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: J3YZ9

Calculation Name: 2QY6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QY6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XCQ7

Base Structure: X-ray

Registration Date: 2023-03-14

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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3369111.099197
FMO2-HF: Nuclear repulsion 3270899.926665
FMO2-HF: Total energy -98211.172532
FMO2-MP2: Total energy -98499.11608


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:20:SER)


Summations of interaction energy for fragment #1(A:20:SER)
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.
-22.505-19.3638.549-6.108-5.584-0.041
Interaction energy analysis for fragmet #1(A:20:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.008
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].
3A22LYS10.9180.9703.289-5.066-2.5120.038-1.230-1.3620.005
4A23HIS00.0260.0013.237-0.4090.4290.039-0.265-0.6130.001
5A24TYR00.0090.0062.920-0.6690.5410.097-0.573-0.7340.001
6A25SER0-0.0070.0011.830-15.707-17.2508.376-4.018-2.815-0.048
7A26ILE0-0.0260.0074.5850.8570.940-0.001-0.022-0.0600.000
8A27GLN0-0.0020.0026.109-0.690-0.6900.0000.0000.0000.000
9A28PRO0-0.040-0.0427.2750.2610.2610.0000.0000.0000.000
10A29ALA0-0.036-0.00710.487-0.029-0.0290.0000.0000.0000.000
11A30ASN0-0.010-0.00413.8130.0990.0990.0000.0000.0000.000
12A31LEU0-0.032-0.01815.0790.0230.0230.0000.0000.0000.000
13A32GLU-1-0.869-0.91518.465-0.167-0.1670.0000.0000.0000.000
14A33PHE0-0.029-0.02420.795-0.002-0.0020.0000.0000.0000.000
15A34ASN0-0.011-0.01625.0050.0130.0130.0000.0000.0000.000
16A35ALA00.0100.00228.0410.0080.0080.0000.0000.0000.000
17A36GLU-1-0.861-0.89531.636-0.101-0.1010.0000.0000.0000.000
18A37GLY00.0190.01128.8750.0040.0040.0000.0000.0000.000
19A38THR0-0.019-0.03627.6460.0000.0000.0000.0000.0000.000
20A39PRO0-0.0230.01622.997-0.006-0.0060.0000.0000.0000.000
21A40VAL00.004-0.01722.7010.0000.0000.0000.0000.0000.000
22A41SER0-0.045-0.02417.850-0.010-0.0100.0000.0000.0000.000
23A42ARG10.7750.83817.9750.2490.2490.0000.0000.0000.000
24A43ASP-1-0.829-0.89314.257-0.584-0.5840.0000.0000.0000.000
25A44PHE0-0.014-0.01217.034-0.011-0.0110.0000.0000.0000.000
26A45ASP-1-0.825-0.89020.520-0.235-0.2350.0000.0000.0000.000
27A46ASP-1-0.841-0.90623.044-0.156-0.1560.0000.0000.0000.000
28A47VAL0-0.022-0.00323.805-0.014-0.0140.0000.0000.0000.000
29A48TYR00.009-0.00518.296-0.012-0.0120.0000.0000.0000.000
30A49PHE0-0.032-0.01625.1250.0030.0030.0000.0000.0000.000
31A50SER0-0.032-0.01728.9210.0020.0020.0000.0000.0000.000
32A51ASN0-0.014-0.02431.4850.0080.0080.0000.0000.0000.000
33A52ASP-1-0.792-0.88532.909-0.083-0.0830.0000.0000.0000.000
