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: QY23Y

Calculation Name: 3QKA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKA

Chain ID: A

ChEMBL ID:

UniProt ID: B2HSK3

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2607641.878144
FMO2-HF: Nuclear repulsion 2521191.222268
FMO2-HF: Total energy -86450.655876
FMO2-MP2: Total energy -86699.793572


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:3:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
-10.694-3.4210.207-3.45-4.030.022
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.900 / q_NPA : -0.962
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].
3A5VAL0-0.016-0.0132.948-21.132-16.1120.072-2.640-2.4520.023
4A6GLN00.0210.0313.3007.3518.6160.116-0.534-0.847-0.001
5A7VAL00.0250.0034.795-5.065-4.958-0.001-0.005-0.1010.000
6A8GLU-1-0.886-0.9277.95325.18925.1890.0000.0000.0000.000
7A9ARG10.8940.94910.683-21.331-21.3310.0000.0000.0000.000
8A10ASN00.0130.01214.130-0.634-0.6340.0000.0000.0000.000
9A11GLY00.0240.00817.449-0.705-0.7050.0000.0000.0000.000
10A12PRO00.0110.01518.9760.6930.6930.0000.0000.0000.000
11A13VAL00.0290.02217.1490.0780.0780.0000.0000.0000.000
12A14THR0-0.015-0.01012.5950.9750.9750.0000.0000.0000.000
13A15THR0-0.047-0.06411.714-0.931-0.9310.0000.0000.0000.000
14A16VAL0-0.029-0.0129.0522.4472.4470.0000.0000.0000.000
15A17ILE00.030-0.0017.546-2.407-2.4070.0000.0000.0000.000
16A18ILE0-0.026-0.0167.0524.9254.9250.0000.0000.0000.000
17A19ASN0-0.030-0.0242.917-8.344-7.6270.021-0.262-0.4760.000
18A20ARG10.8110.8805.568-24.415-24.4150.0000.0000.0000.000
19A21PRO00.0770.0527.564-2.645-2.6450.0000.0000.0000.000
20A22GLN00.0260.0047.201-2.281-2.2810.0000.0000.0000.000
21A23ALA0-0.039-0.02011.398-1.380-1.3800.0000.0000.0000.000
22A24ARG10.9190.95513.175-16.008-16.0080.0000.0000.0000.000
23A25ASN0-0.005-0.01510.3341.0731.0730.0000.0000.0000.000
24A26ALA00.0150.01012.263-0.083-0.0830.0000.0000.0000.000
25A27VAL0-0.011-0.00711.2252.1932.1930.0000.0000.0000.000
26A28ASN00.0400.0209.589-0.081-0.0810.0000.0000.0000.000
27A29GLY00.0360.01011.7371.0071.0070.0000.0000.0000.000
28A30PRO00.0100.0037.8500.6660.6660.0000.0000.0000.000
29A31THR0-0.001-0.0077.0334.7974.7970.0000.0000.0000.000
30A32ALA00.0160.0108.1131.0621.0620.0000.0000.0000.000
31A33ALA0-0.022-0.0119.010-0.911-0.9110.0000.0000.0000.000
32A34ALA00.0450.0214.600-1.361-1.197-0.001-0.009-0.1540.000
33A35LEU00.0100.0016.639-0.937-0.9370.0000.0000.0000.000
34A36TYR0-0.028-0.0139.258-2.119-2.1190.0000.0000.0000.000
35A37SER0-0.024-0.0178.069-2.270-2.2700.0000.0000.0000.000
36A38ALA00.0270.0307.795-1.436-1.4360.0000.0000.0000.000
