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: N2NQQ

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 OptHSide
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 -2236518.409681
FMO2-HF: Nuclear repulsion 2151612.658557
FMO2-HF: Total energy -84905.751124
FMO2-MP2: Total energy -85146.32209


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.
-11.903-4.5623.788-4.595-6.534-0.016
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 : -0.021 / q_NPA : -0.025
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].
3A6CYS0-0.062-0.0073.814-1.775-0.117-0.012-0.746-0.8990.000
4A7GLU-1-0.912-0.9695.8111.7211.7210.0000.0000.0000.000
5A8THR0-0.077-0.0357.7680.1290.1290.0000.0000.0000.000
6A9GLU-1-0.785-0.8689.926-0.224-0.2240.0000.0000.0000.000
7A10GLY00.0120.00913.0770.0280.0280.0000.0000.0000.000
8A11SER0-0.084-0.03310.5140.0180.0180.0000.0000.0000.000
9A12SER0-0.002-0.0189.2480.0730.0730.0000.0000.0000.000
10A13ILE0-0.0220.0082.952-0.530-0.0710.124-0.135-0.448-0.001
11A14SER0-0.016-0.0176.3430.3440.3440.0000.0000.0000.000
12A15PHE0-0.008-0.0072.226-1.294-0.4341.622-1.117-1.364-0.002
13A16THR0-0.005-0.0107.7840.2930.2930.0000.0000.0000.000
14A17VAL0-0.018-0.00410.792-0.040-0.0400.0000.0000.0000.000
15A18GLU-1-0.775-0.88712.598-0.445-0.4450.0000.0000.0000.000
16A19LYS10.8490.94415.0510.2520.2520.0000.0000.0000.000
17A20ALA0-0.0300.00015.855-0.028-0.0280.0000.0000.0000.000
18A21GLY00.004-0.01316.6000.0250.0250.0000.0000.0000.000
19A22HIS0-0.054-0.01811.887-0.017-0.0170.0000.0000.0000.000
20A23VAL0-0.016-0.0178.5020.0240.0240.0000.0000.0000.000
21A24VAL0-0.026-0.0045.461-0.103-0.1030.0000.0000.0000.000
22A25ARG10.9150.9574.060-0.1550.055-0.001-0.060-0.1500.000
23A26PHE00.002-0.0022.293-9.897-6.9092.015-2.336-2.667-0.013
24A27ASN00.0260.0083.5190.0350.7290.007-0.081-0.6200.000
25A28CYS0-0.0540.0125.522-1.004-1.0040.0000.0000.0000.000
26A29PRO00.0820.0507.3970.2150.2150.0000.0000.0000.000
27A30SER00.008-0.0178.919-0.089-0.0890.0000.0000.0000.000
28A31THR0-0.062-0.01912.209-0.046-0.0460.0000.0000.0000.000
29A32LEU0-0.043-0.02410.894-0.034-0.0340.0000.0000.0000.000
30A33GLU-1-0.816-0.88512.3810.0310.0310.0000.0000.0000.000
31A34GLU-1-0.788-0.83112.786-0.057-0.0570.0000.0000.0000.000
32A35ILE0-0.039-0.03910.844-0.063-0.0630.0000.0000.0000.000
33A36LYS10.8420.93614.1380.2810.2810.0000.0000.0000.000
34A37PRO00.029-0.02915.065-0.074-0.0740.0000.0000.0000.000
35A38ALA00.0040.01116.957-0.002-0.0020.0000.0000.0000.000
36A39TYR0-0.008-0.02714.6500.0120.0120.0000.0000.0000.000
37A40GLU-1-0.909-0.93917.468-0.022-0.0220.0000.0000.0000.000
