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

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FMODB ID: YZY82

Calculation Name: 3Q0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q0X

Chain ID: A

ChEMBL ID:

UniProt ID: A9CQL4

Base Structure: X-ray

Registration Date: 2023-06-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066826.929237
FMO2-HF: Nuclear repulsion 1984877.515542
FMO2-HF: Total energy -81949.413695
FMO2-MP2: Total energy -82191.330779


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:16:PHE)


Summations of interaction energy for fragment #1(A:16:PHE)
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.
-20.541-8.95916.911-6.084-22.406-0.033
Interaction energy analysis for fragmet #1(A:16:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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].
3A18LEU00.0340.0082.420-1.9731.6142.554-1.638-4.5030.006
4A19SER0-0.055-0.0174.921-0.589-0.3140.000-0.029-0.2460.000
5A20THR0-0.038-0.0366.393-0.042-0.0420.0000.0000.0000.000
6A21ALA0-0.050-0.0022.835-1.079-0.3140.264-0.276-0.7540.002
7A22THR00.0110.0064.1510.0380.2020.000-0.018-0.1460.000
8A23THR0-0.035-0.0145.467-0.165-0.1650.0000.0000.0000.000
9A24LEU0-0.026-0.0157.4750.0610.0610.0000.0000.0000.000
10A25PHE00.0450.0159.5260.0530.0530.0000.0000.0000.000
11A26TRP00.004-0.02210.224-0.043-0.0430.0000.0000.0000.000
12A27ARG10.9460.98812.6300.1410.1410.0000.0000.0000.000
13A28PRO00.0280.01815.825-0.007-0.0070.0000.0000.0000.000
14A29VAL0-0.007-0.00116.9000.0040.0040.0000.0000.0000.000
15A30PRO00.0740.04619.651-0.002-0.0020.0000.0000.0000.000
16A31VAL0-0.070-0.04118.7050.0000.0000.0000.0000.0000.000
17A32HIS00.0040.00822.1470.0040.0040.0000.0000.0000.000
18A33VAL0-0.041-0.02221.964-0.003-0.0030.0000.0000.0000.000
19A34LYS10.9070.94023.9540.0710.0710.0000.0000.0000.000
20A35GLN00.0440.02423.275-0.008-0.0080.0000.0000.0000.000
21A36GLN0-0.023-0.01726.3510.0060.0060.0000.0000.0000.000
22A37ASP-1-0.922-0.96328.533-0.054-0.0540.0000.0000.0000.000
23A38ARG10.8530.94023.6560.0850.0850.0000.0000.0000.000
24A39GLU-1-0.902-0.94330.582-0.052-0.0520.0000.0000.0000.000
25A40ASP-1-0.882-0.93628.721-0.068-0.0680.0000.0000.0000.000
26A41VAL0-0.019-0.01725.9510.0030.0030.0000.0000.0000.000
27A42LEU0-0.048-0.01225.231-0.004-0.0040.0000.0000.0000.000
28A43GLU-1-0.907-0.96222.547-0.092-0.0920.0000.0000.0000.000
29A44GLU-1-0.901-0.95021.306-0.093-0.0930.0000.0000.0000.000
30A45LEU0-0.030-0.01716.851-0.005-0.0050.0000.0000.0000.000
31A46THR0-0.033-0.01512.8710.0020.0020.0000.0000.0000.000
32A47PHE00.0170.01512.317-0.011-0.0110.0000.0000.0000.000