34A53ASN0-0.088-0.05935.5260.0080.0080.0000.0000.0000.000
35A54GLY00.0200.02332.3370.0000.0000.0000.0000.0000.000
36A55LEU00.0300.03833.240-0.005-0.0050.0000.0000.0000.000
37A56GLU-1-0.823-0.91134.439-0.067-0.0670.0000.0000.0000.000
38A57GLU-1-0.870-0.91633.806-0.109-0.1090.0000.0000.0000.000
39A58THR00.011-0.00531.409-0.004-0.0040.0000.0000.0000.000
40A59ARG10.8170.86933.7330.0660.0660.0000.0000.0000.000
41A60TYR0-0.070-0.04336.9910.0040.0040.0000.0000.0000.000
42A61VAL0-0.009-0.01633.4600.0030.0030.0000.0000.0000.000
43A62PHE00.0040.00630.1400.0010.0010.0000.0000.0000.000
44A63LEU00.0410.02833.9940.0010.0010.0000.0000.0000.000
45A64GLY00.0240.01136.7210.0040.0040.0000.0000.0000.000
46A65GLY0-0.045-0.02837.5350.0030.0030.0000.0000.0000.000
47A66ASN0-0.0210.00533.7690.0010.0010.0000.0000.0000.000
48A67GLN0-0.009-0.00937.7560.0030.0030.0000.0000.0000.000
49A68LEU0-0.0060.00434.7840.0030.0030.0000.0000.0000.000
50A69GLU-1-0.881-0.95139.447-0.061-0.0610.0000.0000.0000.000
51A70ALA0-0.047-0.01841.9460.0030.0030.0000.0000.0000.000
52A71ARG10.8320.89637.7890.0740.0740.0000.0000.0000.000
53A72PHE0-0.015-0.01236.7100.0010.0010.0000.0000.0000.000
54A73PRO0-0.017-0.00242.3470.0010.0010.0000.0000.0000.000
55A74GLU-1-0.917-0.96045.941-0.037-0.0370.0000.0000.0000.000
56A75HIS0-0.048-0.01238.6020.0010.0010.0000.0000.0000.000
57A76PRO00.0050.01343.1520.0020.0020.0000.0000.0000.000
58A77HIS0-0.026-0.03340.1040.0020.0020.0000.0000.0000.000
59A78PRO0-0.041-0.01939.7610.0000.0000.0000.0000.0000.000
60A79LEU0-0.075-0.03733.3180.0010.0010.0000.0000.0000.000
61A80PHE00.0410.03434.8810.0000.0000.0000.0000.0000.000
62A81VAL0-0.006-0.01430.438-0.002-0.0020.0000.0000.0000.000
63A82VAL0-0.0040.00229.9310.0010.0010.0000.0000.0000.000
64A83ALA00.0130.01226.494-0.005-0.0050.0000.0000.0000.000
65A84GLU-1-0.743-0.86224.303-0.176-0.1760.0000.0000.0000.000
66A85SER0-0.003-0.04422.740-0.004-0.0040.0000.0000.0000.000
67A86GLY00.0290.00420.463-0.032-0.0320.0000.0000.0000.000
68A87PHE0-0.0320.02419.9090.0250.0250.0000.0000.0000.000
69A88GLY00.0370.01119.6500.0270.0270.0000.0000.0000.000
70A89THR0-0.050-0.03020.1860.0000.0000.0000.0000.0000.000
71A90GLY00.0490.00222.5710.0210.0210.0000.0000.0000.000
72A91LEU0-0.024-0.00324.3190.0140.0140.0000.0000.0000.000
73A92ASN0-0.025-0.02927.0900.0230.0230.0000.0000.0000.000
74A93PHE00.0320.01926.3850.0100.0100.0000.0000.0000.000
75A94LEU00.0010.00126.6350.0110.0110.0000.0000.0000.000
76A95THR00.006-0.01429.8210.0110.0110.0000.0000.0000.000
77A96LEU0-0.028-0.01031.0270.0070.0070.0000.0000.0000.000
78A97TRP0-0.030-0.01328.7260.0020.0020.0000.0000.0000.000
79A98GLN0-0.013-0.01133.1790.0050.0050.0000.0000.0000.000
80A99ALA00.0500.02435.6230.0050.0050.0000.0000.0000.000
