Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: LN1R9

Calculation Name: 2QOP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QOP

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACS9

Base Structure: X-ray

Registration Date: 2023-09-24

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2360681.634942
FMO2-HF: Nuclear repulsion 2276575.28053
FMO2-HF: Total energy -84106.354412
FMO2-MP2: Total energy -84347.967146


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:7:GLN)


Summations of interaction energy for fragment #1(A:7:GLN)
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.
-1.6672.5160.587-2.028-2.743-0.001
Interaction energy analysis for fragmet #1(A:7:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.050
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].
3A9ALA0-0.023-0.0093.338-1.0441.5690.014-1.261-1.3660.005
4A10GLN00.036-0.0072.842-0.2831.0430.574-0.737-1.164-0.006
5A11GLU-1-0.912-0.9354.661-3.017-2.773-0.001-0.030-0.2130.000
6A12THR0-0.053-0.0456.5510.8900.8900.0000.0000.0000.000
7A13ARG10.7520.8678.0520.1660.1660.0000.0000.0000.000
8A14GLN00.0760.0319.5520.2730.2730.0000.0000.0000.000
9A15HIS0-0.0050.00211.1770.1110.1110.0000.0000.0000.000
10A16ILE0-0.021-0.01412.5570.0920.0920.0000.0000.0000.000
11A17LEU00.0210.01813.6340.0580.0580.0000.0000.0000.000
12A18ASP-1-0.818-0.88015.234-0.556-0.5560.0000.0000.0000.000
13A19VAL0-0.081-0.04717.0910.0470.0470.0000.0000.0000.000
14A20ALA00.0160.00318.6080.0410.0410.0000.0000.0000.000
15A21LEU00.0150.01920.1550.0310.0310.0000.0000.0000.000
16A22ARG10.9320.97118.1850.5630.5630.0000.0000.0000.000
17A23LEU00.0310.00422.3200.0220.0220.0000.0000.0000.000
18A24PHE0-0.026-0.02522.5130.0210.0210.0000.0000.0000.000
19A25SER00.0050.00526.4210.0220.0220.0000.0000.0000.000
20A26GLN0-0.051-0.02126.819-0.005-0.0050.0000.0000.0000.000
21A27GLN0-0.039-0.02528.7190.0010.0010.0000.0000.0000.000
22A28GLY00.0370.04029.9790.0120.0120.0000.0000.0000.000
23A29VAL00.0180.01026.662-0.015-0.0150.0000.0000.0000.000
24A30SER00.0190.00428.7970.0010.0010.0000.0000.0000.000
25A31SER0-0.078-0.03631.5390.0110.0110.0000.0000.0000.000
26A32THR0-0.0050.00725.289-0.014-0.0140.0000.0000.0000.000
27A33SER0-0.086-0.06026.1320.0080.0080.0000.0000.0000.000
28A34LEU00.0890.01519.911-0.027-0.0270.0000.0000.0000.000
29A35GLY0-0.052-0.04521.183-0.034-0.0340.0000.0000.0000.000
30A36GLU-1-0.819-0.88523.166-0.242-0.2420.0000.0000.0000.000
31A37ILE00.0210.02418.502-0.029-0.0290.0000.0000.0000.000
32A38ALA0-0.0180.00118.317-0.058-0.0580.0000.0000.0000.000
33A39LYS10.9150.94818.4630.3070.3070.0000.0000.0000.000
34A40ALA00.0090.00919.5670.0290.0290.0000.0000.0000.000
35A41ALA00.0290.02515.171-0.022-0.0220.0000.0000.0000.000
36A42GLY0-0.054-0.00415.427-0.134-0.1340.0000.0000.0000.000
37A43VAL00.0120.00812.993-0.136-0.1360.0000.0000.0000.000
38A44THR00.0130.00115.2730.1140.1140.0000.0000.0000.000
39A45ARG11.0140.98416.8550.2230.2230.0000.0000.0000.000
40A46GLY0-0.010-0.01018.0680.0390.0390.0000.0000.0000.000
41A47ALA00.0220.01512.7030.0610.0610.0000.0000.0000.000
42A48ILE0-0.013-0.00313.8470.0450.0450.0000.0000.0000.000
43A49TYR0-0.025-0.01816.0130.0110.0110.0000.0000.0000.000
44A50TRP0-0.048-0.00110.809-0.031-0.0310.0000.0000.0000.000