38A41ALA0-0.0010.01518.378-0.021-0.0210.0000.0000.0000.000
39A42GLY00.013-0.00818.947-0.004-0.0040.0000.0000.0000.000
40A43ASP-1-0.875-0.96320.634-0.114-0.1140.0000.0000.0000.000
41A44SER0-0.0020.00222.751-0.012-0.0120.0000.0000.0000.000
42A45THR0-0.059-0.01916.182-0.008-0.0080.0000.0000.0000.000
43A46LYS10.8900.93918.7200.1660.1660.0000.0000.0000.000
44A47VAL00.0150.00315.412-0.021-0.0210.0000.0000.0000.000
45A48CYS0-0.097-0.04116.1710.0830.0830.0000.0000.0000.000
46A49THR00.019-0.01017.131-0.034-0.0340.0000.0000.0000.000
47A50THR0-0.037-0.02218.9310.0000.0000.0000.0000.0000.000
48A51ALA00.012-0.00315.253-0.014-0.0140.0000.0000.0000.000
49A52ASP-1-0.793-0.88115.693-0.332-0.3320.0000.0000.0000.000
50A54SER0-0.021-0.01119.2100.0350.0350.0000.0000.0000.000
51A55ASN0-0.062-0.02621.7440.0240.0240.0000.0000.0000.000
52A56GLU-1-0.801-0.89720.192-0.239-0.2390.0000.0000.0000.000
53A57ALA0-0.018-0.00320.9810.0240.0240.0000.0000.0000.000
54A58ALA00.0510.02720.865-0.015-0.0150.0000.0000.0000.000
55A59LEU00.0340.00716.083-0.010-0.0100.0000.0000.0000.000
56A60LYS10.8670.94619.5490.1260.1260.0000.0000.0000.000
57A61ASP-1-0.925-0.97222.251-0.144-0.1440.0000.0000.0000.000
58A62VAL0-0.084-0.03919.462-0.001-0.0010.0000.0000.0000.000
59A63LEU0-0.026-0.01915.727-0.014-0.0140.0000.0000.0000.000
60A64LYS10.8990.96119.9240.1890.1890.0000.0000.0000.000
61A65SER0-0.038-0.00920.6320.0230.0230.0000.0000.0000.000
62A66ALA00.0680.03515.794-0.019-0.0190.0000.0000.0000.000
63A67SER0-0.047-0.03015.4370.0410.0410.0000.0000.0000.000
64A68LEU00.0420.02810.462-0.048-0.0480.0000.0000.0000.000
65A69ALA0-0.0410.00412.1820.0350.0350.0000.0000.0000.000
66A70GLN00.0660.01711.485-0.060-0.0600.0000.0000.0000.000
67A71ALA0-0.049-0.02411.663-0.021-0.0210.0000.0000.0000.000
68A72GLU-1-0.908-0.93311.7150.3590.3590.0000.0000.0000.000
69A73GLY00.0040.0059.4610.1220.1220.0000.0000.0000.000
70A74SER0-0.107-0.0669.634-0.099-0.0990.0000.0000.0000.000
71A75GLY00.0200.0306.4460.0410.0410.0000.0000.0000.000
72A76PRO0-0.028-0.0363.386-0.895-0.4160.034-0.096-0.4180.000
73A77SER00.0240.0134.3530.004-0.003-0.001-0.0240.0320.000
74A78GLY0-0.014-0.0097.645-0.207-0.2070.0000.0000.0000.000
75A79GLY00.0280.0118.6770.1180.1180.0000.0000.0000.000
76A80ASN0-0.041-0.0089.8070.0330.0330.0000.0000.0000.000
77A81ASP-1-0.800-0.8966.3651.8871.8870.0000.0000.0000.000
78A82PHE00.025-0.0057.011-0.220-0.2200.0000.0000.0000.000
79A83THR0-0.051-0.0386.7010.0970.0970.0000.0000.0000.000
80A84LEU00.0140.0208.5520.0390.0390.0000.0000.0000.000
81A85THR00.001-0.00710.337-0.079-0.0790.0000.0000.0000.000
82A86VAL00.0200.01213.0210.0100.0100.0000.0000.0000.000
