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: LNMY9

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 OptH
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 -2125527.86033
FMO2-HF: Nuclear repulsion 2046395.647571
FMO2-HF: Total energy -79132.21276
FMO2-MP2: Total energy -79364.841664


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.
-15.152-12.7042.551-2.11-2.8910.013
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 : 0.025 / q_NPA : 0.000
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].
3A10ARG11.0531.0153.8520.5141.898-0.010-0.783-0.5920.001
4A11GLU-1-0.921-0.9377.0562.1482.1480.0000.0000.0000.000
5A12ARG10.8910.9352.649-14.888-13.8242.561-1.327-2.2990.012
6A13TYR00.1210.0606.781-0.350-0.3500.0000.0000.0000.000
7A14ARG10.8990.9579.123-1.593-1.5930.0000.0000.0000.000
8A15THR0-0.016-0.0176.4040.0650.0650.0000.0000.0000.000
9A16GLN00.0540.0199.502-0.126-0.1260.0000.0000.0000.000
10A17VAL00.0230.03912.325-0.067-0.0670.0000.0000.0000.000
11A18ARG10.9440.9678.480-1.734-1.7340.0000.0000.0000.000
12A19ALA0-0.0040.00313.557-0.055-0.0550.0000.0000.0000.000
13A20GLU-1-0.816-0.90515.2370.1970.1970.0000.0000.0000.000
14A21ILE0-0.097-0.05317.008-0.035-0.0350.0000.0000.0000.000
15A22LYS10.8170.88313.626-0.646-0.6460.0000.0000.0000.000
16A23ASP-1-0.844-0.90419.1580.1960.1960.0000.0000.0000.000
17A24HIS10.7510.83921.163-0.272-0.2720.0000.0000.0000.000
18A25ALA0-0.019-0.01322.206-0.020-0.0200.0000.0000.0000.000
19A26TRP00.1050.05420.546-0.024-0.0240.0000.0000.0000.000
20A27GLU-1-0.817-0.87925.1580.1640.1640.0000.0000.0000.000
21A28GLN00.0110.00727.301-0.019-0.0190.0000.0000.0000.000
22A29ILE0-0.0330.00625.422-0.007-0.0070.0000.0000.0000.000
23A30ALA0-0.008-0.00928.993-0.012-0.0120.0000.0000.0000.000
24A31THR0-0.099-0.07030.902-0.008-0.0080.0000.0000.0000.000
25A32ALA0-0.034-0.02532.291-0.008-0.0080.0000.0000.0000.000
26A33GLY00.0350.03832.306-0.001-0.0010.0000.0000.0000.000
27A34ALA00.0610.00828.9530.0130.0130.0000.0000.0000.000
28A35SER0-0.102-0.04729.407-0.007-0.0070.0000.0000.0000.000
29A36ALA00.0170.02131.3220.0050.0050.0000.0000.0000.000
30A37LEU0-0.0370.00224.8510.0050.0050.0000.0000.0000.000
31A38SER00.018-0.00727.9930.0160.0160.0000.0000.0000.000
32A39LEU00.0620.01221.665-0.014-0.0140.0000.0000.0000.000
33A40ASN00.0430.01025.3800.0270.0270.0000.0000.0000.000
34A41ALA0-0.0380.00228.164-0.010-0.0100.0000.0000.0000.000
35A42ILE00.0180.01922.279-0.015-0.0150.0000.0000.0000.000
36A43ALA0-0.0010.00024.486-0.006-0.0060.0000.0000.0000.000
37A44LYS10.9580.97825.438-0.193-0.1930.0000.0000.0000.000
