Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 8N9MY

Calculation Name: 2WNK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WNK

Chain ID: A

ChEMBL ID:

UniProt ID: Q6RUA7

Base Structure: X-ray

Registration Date: 2023-09-27

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2235781.986352
FMO2-HF: Nuclear repulsion 2150877.72513
FMO2-HF: Total energy -84904.261221
FMO2-MP2: Total energy -85144.894055


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-12.347-4.7123.185-4.385-6.435-0.013
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.027
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].
3A6CYS0-0.057-0.0063.689-2.066-0.372-0.008-0.742-0.9440.001
4A7GLU-1-0.924-0.9705.5821.6001.6000.0000.0000.0000.000
5A8THR0-0.078-0.0387.7650.0620.0620.0000.0000.0000.000
6A9GLU-1-0.848-0.9319.924-0.147-0.1470.0000.0000.0000.000
7A10GLY0-0.0030.00413.0750.0160.0160.0000.0000.0000.000
8A11SER0-0.082-0.03310.4770.0000.0000.0000.0000.0000.000
9A12SER00.000-0.0219.2260.0720.0720.0000.0000.0000.000
10A13ILE0-0.0290.0103.016-0.518-0.0610.097-0.131-0.4230.000
11A14SER0-0.029-0.0276.3440.3240.3240.0000.0000.0000.000
12A15PHE00.0060.0042.302-1.223-0.3931.123-0.804-1.150-0.001
13A16THR00.000-0.0067.7860.2990.2990.0000.0000.0000.000
14A17VAL0-0.026-0.00710.994-0.055-0.0550.0000.0000.0000.000
15A18GLU-1-0.824-0.93712.781-0.480-0.4800.0000.0000.0000.000
16A19LYS10.8730.94915.2460.3020.3020.0000.0000.0000.000
17A20ALA0-0.0300.00116.035-0.030-0.0300.0000.0000.0000.000
18A21GLY00.003-0.01316.7500.0220.0220.0000.0000.0000.000
19A22HIS0-0.061-0.01912.103-0.024-0.0240.0000.0000.0000.000
20A23VAL0-0.005-0.0088.2130.0350.0350.0000.0000.0000.000
21A24VAL0-0.024-0.0045.670-0.134-0.1340.0000.0000.0000.000
22A25ARG10.9280.9644.1380.1130.310-0.001-0.051-0.1440.000
23A26PHE00.000-0.0022.352-10.511-7.1821.937-2.511-2.755-0.014
24A27ASN00.0340.0263.3850.0290.7050.009-0.012-0.6740.001
25A28CYS0-0.0530.0145.403-0.958-0.959-0.002-0.0080.0120.000
26A29PRO00.0660.0447.3420.1670.1670.0000.0000.0000.000
27A30SER0-0.005-0.0218.826-0.143-0.1430.0000.0000.0000.000
28A31THR0-0.029-0.00812.125-0.062-0.0620.0000.0000.0000.000
29A32LEU0-0.053-0.02710.983-0.050-0.0500.0000.0000.0000.000
30A33GLU-1-0.807-0.89112.3270.1120.1120.0000.0000.0000.000
31A34GLU-1-0.816-0.86412.8230.0250.0250.0000.0000.0000.000
32A35ILE0-0.052-0.04611.005-0.055-0.0550.0000.0000.0000.000
33A36LYS10.9010.97613.9730.1990.1990.0000.0000.0000.000
34A37PRO00.045-0.03315.063-0.064-0.0640.0000.0000.0000.000
35A38ALA00.0160.01616.8340.0020.0020.0000.0000.0000.000
36A39TYR0-0.008-0.01614.9870.0050.0050.0000.0000.0000.000