81A100PHE0-0.036-0.02035.6490.0040.0040.0000.0000.0000.000
82A101ASP-1-0.775-0.89635.895-0.049-0.0490.0000.0000.0000.000
83A102GLN0-0.020-0.01338.5810.0030.0030.0000.0000.0000.000
84A103PHE0-0.033-0.01540.5530.0030.0030.0000.0000.0000.000
85A104ARG10.8030.89238.9800.0420.0420.0000.0000.0000.000
86A105GLU-1-0.931-0.96242.259-0.027-0.0270.0000.0000.0000.000
87A106ALA0-0.059-0.02544.5530.0020.0020.0000.0000.0000.000
88A107HIS0-0.026-0.00845.6240.0030.0030.0000.0000.0000.000
89A108PRO00.0340.03745.384-0.001-0.0010.0000.0000.0000.000
90A109GLN0-0.014-0.03045.949-0.001-0.0010.0000.0000.0000.000
91A110ALA00.0300.03145.4800.0010.0010.0000.0000.0000.000
92A111GLN0-0.009-0.00644.3040.0000.0000.0000.0000.0000.000
93A112LEU0-0.0220.02038.2650.0000.0000.0000.0000.0000.000
94A113GLN0-0.026-0.00840.8340.0010.0010.0000.0000.0000.000
95A114ARG10.9390.97735.0110.0460.0460.0000.0000.0000.000
96A115LEU00.0220.00932.126-0.001-0.0010.0000.0000.0000.000
97A116HIS0-0.049-0.02526.4770.0070.0070.0000.0000.0000.000
98A117PHE00.0160.01025.3410.0000.0000.0000.0000.0000.000
99A118ILE0-0.033-0.01023.353-0.005-0.0050.0000.0000.0000.000
100A119SER0-0.020-0.04222.365-0.008-0.0080.0000.0000.0000.000
101A120PHE00.0250.00217.984-0.010-0.0100.0000.0000.0000.000
102A121GLU-1-0.825-0.90615.592-0.405-0.4050.0000.0000.0000.000
103A122LYS10.8960.95012.2530.6250.6250.0000.0000.0000.000
104A123PHE0-0.017-0.02011.942-0.193-0.1930.0000.0000.0000.000
105A124PRO0-0.0040.01211.5670.1050.1050.0000.0000.0000.000
106A125LEU00.0510.02413.153-0.032-0.0320.0000.0000.0000.000
107A126THR0-0.030-0.04312.9510.0310.0310.0000.0000.0000.000
108A127ARG10.8480.89715.2090.0440.0440.0000.0000.0000.000
109A128ALA0-0.0010.01017.8660.0090.0090.0000.0000.0000.000
110A129ASP-1-0.785-0.86616.641-0.191-0.1910.0000.0000.0000.000
111A130LEU00.000-0.00119.3300.0050.0050.0000.0000.0000.000
112A131ALA0-0.017-0.00421.0900.0070.0070.0000.0000.0000.000
113A132LEU0-0.005-0.00121.8650.0050.0050.0000.0000.0000.000
114A133ALA00.004-0.00723.1980.0020.0020.0000.0000.0000.000
115A134HIS10.8470.92824.0920.1190.1190.0000.0000.0000.000
116A135GLN0-0.021-0.00527.1750.0070.0070.0000.0000.0000.000
117A136HIS0-0.0170.00228.0240.0070.0070.0000.0000.0000.000
118A137TRP0-0.005-0.00726.0460.0020.0020.0000.0000.0000.000
119A138PRO00.0150.00332.7070.0010.0010.0000.0000.0000.000
120A139GLU-1-0.806-0.86034.552-0.057-0.0570.0000.0000.0000.000
121A140LEU00.0210.00831.0600.0020.0020.0000.0000.0000.000
122A141ALA0-0.0040.01331.458-0.002-0.0020.0000.0000.0000.000
123A142PRO00.0540.01931.320-0.001-0.0010.0000.0000.0000.000
124A143TRP0-0.024-0.00731.0110.0020.0020.0000.0000.0000.000
125A144ALA0-0.009-0.01827.688-0.006-0.0060.0000.0000.0000.000