38A45ARG10.8930.94526.423-0.197-0.1970.0000.0000.0000.000
39A46MET0-0.041-0.01219.398-0.007-0.0070.0000.0000.0000.000
40A47GLY00.0020.02324.8230.0010.0010.0000.0000.0000.000
41A48MET0-0.039-0.01019.3930.0090.0090.0000.0000.0000.000
42A49SER00.0120.00024.717-0.009-0.0090.0000.0000.0000.000
43A50GLY00.0550.01024.3600.0290.0290.0000.0000.0000.000
44A51PRO00.042-0.00324.3750.0270.0270.0000.0000.0000.000
45A52ALA00.0050.01720.8410.0490.0490.0000.0000.0000.000
46A53LEU00.0400.01419.5450.0740.0740.0000.0000.0000.000
47A54TYR00.0350.00819.7690.0350.0350.0000.0000.0000.000
48A55ARG10.8410.94217.589-0.637-0.6370.0000.0000.0000.000
49A56TYR0-0.101-0.05713.1320.2060.2060.0000.0000.0000.000
50A57PHE00.0440.01215.5140.0830.0830.0000.0000.0000.000
51A58ASP-1-0.945-0.94018.3980.4880.4880.0000.0000.0000.000
52A59GLY00.0390.00720.773-0.038-0.0380.0000.0000.0000.000
53A60ARG10.8800.92422.330-0.254-0.2540.0000.0000.0000.000
54A61ASP-1-0.794-0.90123.8440.3280.3280.0000.0000.0000.000
55A62GLU-1-0.819-0.90818.0360.7620.7620.0000.0000.0000.000
56A63LEU0-0.048-0.01619.0110.0320.0320.0000.0000.0000.000
57A64ILE0-0.016-0.00620.263-0.009-0.0090.0000.0000.0000.000
58A65THR00.0150.00718.837-0.027-0.0270.0000.0000.0000.000
59A66GLU-1-0.947-0.97614.5200.7720.7720.0000.0000.0000.000
60A67LEU0-0.048-0.00917.757-0.018-0.0180.0000.0000.0000.000
61A68ILE00.0440.01620.153-0.033-0.0330.0000.0000.0000.000
62A69ARG10.8600.92514.866-0.628-0.6280.0000.0000.0000.000
63A70ASP-1-0.835-0.91215.4480.4600.4600.0000.0000.0000.000
64A71ALA0-0.014-0.00517.889-0.048-0.0480.0000.0000.0000.000
65A72TYR00.0430.00620.802-0.034-0.0340.0000.0000.0000.000
66A73ARG10.9290.97914.063-0.435-0.4350.0000.0000.0000.000
67A74SER00.0290.01618.818-0.042-0.0420.0000.0000.0000.000
68A75GLN00.0210.01420.514-0.040-0.0400.0000.0000.0000.000
69A76ALA0-0.031-0.01920.478-0.023-0.0230.0000.0000.0000.000
70A77ASP-1-0.875-0.93817.8240.0220.0220.0000.0000.0000.000
71A78SER0-0.046-0.01721.069-0.031-0.0310.0000.0000.0000.000
72A79LEU00.030-0.00924.476-0.014-0.0140.0000.0000.0000.000
73A80ARG10.7960.89718.280-0.037-0.0370.0000.0000.0000.000
74A81ALA0-0.021-0.00623.353-0.017-0.0170.0000.0000.0000.000
75A82ALA00.0170.01424.765-0.010-0.0100.0000.0000.0000.000
76A83ALA00.0250.00927.326-0.005-0.0050.0000.0000.0000.000
77A84ALA0-0.047-0.01924.409-0.009-0.0090.0000.0000.0000.000
78A85SER0-0.073-0.03726.406-0.012-0.0120.0000.0000.0000.000
79A86GLY0-0.038-0.01428.9920.0020.0020.0000.0000.0000.000
80A87ALA0-0.0410.00131.3230.0050.0050.0000.0000.0000.000
81A88ASP-1-0.819-0.91733.150-0.023-0.0230.0000.0000.0000.000