33A48ARG10.8180.8897.3080.2990.2990.0000.0000.0000.000
34A49ILE0-0.012-0.0027.5080.0270.0270.0000.0000.0000.000
35A50LEU00.0160.0082.497-1.105-0.1710.392-0.246-1.080-0.001
36A51THR00.002-0.0073.703-0.2900.5660.027-0.248-0.636-0.001
37A52GLY00.0330.0032.073-0.695-1.6795.025-1.951-2.0900.001
38A53VAL00.0210.0222.5324.5050.4050.1925.107-1.198-0.007
39A54ALA00.0560.0352.153-5.302-3.4186.052-4.094-3.841-0.036
40A55LYS10.8740.9373.177-4.888-3.9700.091-0.079-0.9290.006
41A56GLN00.024-0.0064.1110.8771.2790.006-0.066-0.3420.000
42A57ASN00.0640.0356.583-0.623-0.6230.0000.0000.0000.000
43A58HIS00.0200.0076.879-0.274-0.2740.0000.0000.0000.000
44A59ASN0-0.040-0.0288.420-0.280-0.2800.0000.0000.0000.000
45A60LEU0-0.0220.0106.695-0.080-0.0800.0000.0000.0000.000
46A61ARG10.9520.9855.2100.5710.5710.0000.0000.0000.000
47A62ILE0-0.026-0.0142.429-2.2300.0291.588-0.904-2.9430.000
48A63LEU0-0.0020.0033.639-0.679-0.1500.024-0.206-0.347-0.001
49A64ARG10.8610.9282.798-1.3940.9870.621-0.769-2.2320.003
50A65ILE00.0020.0015.220-0.449-0.377-0.001-0.005-0.0650.000
51A66HIS0-0.019-0.0184.9290.0610.0610.0000.0000.0000.000
52A67ILE00.0300.0228.9480.0050.0050.0000.0000.0000.000
53A68SER00.006-0.01612.616-0.018-0.0180.0000.0000.0000.000
54A69SER00.0500.02214.3430.0100.0100.0000.0000.0000.000
55A70ASP-1-0.925-0.95817.713-0.134-0.1340.0000.0000.0000.000
56A71SER0-0.047-0.02419.2770.0090.0090.0000.0000.0000.000
57A72ASP-1-0.838-0.92920.453-0.106-0.1060.0000.0000.0000.000
58A73LEU0-0.021-0.01817.859-0.011-0.0110.0000.0000.0000.000
59A74PHE0-0.027-0.02017.046-0.013-0.0130.0000.0000.0000.000
60A75PHE0-0.0340.01816.031-0.016-0.0160.0000.0000.0000.000
61A76LEU00.003-0.0209.819-0.016-0.0160.0000.0000.0000.000
62A77HIS00.0250.05512.838-0.002-0.0020.0000.0000.0000.000
63A78THR0-0.078-0.0307.912-0.050-0.0500.0000.0000.0000.000
64A79LEU00.0560.0408.849-0.013-0.0130.0000.0000.0000.000
65A80GLU-1-0.907-0.9733.297-4.235-2.5950.076-0.662-1.054-0.005
66A81VAL00.0440.0457.290-0.114-0.1140.0000.0000.0000.000
67A82SER00.0570.0166.575-0.009-0.0090.0000.0000.0000.000
68A83GLU-1-0.917-0.9927.655-0.234-0.2340.0000.0000.0000.000
69A84GLU-1-1.006-0.99510.2540.0770.0770.0000.0000.0000.000
70A85ASP-1-0.915-0.96410.214-0.189-0.1890.0000.0000.0000.000
71A86PHE00.0000.00212.1160.0170.0170.0000.0000.0000.000
72A87GLN0-0.033-0.02513.5660.0090.0090.0000.0000.0000.000
73A88SER00.0100.00815.9050.0120.0120.0000.0000.0000.000
74A89LEU00.0360.02712.9990.0080.0080.0000.0000.0000.000
75A90LYS10.8570.93316.5930.1120.1120.0000.0000.0000.000
76A91ASN00.0150.00018.9680.0050.0050.0000.0000.0000.000
