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: 827ZY

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 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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3358641.223995
FMO2-HF: Nuclear repulsion 3260432.066559
FMO2-HF: Total energy -98209.157435
FMO2-MP2: Total energy -98497.333357


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.
-7.122-1.0244.014-3.677-6.4350.006
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 : 0.048 / q_NPA : -0.004
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].
3A22LYS10.8840.9522.639-7.442-4.5161.070-1.380-2.6160.014
4A23HIS00.0390.0132.221-2.031-1.1801.050-0.813-1.0880.003
5A24TYR0-0.0030.0062.431-0.4090.8890.477-0.794-0.982-0.003
6A25SER0-0.005-0.0052.6822.2363.2091.418-0.688-1.702-0.008
7A26ILE0-0.0300.0045.1960.2020.252-0.001-0.002-0.0470.000
8A27GLN00.0300.0135.9300.1740.1740.0000.0000.0000.000
9A28PRO0-0.051-0.0397.263-0.040-0.0400.0000.0000.0000.000
10A29ALA0-0.017-0.00810.5200.0040.0040.0000.0000.0000.000
11A30ASN0-0.035-0.00413.8360.0180.0180.0000.0000.0000.000
12A31LEU0-0.019-0.01715.246-0.015-0.0150.0000.0000.0000.000
13A32GLU-1-0.889-0.92718.7940.0660.0660.0000.0000.0000.000
14A33PHE0-0.048-0.03120.882-0.004-0.0040.0000.0000.0000.000
15A34ASN00.0470.02824.787-0.001-0.0010.0000.0000.0000.000
16A35ALA00.019-0.00827.8890.0010.0010.0000.0000.0000.000
17A36GLU-1-0.959-0.96731.1700.0330.0330.0000.0000.0000.000
18A37GLY0-0.004-0.00428.6570.0000.0000.0000.0000.0000.000
19A38THR0-0.0040.00627.5670.0020.0020.0000.0000.0000.000
20A39PRO00.0020.02323.0690.0020.0020.0000.0000.0000.000
21A40VAL0-0.008-0.01123.428-0.007-0.0070.0000.0000.0000.000
22A41SER00.0190.02318.7150.0070.0070.0000.0000.0000.000
23A42ARG10.8110.87417.800-0.067-0.0670.0000.0000.0000.000
24A43ASP-1-0.879-0.93014.6320.1140.1140.0000.0000.0000.000
25A44PHE0-0.012-0.02117.182-0.003-0.0030.0000.0000.0000.000
26A45ASP-1-0.872-0.92120.9350.0480.0480.0000.0000.0000.000
27A46ASP-1-0.923-0.96423.4330.0270.0270.0000.0000.0000.000
28A47VAL0-0.038-0.01624.1780.0050.0050.0000.0000.0000.000
29A48TYR00.032-0.00318.3350.0000.0000.0000.0000.0000.000
30A49PHE0-0.022-0.00525.218-0.003-0.0030.0000.0000.0000.000
31A50SER0-0.032-0.01628.8370.0010.0010.0000.0000.0000.000
32A51ASN0-0.005-0.02131.471-0.002-0.0020.0000.0000.0000.000
33A52ASP-1-0.874-0.92332.9340.0260.0260.0000.0000.0000.000
34A53ASN0-0.035-0.02935.585-0.001-0.0010.0000.0000.0000.000
35A54GLY00.0250.02432.386-0.002-0.0020.0000.0000.0000.000
36A55LEU00.0440.04233.194-0.001-0.0010.0000.0000.0000.000
37A56GLU-1-0.806-0.89434.4510.0130.0130.0000.0000.0000.000
