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: J2QG9

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238432.911179
FMO2-HF: Nuclear repulsion 2153526.443978
FMO2-HF: Total energy -84906.4672
FMO2-MP2: Total energy -85147.049021


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.
-14.275-7.7497.171-5.985-7.712-0.022
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 : -0.016 / 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].
3A6CYS0-0.0490.0023.792-1.745-0.133-0.007-0.764-0.8410.001
4A7GLU-1-0.878-0.9285.9291.9081.9080.0000.0000.0000.000
5A8THR0-0.076-0.0517.9780.0750.0750.0000.0000.0000.000
6A9GLU-1-0.749-0.83910.095-0.162-0.1620.0000.0000.0000.000
7A10GLY0-0.009-0.00113.1220.0100.0100.0000.0000.0000.000
8A11SER0-0.074-0.02010.6620.0080.0080.0000.0000.0000.000
9A12SER0-0.007-0.0249.2120.0570.0570.0000.0000.0000.000
10A13ILE0-0.0040.0233.082-0.5090.0180.083-0.150-0.460-0.001
11A14SER0-0.033-0.0265.9210.4860.4860.0000.0000.0000.000
12A15PHE0-0.0050.0012.114-1.158-0.5532.374-1.478-1.502-0.003
13A16THR0-0.023-0.0287.6690.3360.3360.0000.0000.0000.000
14A17VAL0-0.0160.01011.025-0.049-0.0490.0000.0000.0000.000
15A18GLU-1-0.776-0.88212.569-0.466-0.4660.0000.0000.0000.000
16A19LYS10.8340.92715.0280.3220.3220.0000.0000.0000.000
17A20ALA00.0090.01315.997-0.034-0.0340.0000.0000.0000.000
18A21GLY00.004-0.00616.6750.0250.0250.0000.0000.0000.000
19A22HIS0-0.050-0.02011.955-0.035-0.0350.0000.0000.0000.000
20A23VAL0-0.010-0.0138.6320.0520.0520.0000.0000.0000.000
21A24VAL0-0.016-0.0035.612-0.127-0.1270.0000.0000.0000.000
22A25ARG10.8960.9463.8630.1200.431-0.001-0.124-0.1860.000
23A26PHE00.0100.0042.093-12.669-10.2454.686-3.521-3.588-0.020
24A27ASN00.0370.0053.3350.0440.5570.0150.241-0.7680.001
25A28CYS0-0.0170.0135.285-1.001-1.011-0.002-0.0100.0220.000
26A29PRO00.0940.0617.0610.1230.1230.0000.0000.0000.000
27A30SER0-0.018-0.0288.649-0.130-0.1300.0000.0000.0000.000
28A31THR0-0.067-0.02312.132-0.057-0.0570.0000.0000.0000.000
29A32LEU0-0.084-0.05011.002-0.050-0.0500.0000.0000.0000.000
30A33GLU-1-0.837-0.89612.2340.1030.1030.0000.0000.0000.000
31A34GLU-1-0.811-0.86312.851-0.017-0.0170.0000.0000.0000.000
32A35ILE0-0.0140.00010.942-0.055-0.0550.0000.0000.0000.000
33A36LYS10.7970.90514.1470.2500.2500.0000.0000.0000.000
34A37PRO00.043-0.02114.836-0.074-0.0740.0000.0000.0000.000
35A38ALA00.0110.01316.580-0.004-0.0040.0000.0000.0000.000
36A39TYR0-0.031-0.03614.4470.0040.0040.0000.0000.0000.000
37A40GLU-1-0.860-0.93717.062-0.028-0.0280.0000.0000.0000.000
38A41ALA0-0.0020.02818.057-0.023-0.0230.0000.0000.0000.000
39A42GLY0-0.006-0.01118.9430.0000.0000.0000.0000.0000.000