37A40GLU-1-0.909-0.94217.336-0.004-0.0040.0000.0000.0000.000
38A41ALA0-0.0030.02418.308-0.021-0.0210.0000.0000.0000.000
39A42GLY00.018-0.00618.906-0.005-0.0050.0000.0000.0000.000
40A43ASP-1-0.903-0.96720.603-0.104-0.1040.0000.0000.0000.000
41A44SER00.0040.00322.634-0.009-0.0090.0000.0000.0000.000
42A45THR0-0.061-0.02816.108-0.005-0.0050.0000.0000.0000.000
43A46LYS10.9140.96718.6490.1260.1260.0000.0000.0000.000
44A47VAL00.0110.00115.430-0.016-0.0160.0000.0000.0000.000
45A48CYS0-0.114-0.04716.1780.0780.0780.0000.0000.0000.000
46A49THR00.002-0.01917.131-0.038-0.0380.0000.0000.0000.000
47A50THR00.0120.00218.923-0.003-0.0030.0000.0000.0000.000
48A51ALA00.012-0.00415.200-0.010-0.0100.0000.0000.0000.000
49A52ASP-1-0.843-0.93015.716-0.275-0.2750.0000.0000.0000.000
50A54SER0-0.0090.01419.2220.0230.0230.0000.0000.0000.000
51A55ASN0-0.056-0.01821.7470.0230.0230.0000.0000.0000.000
52A56GLU-1-0.857-0.94220.330-0.186-0.1860.0000.0000.0000.000
53A57ALA0-0.038-0.01720.9500.0200.0200.0000.0000.0000.000
54A58ALA00.0500.02820.836-0.012-0.0120.0000.0000.0000.000
55A59LEU00.0220.00316.122-0.007-0.0070.0000.0000.0000.000
56A60LYS10.8510.92319.5510.1270.1270.0000.0000.0000.000
57A61ASP-1-0.890-0.94422.276-0.134-0.1340.0000.0000.0000.000
58A62VAL0-0.106-0.04919.353-0.002-0.0020.0000.0000.0000.000
59A63LEU0-0.031-0.02315.754-0.015-0.0150.0000.0000.0000.000
60A64LYS10.9410.96819.9950.1860.1860.0000.0000.0000.000
61A65SER0-0.0140.00020.9370.0180.0180.0000.0000.0000.000
62A66ALA00.0540.02815.861-0.021-0.0210.0000.0000.0000.000
63A67SER0-0.040-0.01915.4770.0400.0400.0000.0000.0000.000
64A68LEU00.0510.03110.406-0.056-0.0560.0000.0000.0000.000
65A69ALA0-0.037-0.00412.1390.0380.0380.0000.0000.0000.000
66A70GLN00.0620.01311.394-0.043-0.0430.0000.0000.0000.000
67A71ALA0-0.051-0.02811.552-0.038-0.0380.0000.0000.0000.000
68A72GLU-1-0.896-0.92611.6180.4310.4310.0000.0000.0000.000
69A73GLY0-0.0060.0109.6220.1240.1240.0000.0000.0000.000
70A74SER0-0.089-0.0699.635-0.125-0.1250.0000.0000.0000.000
71A75GLY00.0180.0316.685-0.009-0.0090.0000.0000.0000.000
72A76PRO0-0.028-0.0363.318-0.875-0.4310.031-0.089-0.3860.000
73A77SER00.0120.0084.2430.1690.178-0.001-0.0370.0290.000
74A78GLY0-0.003-0.0027.569-0.201-0.2010.0000.0000.0000.000
75A79GLY00.0280.0108.7020.1650.1650.0000.0000.0000.000
76A80ASN0-0.0280.0009.869-0.006-0.0060.0000.0000.0000.000
77A81ASP-1-0.825-0.9106.8772.1502.1500.0000.0000.0000.000
78A82PHE00.016-0.0106.860-0.291-0.2910.0000.0000.0000.000
79A83THR0-0.059-0.0416.6280.0090.0090.0000.0000.0000.000
80A84LEU00.0140.0158.5860.0620.0620.0000.0000.0000.000
81A85THR0-0.002-0.00810.420-0.107-0.1070.0000.0000.0000.000