38A57GLU-1-0.877-0.92334.2530.0170.0170.0000.0000.0000.000
39A58THR00.009-0.00330.879-0.002-0.0020.0000.0000.0000.000
40A59ARG10.8340.87133.563-0.019-0.0190.0000.0000.0000.000
41A60TYR0-0.047-0.02936.584-0.002-0.0020.0000.0000.0000.000
42A61VAL0-0.021-0.03033.574-0.002-0.0020.0000.0000.0000.000
43A62PHE00.0230.01030.109-0.002-0.0020.0000.0000.0000.000
44A63LEU00.0490.03434.329-0.002-0.0020.0000.0000.0000.000
45A64GLY0-0.006-0.01536.918-0.001-0.0010.0000.0000.0000.000
46A65GLY0-0.057-0.02737.920-0.001-0.0010.0000.0000.0000.000
47A66ASN0-0.0070.00333.980-0.003-0.0030.0000.0000.0000.000
48A67GLN0-0.037-0.01938.188-0.002-0.0020.0000.0000.0000.000
49A68LEU0-0.007-0.00234.886-0.001-0.0010.0000.0000.0000.000
50A69GLU-1-0.904-0.96039.5470.0070.0070.0000.0000.0000.000
51A70ALA0-0.024-0.01441.9700.0000.0000.0000.0000.0000.000
52A71ARG10.8640.92338.1290.0050.0050.0000.0000.0000.000
53A72PHE00.0010.00736.412-0.001-0.0010.0000.0000.0000.000
54A73PRO0-0.025-0.01142.313-0.001-0.0010.0000.0000.0000.000
55A74GLU-1-0.929-0.96445.553-0.002-0.0020.0000.0000.0000.000
56A75HIS0-0.080-0.02938.6920.0000.0000.0000.0000.0000.000
57A76PRO00.0180.01743.0240.0000.0000.0000.0000.0000.000
58A77HIS0-0.067-0.04740.190-0.002-0.0020.0000.0000.0000.000
59A78PRO0-0.014-0.00539.6280.0010.0010.0000.0000.0000.000
60A79LEU0-0.066-0.03432.9650.0010.0010.0000.0000.0000.000
61A80PHE00.0330.02634.7060.0000.0000.0000.0000.0000.000
62A81VAL0-0.018-0.02230.1750.0000.0000.0000.0000.0000.000
63A82VAL00.0050.00529.4830.0010.0010.0000.0000.0000.000
64A83ALA0-0.0030.01326.678-0.003-0.0030.0000.0000.0000.000
65A84GLU-1-0.747-0.88124.8300.0100.0100.0000.0000.0000.000
66A85SER0-0.013-0.03123.402-0.005-0.0050.0000.0000.0000.000
67A86GLY00.022-0.00321.090-0.002-0.0020.0000.0000.0000.000
68A87PHE0-0.0440.01219.8290.0030.0030.0000.0000.0000.000
69A88GLY00.0400.01120.1560.0040.0040.0000.0000.0000.000
70A89THR0-0.036-0.03020.0880.0030.0030.0000.0000.0000.000
71A90GLY00.0510.01622.4790.0030.0030.0000.0000.0000.000
72A91LEU0-0.0300.00324.258-0.003-0.0030.0000.0000.0000.000
73A92ASN0-0.049-0.06327.2640.0000.0000.0000.0000.0000.000
74A93PHE00.0330.01326.022-0.002-0.0020.0000.0000.0000.000
75A94LEU0-0.008-0.00826.403-0.001-0.0010.0000.0000.0000.000
76A95THR0-0.016-0.01629.575-0.001-0.0010.0000.0000.0000.000
77A96LEU0-0.034-0.01830.853-0.001-0.0010.0000.0000.0000.000
78A97TRP0-0.0090.00428.2380.0000.0000.0000.0000.0000.000
79A98GLN00.0140.01932.764-0.001-0.0010.0000.0000.0000.000
80A99ALA00.0320.01935.456-0.001-0.0010.0000.0000.0000.000
81A100PHE0-0.044-0.03435.305-0.002-0.0020.0000.0000.0000.000
82A101ASP-1-0.794-0.90436.0430.0100.0100.0000.0000.0000.000
83A102GLN0-0.030-0.01938.148-0.001-0.0010.0000.0000.0000.000
