000.000
135A142LEU0-0.025-0.03139.4130.0020.0020.0000.0000.0000.000
136A143PRO0-0.0310.00741.8510.0010.0010.0000.0000.0000.000
137A144PRO00.0010.00140.5850.0010.0010.0000.0000.0000.000
138A145SER0-0.048-0.05442.375-0.001-0.0010.0000.0000.0000.000
139A146ASP-1-0.890-0.93443.6370.0220.0220.0000.0000.0000.000
140A147GLY0-0.032-0.00944.691-0.002-0.0020.0000.0000.0000.000
141A148THR0-0.024-0.01145.455-0.001-0.0010.0000.0000.0000.000
142A149ASP-1-0.912-0.94647.0940.0090.0090.0000.0000.0000.000
143A150GLY00.0590.02248.995-0.002-0.0020.0000.0000.0000.000
144A151ALA0-0.035-0.03348.2470.0020.0020.0000.0000.0000.000
145A152PHE0-0.022-0.01040.2560.0020.0020.0000.0000.0000.000
146A153ASP-1-0.758-0.90443.3200.0140.0140.0000.0000.0000.000
147A154ALA00.0160.01243.7250.0030.0030.0000.0000.0000.000
148A155HIS0-0.022-0.00541.0340.0040.0040.0000.0000.0000.000
149A156LEU00.001-0.01438.7140.0030.0030.0000.0000.0000.000
150A157ASP-1-0.879-0.89739.4970.0350.0350.0000.0000.0000.000
151A158THR0-0.028-0.01240.5700.0050.0050.0000.0000.0000.000
152A159HIS0-0.109-0.04538.2830.0080.0080.0000.0000.0000.000
153A160ARG10.9010.93835.532-0.044-0.0440.0000.0000.0000.000
154A161GLN0-0.028-0.02232.214-0.004-0.0040.0000.0000.0000.000
155A162TRP0-0.0100.02329.8270.0060.0060.0000.0000.0000.000
156A163ALA00.0550.02129.815-0.010-0.0100.0000.0000.0000.000
157A164GLY0-0.134-0.06630.3840.0070.0070.0000.0000.0000.000
158A165ASP-1-0.874-0.93330.6340.0920.0920.0000.0000.0000.000
159A166ARG10.8790.90729.661-0.026-0.0260.0000.0000.0000.000
160A167PRO0-0.0330.01932.698-0.005-0.0050.0000.0000.0000.000
161A168ALA00.015-0.00635.561-0.002-0.0020.0000.0000.0000.000
162A169PRO00.0940.06637.3740.0040.0040.0000.0000.0000.000
163A170SER00.014-0.04539.658-0.002-0.0020.0000.0000.0000.000
164A171SER00.0270.01140.598-0.001-0.0010.0000.0000.0000.000
165A172ALA0-0.0080.00637.728-0.004-0.0040.0000.0000.0000.000
166A173LEU00.0130.01134.537-0.004-0.0040.0000.0000.0000.000
167A174HIS10.8890.94037.370-0.007-0.0070.0000.0000.0000.000
168A175ARG10.9510.97739.3430.0090.0090.0000.0000.0000.000
169A176ALA00.0770.02234.219-0.004-0.0040.0000.0000.0000.000
170A177LEU0-0.020-0.00834.846-0.004-0.0040.0000.0000.0000.000
171A178SER0-0.029-0.01436.971-0.001-0.0010.0000.0000.0000.000
172A179PHE00.0550.02432.946-0.002-0.0020.0000.0000.0000.000
173A180TRP00.0390.01528.678-0.007-0.0070.0000.0000.0000.000
174A181SER0-0.061-0.05035.285-0.004-0.0040.0000.0000.0000.000
175A182ARG10.8100.88138.0240.0160.0160.0000.0000.0000.000
176A183LEU00.0240.01435.986-0.003-0.0030.0000.0000.0000.000
177A184HIS10.8700.93631.0400.0330.0330.0000.0000.0000.000
178A185GLY00.0230.04436.383-0.001-0.0010.0000.0000.0000.000
179A186VAL00.0030.00039.404-0.001-0.0010.0000.0000.0000.000
180A187LEU00.0090.01233.598-0.003-0.0030.0000.0000.0000.000
181A188SER0-0.072-0.04835.975-0.002-0.0020.0000.0000.0000.000
182A189LEU00.0180.01437.2260.0000.0000.0000.0000.0000.000
183A190GLU-1-0.765-0.84138.601-0.057-0.0570.0000.0000.0000.000
184A191LEU0-0.0100.00033.323-0.002-0.0020.0000.0000.0000.000
185A192ALA0-0.045-0.01237.443-0.001-0.0010.0000.0000.0000.000
186A193GLY00.0010.01139.3940.0030.0030.0000.0000.0000.000
187A194GLN0-0.079-0.05142.2030.0040.0040.0000.0000.0000.000
188A195PHE00.0580.00842.6390.0020.0020.0000.0000.0000.000
189A196THR0-0.014-0.01244.632-0.003-0.0030.0000.0000.0000.000
190A197GLY0-0.049-0.01846.7500.0030.0030.0000.0000.0000.000
191A198MET0-0.0130.00449.0110.0020.0020.0000.0000.0000.000
192A199GLY0-0.062-0.02549.9300.0010.0010.0000.0000.0000.000
193A200PHE0-0.0020.01146.648-0.001-0.0010.0000.0000.0000.000
194A201ASP-1-0.843-0.92844.851-0.058-0.0580.0000.0000.0000.000
195A202SER0-0.002-0.03041.9640.0010.0010.0000.0000.0000.000
196A203ALA00.0360.01941.5610.0010.0010.0000.0000.0000.000
197A204LEU0-0.032-0.01842.5240.0000.0000.0000.0000.0000.000
198A205LEU00.0010.01244.7700.0020.0020.0000.0000.0000.000
199A206PHE00.0150.00136.2650.0020.0020.0000.0000.0000.000
200A207GLU-1-0.798-0.88641.250-0.053-0.0530.0000.0000.0000.000
201A208ALA0-0.073-0.03443.3650.0020.0020.0000.0000.0000.000
202A209GLU-1-0.845-0.92442.717-0.021-0.0210.0000.0000.0000.000
203A210LEU0-0.0040.00838.8540.0030.0030.0000.0000.0000.000
204A211LYS10.8240.88941.9410.0460.0460.0000.0000.0000.000
205A212ASP-1-0.880-0.92144.902-0.017-0.0170.0000.0000.0000.000
206A213LEU0-0.0190.00439.1370.0030.0030.0000.0000.0000.000
207A214LEU0-0.064-0.03440.7400.0030.0030.0000.0000.0000.000
208A215GLY0-0.069-0.03543.0870.0000.0000.0000.0000.0000.000
209A216PRO0-0.0230.01245.1540.0020.0020.0000.0000.0000.000