40A43ASP-1-0.883-0.95120.417-0.132-0.1320.0000.0000.0000.000
41A44SER0-0.016-0.00622.364-0.012-0.0120.0000.0000.0000.000
42A45THR0-0.065-0.03216.274-0.006-0.0060.0000.0000.0000.000
43A46LYS10.8730.93318.4610.1620.1620.0000.0000.0000.000
44A47VAL00.0160.00914.996-0.024-0.0240.0000.0000.0000.000
45A48CYS0-0.082-0.02115.8970.0820.0820.0000.0000.0000.000
46A49THR00.021-0.00516.817-0.040-0.0400.0000.0000.0000.000
47A50THR0-0.060-0.04118.460-0.001-0.0010.0000.0000.0000.000
48A51ALA00.0180.00314.770-0.013-0.0130.0000.0000.0000.000
49A52ASP-1-0.750-0.84215.435-0.302-0.3020.0000.0000.0000.000
50A54SER0-0.003-0.01618.7800.0350.0350.0000.0000.0000.000
51A55ASN0-0.081-0.04121.3690.0240.0240.0000.0000.0000.000
52A56GLU-1-0.781-0.88519.730-0.230-0.2300.0000.0000.0000.000
53A57ALA0-0.0240.00020.7980.0260.0260.0000.0000.0000.000
54A58ALA00.0660.02920.784-0.012-0.0120.0000.0000.0000.000
55A59LEU0-0.001-0.00415.592-0.014-0.0140.0000.0000.0000.000
56A60LYS10.8570.92719.0200.1410.1410.0000.0000.0000.000
57A61ASP-1-0.882-0.94121.902-0.154-0.1540.0000.0000.0000.000
58A62VAL0-0.023-0.00119.0860.0060.0060.0000.0000.0000.000
59A63LEU0-0.017-0.01815.639-0.018-0.0180.0000.0000.0000.000
60A64LYS10.8110.90519.8460.1970.1970.0000.0000.0000.000
61A65SER0-0.040-0.00920.6530.0290.0290.0000.0000.0000.000
62A66ALA00.0450.02115.883-0.027-0.0270.0000.0000.0000.000
63A67SER0-0.029-0.01615.5430.0450.0450.0000.0000.0000.000
64A68LEU00.0320.01210.493-0.071-0.0710.0000.0000.0000.000
65A69ALA0-0.0300.01111.9200.0450.0450.0000.0000.0000.000
66A70GLN00.034-0.00211.044-0.085-0.0850.0000.0000.0000.000
67A71ALA0-0.047-0.02211.172-0.029-0.0290.0000.0000.0000.000
68A72GLU-1-0.891-0.94411.7370.3480.3480.0000.0000.0000.000
69A73GLY0-0.039-0.0159.3490.0950.0950.0000.0000.0000.000
70A74SER0-0.079-0.0449.301-0.085-0.0850.0000.0000.0000.000
71A75GLY0-0.033-0.0055.968-0.015-0.0150.0000.0000.0000.000
72A76PRO0-0.042-0.0343.522-0.825-0.3990.022-0.089-0.3600.000
73A77SER00.002-0.0273.9220.0390.1570.001-0.090-0.0290.000
74A78GLY00.0050.0207.428-0.242-0.2420.0000.0000.0000.000
75A79GLY00.0140.0058.7140.0770.0770.0000.0000.0000.000
76A80ASN0-0.033-0.0129.747-0.007-0.0070.0000.0000.0000.000
77A81ASP-1-0.751-0.8496.1422.0602.0600.0000.0000.0000.000
78A82PHE00.0470.0076.600-0.338-0.3380.0000.0000.0000.000
79A83THR0-0.074-0.0536.3730.1420.1420.0000.0000.0000.000
80A84LEU00.0240.0348.2870.0950.0950.0000.0000.0000.000
81A85THR00.001-0.00910.040-0.100-0.1000.0000.0000.0000.000
82A86VAL00.0230.01112.8870.0140.0140.0000.0000.0000.000
83A87ASP-1-0.876-0.93815.421-0.203-0.2030.0000.0000.0000.000