37A39PHE00.032-0.0109.581-2.147-2.1470.0000.0000.0000.000
38A40ALA0-0.019-0.00612.899-1.727-1.7270.0000.0000.0000.000
39A41GLU-1-0.986-0.9999.78430.17930.1790.0000.0000.0000.000
40A42PHE0-0.0040.00013.359-1.174-1.1740.0000.0000.0000.000
41A43ASP-1-0.827-0.92315.01814.44914.4490.0000.0000.0000.000
42A44ARG10.9320.96714.167-21.147-21.1470.0000.0000.0000.000
43A45ASP-1-0.835-0.90816.35317.79017.7900.0000.0000.0000.000
44A46GLU-1-0.916-0.95318.45113.02213.0220.0000.0000.0000.000
45A47SER0-0.111-0.05019.371-0.472-0.4720.0000.0000.0000.000
46A48ALA0-0.070-0.03617.3140.0870.0870.0000.0000.0000.000
47A49SER0-0.047-0.04119.386-0.638-0.6380.0000.0000.0000.000
48A50VAL0-0.009-0.00920.415-0.385-0.3850.0000.0000.0000.000
49A51ALA0-0.0040.01315.3660.7140.7140.0000.0000.0000.000
50A52VAL00.0250.01015.432-1.162-1.1620.0000.0000.0000.000
51A53LEU0-0.0070.01312.4111.6181.6180.0000.0000.0000.000
52A54CYS0-0.032-0.00512.499-1.420-1.4200.0000.0000.0000.000
53A55GLY00.0430.03111.4042.0542.0540.0000.0000.0000.000
54A56ASN00.000-0.0207.192-3.315-3.3150.0000.0000.0000.000
55A57GLY0-0.038-0.02111.044-0.224-0.2240.0000.0000.0000.000
56A58GLY00.0030.00913.252-0.849-0.8490.0000.0000.0000.000
57A59THR0-0.011-0.01614.661-1.362-1.3620.0000.0000.0000.000
58A60PHE0-0.0300.01214.6571.3651.3650.0000.0000.0000.000
59A61CYS0-0.0210.01714.3621.1731.1730.0000.0000.0000.000
60A62ALA00.0140.00516.000-1.172-1.1720.0000.0000.0000.000
61A63GLY00.007-0.01316.991-0.975-0.9750.0000.0000.0000.000
62A64ALA00.0690.03116.0791.2381.2380.0000.0000.0000.000
63A65ASP-1-0.859-0.90414.03719.28119.2810.0000.0000.0000.000
64A66LEU0-0.001-0.01316.162-0.306-0.3060.0000.0000.0000.000
65A67LYS10.8880.94717.450-14.709-14.7090.0000.0000.0000.000
66A68ALA00.0520.04514.716-0.010-0.0100.0000.0000.0000.000
67A69PHE0-0.0050.00116.791-0.136-0.1360.0000.0000.0000.000
68A70GLY0-0.008-0.00319.947-0.331-0.3310.0000.0000.0000.000
69A71THR0-0.034-0.01416.4620.1170.1170.0000.0000.0000.000
70A72ALA00.0240.00415.533-0.025-0.0250.0000.0000.0000.000
71A73GLU-1-0.915-0.96211.35922.98422.9840.0000.0000.0000.000
72A74ALA0-0.021-0.00213.7140.8240.8240.0000.0000.0000.000
73A75ASN0-0.035-0.04415.2340.3320.3320.0000.0000.0000.000
74A76ALA00.0120.01416.151-0.993-0.9930.0000.0000.0000.000
75A77VAL00.0100.00118.046-0.098-0.0980.0000.0000.0000.000
76A78HIS00.0600.03819.467-1.249-1.2490.0000.0000.0000.000
77A79ARG10.9680.98023.068-10.752-10.7520.0000.0000.0000.000
78A80THR0-0.025-0.01223.936-0.072-0.0720.0000.0000.0000.000
79A81GLY00.0480.02420.1660.3390.3390.0000.0000.0000.000
80A82PRO00.0340.01015.571-0.753-0.7530.0000.0000.0000.000