83A87ASP-1-0.883-0.93715.360-0.143-0.1430.0000.0000.0000.000
84A88ALA0-0.024-0.02418.5390.0170.0170.0000.0000.0000.000
85A89LEU0-0.072-0.01316.798-0.017-0.0170.0000.0000.0000.000
86A90PRO00.0130.01618.9870.0300.0300.0000.0000.0000.000
87A91GLU-1-0.870-0.94021.985-0.178-0.1780.0000.0000.0000.000
88A92ALA0-0.031-0.01324.0020.0050.0050.0000.0000.0000.000
89A93GLU-1-0.920-0.96218.581-0.420-0.4200.0000.0000.0000.000
90A94THR0-0.022-0.01518.5540.0150.0150.0000.0000.0000.000
91A95SER00.011-0.00715.511-0.037-0.0370.0000.0000.0000.000
92A96VAL0-0.056-0.01612.9420.0690.0690.0000.0000.0000.000
93A97PHE0-0.003-0.01612.661-0.134-0.1340.0000.0000.0000.000
94A98PHE00.0140.00910.6870.1060.1060.0000.0000.0000.000
95A99LEU0-0.008-0.01012.058-0.090-0.0900.0000.0000.0000.000
96A101GLN0-0.009-0.03012.213-0.040-0.0400.0000.0000.0000.000
97A102ARG10.8270.88215.6150.1200.1200.0000.0000.0000.000
98A103THR0-0.005-0.03617.876-0.016-0.0160.0000.0000.0000.000
99A104GLY0-0.029-0.02119.5130.0040.0040.0000.0000.0000.000
100A105ALA0-0.130-0.04219.931-0.019-0.0190.0000.0000.0000.000
101A115ALA0-0.045-0.04117.755-0.013-0.0130.0000.0000.0000.000
102A116VAL00.0290.02612.7070.0120.0120.0000.0000.0000.000
103A117PRO00.0030.00116.0720.0360.0360.0000.0000.0000.000
104A118SER00.009-0.00916.395-0.025-0.0250.0000.0000.0000.000
105A119ASP-1-0.932-0.96217.285-0.174-0.1740.0000.0000.0000.000
106A120LYS10.8900.94614.5080.2310.2310.0000.0000.0000.000
107A122GLY00.0260.01810.6250.0350.0350.0000.0000.0000.000
108A123VAL00.0170.0076.629-0.322-0.3220.0000.0000.0000.000
109A124HIS00.0130.0258.7410.3330.3330.0000.0000.0000.000
110A125ILE0-0.008-0.0148.241-0.247-0.2470.0000.0000.0000.000
111A126LEU0-0.0050.01010.8260.1530.1530.0000.0000.0000.000
112A127VAL0-0.022-0.01713.404-0.050-0.0500.0000.0000.0000.000
113A128LYS10.8980.93615.5170.5330.5330.0000.0000.0000.000
114A129ALA00.0120.00218.1820.0110.0110.0000.0000.0000.000
115A130ALA0-0.001-0.00821.559-0.005-0.0050.0000.0000.0000.000
116A131PRO0-0.002-0.00121.7910.0110.0110.0000.0000.0000.000
117A132GLN0-0.054-0.03224.9550.0210.0210.0000.0000.0000.000
118A133ALA0-0.035-0.01927.8930.0090.0090.0000.0000.0000.000
119A134PRO0-0.0030.01828.267-0.004-0.0040.0000.0000.0000.000
120A135VAL00.0500.01324.567-0.003-0.0030.0000.0000.0000.000
121A136CYS0-0.110-0.01427.1480.0140.0140.0000.0000.0000.000
122A137SER00.006-0.00924.626-0.006-0.0060.0000.0000.0000.000
123A138ALA0-0.0020.00326.2660.0060.0060.0000.0000.0000.000
124A139GLN00.008-0.03228.9950.0020.0020.0000.0000.0000.000
125A140ASP-1-0.920-0.95130.445-0.005-0.0050.0000.0000.0000.000
126A141HIS00.0170.02832.0060.0040.0040.0000.0000.0000.000
