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: MN64Z

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2133462.361189
FMO2-HF: Nuclear repulsion 2054327.870799
FMO2-HF: Total energy -79134.49039
FMO2-MP2: Total energy -79366.905807


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.
-15.201-18.13212.394-4.615-4.8470.033
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 : 0.048 / q_NPA : 0.021
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].
3A10ARG11.0160.9943.9300.1881.182-0.008-0.476-0.5100.002
4A11GLU-1-0.816-0.8886.6330.3570.3570.0000.0000.0000.000
5A12ARG10.9400.9552.007-16.303-20.22812.402-4.139-4.3370.031
6A13TYR00.0850.0445.529-0.191-0.1910.0000.0000.0000.000
7A14ARG10.8300.9008.234-0.094-0.0940.0000.0000.0000.000
8A15THR0-0.025-0.0276.0290.4010.4010.0000.0000.0000.000
9A16GLN00.0200.0188.952-0.063-0.0630.0000.0000.0000.000
10A17VAL00.0280.02711.5760.0930.0930.0000.0000.0000.000
11A18ARG10.9040.9517.7910.2390.2390.0000.0000.0000.000
12A19ALA00.0070.01713.1730.0530.0530.0000.0000.0000.000
13A20GLU-1-0.761-0.87014.832-0.250-0.2500.0000.0000.0000.000
14A21ILE0-0.065-0.04016.4160.0490.0490.0000.0000.0000.000
15A22LYS10.8270.89314.1870.2500.2500.0000.0000.0000.000
16A23ASP-1-0.857-0.91618.940-0.319-0.3190.0000.0000.0000.000
17A24HIS10.7400.81220.9130.2560.2560.0000.0000.0000.000
18A25ALA0-0.016-0.01421.7840.0250.0250.0000.0000.0000.000
19A26TRP00.0740.03420.5050.0370.0370.0000.0000.0000.000
20A27GLU-1-0.800-0.86424.829-0.167-0.1670.0000.0000.0000.000
21A28GLN00.0000.01126.1160.0230.0230.0000.0000.0000.000
22A29ILE0-0.015-0.00624.9570.0120.0120.0000.0000.0000.000
23A30ALA00.004-0.00128.7700.0080.0080.0000.0000.0000.000
24A31THR0-0.097-0.05930.6620.0050.0050.0000.0000.0000.000
25A32ALA0-0.039-0.01932.0700.0060.0060.0000.0000.0000.000
26A33GLY00.0470.04231.7290.0090.0090.0000.0000.0000.000
27A34ALA00.031-0.00428.8750.0020.0020.0000.0000.0000.000
28A35SER0-0.029-0.02428.9310.0080.0080.0000.0000.0000.000
29A36ALA00.0020.02230.5510.0070.0070.0000.0000.0000.000
30A37LEU0-0.044-0.00423.8500.0000.0000.0000.0000.0000.000
31A38SER00.001-0.00827.2280.0150.0150.0000.0000.0000.000
32A39LEU00.0570.02821.270-0.020-0.0200.0000.0000.0000.000
33A40ASN00.0160.00124.527-0.008-0.0080.0000.0000.0000.000
34A41ALA0-0.0070.01227.204-0.009-0.0090.0000.0000.0000.000
35A42ILE00.0250.01921.316-0.012-0.0120.0000.0000.0000.000
36A43ALA0-0.006-0.01023.479-0.017-0.0170.0000.0000.0000.000
37A44LYS10.9700.98424.4530.0380.0380.0000.0000.0000.000
38A45ARG10.8170.89025.3930.1640.1640.0000.0000.0000.000