45A51HIS0-0.022-0.0048.0660.2060.2060.0000.0000.0000.000
46A52PHE00.0360.01313.2260.0390.0390.0000.0000.0000.000
47A53LYS10.8570.93016.724-0.120-0.1200.0000.0000.0000.000
48A54ASP-1-0.835-0.94620.013-0.008-0.0080.0000.0000.0000.000
49A55LYS10.8860.94221.6100.0990.0990.0000.0000.0000.000
50A56SER00.0290.01823.524-0.018-0.0180.0000.0000.0000.000
51A57ASP-1-0.857-0.90518.4610.0950.0950.0000.0000.0000.000
52A58LEU0-0.0090.00317.5470.0010.0010.0000.0000.0000.000
53A59PHE00.006-0.01119.416-0.019-0.0190.0000.0000.0000.000
54A60SER0-0.014-0.03521.3500.0000.0000.0000.0000.0000.000
55A61GLU-1-0.802-0.86413.3710.0950.0950.0000.0000.0000.000
56A62ILE0-0.0170.00117.214-0.015-0.0150.0000.0000.0000.000
57A63TRP00.006-0.01619.318-0.015-0.0150.0000.0000.0000.000
58A64GLU-1-0.961-0.95716.9520.1300.1300.0000.0000.0000.000
59A65LEU0-0.049-0.01412.1680.0130.0130.0000.0000.0000.000
60A66SER0-0.066-0.03916.280-0.028-0.0280.0000.0000.0000.000
61A67GLU-1-0.778-0.86118.340-0.094-0.0940.0000.0000.0000.000
62A68SER0-0.017-0.02120.9300.0190.0190.0000.0000.0000.000
63A69ASN00.0410.02320.6720.0070.0070.0000.0000.0000.000
64A70ILE0-0.002-0.02422.5440.0060.0060.0000.0000.0000.000
65A71GLY0-0.0040.00725.2890.0030.0030.0000.0000.0000.000
66A72GLU-1-0.899-0.95219.9790.1430.1430.0000.0000.0000.000
67A73LEU0-0.014-0.01123.632-0.003-0.0030.0000.0000.0000.000
68A74GLU-1-0.960-0.98126.0390.0590.0590.0000.0000.0000.000
69A75LEU00.0110.00225.0920.0000.0000.0000.0000.0000.000
70A76GLU-1-0.911-0.93324.946-0.021-0.0210.0000.0000.0000.000
71A77TYR00.004-0.02926.846-0.001-0.0010.0000.0000.0000.000
72A78GLN00.002-0.00330.2890.0060.0060.0000.0000.0000.000
73A79ALA0-0.038-0.00229.0330.0040.0040.0000.0000.0000.000
74A80LYS10.8060.91028.6700.0130.0130.0000.0000.0000.000
75A81PHE0-0.043-0.01932.538-0.006-0.0060.0000.0000.0000.000
76A82PRO00.0190.01335.0920.0040.0040.0000.0000.0000.000
77A83GLY0-0.025-0.01136.781-0.003-0.0030.0000.0000.0000.000
78A84ASP-1-0.823-0.89038.1860.0160.0160.0000.0000.0000.000
79A85PRO00.0400.01537.276-0.003-0.0030.0000.0000.0000.000
80A86LEU00.0570.00737.710-0.003-0.0030.0000.0000.0000.000
81A87SER0-0.042-0.05237.441-0.009-0.0090.0000.0000.0000.000
82A88VAL0-0.0070.01832.364-0.006-0.0060.0000.0000.0000.000
83A89LEU0-0.017-0.01133.808-0.004-0.0040.0000.0000.0000.000
84A90ARG10.8100.89435.8810.0030.0030.0000.0000.0000.000
85A91GLU-1-0.726-0.84532.565-0.034-0.0340.0000.0000.0000.000
86A92ILE00.0030.01629.444-0.010-0.0100.0000.0000.0000.000
87A93LEU0-0.018-0.01431.204-0.010-0.0100.0000.0000.0000.000
88A94ILE0-0.006-0.00133.236-0.007-0.0070.0000.0000.0000.000
89A95HIS00.0360.02925.1850.0030.0030.0000.0000.0000.000
90A96VAL0-0.0090.00829.189-0.015-0.0150.0000.0000.0000.000
91A97LEU0-0.006-0.00330.401-0.011-0.0110.0000.0000.0000.000
92A98GLU-1-0.912-0.95830.821-0.092-0.0920.0000.0000.0000.000
93A99SER0-0.013-0.01526.016-0.016-0.0160.0000.0000.0000.000
94A100THR0-0.007-0.01827.297-0.018-0.0180.0000.0000.0000.000
95A101VAL0-0.0220.00129.465-0.007-0.0070.0000.0000.0000.000
96A102THR0-0.028-0.02926.873-0.013-0.0130.0000.0000.0000.000
97A103GLU-1-0.871-0.93322.954-0.184-0.1840.0000.0000.0000.000
98A104GLU-1-0.820-0.89821.777-0.284-0.2840.0000.0000.0000.000
99A105ARG10.8290.87314.1970.4860.4860.0000.0000.0000.000