77A92ASP-1-0.883-0.92519.472-0.079-0.0790.0000.0000.0000.000
78A93GLN0-0.082-0.07319.541-0.007-0.0070.0000.0000.0000.000
79A94GLY00.0240.03122.4750.0040.0040.0000.0000.0000.000
80A95ILE0-0.086-0.03817.6490.0010.0010.0000.0000.0000.000
81A96LEU00.0350.00921.175-0.002-0.0020.0000.0000.0000.000
82A97VAL0-0.039-0.01717.3070.0020.0020.0000.0000.0000.000
83A98ASP-1-0.815-0.90215.724-0.157-0.1570.0000.0000.0000.000
84A99PHE00.0330.0177.2240.0050.0050.0000.0000.0000.000
85A100ALA00.0200.00511.579-0.022-0.0220.0000.0000.0000.000
86A101SER0-0.039-0.04012.640-0.009-0.0090.0000.0000.0000.000
87A102PHE0-0.041-0.01111.8080.0090.0090.0000.0000.0000.000
88A103PRO00.0320.0139.8690.0180.0180.0000.0000.0000.000
89A104GLY00.0520.02712.0010.0090.0090.0000.0000.0000.000
90A105LYS10.9280.97315.2040.1200.1200.0000.0000.0000.000
91A106ILE00.006-0.00212.9900.0110.0110.0000.0000.0000.000
92A107ILE00.0020.00311.8350.0060.0060.0000.0000.0000.000
93A108SER00.0110.01515.6730.0130.0130.0000.0000.0000.000
94A109LEU0-0.045-0.02018.8020.0090.0090.0000.0000.0000.000
95A110LEU00.0320.00614.3050.0060.0060.0000.0000.0000.000
96A111GLU-1-0.944-0.97218.577-0.122-0.1220.0000.0000.0000.000
97A112LYS10.9260.97220.6860.0920.0920.0000.0000.0000.000
98A113CYS0-0.057-0.03321.5550.0050.0050.0000.0000.0000.000
99A114ILE0-0.041-0.02118.8010.0030.0030.0000.0000.0000.000
100A115LEU0-0.041-0.02123.0810.0040.0040.0000.0000.0000.000
101A116ALA0-0.0130.02626.1620.0050.0050.0000.0000.0000.000
102A117GLN0-0.025-0.00728.297-0.001-0.0010.0000.0000.0000.000
103A118PRO0-0.055-0.05231.6960.0010.0010.0000.0000.0000.000
104A119GLY0-0.019-0.01534.0360.0000.0000.0000.0000.0000.000
105A120ASP-1-0.865-0.91731.488-0.058-0.0580.0000.0000.0000.000
106A121SER0-0.012-0.01434.4470.0000.0000.0000.0000.0000.000
107A122PRO0-0.0170.00831.5790.0020.0020.0000.0000.0000.000
108A123ARG10.9280.97129.8640.0590.0590.0000.0000.0000.000
109A124PHE0-0.006-0.01024.719-0.001-0.0010.0000.0000.0000.000
110A125GLN00.0060.00125.601-0.001-0.0010.0000.0000.0000.000
111A126ALA00.0590.02820.368-0.002-0.0020.0000.0000.0000.000
112A127VAL0-0.060-0.03521.9410.0040.0040.0000.0000.0000.000
113A128LEU00.0220.02817.452-0.004-0.0040.0000.0000.0000.000
114A129THR0-0.031-0.00920.9290.0080.0080.0000.0000.0000.000
115A130ILE00.000-0.01620.287-0.007-0.0070.0000.0000.0000.000
116A131ARG10.8830.93322.4860.0830.0830.0000.0000.0000.000
117A132GLY00.0170.02822.3950.0060.0060.0000.0000.0000.000
118A133GLY0-0.023-0.01819.5630.0040.0040.0000.0000.0000.000
119A134GLU-1-0.897-0.95517.193-0.169-0.1690.0000.0000.0000.000
120A135SER0-0.053-0.06716.8100.0110.0110.0000.0000.0000.000