84A103PHE0-0.036-0.02540.175-0.001-0.0010.0000.0000.0000.000
85A104ARG10.9130.95038.909-0.003-0.0030.0000.0000.0000.000
86A105GLU-1-0.955-0.96542.1590.0090.0090.0000.0000.0000.000
87A106ALA0-0.044-0.01644.3910.0000.0000.0000.0000.0000.000
88A107HIS0-0.037-0.01745.365-0.001-0.0010.0000.0000.0000.000
89A108PRO00.0130.02545.122-0.001-0.0010.0000.0000.0000.000
90A109GLN0-0.056-0.05545.957-0.001-0.0010.0000.0000.0000.000
91A110ALA00.0570.05244.888-0.001-0.0010.0000.0000.0000.000
92A111GLN00.0120.00744.1970.0000.0000.0000.0000.0000.000
93A112LEU0-0.0460.00338.165-0.001-0.0010.0000.0000.0000.000
94A113GLN0-0.069-0.03640.2910.0020.0020.0000.0000.0000.000
95A114ARG10.9440.97135.0710.0150.0150.0000.0000.0000.000
96A115LEU00.0480.02431.632-0.001-0.0010.0000.0000.0000.000
97A116HIS0-0.045-0.01626.2500.0040.0040.0000.0000.0000.000
98A117PHE00.0240.00925.3180.0010.0010.0000.0000.0000.000
99A118ILE0-0.020-0.00623.199-0.003-0.0030.0000.0000.0000.000
100A119SER00.008-0.01021.9300.0040.0040.0000.0000.0000.000
101A120PHE00.0050.00118.481-0.013-0.0130.0000.0000.0000.000
102A121GLU-1-0.814-0.90915.6940.0470.0470.0000.0000.0000.000
103A122LYS10.9720.99411.993-0.114-0.1140.0000.0000.0000.000
104A123PHE0-0.032-0.01711.9790.0090.0090.0000.0000.0000.000
105A124PRO00.0050.02211.3670.0030.0030.0000.0000.0000.000
106A125LEU00.0550.03013.2770.0260.0260.0000.0000.0000.000
107A126THR00.0260.01812.7100.0030.0030.0000.0000.0000.000
108A127ARG10.9310.95514.978-0.130-0.1300.0000.0000.0000.000
109A128ALA00.0010.00717.535-0.014-0.0140.0000.0000.0000.000
110A129ASP-1-0.800-0.91117.2050.1150.1150.0000.0000.0000.000
111A130LEU0-0.052-0.03219.120-0.014-0.0140.0000.0000.0000.000
112A131ALA0-0.019-0.00520.879-0.010-0.0100.0000.0000.0000.000
113A132LEU00.0110.00622.277-0.008-0.0080.0000.0000.0000.000
114A133ALA0-0.016-0.00723.246-0.007-0.0070.0000.0000.0000.000
115A134HIS10.8630.92323.947-0.057-0.0570.0000.0000.0000.000
116A135GLN0-0.0200.00727.1500.0010.0010.0000.0000.0000.000
117A136HIS0-0.027-0.01727.916-0.006-0.0060.0000.0000.0000.000
118A137TRP0-0.012-0.00526.416-0.002-0.0020.0000.0000.0000.000
119A138PRO00.0350.00832.595-0.001-0.0010.0000.0000.0000.000
120A139GLU-1-0.826-0.89734.5400.0200.0200.0000.0000.0000.000
121A140LEU0-0.007-0.01430.875-0.001-0.0010.0000.0000.0000.000
122A141ALA00.0020.01231.0950.0000.0000.0000.0000.0000.000
123A142PRO00.0640.03631.1790.0020.0020.0000.0000.0000.000
124A143TRP0-0.041-0.01830.5210.0020.0020.0000.0000.0000.000
125A144ALA0-0.005-0.01327.3840.0010.0010.0000.0000.0000.000
126A145GLU-1-0.948-0.98326.3020.0490.0490.0000.0000.0000.000
127A146GLN0-0.015-0.01226.6480.0030.0030.0000.0000.0000.000