81A83GLY0-0.0120.01117.750-0.674-0.6740.0000.0000.0000.000
82A84PRO00.0160.00616.6621.1541.1540.0000.0000.0000.000
83A85MET0-0.063-0.01915.1471.2701.2700.0000.0000.0000.000
84A86GLY00.0390.01512.9351.6501.6500.0000.0000.0000.000
85A87PRO00.004-0.00912.975-0.840-0.8400.0000.0000.0000.000
86A88SER0-0.051-0.05115.474-0.958-0.9580.0000.0000.0000.000
87A89ARG10.8210.88718.725-15.431-15.4310.0000.0000.0000.000
88A90MET0-0.0460.01315.193-0.291-0.2910.0000.0000.0000.000
89A91MET0-0.0190.00220.067-0.314-0.3140.0000.0000.0000.000
90A92LEU0-0.0060.00617.049-0.044-0.0440.0000.0000.0000.000
91A93SER0-0.003-0.00821.131-0.861-0.8610.0000.0000.0000.000
92A94LYS10.8220.93019.614-16.470-16.4700.0000.0000.0000.000
93A95PRO0-0.0110.00121.2150.3500.3500.0000.0000.0000.000
94A96VAL00.018-0.00516.7440.7290.7290.0000.0000.0000.000
95A97ILE0-0.031-0.00219.299-0.776-0.7760.0000.0000.0000.000
96A98ALA00.009-0.01418.1740.9530.9530.0000.0000.0000.000
97A99ALA00.0020.00816.876-0.942-0.9420.0000.0000.0000.000
98A100VAL0-0.042-0.04117.4880.8560.8560.0000.0000.0000.000
99A101SER00.0750.04516.829-0.643-0.6430.0000.0000.0000.000
100A102GLY00.0480.02019.2350.4910.4910.0000.0000.0000.000
101A103TYR0-0.002-0.00219.611-0.603-0.6030.0000.0000.0000.000
102A104ALA00.0270.02519.1521.0111.0110.0000.0000.0000.000
103A105VAL0-0.012-0.00720.516-0.807-0.8070.0000.0000.0000.000
104A106ALA0-0.054-0.02920.8470.6850.6850.0000.0000.0000.000
105A107GLY00.0820.02319.255-0.055-0.0550.0000.0000.0000.000
106A108GLY00.038-0.00617.7520.5510.5510.0000.0000.0000.000
107A109LEU0-0.021-0.00518.715-0.006-0.0060.0000.0000.0000.000
108A110GLU-1-0.803-0.92420.78113.49213.4920.0000.0000.0000.000
109A111LEU0-0.0010.00114.371-0.151-0.1510.0000.0000.0000.000
110A112ALA00.0310.01818.547-0.001-0.0010.0000.0000.0000.000
111A113LEU0-0.086-0.04720.673-0.491-0.4910.0000.0000.0000.000
112A114TRP0-0.065-0.04016.000-0.302-0.3020.0000.0000.0000.000
113A115CYS0-0.0310.01518.6060.3330.3330.0000.0000.0000.000
114A116ASP-1-0.747-0.85220.97712.91212.9120.0000.0000.0000.000
115A117LEU0-0.053-0.02223.219-0.734-0.7340.0000.0000.0000.000
116A118ARG10.8240.91422.657-11.711-11.7110.0000.0000.0000.000
117A119VAL00.0020.00622.017-0.736-0.7360.0000.0000.0000.000
118A120ALA00.003-0.00922.2180.6140.6140.0000.0000.0000.000
119A121GLU-1-0.785-0.89520.56413.75913.7590.0000.0000.0000.000
120A122GLN0-0.022-0.01024.552-0.096-0.0960.0000.0000.0000.000
121A123ASP-1-0.841-0.90725.66710.39710.3970.0000.0000.0000.000
122A124ALA0-0.078-0.02423.2180.2170.2170.0000.0000.0000.000
123A125VAL0-0.050-0.03523.801-0.573-0.5730.0000.0000.0000.000