82A86VAL00.0090.00513.1000.0220.0220.0000.0000.0000.000
83A87ASP-1-0.898-0.94115.472-0.161-0.1610.0000.0000.0000.000
84A88ALA0-0.019-0.01818.6540.0150.0150.0000.0000.0000.000
85A89LEU0-0.083-0.02216.941-0.016-0.0160.0000.0000.0000.000
86A90PRO00.0020.01419.0680.0310.0310.0000.0000.0000.000
87A91GLU-1-0.868-0.95222.116-0.189-0.1890.0000.0000.0000.000
88A92ALA0-0.037-0.01524.1020.0050.0050.0000.0000.0000.000
89A93GLU-1-0.914-0.95518.696-0.410-0.4100.0000.0000.0000.000
90A94THR0-0.028-0.01918.5200.0170.0170.0000.0000.0000.000
91A95SER00.012-0.01815.467-0.042-0.0420.0000.0000.0000.000
92A96VAL0-0.057-0.01412.9870.0670.0670.0000.0000.0000.000
93A97PHE0-0.004-0.01312.676-0.123-0.1230.0000.0000.0000.000
94A98PHE00.0150.00910.4830.0960.0960.0000.0000.0000.000
95A99LEU0-0.008-0.00912.070-0.079-0.0790.0000.0000.0000.000
96A101GLN00.007-0.01512.222-0.061-0.0610.0000.0000.0000.000
97A102ARG10.9200.96515.6150.0540.0540.0000.0000.0000.000
98A103THR00.019-0.01817.791-0.017-0.0170.0000.0000.0000.000
99A104GLY0-0.045-0.02319.484-0.001-0.0010.0000.0000.0000.000
100A105ALA0-0.091-0.01819.999-0.021-0.0210.0000.0000.0000.000
101A115ALA0-0.048-0.04617.645-0.013-0.0130.0000.0000.0000.000
102A116VAL00.0240.03012.7890.0080.0080.0000.0000.0000.000
103A117PRO00.0040.00016.0720.0310.0310.0000.0000.0000.000
104A118SER00.015-0.00916.393-0.019-0.0190.0000.0000.0000.000
105A119ASP-1-0.956-0.97017.284-0.105-0.1050.0000.0000.0000.000
106A120LYS10.8920.94514.5100.1790.1790.0000.0000.0000.000
107A122GLY00.0170.01010.6340.0380.0380.0000.0000.0000.000
108A123VAL00.0240.0146.741-0.280-0.2800.0000.0000.0000.000
109A124HIS00.0140.0338.7630.2930.2930.0000.0000.0000.000
110A125ILE0-0.002-0.0128.621-0.239-0.2390.0000.0000.0000.000
111A126LEU0-0.0040.01010.8240.1460.1460.0000.0000.0000.000
112A127VAL0-0.023-0.01613.397-0.056-0.0560.0000.0000.0000.000
113A128LYS10.9210.95515.6620.5450.5450.0000.0000.0000.000
114A129ALA00.0170.00318.3350.0100.0100.0000.0000.0000.000
115A130ALA00.003-0.00321.743-0.009-0.0090.0000.0000.0000.000
116A131PRO0-0.009-0.00421.9800.0110.0110.0000.0000.0000.000
117A132GLN0-0.043-0.01625.1510.0220.0220.0000.0000.0000.000
118A133ALA0-0.038-0.01828.1760.0090.0090.0000.0000.0000.000
119A134PRO0-0.0080.01828.463-0.005-0.0050.0000.0000.0000.000
120A135VAL00.0520.01224.855-0.005-0.0050.0000.0000.0000.000
121A136CYS0-0.114-0.01727.3450.0180.0180.0000.0000.0000.000
122A137SER0-0.004-0.01724.713-0.007-0.0070.0000.0000.0000.000
123A138ALA00.0090.01226.4370.0050.0050.0000.0000.0000.000
124A139GLN00.052-0.00529.1650.0020.0020.0000.0000.0000.000
125A140ASP-1-0.963-0.97330.615-0.023-0.0230.0000.0000.0000.000
126A141HIS00.0010.01932.3780.0060.0060.0000.0000.0000.000