100A106ARG10.7910.87321.8080.1270.1270.0000.0000.0000.000
101A107ARG10.7560.87424.9400.2400.2400.0000.0000.0000.000
102A108LEU0-0.042-0.03323.0890.0100.0100.0000.0000.0000.000
103A109LEU00.0290.01923.6270.0080.0080.0000.0000.0000.000
104A110MET0-0.010-0.01425.5040.0170.0170.0000.0000.0000.000
105A111GLU-1-0.785-0.87528.769-0.136-0.1360.0000.0000.0000.000
106A112ILE0-0.048-0.02325.8960.0050.0050.0000.0000.0000.000
107A113ILE0-0.057-0.03027.2100.0110.0110.0000.0000.0000.000
108A114PHE0-0.012-0.01530.9590.0100.0100.0000.0000.0000.000
109A115HIS0-0.0040.02033.0270.0050.0050.0000.0000.0000.000
110A116LYS10.7490.87830.3700.1580.1580.0000.0000.0000.000
111A117CYS0-0.030-0.01630.435-0.007-0.0070.0000.0000.0000.000
112A118GLU-1-0.884-0.95530.515-0.084-0.0840.0000.0000.0000.000
113A119PHE00.012-0.02230.8880.0060.0060.0000.0000.0000.000
114A120VAL0-0.0020.00334.2240.0060.0060.0000.0000.0000.000
115A121GLY00.0230.01234.5110.0070.0070.0000.0000.0000.000
116A122GLU-1-0.874-0.95628.629-0.002-0.0020.0000.0000.0000.000
117A123MET0-0.048-0.00126.8610.0070.0070.0000.0000.0000.000
118A124ALA00.0160.00830.7000.0010.0010.0000.0000.0000.000
119A125VAL00.0100.00228.5410.0080.0080.0000.0000.0000.000
120A126VAL00.0540.01725.7700.0100.0100.0000.0000.0000.000
121A127GLN00.0380.04528.5870.0080.0080.0000.0000.0000.000
122A128GLN0-0.015-0.01931.949-0.001-0.0010.0000.0000.0000.000
123A129ALA00.0080.01427.2170.0080.0080.0000.0000.0000.000
124A130GLN00.0290.00228.2810.0030.0030.0000.0000.0000.000
125A131ARG10.8460.93230.139-0.004-0.0040.0000.0000.0000.000
126A132ASN00.0330.00031.219-0.004-0.0040.0000.0000.0000.000
127A133LEU00.0190.03226.1530.0050.0050.0000.0000.0000.000
128A134CYS0-0.052-0.02630.412-0.004-0.0040.0000.0000.0000.000
129A135LEU0-0.030-0.03333.581-0.001-0.0010.0000.0000.0000.000
130A136GLU-1-0.889-0.93431.5680.0780.0780.0000.0000.0000.000
131A137SER0-0.056-0.00732.104-0.001-0.0010.0000.0000.0000.000
132A138TYR0-0.022-0.01933.529-0.003-0.0030.0000.0000.0000.000
133A139ASP-1-0.791-0.88636.3550.0460.0460.0000.0000.0000.000
134A140ARG10.9660.99127.822-0.064-0.0640.0000.0000.0000.000
135A141ILE00.0090.01134.4110.0000.0000.0000.0000.0000.000
136A142GLU-1-0.798-0.87236.8270.0340.0340.0000.0000.0000.000
137A143GLN00.015-0.00137.101-0.001-0.0010.0000.0000.0000.000
138A144THR00.0320.02735.5820.0030.0030.0000.0000.0000.000
139A145LEU0-0.019-0.01637.891-0.002-0.0020.0000.0000.0000.000
140A146LYS10.8950.93641.394-0.040-0.0400.0000.0000.0000.000
141A147HIS00.0050.01237.6290.0010.0010.0000.0000.0000.000
142A148CYS0-0.012-0.00540.377-0.001-0.0010.0000.0000.0000.000
143A149ILE0-0.083-0.03142.968-0.002-0.0020.0000.0000.0000.000
144A150GLU-1-0.923-0.96342.4330.0580.0580.0000.0000.0000.000
145A151ALA0-0.014-0.00143.3570.0010.0010.0000.0000.0000.000
146A152LYS10.8580.93045.498-0.035-0.0350.0000.0000.0000.000
147A153MET00.0070.01442.690-0.003-0.0030.0000.0000.0000.000
148A154LEU00.0080.00843.558-0.004-0.0040.0000.0000.0000.000
149A155PRO0-0.039-0.01547.5520.0030.0030.0000.0000.0000.000
150A156ALA00.0310.00349.8700.0010.0010.0000.0000.0000.000
151A157ASP-1-0.882-0.92151.2960.0180.0180.0000.0000.0000.000
152A158LEU00.0210.02146.028-0.003-0.0030.0000.0000.0000.000