128A147LEU0-0.0100.00222.2030.0010.0010.0000.0000.0000.000
129A148GLN0-0.023-0.02922.0730.0000.0000.0000.0000.0000.000
130A149ALA0-0.029-0.01021.6140.0110.0110.0000.0000.0000.000
131A150GLN0-0.051-0.02621.6360.0020.0020.0000.0000.0000.000
132A151TRP0-0.055-0.01315.847-0.018-0.0180.0000.0000.0000.000
133A152PRO00.0270.02615.3340.0190.0190.0000.0000.0000.000
134A153MET0-0.009-0.02110.7890.0550.0550.0000.0000.0000.000
135A154PRO00.0000.0138.346-0.056-0.0560.0000.0000.0000.000
136A155LEU0-0.005-0.0127.126-0.116-0.1160.0000.0000.0000.000
137A156PRO00.0380.0097.5800.1340.1340.0000.0000.0000.000
138A157GLY0-0.0070.01710.538-0.012-0.0120.0000.0000.0000.000
139A158CYS0-0.0010.01014.2100.0370.0370.0000.0000.0000.000
140A159HIS10.8320.90513.1060.1520.1520.0000.0000.0000.000
141A160ARG10.8780.92318.2600.0580.0580.0000.0000.0000.000
142A161LEU0-0.029-0.01219.9610.0040.0040.0000.0000.0000.000
143A162LEU0-0.023-0.01923.681-0.003-0.0030.0000.0000.0000.000
144A163LEU0-0.0050.00025.6440.0060.0060.0000.0000.0000.000
145A164ASP-1-0.800-0.90129.1570.0050.0050.0000.0000.0000.000
146A165GLU-1-0.968-0.98032.8690.0030.0030.0000.0000.0000.000
147A166GLY0-0.069-0.03633.230-0.002-0.0020.0000.0000.0000.000
148A167ARG10.7910.88533.619-0.002-0.0020.0000.0000.0000.000
149A168VAL00.0620.03129.421-0.001-0.0010.0000.0000.0000.000
150A169THR0-0.0470.00026.5650.0000.0000.0000.0000.0000.000
151A170LEU0-0.0010.01022.3780.0000.0000.0000.0000.0000.000
152A171ASP-1-0.784-0.88022.020-0.050-0.0500.0000.0000.0000.000
153A172LEU00.0160.00017.8560.0030.0030.0000.0000.0000.000
154A173TRP00.0020.00116.810-0.030-0.0300.0000.0000.0000.000
155A174PHE0-0.033-0.02012.1270.0270.0270.0000.0000.0000.000
156A175GLY00.022-0.01611.799-0.067-0.0670.0000.0000.0000.000
157A176ASP-1-0.852-0.92212.7310.0330.0330.0000.0000.0000.000
158A177ILE00.0410.01815.184-0.017-0.0170.0000.0000.0000.000
159A178ASN00.0210.03818.752-0.011-0.0110.0000.0000.0000.000
160A179GLU-1-0.893-0.95114.666-0.037-0.0370.0000.0000.0000.000
161A180LEU0-0.088-0.03414.511-0.018-0.0180.0000.0000.0000.000
162A181ILE0-0.018-0.01018.086-0.005-0.0050.0000.0000.0000.000
163A182SER0-0.009-0.01020.425-0.001-0.0010.0000.0000.0000.000
164A183GLN0-0.015-0.01618.380-0.001-0.0010.0000.0000.0000.000
165A184LEU0-0.070-0.01121.4760.0010.0010.0000.0000.0000.000
166A185ASP-1-0.759-0.85624.532-0.063-0.0630.0000.0000.0000.000
167A186ASP-1-0.910-0.97926.628-0.046-0.0460.0000.0000.0000.000
168A187SER0-0.132-0.07528.3060.0060.0060.0000.0000.0000.000
169A188LEU0-0.040-0.03426.2740.0040.0040.0000.0000.0000.000
170A189ASN00.0490.03330.2050.0020.0020.0000.0000.0000.000
171A190GLN0-0.063-0.03332.5830.0030.0030.0000.0000.0000.000