127A142THR0-0.011-0.02434.012-0.001-0.0010.0000.0000.0000.000
128A143LEU0-0.0260.00231.4610.0010.0010.0000.0000.0000.000
129A144GLU-1-0.943-0.98034.983-0.050-0.0500.0000.0000.0000.000
130A145LEU0-0.021-0.00133.433-0.004-0.0040.0000.0000.0000.000
131A146GLN0-0.010-0.02238.0670.0050.0050.0000.0000.0000.000
132A147ILE00.0090.02438.374-0.004-0.0040.0000.0000.0000.000
133A148THR0-0.027-0.03741.8750.0030.0030.0000.0000.0000.000
134A149ALA00.0160.01444.1040.0030.0030.0000.0000.0000.000
135A150ALA00.0420.02544.067-0.002-0.0020.0000.0000.0000.000
136A151ASN0-0.096-0.06542.421-0.002-0.0020.0000.0000.0000.000
137A152SER0-0.036-0.01440.223-0.003-0.0030.0000.0000.0000.000
138A153ASP-1-0.907-0.97135.134-0.111-0.1110.0000.0000.0000.000
139A154THR00.0300.02535.3300.0010.0010.0000.0000.0000.000
140A155SER00.015-0.00829.922-0.006-0.0060.0000.0000.0000.000
141A156PHE0-0.010-0.00928.5930.0070.0070.0000.0000.0000.000
142A157VAL00.0540.02023.224-0.009-0.0090.0000.0000.0000.000
143A158CYS0-0.0510.01523.9120.0090.0090.0000.0000.0000.000
144A159GLY00.0510.00322.034-0.023-0.0230.0000.0000.0000.000
145A160GLY00.0280.00820.5700.0190.0190.0000.0000.0000.000
146A161THR0-0.008-0.01819.723-0.018-0.0180.0000.0000.0000.000
147A162PHE0-0.071-0.02520.9660.0130.0130.0000.0000.0000.000
148A163ASN0-0.016-0.02418.3300.0000.0000.0000.0000.0000.000
149A164VAL00.0290.03221.244-0.016-0.0160.0000.0000.0000.000
150A165ILE00.0260.02023.1980.0070.0070.0000.0000.0000.000
151A166LYS10.8440.96126.3140.0550.0550.0000.0000.0000.000
152A167PRO00.1270.03729.423-0.001-0.0010.0000.0000.0000.000
153A168ALA00.0040.00826.165-0.007-0.0070.0000.0000.0000.000
154A169ASN0-0.030-0.02227.522-0.014-0.0140.0000.0000.0000.000
155A170ALA00.0440.01329.1250.0040.0040.0000.0000.0000.000
156A171ALA00.0100.01530.8820.0010.0010.0000.0000.0000.000
157A172LYS10.8390.94133.3650.0510.0510.0000.0000.0000.000
158A173VAL0-0.0120.00033.879-0.006-0.0060.0000.0000.0000.000
159A174LEU00.0100.01033.6490.0050.0050.0000.0000.0000.000
160A175GLN00.007-0.01037.389-0.003-0.0030.0000.0000.0000.000
161A176GLY0-0.0090.02040.4140.0000.0000.0000.0000.0000.000
162A177ASP-1-0.813-0.92741.765-0.036-0.0360.0000.0000.0000.000
163A178SER0-0.042-0.03440.552-0.002-0.0020.0000.0000.0000.000
164A179CYS0-0.062-0.01736.173-0.003-0.0030.0000.0000.0000.000
165A180GLU-1-0.906-0.95536.538-0.022-0.0220.0000.0000.0000.000
166A181THR0-0.050-0.02838.3650.0020.0020.0000.0000.0000.000
167A182GLU-1-0.914-0.95434.239-0.049-0.0490.0000.0000.0000.000
168A183VAL0-0.010-0.01038.0800.0030.0030.0000.0000.0000.000
169A184ASP-1-0.848-0.93038.066-0.051-0.0510.0000.0000.0000.000