84A88ALA0-0.046-0.03318.3400.0200.0200.0000.0000.0000.000
85A89LEU0-0.0100.01016.953-0.014-0.0140.0000.0000.0000.000
86A90PRO00.0160.02219.0690.0330.0330.0000.0000.0000.000
87A91GLU-1-0.859-0.93122.087-0.195-0.1950.0000.0000.0000.000
88A92ALA0-0.032-0.02123.7360.0100.0100.0000.0000.0000.000
89A93GLU-1-0.915-0.95718.688-0.434-0.4340.0000.0000.0000.000
90A94THR0-0.023-0.01318.3770.0190.0190.0000.0000.0000.000
91A95SER00.006-0.01915.219-0.038-0.0380.0000.0000.0000.000
92A96VAL0-0.045-0.00812.6920.0730.0730.0000.0000.0000.000
93A97PHE0-0.013-0.02112.390-0.135-0.1350.0000.0000.0000.000
94A98PHE00.0310.01410.4850.0960.0960.0000.0000.0000.000
95A99LEU0-0.016-0.01411.968-0.086-0.0860.0000.0000.0000.000
96A101GLN00.020-0.01411.978-0.043-0.0430.0000.0000.0000.000
97A102ARG10.8240.88115.4180.0570.0570.0000.0000.0000.000
98A103THR0-0.001-0.03417.609-0.026-0.0260.0000.0000.0000.000
99A104GLY0-0.022-0.00219.2370.0030.0030.0000.0000.0000.000
100A105ALA0-0.105-0.04519.888-0.036-0.0360.0000.0000.0000.000
101A115ALA0-0.037-0.03417.926-0.013-0.0130.0000.0000.0000.000
102A116VAL00.0170.02012.6140.0090.0090.0000.0000.0000.000
103A117PRO00.004-0.00215.9730.0330.0330.0000.0000.0000.000
104A118SER00.011-0.01216.435-0.018-0.0180.0000.0000.0000.000
105A119ASP-1-0.930-0.95917.663-0.114-0.1140.0000.0000.0000.000
106A120LYS10.8320.91314.5390.1790.1790.0000.0000.0000.000
107A122GLY00.0110.01010.5750.0320.0320.0000.0000.0000.000
108A123VAL00.019-0.0046.294-0.326-0.3260.0000.0000.0000.000
109A124HIS00.0050.0278.5690.2720.2720.0000.0000.0000.000
110A125ILE0-0.013-0.0198.175-0.320-0.3200.0000.0000.0000.000
111A126LEU00.0110.02410.5710.1570.1570.0000.0000.0000.000
112A127VAL0-0.035-0.03012.996-0.080-0.0800.0000.0000.0000.000
113A128LYS10.8840.93515.6920.5550.5550.0000.0000.0000.000
114A129ALA00.0230.01118.4180.0110.0110.0000.0000.0000.000
115A130ALA0-0.011-0.00721.645-0.010-0.0100.0000.0000.0000.000
116A131PRO00.001-0.01121.6910.0160.0160.0000.0000.0000.000
117A132GLN0-0.058-0.02524.8300.0230.0230.0000.0000.0000.000
118A133ALA0-0.039-0.02227.9390.0110.0110.0000.0000.0000.000
119A134PRO0-0.0170.00928.253-0.005-0.0050.0000.0000.0000.000
120A135VAL00.0410.00824.664-0.004-0.0040.0000.0000.0000.000
121A136CYS0-0.096-0.01826.9900.0170.0170.0000.0000.0000.000
122A137SER0-0.007-0.00524.180-0.009-0.0090.0000.0000.0000.000
123A138ALA00.003-0.00925.9310.0040.0040.0000.0000.0000.000
124A139GLN0-0.002-0.02228.5840.0020.0020.0000.0000.0000.000
125A140ASP-1-0.922-0.95330.432-0.028-0.0280.0000.0000.0000.000
126A141HIS00.0210.02031.7200.0060.0060.0000.0000.0000.000
127A142THR0-0.025-0.03133.8460.0000.0000.0000.0000.0000.000