82A89LEU0-0.008-0.03434.6340.0030.0030.0000.0000.0000.000
83A90ALA00.0230.02435.6260.0060.0060.0000.0000.0000.000
84A91GLY00.0490.02733.9700.0030.0030.0000.0000.0000.000
85A92LEU0-0.009-0.01630.0250.0030.0030.0000.0000.0000.000
86A93ALA0-0.009-0.00631.8310.0090.0090.0000.0000.0000.000
87A94HIS0-0.062-0.05234.0430.0030.0030.0000.0000.0000.000
88A95ALA0-0.0090.01228.5120.0020.0020.0000.0000.0000.000
89A96LEU0-0.040-0.02529.6030.0090.0090.0000.0000.0000.000
90A97ARG10.8310.90030.724-0.020-0.0200.0000.0000.0000.000
91A98ALA00.0290.01630.3880.0070.0070.0000.0000.0000.000
92A99TRP00.0320.01823.4450.0030.0030.0000.0000.0000.000
93A100ALA0-0.024-0.02028.1630.0130.0130.0000.0000.0000.000
94A101LEU0-0.067-0.05430.5810.0060.0060.0000.0000.0000.000
95A102ASP-1-0.984-0.97826.3680.0480.0480.0000.0000.0000.000
96A103ASP-1-0.867-0.93725.4070.1390.1390.0000.0000.0000.000
97A104PRO00.0480.01428.5380.0120.0120.0000.0000.0000.000
98A105GLN0-0.028-0.01828.3140.0150.0150.0000.0000.0000.000
99A106ARG10.9050.96622.502-0.098-0.0980.0000.0000.0000.000
100A107TYR00.0180.00826.4480.0070.0070.0000.0000.0000.000
101A108PHE0-0.007-0.03129.0090.0040.0040.0000.0000.0000.000
102A109LEU0-0.0430.00523.8230.0060.0060.0000.0000.0000.000
103A110ILE0-0.069-0.01824.0610.0140.0140.0000.0000.0000.000
104A111PHE0-0.067-0.05427.881-0.003-0.0030.0000.0000.0000.000
105A112GLY00.0130.02431.450-0.011-0.0110.0000.0000.0000.000
106A113THR0-0.064-0.03533.4820.0010.0010.0000.0000.0000.000
107A114PRO00.0620.04331.7780.0100.0100.0000.0000.0000.000
108A115VAL0-0.002-0.01028.553-0.004-0.0040.0000.0000.0000.000
109A116PRO00.0230.00531.4170.0070.0070.0000.0000.0000.000
110A117GLY0-0.021-0.01932.5750.0090.0090.0000.0000.0000.000
111A118TYR0-0.074-0.04823.0850.0000.0000.0000.0000.0000.000
112A119ARG10.9330.95928.441-0.276-0.2760.0000.0000.0000.000
113A120ALA00.0280.01724.5700.0200.0200.0000.0000.0000.000
114A121PRO0-0.0010.00820.843-0.014-0.0140.0000.0000.0000.000
115A122ASP-1-0.871-0.95223.6810.2840.2840.0000.0000.0000.000
116A123ASP-1-0.899-0.94919.0320.4730.4730.0000.0000.0000.000
117A124ILE0-0.009-0.01220.6320.0060.0060.0000.0000.0000.000
118A125THR00.0380.00822.657-0.024-0.0240.0000.0000.0000.000
119A126GLU-1-0.936-0.94921.6540.1960.1960.0000.0000.0000.000
120A127ILE0-0.079-0.03116.9410.0020.0020.0000.0000.0000.000
121A128ALA0-0.027-0.01721.267-0.017-0.0170.0000.0000.0000.000
122A129ALA0-0.003-0.01524.706-0.022-0.0220.0000.0000.0000.000
123A130GLU-1-0.807-0.87819.6230.0570.0570.0000.0000.0000.000
124A131THR0-0.001-0.02623.394-0.015-0.0150.0000.0000.0000.000