126A145GLU-1-0.912-0.96526.485-0.041-0.0410.0000.0000.0000.000
127A146GLN0-0.033-0.02726.7570.0040.0040.0000.0000.0000.000
128A147LEU00.0060.00722.520-0.001-0.0010.0000.0000.0000.000
129A148GLN0-0.015-0.02522.460-0.013-0.0130.0000.0000.0000.000
130A149ALA0-0.034-0.01222.0890.0060.0060.0000.0000.0000.000
131A150GLN00.009-0.02022.1750.0070.0070.0000.0000.0000.000
132A151TRP0-0.048-0.00515.9510.0020.0020.0000.0000.0000.000
133A152PRO00.0230.03115.6760.0300.0300.0000.0000.0000.000
134A153MET0-0.004-0.01211.2200.0180.0180.0000.0000.0000.000
135A154PRO00.0200.0178.884-0.016-0.0160.0000.0000.0000.000
136A155LEU00.002-0.0057.335-0.283-0.2830.0000.0000.0000.000
137A156PRO00.0260.0067.5690.1280.1280.0000.0000.0000.000
138A157GLY00.0160.01910.3980.1410.1410.0000.0000.0000.000
139A158CYS0-0.0280.00314.099-0.007-0.0070.0000.0000.0000.000
140A159HIS10.7870.88413.0820.3670.3670.0000.0000.0000.000
141A160ARG10.8780.91418.5740.0890.0890.0000.0000.0000.000
142A161LEU0-0.015-0.00120.1340.0110.0110.0000.0000.0000.000
143A162LEU0-0.024-0.02023.971-0.002-0.0020.0000.0000.0000.000
144A163LEU0-0.018-0.00426.4780.0050.0050.0000.0000.0000.000
145A164ASP-1-0.794-0.90230.006-0.037-0.0370.0000.0000.0000.000
146A165GLU-1-0.949-0.96133.500-0.016-0.0160.0000.0000.0000.000
147A166GLY0-0.055-0.03833.2240.0010.0010.0000.0000.0000.000
148A167ARG10.8010.88834.2880.0310.0310.0000.0000.0000.000
149A168VAL00.0520.03229.930-0.004-0.0040.0000.0000.0000.000
150A169THR0-0.081-0.03926.9670.0050.0050.0000.0000.0000.000
151A170LEU0-0.0010.01223.078-0.004-0.0040.0000.0000.0000.000
152A171ASP-1-0.772-0.85622.145-0.120-0.1200.0000.0000.0000.000
153A172LEU00.0050.00418.126-0.014-0.0140.0000.0000.0000.000
154A173TRP00.012-0.01116.898-0.013-0.0130.0000.0000.0000.000
155A174PHE0-0.022-0.00712.149-0.025-0.0250.0000.0000.0000.000
156A175GLY00.052-0.00411.523-0.075-0.0750.0000.0000.0000.000
157A176ASP-1-0.811-0.88712.464-0.428-0.4280.0000.0000.0000.000
158A177ILE00.0440.03214.7200.0360.0360.0000.0000.0000.000
159A178ASN0-0.050-0.02618.0740.0760.0760.0000.0000.0000.000
160A179GLU-1-0.858-0.93314.679-0.285-0.2850.0000.0000.0000.000
161A180LEU0-0.039-0.00914.0780.0440.0440.0000.0000.0000.000
162A181ILE0-0.034-0.01317.6730.0340.0340.0000.0000.0000.000
163A182SER0-0.052-0.04019.4540.0310.0310.0000.0000.0000.000
164A183GLN0-0.032-0.01018.6550.0140.0140.0000.0000.0000.000
165A184LEU0-0.0220.00121.0590.0180.0180.0000.0000.0000.000
166A185ASP-1-0.760-0.84724.065-0.079-0.0790.0000.0000.0000.000
167A186ASP-1-0.819-0.92126.373-0.083-0.0830.0000.0000.0000.000
168A187SER0-0.114-0.06628.6890.0040.0040.0000.0000.0000.000
169A188LEU0-0.021-0.03425.9860.0040.0040.0000.0000.0000.000
170A189ASN0-0.021-0.01030.042-0.010-0.0100.0000.0000.0000.000