39A46MET0-0.0300.00618.566-0.010-0.0100.0000.0000.0000.000
40A47GLY00.0030.01823.899-0.010-0.0100.0000.0000.0000.000
41A48MET0-0.039-0.00418.371-0.002-0.0020.0000.0000.0000.000
42A49SER00.0160.00023.7850.0120.0120.0000.0000.0000.000
43A50GLY00.0470.00723.6630.0030.0030.0000.0000.0000.000
44A51PRO00.0230.00223.7010.0020.0020.0000.0000.0000.000
45A52ALA00.002-0.00120.0800.0270.0270.0000.0000.0000.000
46A53LEU00.0190.01018.8080.0050.0050.0000.0000.0000.000
47A54TYR0-0.001-0.01518.8020.0040.0040.0000.0000.0000.000
48A55ARG10.7410.87316.696-0.187-0.1870.0000.0000.0000.000
49A56TYR0-0.073-0.04212.1840.0260.0260.0000.0000.0000.000
50A57PHE00.0450.01014.867-0.004-0.0040.0000.0000.0000.000
51A58ASP-1-0.812-0.87817.6710.2160.2160.0000.0000.0000.000
52A59GLY00.028-0.00220.341-0.010-0.0100.0000.0000.0000.000
53A60ARG10.7880.88521.977-0.055-0.0550.0000.0000.0000.000
54A61ASP-1-0.773-0.88823.6380.0730.0730.0000.0000.0000.000
55A62GLU-1-0.840-0.89218.0470.2790.2790.0000.0000.0000.000
56A63LEU0-0.030-0.01418.917-0.013-0.0130.0000.0000.0000.000
57A64ILE00.004-0.00120.087-0.027-0.0270.0000.0000.0000.000
58A65THR00.0260.01619.231-0.014-0.0140.0000.0000.0000.000
59A66GLU-1-0.851-0.91215.0240.1040.1040.0000.0000.0000.000
60A67LEU0-0.046-0.00617.315-0.055-0.0550.0000.0000.0000.000
61A68ILE00.0450.01820.039-0.022-0.0220.0000.0000.0000.000
62A69ARG10.7460.83514.873-0.170-0.1700.0000.0000.0000.000
63A70ASP-1-0.787-0.86815.618-0.296-0.2960.0000.0000.0000.000
64A71ALA00.0050.01518.259-0.025-0.0250.0000.0000.0000.000
65A72TYR00.0310.00521.074-0.009-0.0090.0000.0000.0000.000
66A73ARG10.8660.93914.2390.1870.1870.0000.0000.0000.000
67A74SER00.0290.00518.933-0.004-0.0040.0000.0000.0000.000
68A75GLN00.0090.01020.7060.0010.0010.0000.0000.0000.000
69A76ALA00.0280.01020.7230.0020.0020.0000.0000.0000.000
70A77ASP-1-0.849-0.92918.006-0.287-0.2870.0000.0000.0000.000
71A78SER0-0.050-0.01521.019-0.008-0.0080.0000.0000.0000.000
72A79LEU00.0190.00024.5240.0040.0040.0000.0000.0000.000
73A80ARG10.7440.82818.3780.1680.1680.0000.0000.0000.000
74A81ALA0-0.021-0.00222.801-0.001-0.0010.0000.0000.0000.000
75A82ALA00.0170.01424.1790.0040.0040.0000.0000.0000.000
76A83ALA00.0280.01826.4960.0050.0050.0000.0000.0000.000
77A84ALA0-0.043-0.01623.7960.0060.0060.0000.0000.0000.000
78A85SER0-0.126-0.07325.861-0.002-0.0020.0000.0000.0000.000
79A86GLY0-0.002-0.00228.4740.0040.0040.0000.0000.0000.000
80A87ALA0-0.064-0.01730.7110.0090.0090.0000.0000.0000.000
81A88ASP-1-0.770-0.89232.489-0.064-0.0640.0000.0000.0000.000
82A89LEU00.005-0.01134.179-0.005-0.0050.0000.0000.0000.000