125A132MET0-0.007-0.00325.425-0.017-0.0170.0000.0000.0000.000
126A133ALA00.0000.00525.935-0.011-0.0110.0000.0000.0000.000
127A134VAL00.0340.02825.510-0.011-0.0110.0000.0000.0000.000
128A135ILE0-0.0030.00528.319-0.008-0.0080.0000.0000.0000.000
129A136VAL0-0.028-0.02131.334-0.005-0.0050.0000.0000.0000.000
130A137ASP-1-0.884-0.93328.586-0.011-0.0110.0000.0000.0000.000
131A138ALA00.0110.00532.090-0.005-0.0050.0000.0000.0000.000
132A139CYS0-0.119-0.05534.284-0.001-0.0010.0000.0000.0000.000
133A140ALA0-0.0330.00735.8790.0020.0020.0000.0000.0000.000
134A141ALA00.0080.00737.477-0.007-0.0070.0000.0000.0000.000
135A142LEU0-0.023-0.02639.6510.0020.0020.0000.0000.0000.000
136A143PRO0-0.0290.00742.101-0.003-0.0030.0000.0000.0000.000
137A144PRO0-0.005-0.00240.7730.0030.0030.0000.0000.0000.000
138A145SER0-0.043-0.05442.554-0.001-0.0010.0000.0000.0000.000
139A146ASP-1-0.895-0.93643.8310.0010.0010.0000.0000.0000.000
140A147GLY0-0.034-0.01044.8660.0000.0000.0000.0000.0000.000
141A148THR0-0.016-0.00245.599-0.002-0.0020.0000.0000.0000.000
142A149ASP-1-0.883-0.93247.1890.0160.0160.0000.0000.0000.000
143A150GLY00.0540.02049.0380.0000.0000.0000.0000.0000.000
144A151ALA0-0.043-0.03648.3130.0010.0010.0000.0000.0000.000
145A152PHE0-0.019-0.01440.1610.0020.0020.0000.0000.0000.000
146A153ASP-1-0.754-0.90343.3940.0330.0330.0000.0000.0000.000
147A154ALA00.0190.01343.8510.0010.0010.0000.0000.0000.000
148A155HIS0-0.032-0.01041.061-0.001-0.0010.0000.0000.0000.000
149A156LEU0-0.006-0.01738.9960.0040.0040.0000.0000.0000.000
150A157ASP-1-0.901-0.92639.6650.0330.0330.0000.0000.0000.000
151A158THR0-0.043-0.01740.8260.0000.0000.0000.0000.0000.000
152A159HIS0-0.111-0.04538.4700.0100.0100.0000.0000.0000.000
153A160ARG10.9310.93535.690-0.037-0.0370.0000.0000.0000.000
154A161GLN0-0.019-0.01732.3710.0000.0000.0000.0000.0000.000
155A162TRP0-0.0150.02229.9700.0060.0060.0000.0000.0000.000
156A163ALA00.0540.01629.964-0.005-0.0050.0000.0000.0000.000
157A164GLY0-0.134-0.05930.650-0.001-0.0010.0000.0000.0000.000
158A165ASP-1-0.874-0.93130.9930.0530.0530.0000.0000.0000.000
159A166ARG10.9060.91529.860-0.023-0.0230.0000.0000.0000.000
160A167PRO0-0.0410.01833.0220.0040.0040.0000.0000.0000.000
161A168ALA00.021-0.00235.807-0.001-0.0010.0000.0000.0000.000
162A169PRO00.0820.07837.5890.0070.0070.0000.0000.0000.000
163A170SER00.023-0.02339.7870.0020.0020.0000.0000.0000.000
164A171SER00.0180.00740.6720.0040.0040.0000.0000.0000.000
165A172ALA00.0110.00937.7710.0010.0010.0000.0000.0000.000
166A173LEU00.0160.00934.7080.0020.0020.0000.0000.0000.000