128A143LEU0-0.0230.00331.0740.0010.0010.0000.0000.0000.000
129A144GLU-1-0.928-0.96734.590-0.053-0.0530.0000.0000.0000.000
130A145LEU0-0.019-0.00433.373-0.005-0.0050.0000.0000.0000.000
131A146GLN0-0.011-0.01438.0810.0050.0050.0000.0000.0000.000
132A147ILE00.0170.02138.123-0.004-0.0040.0000.0000.0000.000
133A148THR0-0.015-0.02441.8460.0030.0030.0000.0000.0000.000
134A149ALA00.0130.01444.2620.0030.0030.0000.0000.0000.000
135A150ALA00.0190.01744.232-0.002-0.0020.0000.0000.0000.000
136A151ASN0-0.060-0.04142.451-0.003-0.0030.0000.0000.0000.000
137A152SER0-0.041-0.00740.320-0.003-0.0030.0000.0000.0000.000
138A153ASP-1-0.820-0.91834.410-0.119-0.1190.0000.0000.0000.000
139A154THR00.0420.03835.0230.0000.0000.0000.0000.0000.000
140A155SER0-0.011-0.01930.066-0.006-0.0060.0000.0000.0000.000
141A156PHE00.0000.00028.4340.0060.0060.0000.0000.0000.000
142A157VAL00.0420.01823.130-0.009-0.0090.0000.0000.0000.000
143A158CYS00.0000.04123.7310.0130.0130.0000.0000.0000.000
144A159GLY00.0900.03621.407-0.027-0.0270.0000.0000.0000.000
145A160GLY00.0390.00819.7760.0220.0220.0000.0000.0000.000
146A161THR00.008-0.00919.602-0.013-0.0130.0000.0000.0000.000
147A162PHE0-0.074-0.01420.7730.0100.0100.0000.0000.0000.000
148A163ASN0-0.050-0.02918.943-0.019-0.0190.0000.0000.0000.000
149A164VAL00.0260.01721.014-0.016-0.0160.0000.0000.0000.000
150A165ILE00.0280.00522.9710.0010.0010.0000.0000.0000.000
151A166LYS10.7850.91626.3560.0470.0470.0000.0000.0000.000
152A167PRO00.0780.02829.644-0.002-0.0020.0000.0000.0000.000
153A168ALA00.0230.01226.251-0.008-0.0080.0000.0000.0000.000
154A169ASN0-0.013-0.00827.706-0.016-0.0160.0000.0000.0000.000
155A170ALA00.0630.02829.2970.0020.0020.0000.0000.0000.000
156A171ALA0-0.0030.00430.9800.0010.0010.0000.0000.0000.000
157A172LYS10.7630.89433.4070.0480.0480.0000.0000.0000.000
158A173VAL0-0.0070.00734.101-0.007-0.0070.0000.0000.0000.000
159A174LEU0-0.009-0.00233.3960.0050.0050.0000.0000.0000.000
160A175GLN00.0070.00137.386-0.003-0.0030.0000.0000.0000.000
161A176GLY00.0120.01740.6210.0010.0010.0000.0000.0000.000
162A177ASP-1-0.784-0.89741.434-0.039-0.0390.0000.0000.0000.000
163A178SER0-0.078-0.06940.494-0.002-0.0020.0000.0000.0000.000
164A179CYS0-0.062-0.01736.547-0.005-0.0050.0000.0000.0000.000
165A180GLU-1-0.784-0.87236.525-0.028-0.0280.0000.0000.0000.000
166A181THR0-0.059-0.02938.0140.0010.0010.0000.0000.0000.000
167A182GLU-1-0.875-0.94533.806-0.048-0.0480.0000.0000.0000.000
168A183VAL0-0.006-0.00737.8460.0040.0040.0000.0000.0000.000
169A184ASP-1-0.810-0.90438.109-0.047-0.0470.0000.0000.0000.000
170A185LEU0-0.0030.02035.3540.0020.0020.0000.0000.0000.000