127A142THR0-0.032-0.03133.8210.0000.0000.0000.0000.0000.000
128A143LEU0-0.0180.00231.1700.0000.0000.0000.0000.0000.000
129A144GLU-1-0.936-0.97534.784-0.039-0.0390.0000.0000.0000.000
130A145LEU0-0.023-0.00333.193-0.004-0.0040.0000.0000.0000.000
131A146GLN00.003-0.01837.8540.0050.0050.0000.0000.0000.000
132A147ILE00.0000.02038.003-0.004-0.0040.0000.0000.0000.000
133A148THR0-0.017-0.03041.6520.0030.0030.0000.0000.0000.000
134A149ALA00.0100.01143.8790.0030.0030.0000.0000.0000.000
135A150ALA00.0390.02543.864-0.002-0.0020.0000.0000.0000.000
136A151ASN0-0.082-0.05742.331-0.003-0.0030.0000.0000.0000.000
137A152SER0-0.028-0.01240.032-0.003-0.0030.0000.0000.0000.000
138A153ASP-1-0.824-0.91334.310-0.108-0.1080.0000.0000.0000.000
139A154THR00.0370.02535.1720.0000.0000.0000.0000.0000.000
140A155SER00.005-0.00629.716-0.005-0.0050.0000.0000.0000.000
141A156PHE0-0.008-0.00928.3190.0060.0060.0000.0000.0000.000
142A157VAL00.0480.02023.022-0.008-0.0080.0000.0000.0000.000
143A158CYS0-0.0470.02123.7510.0090.0090.0000.0000.0000.000
144A159GLY00.0810.02321.833-0.020-0.0200.0000.0000.0000.000
145A160GLY00.0320.01120.3980.0190.0190.0000.0000.0000.000
146A161THR0-0.003-0.01519.466-0.012-0.0120.0000.0000.0000.000
147A162PHE0-0.091-0.03720.7920.0160.0160.0000.0000.0000.000
148A163ASN0-0.029-0.02818.654-0.009-0.0090.0000.0000.0000.000
149A164VAL00.0420.03621.131-0.015-0.0150.0000.0000.0000.000
150A165ILE00.0200.02223.1640.0050.0050.0000.0000.0000.000
151A166LYS10.7810.92226.2730.0160.0160.0000.0000.0000.000
152A167PRO00.0920.02529.379-0.002-0.0020.0000.0000.0000.000
153A168ALA00.0170.01226.144-0.007-0.0070.0000.0000.0000.000
154A169ASN0-0.025-0.01827.457-0.015-0.0150.0000.0000.0000.000
155A170ALA00.0480.01729.0510.0030.0030.0000.0000.0000.000
156A171ALA00.0150.01530.8150.0000.0000.0000.0000.0000.000
157A172LYS10.7880.90033.2980.0340.0340.0000.0000.0000.000
158A173VAL0-0.0070.00133.822-0.005-0.0050.0000.0000.0000.000
159A174LEU00.0040.00533.4630.0050.0050.0000.0000.0000.000
160A175GLN00.009-0.00237.345-0.004-0.0040.0000.0000.0000.000
161A176GLY0-0.0160.01740.3790.0010.0010.0000.0000.0000.000
162A177ASP-1-0.771-0.90041.509-0.027-0.0270.0000.0000.0000.000
163A178SER0-0.060-0.07140.346-0.002-0.0020.0000.0000.0000.000
164A179CYS0-0.076-0.02736.191-0.002-0.0020.0000.0000.0000.000
165A180GLU-1-0.828-0.89536.506-0.007-0.0070.0000.0000.0000.000
166A181THR0-0.039-0.02038.3240.0010.0010.0000.0000.0000.000
167A182GLU-1-0.900-0.95433.874-0.030-0.0300.0000.0000.0000.000
168A183VAL0-0.003-0.00438.0270.0030.0030.0000.0000.0000.000
169A184ASP-1-0.817-0.90238.006-0.036-0.0360.0000.0000.0000.000