172A191LYS10.8790.94032.0740.0300.0300.0000.0000.0000.000
173A192VAL00.0070.01429.5050.0010.0010.0000.0000.0000.000
174A193ASP-1-0.808-0.89332.727-0.013-0.0130.0000.0000.0000.000
175A194ALA0-0.008-0.00233.6610.0020.0020.0000.0000.0000.000
176A195TRP00.0420.01425.897-0.001-0.0010.0000.0000.0000.000
177A196PHE0-0.024-0.02228.5030.0020.0020.0000.0000.0000.000
178A197LEU00.0120.00527.214-0.001-0.0010.0000.0000.0000.000
179A198ASP-1-0.778-0.88926.2730.0190.0190.0000.0000.0000.000
180A199GLY00.0290.01223.656-0.002-0.0020.0000.0000.0000.000
181A200PHE00.0010.00120.3190.0010.0010.0000.0000.0000.000
182A201ALA00.0380.00124.629-0.004-0.0040.0000.0000.0000.000
183A202PRO0-0.010-0.00225.9940.0020.0020.0000.0000.0000.000
184A203ALA0-0.017-0.01126.6430.0010.0010.0000.0000.0000.000
185A204LYS10.8280.91224.398-0.034-0.0340.0000.0000.0000.000
186A205ASN00.0270.00919.6230.0090.0090.0000.0000.0000.000
187A206PRO00.0040.00122.557-0.005-0.0050.0000.0000.0000.000
188A207ASP-1-0.887-0.93818.6960.0370.0370.0000.0000.0000.000
189A208MET0-0.055-0.02320.864-0.006-0.0060.0000.0000.0000.000
190A209TRP0-0.057-0.02322.092-0.009-0.0090.0000.0000.0000.000
191A210THR00.032-0.00223.462-0.001-0.0010.0000.0000.0000.000
192A211GLN00.013-0.02026.3830.0000.0000.0000.0000.0000.000
193A212ASN0-0.049-0.02322.625-0.004-0.0040.0000.0000.0000.000
194A213LEU00.0460.03023.876-0.004-0.0040.0000.0000.0000.000
195A214PHE0-0.009-0.01625.985-0.001-0.0010.0000.0000.0000.000
196A215ASN00.0580.01329.4290.0010.0010.0000.0000.0000.000
197A216ALA0-0.0070.00726.476-0.001-0.0010.0000.0000.0000.000
198A217MET0-0.010-0.01226.8260.0000.0000.0000.0000.0000.000
199A218ALA00.007-0.00229.6400.0000.0000.0000.0000.0000.000
200A219ARG10.8390.92826.0960.0470.0470.0000.0000.0000.000
201A220LEU0-0.013-0.01226.542-0.001-0.0010.0000.0000.0000.000
202A221ALA0-0.0220.00631.2120.0010.0010.0000.0000.0000.000
203A222ARG10.9100.96934.1350.0160.0160.0000.0000.0000.000
204A223PRO00.0530.01737.1090.0010.0010.0000.0000.0000.000
205A224GLY0-0.030-0.01340.4160.0000.0000.0000.0000.0000.000
206A225GLY0-0.0330.00137.3270.0010.0010.0000.0000.0000.000
207A226THR0-0.038-0.04736.8430.0000.0000.0000.0000.0000.000
208A227LEU00.0020.00631.605-0.001-0.0010.0000.0000.0000.000
209A228ALA0-0.012-0.00133.6310.0010.0010.0000.0000.0000.000
210A229THR0-0.007-0.00630.7540.0000.0000.0000.0000.0000.000
211A230PHE00.0580.02228.0880.0000.0000.0000.0000.0000.000
212A231THR0-0.034-0.00431.1390.0010.0010.0000.0000.0000.000
213A232SER0-0.020-0.07133.605-0.001-0.0010.0000.0000.0000.000
214A233ALA00.0010.01233.013-0.001-0.0010.0000.0000.0000.000
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