171A186VAL00.007-0.00938.7030.0010.0010.0000.0000.0000.000
172A187SER0-0.108-0.06441.4740.0030.0030.0000.0000.0000.000
173A188LEU00.0160.01641.0720.0020.0020.0000.0000.0000.000
174A189VAL00.001-0.01941.9420.0010.0010.0000.0000.0000.000
175A190PRO00.0260.01442.380-0.003-0.0030.0000.0000.0000.000
176A191HIS0-0.027-0.01641.603-0.002-0.0020.0000.0000.0000.000
177A192ALA0-0.0370.00739.078-0.005-0.0050.0000.0000.0000.000
178A193SER0-0.021-0.01634.771-0.001-0.0010.0000.0000.0000.000
179A194ARG10.8530.92927.3030.1070.1070.0000.0000.0000.000
180A195SER0-0.0060.00227.1480.0040.0040.0000.0000.0000.000
181A196ALA00.010-0.00624.0620.0080.0080.0000.0000.0000.000
182A197LEU0-0.0130.00421.6110.0010.0010.0000.0000.0000.000
183A198GLU-1-0.852-0.89120.877-0.278-0.2780.0000.0000.0000.000
184A199GLN0-0.032-0.03315.3500.0620.0620.0000.0000.0000.000
185A200SER00.028-0.02117.3750.0010.0010.0000.0000.0000.000
186A201GLY0-0.056-0.03819.2980.0180.0180.0000.0000.0000.000
187A202LEU0-0.044-0.00221.6090.0300.0300.0000.0000.0000.000
188A203ILE0-0.033-0.01224.589-0.001-0.0010.0000.0000.0000.000
189A204LYS10.8440.91227.6910.1370.1370.0000.0000.0000.000
190A205LEU00.002-0.00630.9500.0020.0020.0000.0000.0000.000
191A206SER00.021-0.00234.287-0.001-0.0010.0000.0000.0000.000
192A207VAL0-0.005-0.00537.0900.0030.0030.0000.0000.0000.000
193A208THR00.017-0.01440.771-0.002-0.0020.0000.0000.0000.000
194A209ASP-1-0.856-0.90843.191-0.056-0.0560.0000.0000.0000.000
195A210LEU0-0.034-0.01145.125-0.001-0.0010.0000.0000.0000.000
196A211PRO00.0180.02245.5370.0020.0020.0000.0000.0000.000
197A212GLN00.008-0.00948.2200.0020.0020.0000.0000.0000.000
198A213GLN0-0.029-0.01350.3880.0020.0020.0000.0000.0000.000
199A214GLN0-0.0030.00247.089-0.001-0.0010.0000.0000.0000.000
200A215GLN0-0.020-0.00544.1200.0020.0020.0000.0000.0000.000
201A216LYS10.8370.90742.0780.0410.0410.0000.0000.0000.000
202A217LEU00.0190.01937.8420.0020.0020.0000.0000.0000.000
203A219TYR00.035-0.00331.255-0.002-0.0020.0000.0000.0000.000
204A220ARG10.8590.91430.9710.0450.0450.0000.0000.0000.000
205A222GLU-1-0.770-0.90325.424-0.032-0.0320.0000.0000.0000.000
206A223ASP-1-0.749-0.84922.605-0.037-0.0370.0000.0000.0000.000
207A224SER00.003-0.00420.7190.0030.0030.0000.0000.0000.000
208A225SER0-0.108-0.07822.7860.0150.0150.0000.0000.0000.000
209A226GLN0-0.035-0.00125.4550.0040.0040.0000.0000.0000.000
210A227LYS10.9000.96826.6740.0140.0140.0000.0000.0000.000
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212A230LYS10.8470.92130.3680.0350.0350.0000.0000.0000.000
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