121A136VAL00.0270.02517.964-0.005-0.0050.0000.0000.0000.000
122A137PHE00.0180.01016.6040.0050.0050.0000.0000.0000.000
123A138LYS10.9460.97618.7120.0770.0770.0000.0000.0000.000
124A139ILE00.0040.01518.5450.0010.0010.0000.0000.0000.000
125A140VAL0-0.056-0.04022.3490.0020.0020.0000.0000.0000.000
126A141GLU-1-0.859-0.92026.133-0.064-0.0640.0000.0000.0000.000
127A142ILE0-0.033-0.03228.8630.0020.0020.0000.0000.0000.000
128A143ASN00.0310.01532.106-0.001-0.0010.0000.0000.0000.000
129A144ASP-1-0.895-0.94235.358-0.041-0.0410.0000.0000.0000.000
130A145GLU-1-0.956-0.97036.610-0.042-0.0420.0000.0000.0000.000
131A146LYS10.8810.93832.6810.0520.0520.0000.0000.0000.000
132A147GLN00.0480.01629.589-0.003-0.0030.0000.0000.0000.000
133A148LEU0-0.052-0.03228.8480.0010.0010.0000.0000.0000.000
134A149PRO00.003-0.00225.229-0.002-0.0020.0000.0000.0000.000
135A150HIS0-0.032-0.01023.090-0.003-0.0030.0000.0000.0000.000
136A151ILE0-0.031-0.01717.520-0.004-0.0040.0000.0000.0000.000
137A152THR0-0.022-0.02320.2720.0060.0060.0000.0000.0000.000
138A153LEU0-0.0090.00213.920-0.003-0.0030.0000.0000.0000.000
139A154ALA00.0520.02915.8280.0070.0070.0000.0000.0000.000
140A155PHE0-0.019-0.01711.075-0.012-0.0120.0000.0000.0000.000
141A156ARG10.9800.9939.5620.3810.3810.0000.0000.0000.000
142A157PRO0-0.026-0.01212.962-0.029-0.0290.0000.0000.0000.000
143A158GLY0-0.030-0.03112.745-0.021-0.0210.0000.0000.0000.000
144A159ASN00.0460.01913.1580.0210.0210.0000.0000.0000.000
145A160ASP-1-0.786-0.91114.433-0.145-0.1450.0000.0000.0000.000
146A161SER0-0.090-0.04312.126-0.020-0.0200.0000.0000.0000.000
147A162VAL0-0.036-0.0209.014-0.041-0.0410.0000.0000.0000.000
148A163VAL00.0740.04310.401-0.047-0.0470.0000.0000.0000.000
149A164LYS10.9640.98813.0190.1280.1280.0000.0000.0000.000
150A165GLN0-0.065-0.0437.751-0.078-0.0780.0000.0000.0000.000
151A166PHE00.0300.0238.0500.0120.0120.0000.0000.0000.000
152A167LEU00.0470.01710.1140.0310.0310.0000.0000.0000.000
153A168ALA0-0.023-0.00212.4080.0300.0300.0000.0000.0000.000
154A169PHE0-0.036-0.0137.2450.0180.0180.0000.0000.0000.000
155A170ARG10.9330.94910.6280.2080.2080.0000.0000.0000.000
156A171LEU00.0170.01712.4620.0220.0220.0000.0000.0000.000
157A172SER0-0.092-0.04412.7830.0180.0180.0000.0000.0000.000
158A173GLU-1-0.765-0.85310.324-0.201-0.2010.0000.0000.0000.000
159A174VAL0-0.003-0.01113.9180.0070.0070.0000.0000.0000.000
160A175LYS10.9500.94917.0790.0480.0480.0000.0000.0000.000
161A176GLY0-0.0010.01317.5520.0090.0090.0000.0000.0000.000
162A177THR00.0070.00716.7010.0030.0030.0000.0000.0000.000
163A178CYS0-0.043-0.03319.5290.0030.0030.0000.0000.0000.000