167A174HIS10.8820.94037.409-0.032-0.0320.0000.0000.0000.000
168A175ARG10.9260.96239.080-0.006-0.0060.0000.0000.0000.000
169A176ALA00.0770.02034.1400.0010.0010.0000.0000.0000.000
170A177LEU0-0.039-0.02034.7690.0040.0040.0000.0000.0000.000
171A178SER0-0.031-0.02536.8440.0050.0050.0000.0000.0000.000
172A179PHE00.0390.02032.8560.0010.0010.0000.0000.0000.000
173A180TRP00.0180.00928.486-0.001-0.0010.0000.0000.0000.000
174A181SER0-0.037-0.03035.0280.0020.0020.0000.0000.0000.000
175A182ARG11.0010.99537.732-0.030-0.0300.0000.0000.0000.000
176A183LEU00.0500.03035.7720.0000.0000.0000.0000.0000.000
177A184HIS10.8660.94130.845-0.083-0.0830.0000.0000.0000.000
178A185GLY00.0140.06136.1010.0040.0040.0000.0000.0000.000
179A186VAL00.0470.01239.3320.0010.0010.0000.0000.0000.000
180A187LEU00.0110.01433.2690.0010.0010.0000.0000.0000.000
181A188SER0-0.098-0.08335.5840.0040.0040.0000.0000.0000.000
182A189LEU00.0120.02137.0530.0020.0020.0000.0000.0000.000
183A190GLU-1-0.751-0.81038.2770.0380.0380.0000.0000.0000.000
184A191LEU0-0.022-0.00833.1700.0010.0010.0000.0000.0000.000
185A192ALA0-0.057-0.01737.3400.0050.0050.0000.0000.0000.000
186A193GLY0-0.013-0.00739.3200.0000.0000.0000.0000.0000.000
187A194GLN0-0.074-0.04642.144-0.005-0.0050.0000.0000.0000.000
188A195PHE00.0510.01142.554-0.002-0.0020.0000.0000.0000.000
189A196THR00.0120.00944.434-0.005-0.0050.0000.0000.0000.000
190A197GLY0-0.049-0.01946.6780.0010.0010.0000.0000.0000.000
191A198MET0-0.0090.00348.853-0.001-0.0010.0000.0000.0000.000
192A199GLY0-0.065-0.02649.820-0.002-0.0020.0000.0000.0000.000
193A200PHE0-0.0020.01346.418-0.003-0.0030.0000.0000.0000.000
194A201ASP-1-0.853-0.93344.7830.0170.0170.0000.0000.0000.000
195A202SER0-0.024-0.06741.613-0.002-0.0020.0000.0000.0000.000
196A203ALA00.0510.02441.3350.0010.0010.0000.0000.0000.000
197A204LEU0-0.035-0.01842.276-0.003-0.0030.0000.0000.0000.000
198A205LEU00.0040.01344.191-0.001-0.0010.0000.0000.0000.000
199A206PHE0-0.001-0.00335.9230.0010.0010.0000.0000.0000.000
200A207GLU-1-0.850-0.92940.5810.0010.0010.0000.0000.0000.000
201A208ALA0-0.099-0.04243.015-0.003-0.0030.0000.0000.0000.000
202A209GLU-1-0.891-0.95642.5710.0290.0290.0000.0000.0000.000
203A210LEU0-0.0060.00638.3830.0000.0000.0000.0000.0000.000
204A211LYS10.8930.92941.610-0.004-0.0040.0000.0000.0000.000
205A212ASP-1-0.963-0.97244.5980.0160.0160.0000.0000.0000.000
206A213LEU0-0.048-0.00838.9610.0020.0020.0000.0000.0000.000
207A214LEU0-0.057-0.03740.3080.0000.0000.0000.0000.0000.000
208A215GLY0-0.085-0.03942.896-0.002-0.0020.0000.0000.0000.000
209A216PRO0-0.0050.02344.998-0.001-0.0010.0000.0000.0000.000