124A126PHE00.0240.01223.7570.7340.7340.0000.0000.0000.000
125A127GLY00.0690.01825.269-0.544-0.5440.0000.0000.0000.000
126A128VAL00.0330.02225.3710.6560.6560.0000.0000.0000.000
127A129PHE00.034-0.00124.443-0.263-0.2630.0000.0000.0000.000
128A130CYS0-0.0270.00224.275-0.209-0.2090.0000.0000.0000.000
129A131ARG10.8870.95526.097-10.289-10.2890.0000.0000.0000.000
130A132ARG10.9540.97427.675-10.859-10.8590.0000.0000.0000.000
131A133TRP0-0.053-0.03921.778-0.228-0.2280.0000.0000.0000.000
132A134GLY00.0230.03827.7810.0270.0270.0000.0000.0000.000
133A135VAL0-0.021-0.00423.2940.0370.0370.0000.0000.0000.000
134A136PRO0-0.020-0.00926.704-0.043-0.0430.0000.0000.0000.000
135A137LEU0-0.005-0.01225.1060.4380.4380.0000.0000.0000.000
136A138ILE0-0.031-0.01622.486-0.484-0.4840.0000.0000.0000.000
137A139ASP-1-0.755-0.83818.99716.84116.8410.0000.0000.0000.000
138A140GLY00.0460.01121.9590.2140.2140.0000.0000.0000.000
139A141GLY00.0000.01024.690-0.416-0.4160.0000.0000.0000.000
140A142THR0-0.039-0.03626.129-0.265-0.2650.0000.0000.0000.000
141A143VAL0-0.0120.00527.822-0.411-0.4110.0000.0000.0000.000
142A144ARG10.8950.93922.238-13.908-13.9080.0000.0000.0000.000
143A145LEU00.0400.03328.184-0.225-0.2250.0000.0000.0000.000
144A146PRO0-0.014-0.02929.702-0.245-0.2450.0000.0000.0000.000
145A147ARG10.9030.97130.671-10.255-10.2550.0000.0000.0000.000
146A148LEU0-0.047-0.00726.424-0.169-0.1690.0000.0000.0000.000
147A149ILE00.0130.01331.059-0.146-0.1460.0000.0000.0000.000
148A150GLY00.0330.02933.745-0.328-0.3280.0000.0000.0000.000
149A151HIS00.034-0.01635.7580.2500.2500.0000.0000.0000.000
150A152SER0-0.037-0.01037.3010.0990.0990.0000.0000.0000.000
151A153ARG11.0481.01135.518-8.325-8.3250.0000.0000.0000.000
152A154ALA00.0440.04132.8800.1720.1720.0000.0000.0000.000
153A155MET0-0.015-0.01033.5700.2230.2230.0000.0000.0000.000
154A156ASP-1-0.819-0.88635.9728.6968.6960.0000.0000.0000.000
155A157MET00.0170.02328.6940.0900.0900.0000.0000.0000.000
156A158ILE0-0.017-0.01130.5450.2490.2490.0000.0000.0000.000
157A159LEU0-0.025-0.01932.3190.1230.1230.0000.0000.0000.000
158A160THR0-0.013-0.01034.7580.1220.1220.0000.0000.0000.000
159A161GLY0-0.027-0.01130.6070.0440.0440.0000.0000.0000.000
160A162ARG10.6960.82830.249-8.714-8.7140.0000.0000.0000.000
161A163ALA0-0.036-0.02429.0080.2840.2840.0000.0000.0000.000
162A164VAL0-0.016-0.01029.093-0.372-0.3720.0000.0000.0000.000
163A165GLN00.0300.01528.6160.5720.5720.0000.0000.0000.000
164A166ALA00.0780.03027.605-0.146-0.1460.0000.0000.0000.000
165A167ASP-1-0.872-0.92729.2179.1509.1500.0000.0000.0000.000
166A168GLU-1-0.811-0.89532.8898.9058.9050.0000.0000.0000.000