164A179HIS0-0.046-0.00721.9410.0040.0040.0000.0000.0000.000
165A180ASP-1-0.830-0.91920.382-0.049-0.0490.0000.0000.0000.000
166A181LEU0-0.003-0.00323.1280.0020.0020.0000.0000.0000.000
167A182SER0-0.063-0.02825.6470.0030.0030.0000.0000.0000.000
168A183ASP-1-0.896-0.94626.948-0.022-0.0220.0000.0000.0000.000
169A184ASP-1-0.889-0.93626.427-0.041-0.0410.0000.0000.0000.000
170A185LEU0-0.074-0.02229.5610.0020.0020.0000.0000.0000.000
171A186SER0-0.034-0.01031.6510.0020.0020.0000.0000.0000.000
172A187ARG11.0061.00032.2060.0230.0230.0000.0000.0000.000
173A188THR0-0.026-0.03932.4650.0010.0010.0000.0000.0000.000
174A189ARG10.8570.93335.0260.0270.0270.0000.0000.0000.000
175A190ASP-1-0.853-0.92237.237-0.015-0.0150.0000.0000.0000.000
176A191ASP-1-0.970-0.98537.656-0.021-0.0210.0000.0000.0000.000
177A192ARG10.8720.91739.2640.0220.0220.0000.0000.0000.000
178A193ASP-1-0.866-0.93741.160-0.017-0.0170.0000.0000.0000.000
179A194SER00.0110.00842.7560.0020.0020.0000.0000.0000.000
180A195MET0-0.025-0.01142.1880.0010.0010.0000.0000.0000.000
181A196VAL0-0.022-0.00745.2590.0010.0010.0000.0000.0000.000
182A197ALA00.0210.02447.5450.0010.0010.0000.0000.0000.000
183A198GLN0-0.001-0.00845.9260.0000.0000.0000.0000.0000.000
184A199LEU0-0.034-0.00749.2870.0000.0000.0000.0000.0000.000
185A200ALA0-0.004-0.01250.9700.0000.0000.0000.0000.0000.000
186A201GLN00.0170.01052.1080.0000.0000.0000.0000.0000.000
187A202CYS00.0010.00253.3820.0010.0010.0000.0000.0000.000
188A203ARG10.9420.95652.9660.0150.0150.0000.0000.0000.000
189A204GLN00.0010.01057.0530.0000.0000.0000.0000.0000.000
190A205GLN0-0.012-0.01056.0330.0000.0000.0000.0000.0000.000
191A206LEU0-0.0180.00058.4830.0000.0000.0000.0000.0000.000
192A207ALA0-0.027-0.02260.8280.0000.0000.0000.0000.0000.000
193A208GLN00.003-0.00562.3650.0000.0000.0000.0000.0000.000
194A209LEU00.0000.01463.2520.0000.0000.0000.0000.0000.000
195A210ARG10.9410.96262.1290.0110.0110.0000.0000.0000.000
196A211GLU-1-0.885-0.93167.007-0.007-0.0070.0000.0000.0000.000
197A212GLN0-0.024-0.02666.9330.0000.0000.0000.0000.0000.000
198A213TYR0-0.076-0.02369.0490.0000.0000.0000.0000.0000.000
199A214ASP-1-0.862-0.95370.844-0.009-0.0090.0000.0000.0000.000
200A215LYS10.8230.90472.9830.0060.0060.0000.0000.0000.000
201A216HIS0-0.031-0.01773.5380.0000.0000.0000.0000.0000.000
202A217LEU00.005-0.00873.3680.0000.0000.0000.0000.0000.000
203A218LEU0-0.050-0.01176.8040.0000.0000.0000.0000.0000.000
204A219GLU-1-0.844-0.91178.731-0.006-0.0060.0000.0000.0000.000
205A220VAL0-0.075-0.01578.9930.0000.0000.0000.0000.0000.000
206A221GLN0-0.047-0.01980.5050.0000.0000.0000.0000.0000.000