83A90ALA00.005-0.00335.639-0.002-0.0020.0000.0000.0000.000
84A91GLY00.0420.02233.925-0.005-0.0050.0000.0000.0000.000
85A92LEU0-0.001-0.01629.923-0.010-0.0100.0000.0000.0000.000
86A93ALA0-0.0110.00131.560-0.003-0.0030.0000.0000.0000.000
87A94HIS0-0.059-0.04633.835-0.007-0.0070.0000.0000.0000.000
88A95ALA00.0130.01828.409-0.007-0.0070.0000.0000.0000.000
89A96LEU0-0.031-0.00929.208-0.009-0.0090.0000.0000.0000.000
90A97ARG10.8040.86230.5870.0790.0790.0000.0000.0000.000
91A98ALA0-0.008-0.00529.992-0.002-0.0020.0000.0000.0000.000
92A99TRP0-0.003-0.01723.4700.0060.0060.0000.0000.0000.000
93A100ALA0-0.004-0.00928.069-0.002-0.0020.0000.0000.0000.000
94A101LEU0-0.032-0.02830.6770.0030.0030.0000.0000.0000.000
95A102ASP-1-0.886-0.90526.142-0.212-0.2120.0000.0000.0000.000
96A103ASP-1-0.814-0.91025.236-0.171-0.1710.0000.0000.0000.000
97A104PRO00.0510.01428.6500.0100.0100.0000.0000.0000.000
98A105GLN0-0.0170.00027.9340.0180.0180.0000.0000.0000.000
99A106ARG10.7300.85022.6260.1970.1970.0000.0000.0000.000
100A107TYR00.0070.02126.2440.0130.0130.0000.0000.0000.000
101A108PHE0-0.008-0.02929.1550.0140.0140.0000.0000.0000.000
102A109LEU0-0.081-0.02523.6850.0120.0120.0000.0000.0000.000
103A110ILE0-0.063-0.02424.2500.0140.0140.0000.0000.0000.000
104A111PHE0-0.058-0.02728.3590.0110.0110.0000.0000.0000.000
105A112GLY00.0420.02332.008-0.003-0.0030.0000.0000.0000.000
106A113THR0-0.052-0.02933.7990.0070.0070.0000.0000.0000.000
107A114PRO00.0240.02032.135-0.002-0.0020.0000.0000.0000.000
108A115VAL00.0220.00827.974-0.001-0.0010.0000.0000.0000.000
109A116PRO00.0460.01331.2340.0110.0110.0000.0000.0000.000
110A117GLY0-0.024-0.01532.1920.0010.0010.0000.0000.0000.000
111A118TYR0-0.062-0.04323.2090.0050.0050.0000.0000.0000.000
112A119ARG10.9200.95128.038-0.129-0.1290.0000.0000.0000.000
113A120ALA00.0180.01524.7320.0110.0110.0000.0000.0000.000
114A121PRO00.0140.01321.0860.0030.0030.0000.0000.0000.000
115A122ASP-1-0.844-0.91923.6910.1630.1630.0000.0000.0000.000
116A123ASP-1-0.817-0.89319.4200.2110.2110.0000.0000.0000.000
117A124ILE0-0.026-0.02321.162-0.023-0.0230.0000.0000.0000.000
118A125THR0-0.032-0.02922.669-0.029-0.0290.0000.0000.0000.000
119A126GLU-1-0.928-0.95821.5150.1540.1540.0000.0000.0000.000
120A127ILE0-0.070-0.03417.336-0.012-0.0120.0000.0000.0000.000
121A128ALA0-0.0030.00121.214-0.029-0.0290.0000.0000.0000.000
122A129ALA00.006-0.00124.667-0.017-0.0170.0000.0000.0000.000
123A130GLU-1-0.809-0.87519.348-0.083-0.0830.0000.0000.0000.000
124A131THR00.0040.00023.496-0.023-0.0230.0000.0000.0000.000
125A132MET0-0.016-0.01425.431-0.009-0.0090.0000.0000.0000.000