170A185LEU00.0330.02135.6050.0020.0020.0000.0000.0000.000
171A186VAL0-0.017-0.00938.6730.0020.0020.0000.0000.0000.000
172A187SER0-0.094-0.05841.3700.0030.0030.0000.0000.0000.000
173A188LEU00.0020.01040.9890.0020.0020.0000.0000.0000.000
174A189VAL0-0.039-0.03541.5480.0010.0010.0000.0000.0000.000
175A190PRO00.0170.00842.056-0.003-0.0030.0000.0000.0000.000
176A191HIS00.002-0.00241.732-0.002-0.0020.0000.0000.0000.000
177A192ALA0-0.0210.00938.822-0.004-0.0040.0000.0000.0000.000
178A193SER0-0.038-0.02834.460-0.002-0.0020.0000.0000.0000.000
179A194ARG10.9070.97426.9640.1110.1110.0000.0000.0000.000
180A195SER00.0150.01727.4030.0030.0030.0000.0000.0000.000
181A196ALA00.005-0.01024.5390.0070.0070.0000.0000.0000.000
182A197LEU0-0.031-0.02721.703-0.002-0.0020.0000.0000.0000.000
183A198GLU-1-0.887-0.92221.344-0.258-0.2580.0000.0000.0000.000
184A199GLN0-0.010-0.00415.0380.0570.0570.0000.0000.0000.000
185A200SER00.0700.02217.6480.0000.0000.0000.0000.0000.000
186A201GLY0-0.039-0.03119.5740.0190.0190.0000.0000.0000.000
187A202LEU0-0.053-0.01021.9180.0270.0270.0000.0000.0000.000
188A203ILE0-0.031-0.00924.854-0.002-0.0020.0000.0000.0000.000
189A204LYS10.9910.99427.8710.1430.1430.0000.0000.0000.000
190A205LEU0-0.027-0.01131.0290.0020.0020.0000.0000.0000.000
191A206SER00.011-0.00534.243-0.002-0.0020.0000.0000.0000.000
192A207VAL0-0.022-0.01536.8490.0030.0030.0000.0000.0000.000
193A208THR00.0500.02640.503-0.002-0.0020.0000.0000.0000.000
194A209ASP-1-0.881-0.91843.161-0.055-0.0550.0000.0000.0000.000
195A210LEU0-0.062-0.03545.008-0.001-0.0010.0000.0000.0000.000
196A211PRO0-0.0040.01345.4100.0020.0020.0000.0000.0000.000
197A212GLN00.032-0.00148.0610.0020.0020.0000.0000.0000.000
198A213GLN0-0.0180.00150.4010.0010.0010.0000.0000.0000.000
199A214GLN00.006-0.01147.160-0.001-0.0010.0000.0000.0000.000
200A215GLN0-0.0150.00644.1490.0020.0020.0000.0000.0000.000
201A216LYS10.9010.94442.0780.0390.0390.0000.0000.0000.000
202A217LEU0-0.0210.00037.4200.0010.0010.0000.0000.0000.000
203A219TYR00.013-0.00431.054-0.001-0.0010.0000.0000.0000.000
204A220ARG10.8780.94630.1120.0440.0440.0000.0000.0000.000
205A222GLU-1-0.810-0.93625.853-0.033-0.0330.0000.0000.0000.000
206A223ASP-1-0.767-0.88922.879-0.035-0.0350.0000.0000.0000.000
207A224SER0-0.046-0.03021.0310.0010.0010.0000.0000.0000.000
208A225SER0-0.032-0.01223.1880.0160.0160.0000.0000.0000.000
209A226GLN0-0.096-0.04325.840-0.002-0.0020.0000.0000.0000.000
210A227LYS10.9030.97527.4360.0100.0100.0000.0000.0000.000
211A228ALA00.021-0.01728.132-0.007-0.0070.0000.0000.0000.000
212A230LYS10.9590.98130.5860.0310.0310.0000.0000.0000.000
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