171A190GLN0-0.044-0.02632.3500.0090.0090.0000.0000.0000.000
172A191LYS10.8070.90132.3630.0730.0730.0000.0000.0000.000
173A192VAL0-0.0090.01629.3730.0010.0010.0000.0000.0000.000
174A193ASP-1-0.763-0.85732.610-0.067-0.0670.0000.0000.0000.000
175A194ALA0-0.031-0.00533.4790.0040.0040.0000.0000.0000.000
176A195TRP00.0530.02725.763-0.009-0.0090.0000.0000.0000.000
177A196PHE0-0.012-0.02028.3340.0090.0090.0000.0000.0000.000
178A197LEU00.0140.01226.682-0.013-0.0130.0000.0000.0000.000
179A198ASP-1-0.772-0.88626.432-0.165-0.1650.0000.0000.0000.000
180A199GLY00.0630.04623.305-0.021-0.0210.0000.0000.0000.000
181A200PHE00.0230.00720.3980.0170.0170.0000.0000.0000.000
182A201ALA00.0300.01623.992-0.001-0.0010.0000.0000.0000.000
183A202PRO00.005-0.00525.496-0.013-0.0130.0000.0000.0000.000
184A203ALA0-0.046-0.02926.070-0.007-0.0070.0000.0000.0000.000
185A204LYS10.7510.86423.8370.2040.2040.0000.0000.0000.000
186A205ASN00.0340.01819.458-0.049-0.0490.0000.0000.0000.000
187A206PRO0-0.0020.00321.8590.0090.0090.0000.0000.0000.000
188A207ASP-1-0.898-0.94617.729-0.368-0.3680.0000.0000.0000.000
189A208MET0-0.0080.01820.700-0.004-0.0040.0000.0000.0000.000
190A209TRP0-0.067-0.04021.6020.0340.0340.0000.0000.0000.000
191A210THR00.012-0.01422.5000.0270.0270.0000.0000.0000.000
192A211GLN00.000-0.02225.557-0.001-0.0010.0000.0000.0000.000
193A212ASN0-0.063-0.02421.7130.0250.0250.0000.0000.0000.000
194A213LEU00.0330.03023.0490.0080.0080.0000.0000.0000.000
195A214PHE00.005-0.01125.2710.0090.0090.0000.0000.0000.000
196A215ASN00.0630.01729.0750.0090.0090.0000.0000.0000.000
197A216ALA0-0.0100.00725.8250.0090.0090.0000.0000.0000.000
198A217MET0-0.020-0.02625.9230.0090.0090.0000.0000.0000.000
199A218ALA0-0.0010.00429.1100.0080.0080.0000.0000.0000.000
200A219ARG10.8300.90725.6790.1250.1250.0000.0000.0000.000
201A220LEU00.0150.01126.1860.0060.0060.0000.0000.0000.000
202A221ALA0-0.0300.00130.8990.0040.0040.0000.0000.0000.000
203A222ARG10.8720.92133.7130.0690.0690.0000.0000.0000.000
204A223PRO00.0560.02236.911-0.002-0.0020.0000.0000.0000.000
205A224GLY0-0.035-0.01240.1790.0020.0020.0000.0000.0000.000
206A225GLY0-0.0270.00037.1210.0010.0010.0000.0000.0000.000
207A226THR0-0.067-0.06536.3040.0020.0020.0000.0000.0000.000
208A227LEU0-0.0050.00131.206-0.006-0.0060.0000.0000.0000.000
209A228ALA0-0.036-0.01233.1870.0070.0070.0000.0000.0000.000
210A229THR0-0.004-0.02030.051-0.009-0.0090.0000.0000.0000.000
211A230PHE00.0320.01627.9330.0140.0140.0000.0000.0000.000
212A231THR0-0.0210.00530.8830.0080.0080.0000.0000.0000.000
213A232SER0-0.011-0.04733.4160.0020.0020.0000.0000.0000.000
214A233ALA0-0.0080.00032.6170.0050.0050.0000.0000.0000.000
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