126A133ALA0-0.029-0.00325.8710.0000.0000.0000.0000.0000.000
127A134VAL00.0560.02225.120-0.001-0.0010.0000.0000.0000.000
128A135ILE0-0.0130.00528.099-0.003-0.0030.0000.0000.0000.000
129A136VAL0-0.004-0.00431.1530.0010.0010.0000.0000.0000.000
130A137ASP-1-0.839-0.88828.654-0.001-0.0010.0000.0000.0000.000
131A138ALA00.0050.00531.887-0.001-0.0010.0000.0000.0000.000
132A139CYS0-0.089-0.03433.661-0.001-0.0010.0000.0000.0000.000
133A140ALA0-0.051-0.00935.4880.0040.0040.0000.0000.0000.000
134A141ALA0-0.020-0.00737.295-0.002-0.0020.0000.0000.0000.000
135A142LEU0-0.009-0.01939.0350.0030.0030.0000.0000.0000.000
136A143PRO0-0.0310.00441.5370.0010.0010.0000.0000.0000.000
137A144PRO0-0.0030.00140.4810.0020.0020.0000.0000.0000.000
138A145SER0-0.041-0.04942.113-0.001-0.0010.0000.0000.0000.000
139A146ASP-1-0.898-0.93943.1530.0220.0220.0000.0000.0000.000
140A147GLY0-0.033-0.01344.525-0.003-0.0030.0000.0000.0000.000
141A148THR0-0.0140.00645.435-0.001-0.0010.0000.0000.0000.000
142A149ASP-1-0.924-0.95247.3680.0090.0090.0000.0000.0000.000
143A150GLY00.0530.01348.323-0.003-0.0030.0000.0000.0000.000
144A151ALA0-0.045-0.02448.2990.0030.0030.0000.0000.0000.000
145A152PHE0-0.010-0.00940.2090.0030.0030.0000.0000.0000.000
146A153ASP-1-0.780-0.91143.3920.0150.0150.0000.0000.0000.000
147A154ALA00.0300.01443.7740.0030.0030.0000.0000.0000.000
148A155HIS0-0.025-0.00541.2340.0050.0050.0000.0000.0000.000
149A156LEU00.001-0.01138.7330.0040.0040.0000.0000.0000.000
150A157ASP-1-0.853-0.90439.8010.0400.0400.0000.0000.0000.000
151A158THR0-0.037-0.01440.8190.0050.0050.0000.0000.0000.000
152A159HIS0-0.107-0.03638.2220.0100.0100.0000.0000.0000.000
153A160ARG10.9170.96535.754-0.048-0.0480.0000.0000.0000.000
154A161GLN00.007-0.02332.664-0.004-0.0040.0000.0000.0000.000
155A162TRP0-0.025-0.00930.0560.0070.0070.0000.0000.0000.000
156A163ALA0-0.031-0.01629.904-0.008-0.0080.0000.0000.0000.000
157A164GLY0-0.055-0.00131.130-0.004-0.0040.0000.0000.0000.000
158A165ASP-1-0.879-0.95030.6440.1070.1070.0000.0000.0000.000
159A166ARG10.7640.85629.316-0.027-0.0270.0000.0000.0000.000
160A167PRO00.0150.00532.119-0.004-0.0040.0000.0000.0000.000
161A168ALA0-0.0040.01335.061-0.003-0.0030.0000.0000.0000.000
162A169PRO00.0920.05236.8470.0050.0050.0000.0000.0000.000
163A170SER00.003-0.04539.704-0.002-0.0020.0000.0000.0000.000
164A171SER00.0440.01540.847-0.001-0.0010.0000.0000.0000.000
165A172ALA0-0.0040.00637.830-0.004-0.0040.0000.0000.0000.000
166A173LEU00.0130.01234.754-0.004-0.0040.0000.0000.0000.000
167A174HIS10.8820.93137.404-0.006-0.0060.0000.0000.0000.000