153A159MET0-0.0010.01648.8130.0020.0020.0000.0000.0000.000
154A160THR00.005-0.03643.398-0.002-0.0020.0000.0000.0000.000
155A161ARG10.8470.90940.165-0.036-0.0360.0000.0000.0000.000
156A162ARG10.8440.88344.134-0.009-0.0090.0000.0000.0000.000
157A163ALA00.0360.02343.911-0.004-0.0040.0000.0000.0000.000
158A164ALA00.0370.02039.812-0.004-0.0040.0000.0000.0000.000
159A165ILE0-0.044-0.02540.049-0.003-0.0030.0000.0000.0000.000
160A166ILE0-0.0050.00441.877-0.004-0.0040.0000.0000.0000.000
161A167MET00.0240.02935.805-0.003-0.0030.0000.0000.0000.000
162A168ARG10.9700.97031.6380.0010.0010.0000.0000.0000.000
163A169GLY00.0140.01237.729-0.006-0.0060.0000.0000.0000.000
164A170TYR0-0.053-0.04640.216-0.005-0.0050.0000.0000.0000.000
165A171ILE00.0050.00434.658-0.005-0.0050.0000.0000.0000.000
166A172SER0-0.013-0.03935.175-0.007-0.0070.0000.0000.0000.000
167A173GLY00.0170.02536.113-0.006-0.0060.0000.0000.0000.000
168A174LEU00.0150.01038.481-0.005-0.0050.0000.0000.0000.000
169A175MET0-0.048-0.01830.979-0.004-0.0040.0000.0000.0000.000
170A176GLU-1-0.937-0.96935.293-0.074-0.0740.0000.0000.0000.000
171A177ASN0-0.010-0.01936.576-0.005-0.0050.0000.0000.0000.000
172A178TRP0-0.021-0.00132.143-0.008-0.0080.0000.0000.0000.000
173A179LEU0-0.042-0.02931.255-0.007-0.0070.0000.0000.0000.000
174A180PHE0-0.0420.01235.231-0.006-0.0060.0000.0000.0000.000
175A181ALA0-0.024-0.02238.334-0.003-0.0030.0000.0000.0000.000
176A182PRO00.0540.04335.9980.0040.0040.0000.0000.0000.000
177A183GLN0-0.043-0.03738.0810.0000.0000.0000.0000.0000.000
178A184SER0-0.094-0.03541.1910.0060.0060.0000.0000.0000.000
179A185PHE00.0440.01439.2470.0050.0050.0000.0000.0000.000
180A186ASP-1-0.773-0.87537.399-0.115-0.1150.0000.0000.0000.000
181A187LEU00.0400.02134.6740.0060.0060.0000.0000.0000.000
182A188LYS10.8810.93232.8540.1250.1250.0000.0000.0000.000
183A189LYS10.8080.87935.3000.1040.1040.0000.0000.0000.000
184A190GLU-1-0.902-0.93038.359-0.058-0.0580.0000.0000.0000.000
185A191ALA00.0040.02135.5520.0060.0060.0000.0000.0000.000
186A192ARG10.8310.86134.9930.0470.0470.0000.0000.0000.000
187A193ASP-1-0.880-0.92838.940-0.041-0.0410.0000.0000.0000.000
188A194TYR0-0.003-0.00739.2900.0040.0040.0000.0000.0000.000
189A195VAL00.0050.00636.6100.0060.0060.0000.0000.0000.000
190A196ALA00.0140.01540.0510.0060.0060.0000.0000.0000.000
191A197ILE00.0470.02443.1410.0040.0040.0000.0000.0000.000
192A198LEU0-0.071-0.02940.1420.0040.0040.0000.0000.0000.000
193A199LEU00.008-0.01440.0300.0050.0050.0000.0000.0000.000
194A200GLU-1-0.951-0.97043.832-0.011-0.0110.0000.0000.0000.000
195A201MET0-0.042-0.02545.0910.0020.0020.0000.0000.0000.000
196A202TYR0-0.038-0.03142.1970.0010.0010.0000.0000.0000.000
197A203LEU00.010-0.00547.1200.0030.0030.0000.0000.0000.000
198A204LEU0-0.030-0.00450.0160.0010.0010.0000.0000.0000.000
199A205CYS0-0.0370.00750.9840.0000.0000.0000.0000.0000.000
200A206PRO00.0780.03953.0540.0020.0020.0000.0000.0000.000
201A207THR0-0.057-0.00953.896-0.001-0.0010.0000.0000.0000.000
202A208LEU00.014-0.00948.3680.0020.0020.0000.0000.0000.000
203A209ARG10.8670.93851.713-0.008-0.0080.0000.0000.0000.000
204A210ASN0-0.048-0.03653.114-0.002-0.0020.0000.0000.0000.000
205A211PRO00.0100.00756.0380.0010.0010.0000.0000.0000.000
206A212ALA00.0280.02357.3190.0020.0020.0000.0000.0000.000