167A169ALA0-0.007-0.01428.838-0.077-0.0770.0000.0000.0000.000
168A170LEU0-0.0070.00130.5850.0250.0250.0000.0000.0000.000
169A171ALA0-0.036-0.00532.062-0.166-0.1660.0000.0000.0000.000
170A172ILE0-0.112-0.06332.132-0.236-0.2360.0000.0000.0000.000
171A173GLY00.0180.01732.585-0.013-0.0130.0000.0000.0000.000
172A174LEU0-0.034-0.01227.0730.2770.2770.0000.0000.0000.000
173A175ALA0-0.014-0.00427.0010.5770.5770.0000.0000.0000.000
174A176ASN00.0330.01027.211-0.036-0.0360.0000.0000.0000.000
175A177ARG10.9320.95526.644-10.832-10.8320.0000.0000.0000.000
176A178VAL00.0270.02427.0250.3730.3730.0000.0000.0000.000
177A179VAL0-0.018-0.00123.988-0.281-0.2810.0000.0000.0000.000
178A180PRO00.0300.00926.6440.0860.0860.0000.0000.0000.000
179A181ASN0-0.010-0.04724.0520.5840.5840.0000.0000.0000.000
180A182GLY0-0.044-0.01720.546-0.244-0.2440.0000.0000.0000.000
181A183GLN00.0130.00620.4900.3550.3550.0000.0000.0000.000
182A184ALA00.0020.01119.986-0.085-0.0850.0000.0000.0000.000
183A185ARG10.8350.89211.653-20.990-20.9900.0000.0000.0000.000
184A186GLN00.0270.01317.9840.5520.5520.0000.0000.0000.000
185A187ALA00.0780.03720.353-0.214-0.2140.0000.0000.0000.000
186A188ALA0-0.039-0.01619.192-0.342-0.3420.0000.0000.0000.000
187A189GLU-1-0.788-0.86715.37118.20118.2010.0000.0000.0000.000
188A190GLU-1-0.954-0.97119.92211.68711.6870.0000.0000.0000.000
189A191LEU0-0.064-0.02923.597-0.449-0.4490.0000.0000.0000.000
190A192ALA00.026-0.01120.638-0.323-0.3230.0000.0000.0000.000
191A193ALA00.0160.00622.537-0.116-0.1160.0000.0000.0000.000
192A194GLN0-0.034-0.01823.964-0.453-0.4530.0000.0000.0000.000
193A195LEU0-0.030-0.01624.521-0.355-0.3550.0000.0000.0000.000
194A196ALA0-0.008-0.00623.397-0.236-0.2360.0000.0000.0000.000
195A197ALA0-0.0230.00225.564-0.139-0.1390.0000.0000.0000.000
196A198LEU0-0.0350.00128.776-0.462-0.4620.0000.0000.0000.000
197A199PRO00.0240.00030.1390.3120.3120.0000.0000.0000.000
198A200GLN00.0230.00025.9610.4220.4220.0000.0000.0000.000
199A201GLN00.0250.00929.0650.2760.2760.0000.0000.0000.000
200A202CYS00.017-0.00131.007-0.061-0.0610.0000.0000.0000.000
201A203LEU00.0140.03526.782-0.006-0.0060.0000.0000.0000.000
202A204ARG10.9270.94824.409-12.628-12.6280.0000.0000.0000.000
203A205SER00.0100.00528.5090.0600.0600.0000.0000.0000.000
204A206ASP-1-0.882-0.92831.6139.1689.1680.0000.0000.0000.000
205A207ARG10.7760.86522.845-13.157-13.1570.0000.0000.0000.000
206A208LEU0-0.017-0.02126.0120.0930.0930.0000.0000.0000.000
207A209SER00.0240.02129.424-0.070-0.0700.0000.0000.0000.000
208A210ALA00.0220.01131.339-0.143-0.1430.0000.0000.0000.000
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