168A175ARG10.9550.98738.9860.0150.0150.0000.0000.0000.000
169A176ALA00.1000.03333.926-0.005-0.0050.0000.0000.0000.000
170A177LEU0-0.012-0.00734.767-0.005-0.0050.0000.0000.0000.000
171A178SER0-0.035-0.01036.880-0.001-0.0010.0000.0000.0000.000
172A179PHE00.0280.00732.426-0.002-0.0020.0000.0000.0000.000
173A180TRP00.0380.01528.218-0.008-0.0080.0000.0000.0000.000
174A181SER0-0.048-0.05234.948-0.004-0.0040.0000.0000.0000.000
175A182ARG10.7960.87737.8950.0230.0230.0000.0000.0000.000
176A183LEU00.0100.01235.602-0.003-0.0030.0000.0000.0000.000
177A184HIS10.8670.92730.5440.0440.0440.0000.0000.0000.000
178A185GLY00.0340.04235.850-0.001-0.0010.0000.0000.0000.000
179A186VAL0-0.010-0.00339.011-0.001-0.0010.0000.0000.0000.000
180A187LEU00.0180.00933.457-0.003-0.0030.0000.0000.0000.000
181A188SER0-0.057-0.04036.138-0.002-0.0020.0000.0000.0000.000
182A189LEU00.0150.00837.2450.0000.0000.0000.0000.0000.000
183A190GLU-1-0.754-0.82338.413-0.071-0.0710.0000.0000.0000.000
184A191LEU0-0.0090.00633.298-0.003-0.0030.0000.0000.0000.000
185A192ALA0-0.046-0.00937.308-0.001-0.0010.0000.0000.0000.000
186A193GLY00.0160.02039.3640.0040.0040.0000.0000.0000.000
187A194GLN0-0.060-0.03442.1450.0050.0050.0000.0000.0000.000
188A195PHE00.0520.00442.5410.0030.0030.0000.0000.0000.000
189A196THR0-0.039-0.03244.709-0.003-0.0030.0000.0000.0000.000
190A197GLY0-0.037-0.01946.9160.0030.0030.0000.0000.0000.000
191A198MET0-0.027-0.00349.1820.0020.0020.0000.0000.0000.000
192A199GLY0-0.043-0.00950.2620.0010.0010.0000.0000.0000.000
193A200PHE0-0.036-0.01546.216-0.002-0.0020.0000.0000.0000.000
194A201ASP-1-0.825-0.91144.570-0.072-0.0720.0000.0000.0000.000
195A202SER00.011-0.03541.4970.0020.0020.0000.0000.0000.000
196A203ALA00.0130.00541.0050.0000.0000.0000.0000.0000.000
197A204LEU0-0.017-0.01042.0590.0010.0010.0000.0000.0000.000
198A205LEU0-0.0160.00544.6260.0030.0030.0000.0000.0000.000
199A206PHE00.017-0.00135.8680.0030.0030.0000.0000.0000.000
200A207GLU-1-0.807-0.90040.848-0.068-0.0680.0000.0000.0000.000
201A208ALA0-0.043-0.00343.0340.0020.0020.0000.0000.0000.000
202A209GLU-1-0.833-0.92042.294-0.028-0.0280.0000.0000.0000.000
203A210LEU0-0.030-0.00638.2220.0030.0030.0000.0000.0000.000
204A211LYS10.7960.87541.6360.0580.0580.0000.0000.0000.000
205A212ASP-1-0.852-0.90044.755-0.022-0.0220.0000.0000.0000.000
206A213LEU0-0.036-0.00538.4550.0040.0040.0000.0000.0000.000
207A214LEU0-0.057-0.02440.7610.0030.0030.0000.0000.0000.000
208A215GLY0-0.054-0.02142.8440.0000.0000.0000.0000.0000.000
209A216PRO0-0.021-0.00144.9620.0020.0020.0000.0000.0000.000