170A185LEU00.0320.02635.3640.0010.0010.0000.0000.0000.000
171A186VAL0-0.006-0.00638.6110.0010.0010.0000.0000.0000.000
172A187SER0-0.098-0.06241.3040.0030.0030.0000.0000.0000.000
173A188LEU00.0070.01341.0150.0020.0020.0000.0000.0000.000
174A189VAL0-0.027-0.03141.4920.0000.0000.0000.0000.0000.000
175A190PRO00.0190.01141.994-0.003-0.0030.0000.0000.0000.000
176A191HIS0-0.023-0.01141.664-0.002-0.0020.0000.0000.0000.000
177A192ALA0-0.0260.00838.814-0.004-0.0040.0000.0000.0000.000
178A193SER0-0.037-0.02934.416-0.001-0.0010.0000.0000.0000.000
179A194ARG10.8920.97326.9460.0870.0870.0000.0000.0000.000
180A195SER00.0230.02227.2820.0030.0030.0000.0000.0000.000
181A196ALA0-0.008-0.02324.4910.0070.0070.0000.0000.0000.000
182A197LEU0-0.028-0.02421.484-0.003-0.0030.0000.0000.0000.000
183A198GLU-1-0.845-0.88221.102-0.251-0.2510.0000.0000.0000.000
184A199GLN0-0.019-0.02215.4220.0620.0620.0000.0000.0000.000
185A200SER00.029-0.01717.4210.0060.0060.0000.0000.0000.000
186A201GLY0-0.048-0.04519.3530.0200.0200.0000.0000.0000.000
187A202LEU0-0.034-0.00321.6940.0270.0270.0000.0000.0000.000
188A203ILE0-0.037-0.01224.630-0.001-0.0010.0000.0000.0000.000
189A204LYS10.8740.92027.7270.1260.1260.0000.0000.0000.000
190A205LEU0-0.019-0.00830.8960.0030.0030.0000.0000.0000.000
191A206SER00.014-0.00834.195-0.003-0.0030.0000.0000.0000.000
192A207VAL0-0.017-0.01336.7960.0040.0040.0000.0000.0000.000
193A208THR00.0410.01840.448-0.003-0.0030.0000.0000.0000.000
194A209ASP-1-0.876-0.92143.103-0.051-0.0510.0000.0000.0000.000
195A210LEU0-0.037-0.01544.926-0.001-0.0010.0000.0000.0000.000
196A211PRO00.0040.01645.3320.0020.0020.0000.0000.0000.000
197A212GLN00.020-0.00448.0080.0020.0020.0000.0000.0000.000
198A213GLN0-0.0150.00350.3720.0010.0010.0000.0000.0000.000
199A214GLN00.005-0.00547.032-0.001-0.0010.0000.0000.0000.000
200A215GLN0-0.021-0.00244.0420.0030.0030.0000.0000.0000.000
201A216LYS10.8680.92441.9180.0290.0290.0000.0000.0000.000
202A217LEU0-0.024-0.00237.4730.0010.0010.0000.0000.0000.000
203A219TYR00.0260.00231.018-0.001-0.0010.0000.0000.0000.000
204A220ARG10.8580.90930.7010.0200.0200.0000.0000.0000.000
205A222GLU-1-0.735-0.88625.742-0.003-0.0030.0000.0000.0000.000
206A223ASP-1-0.765-0.86722.8590.0100.0100.0000.0000.0000.000
207A224SER0-0.012-0.01321.0470.0010.0010.0000.0000.0000.000
208A225SER0-0.097-0.06823.1740.0150.0150.0000.0000.0000.000
209A226GLN0-0.058-0.01325.657-0.001-0.0010.0000.0000.0000.000
210A227LYS10.9150.97826.835-0.021-0.0210.0000.0000.0000.000
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212A230LYS10.8770.94630.3920.0180.0180.0000.0000.0000.000
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